AMYRIS, INC. (Form: 10-K, Received: 04/02/2014 06:03:10)

Large accelerated filer

Accelerated filer

Non-accelerated filer

¨ (Do not check if a smaller reporting company)

Smaller reporting company

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington D.C. 20549

FORM 10-K

(Mark One)



x	ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the fiscal year ended December 31, 2013



¨	TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the Transition Period from to

Commission File Number: 001-34885

AMYRIS, INC.

(Exact name of registrant as specified in its charter)



Delaware		55-0856151
(State or other jurisdiction of incorporation or organization)		(I.R.S. Employer Identification No.)



5885 Hollis Street, Suite 100, Emeryville, California		94608
(Address of principal executive office)		(Zip Code)

(510) 450-0761

(Registrant’s telephone number, including area code)

Securities registered pursuant to Section 12(b) of the Act:



Title of each class		Name of each exchange on which registered
Common Stock, $0.0001 par value per share		The NASDAQ Stock Market LLC (NASDAQ Global Select Market)

Securities registered pursuant to Section 12(g) of the Act: None

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act. Yes ¨ No x

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act. Yes ¨ No x

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes x No ¨

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files). Yes x No ¨

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K. x

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, or a non-accelerated filer. See definition of “large accelerated filer”, “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one.)

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act.): Yes ¨ No x

As of June 28, 2013, the last business day of the registrant’s most recently completed second fiscal quarter, the aggregate market value of the voting stock held by non-affiliates of the registrant was approximately $107.7 million , based on the closing price of the registrant’s common stock on the NASDAQ Global Select Market on such date.

76,802,434 shares of the Registrant’s common stock, par value $0.0001 per share, were outstanding as of February 28, 2014 .

DOCUMENTS INCORPORATED BY REFERENCE

Portions of registrant’s proxy statement to be delivered to stockholders in connection with the registrant’s 2014 Annual Meeting of Stockholders to be held on or about May 29, 2014 are incorporated by reference into Part III of this Form 10-K. The registrant intends to file its proxy statement within 120 days after its fiscal year end.

AMYRIS, INC.

ANNUAL REPORT ON FORM 10-K

For the Fiscal Year Ended December 31, 2013

INDEX



		Page
	PART I
Item 1.	Business	2
Item 1A.	Risk Factors	12
	Executive Officers of the Registrant	35
Item 1B	Unresolved Staff Comments	37
Item 2.	Properties	37
Item 3.	Legal Proceedings	37
Item 4.	Mine Safety Disclosures	37

	PART II

Item 5.	Market for the Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities	38
Item 6.	Selected Financial Data	41
Item 7.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	43
Item 7A.	Quantitative and Qualitative Disclosures About Market Risk	62
Item 8.	Financial Statements and Supplementary Data	63
Item 9.	Changes in and Disagreements with Accountants on Accounting and Financial Disclosure	126
Item 9A.	Controls and Procedures	126
Item 9B.	Other Information	127

	PART III

Item 10.	Directors, Executive Officers and Corporate Governance	128
Item 11.	Executive Compensation	128
Item 12.	Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters	128
Item 13.	Certain Relationships and Related Transactions, and Director Independence	128
Item 14.	Principal Accounting Fees and Services	129

	PART IV

Item 15.	Exhibits, Financial Statement Schedules	129
	Signatures	146

FORWARD-LOOKING STATEMENTS

This report on Form 10-K, including the sections entitled “Item 1. Business,” “Item 1A. Risk Factors,” and “Item 7. Management’s Discussion and Analysis of Financial Condition and Results of Operations,” contains forward-looking statements reflecting our current expectations that involve risks and uncertainties and which are subject to safe harbors under the Securities Act of 1933, as amended, or the Securities Act, and the Securities Exchange Act of 1934, as amended. These forward-looking statements include, but are not limited to, statements concerning our strategy, future production capacity and other aspects of our future operations, ability to improve our production efficiencies, future financial position, future revenues, projected costs, expectations regarding demand and acceptance for our technologies, growth opportunities and trends in the market in which we operate, prospects and plans and objectives of management. The words “anticipates,” “believes,” “estimates,” “expects,” “intends,” “may,” “plans,” “projects,” “will,” “would” and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. We may not actually achieve the plans, intentions or expectations disclosed in our forward-looking statements and you should not place undue reliance on our forward-looking statements. These forward-looking statements involve risks and uncertainties that could cause our actual results to differ materially from those in the forward-looking statements, including, without limitation, the risks set forth in Part I, Item 1A, “Risk Factors” in this Annual Report on Form 10-K and in our other filings with the Securities and Exchange Commission. We do not assume any obligation to update any forward-looking statements.

TRADEMARKS

Amyris ^® , the Amyris logo, Biofene ^® , No Compromise ^® , Diesel de Cana™ and Neossance™ are trademarks or registered trademarks of Amyris, Inc. This report also contains trademarks and trade names of other business that are the property of their respective holders.

PART I

ITEM 1. BUSINESS

Overview

Amyris, Inc. (referred to as the "Company," " Amyris," "we," "us," or "our") is an renewable products company focused on providing sustainable alternatives to a broad range of petroleum-sourced products. We developed innovative microbial engineering and screening technologies that modify the way microorganisms process sugars. We are using our proprietary synthetic biology platform to design microbes, primarily yeast, and use them as living factories in established fermentation processes to convert plant-sourced sugars into renewable hydrocarbons. We are developing, and, in some cases, already commercializing, products from these hydrocarbons in several target markets, including cosmetics, lubricants, flavors and fragrances, performance materials, and transportation fuels. We call these No Compromise ^® products because we design them to perform comparably to, or better than, currently available products.

We were founded in 2003 in the San Francisco Bay Area by a group of scientists from the University of California, Berkeley. Our first major milestone came in 2005 when, through a grant from the Bill & Melinda Gates Foundation, our scientists developed technology capable of creating microbial strains to produce artemisinic acid - a precursor of artemisinin, an effective anti-malarial drug. In 2008, we granted a royalty-free license (and a royalty-free sublicense from a license we received from the University of California) to this technology to the Institute of One World Health who then sublicensed it to Sanofi-Aventis, which currently distributes artemisinin-based anti-malarial drugs made through our technology.

Building on our success with semi-synthetic artemisinin to combat malaria, we have been applying our industrial synthetic biology platform to provide alternatives to a broad range of petroleum-sourced products. We have focused our development efforts on the production of Biofene ^® , our brand of renewable farnesene, a long-chain, branched liquid hydrocarbon molecule. Using Biofene as a building block molecule, we are developing a wide range of renewable products for our target markets.

While our platform is able to utilize a wide variety of feedstocks, we are focusing our large-scale production plans primarily on the use of Brazilian sugarcane as our feedstock because of its renewability, low cost and relative price stability. We have also been able to produce Biofene through the use of other feedstocks such as sugar beets, corn dextrose, sweet sorghum and cellulosic sugars.

Our first purpose-built, large-scale Biofene production plant commenced operations in southeastern Brazil in December 2012. This plant is in Brotas, in the state of São Paulo, Brazil, and is adjacent to an existing sugar and ethanol mill, Paraíso Bioenergia (or Paraíso). We have also commenced initial construction of a second large-scale production plant in Brazil, located at the São Martinho S.A. (or SMSA, a legal successor by spin-off of Usina São Martinho S.A.) sugar and ethanol mill also in the state of São Paulo, Brazil, and we intend to complete construction when market developments support the start-up of such plant.

Our business strategy is to focus on direct commercialization of renewable products while moving products in commodity industries, including our fuels and base oil lubricants products, into joint venture arrangements with established industry leaders. We believe this approach will permit access to the capital and resources necessary to support large-scale production and global distribution for our commodity products.

We are focused on building our renewable-product leadership position initially with squalane in cosmetics, niche fuel (diesel and jet) opportunities, fragrance oils, and farnesene for liquid polymer applications. We believe that success in these markets will pave the way to accessing larger markets and having a more significant impact in the longer term.

We were incorporated in 2003. We have two operating subsidiaries, Amyris Brasil Ltda. (formerly Amyris Brasil S.A.) (or Amyris Brasil), and Amyris Fuels LLC (or Amyris Fuels). Amyris Brasil oversees the establishment and expansion of our production in Brazil. Amyris Fuels was originally established to help us develop fuel distribution capabilities in the United States. We began selling fuels through Amyris Fuels in June 2008. Amyris Fuels generated revenue from the sale of ethanol and reformulated ethanol-blended gasoline to wholesale customers through a network of terminals in the eastern United States. In the third quarter of 2012, we transitioned out of the ethanol and reformulated ethanol-blended gasoline business, though we continue to maintain the Amyris Fuels subsidiary for activities related to renewable fuel sales.

Our Business Strategy

Petroleum is a fundamental building block for many products, such as consumer products, chemicals, plastics and transportation fuels that are essential to modern economies. Recently, the increased demand for petroleum in the face of limited supply, supply chain uncertainties and negative environmental impacts have created challenges to the current petroleum infrastructure. As a result, there have been many attempts to create products comparable to petroleum derivatives without these drawbacks. However, initial approaches have faced a number of challenges that have limited their success, including exposure to volatile feedstock pricing, questionable environmental sustainability, limited product portfolio, and dependency on government policy.

Our objective is to become the leading provider of renewable, high-performance alternatives to selected petroleum-sourced chemicals and fuels. By leveraging our synthetic biology platform, our partners' know-how, and our experience in industrial fermentation, our products are designed to enable our customers to reduce the environmental impact of their products without compromising performance, and, in some cases, our renewable products provide superior performance to the petroleum-sourced products they are replacing.

Key elements of our strategy include:

Leveraging our technology platform to improve efficiency. We continue applying synthetic biology, primarily our strain engineering platform, to lower the cost of production of our products through improvements in yields and other production process efficiencies. We do this with our industrial platform for yeast strain development at our world-class laboratories. We also support scale up to commercial production in two pilot plant facilities and a demonstration production facility, as well as at various contract manufacturing locations.

Accelerating development through collaborations . In order to accelerate the development of new technologies, production methods or products, we enter into collaborative research, development and commercialization agreements, such as our existing agreements with Total Energies Nouvelles Activités USA, SAS (or Total), Firmenich SA (or Firmenich), , Cosan US, Inc. (or Cosan), Kuraray Co., Ltd. (or Kuraray), and Manufacture Francaise de Pneumatiques Michelin (or Michelin). We have also entered into partnerships with the U.S. government to develop certain technologies and processes capable of improving our ability to produce alternatives to petroleum-sourced products.

Delivering cost efficient manufacturing. Building on our breakthrough technology and experience gained from production through third party contract manufacturing, we built, commissioned and are now operating our own large-scale Biofene production plant in Brotas, in the state of São Paulo, Brazil. We opted to focus on Brazilian sugarcane as the feedstock to support our production ramp because of its renewability, low-cost and relative price stability. As we develop cost efficient manufacturing in our first production facility, we expect to work selectively with other Brazilian sugar and ethanol producers to build additional facilities adjacent to their existing mills, thereby reducing the capital required to establish and scale our production operations.

Targeting product markets to maximize returns . We have begun to commercialize our products derived from Biofene primarily in select specialty chemical markets characterized by higher-margin, lower-volume products, where we believe we can earn positive gross margins with current production process efficiencies. For example, in 2011 we initiated sales of squalane, a cosmetic emollient produced from Biofene. At the end of 2013, we estimate that we achieved a 18% market share in the global squalane market. We have also established sales channels to certain niche diesel markets in metropolitan bus fleets in Brazil to generate revenue while building the know-how and credibility as a reliable fuel supplier. As we lower our production costs through technological and manufacturing improvements, we intend to expand into broader, lower-margin, higher volume commodity product markets, such as the broad-based fuels market and base oil lubricants markets, through joint venture arrangements.

Our Breakthrough Technology

Our synthetic biology platform enables us to modify the genetic pathways of microorganisms, primarily yeast, to turn them into living factories to produce target molecules for which we believe there may be significant market opportunities. In addition to using our synthetic biology platform to identify and improve strains of microbes to produce target molecules, we are using our technology platform to develop production processes that we believe will allow us to scale to commercial levels.

The primary biological pathway within the microbe that we currently use to produce our target molecules is the isoprenoid pathway. Isoprenoids constitute a large, diverse class of organic chemicals with current product applications in a wide range of

industries, including specialty chemicals and fuels. With this pathway, we can potentially produce thousands of different isoprenoid molecules.

The key steps in our strain engineering and scale-up process have been as follows:

Identifying target molecules. We start our process by identifying, usually based on input from collaborators, a commercial application where we can deliver a No Compromise solution that we want to pursue. We identify the key molecular properties that are essential to product performance in a specific commercial application and then analyze the chemical structures that drive those key performance characteristics. Finally, we identify target molecules or derivatives of molecules that are comprised of these key chemical structures and that may be produced by our yeast strains.

Developing initial strains. Once we have chosen a target molecule, we identify the steps required for its production in a biological pathway. We then seek to design a pathway to produce the target, either directly or by producing a molecule that can, through simple chemical steps, be synthesized, or converted, into the target. Once this pathway is identified, we undertake to engineer it into our yeast strains by employing the processes discussed below.

Improving strain performance and process development . After we have established a pathway and verified that it can produce the target molecule, the yeast strain must be improved to increase the level of efficiency of production. Initially, we focus primarily on yield , a measure of the amount of product produced by a defined amount of sugar as the means to improve strain output. As we advance in our scale up and commercial scale process development, we also seek to improve production output through improvements in strain productivity , the rate at which our product is produced by a given yeast strain, and titer , the concentration of product in the fermentation broth. In addition, we seek to develop processes to improve production recovery efficiency, including separation efficiency, which is the amount of product that is captured from a fermentation run, cycle-time, which is the time needed to run a full fermentation cycle, and the evolution of batch process methods to semi-continuous and continuous production methods.

Moving production from lab to commercial scale. Once we have established a pathway and verified that it can produce the target molecule, the yeast strain must be improved to increase the level of efficiency of production. We design our lab scale two-liter fermenters to mimic the conditions found in larger scale fermentation so that our findings may translate predictably from lab scale to pilot, demonstration and commercial scale. In addition to our lab scale fermenters, we have operating pilot plants in our facilities in Emeryville, California and Campinas, Brazil, as well as two 5,000-liter fermenters in our Campinas demonstration facility. To date, most of our efforts have focused on developing yeast strains to produce Biofene and, to a lesser extent, flavors and fragrances, with significant development efforts devoted to chemical synthesis of other products from Biofene. Though our technology platform allows us to develop yeast strains engineered to produce other target molecules, we expect to continue focusing most of our strain-engineering efforts on Biofene production and, to a lesser extent, selected specialty chemical ingredients, for the foreseeable future.

Our Industrial Production

Our industrial production operations generally involve two major steps. First, we produce a target molecule by means of an industrial fermentation process. In some cases this target molecule is itself the desired end product. In other cases, it must be converted into the desired end product by a second step where we use chemical synthesis of the initial target molecule to produce a final target molecule.

Commercial Production of Target Fermentation Molecules

We have initiated commercial production of Biofene, our initial fermentation molecule, at our purpose-built, large-scale Biofene production plant in Brotas, in the State of São Paulo, Brazil. Our Biofene production plant in Brotas is adjacent to an existing sugar and ethanol mill, Paraíso. Under our agreement with Paraíso, they will supply sugarcane juice and other utilities and we were responsible for construction (which commenced in August 2011) and operation of our Biofene production facility. Our Biofene production plant has six 200,000 liter production fermenters and was designed to process sugarcane juice, or its equivalent, from up to one million tons of raw sugarcane annually. In December 2012, following a successful commissioning phase, we began production of Biofene at the facility. Our first shipment of Biofene produced at the facility occurred on February 1, 2013.

Prior to operating our own facility, we relied on multiple contract manufacturing facilities in the United States, Brazil and Spain, which used 100,000 to 240,000 liter fermenters and multiple kinds of feedstock.

We have also advanced initial construction of a second large-scale production plant in Brazil, located at the SMSA sugar and ethanol mill also in the state of São Paulo, which we intend to complete when production economics support start-up of that plant. We entered into agreements with SMSA to establish the facility at SMSA, and to form a joint venture SMA Indústria Química S.A. (or SMA). We formed SMA in 2010, and commenced site preparation in December 2010 and civil construction in February 2011. In early 2012, we suspended construction of the plant pending completion and operation of our Brotas facility. The SMA plant is intended to provide a large-scale production facility to support our longer-term production plans.

Following the completion of our SMA plant, we expect to seek to expand our large-scale production capacity of intermediate molecules by entering into agreements with owners of additional sugar and ethanol mills in Brazil.

Chemical Finishing Process

In some cases, we perform additional chemical finishing steps to convert initial target molecules into other finished products, such as renewable squalane, lubricants, polymers and diesel. We have established an agreement with Glycotech Inc. (or Glycotech), for use of a Leland, North Carolina facility of Salisbury Partners, LLC to convert Biofene into squalane and other final products. We expect to enter into additional agreements with other chemical companies for finishing services to access flexible capacity and an array of services as we develop additional products.

Our Products

We are focused on developing a broad range of products to address five identified markets: cosmetics, flavors and fragrances, performance materials, lubricants and transportation fuels.

Cosmetics

Through basic chemical finishing steps, we are able to convert Biofene into squalane. Squalane is used today as an emollient in cosmetics and other personal care products. Squalane traditionally has been manufactured from olive oil or extracted from deep-sea shark liver oil. We believe Amyris-produced squalane offers a purity that is equal or superior to squalane derived from conventional sources. The relatively high price of squalane to date has meant that its use has been limited to small quantities in mass-market product formulations or to use in luxury products. We believe that we are capable of producing squalane at a price that would permit formulators to use squalane more broadly. We currently have agreements with several regional distributors, including in Japan, South Korea, North America, Brazil and Europe.

Lubricants

Base oils are the building blocks of lubricating oils and are currently derived from the crude oil refining process. Additives are materials added to base oils to change their properties, characteristics, or performance (e.g., anti-foam, anti-wear, corrosion inhibitor, detergent, dispersant, pour point depressant, anti-oxidant, or friction modifier). Lubricants are manufactured by combining a base oil with additives required by lubricant product applications, including engine oils, gear oils, hydraulic oils and turbine oils. Biofene may be chemically modified to serve as a base oil, additive, and/or lubricant. We believe the high-purity, synthetic base oil and additive molecules that can be made from Biofene could enable lubricant products to perform in harsh environments under extremes of temperature, moisture, dirt and/or wear.

In December 2010, we entered into an agreement with Cosan Combustíveis e Lubrificantes S.A. and Cosan S.A. Industria e Comércio (such Cosan entities and their affiliates, collectively or individually referred to as Cosan) to establish a joint venture for the worldwide development, production and commercialization of renewable base oils for the automotive, industrial and commercial lubricants markets. In March 2013, we expanded this collaboration to also include additives and lubricants for the automotive, industrial and commercial lubricants markets. The joint venture is operated through Novvi LLC (or Novvi). We anticipate that Novvi will source Biofene for its products initially from Amyris production facilities, and Amyris and Cosan, as co-owners of Novvi, would share its development, marketing and operating costs. In 2013, Novvi purchased initial quantities of Biofene for base oil production.

Flavors and Fragrances

We believe we are well situated to cost-effectively produce natural oils and aroma chemicals that are commonly used in the flavors and fragrances market. Many of the natural ingredients used in flavors and fragrances market are expensive because there is limited supply and the synthetic alternatives require complex chemical conversions. Amyris intends to offer flavors and fragrances companies a natural route to procure these ingredients without sacrificing cost or quality.

Currently, we are working with partners to develop a variety of flavors and fragrances ingredients that are either direct fermentation target molecules or derivatives of fermentation target molecules.

We plan to participate in the flavors and fragrance market by providing sustainable replacements that are high quality, reliably available, and competitively priced. To begin to develop our product offerings in this area, we have established various partnerships, including:


•	A collaboration agreement with a global flavors and fragrances company for development and commercialization of various compounds for the flavors and fragrances market. Under this agreement, we conduct development activities and grant the partner licenses under our technology for commercialization of the compounds in exchange for funding and a profit sharing arrangement.

•

A joint development and license agreement with a leading global creator of flavors and fragrances for consumer products for specified fragrance molecules. Under the terms of the multi-year agreement, we are jointly developing these fragrance ingredients for the flavors and fragrances market, and we and the collaboration partner will share in the economic value derived from these ingredients. The agreement provides for specified funding during the term of the agreement based upon the achievement of certain technical milestones.

Performance Materials

Polymers are used in the manufacture of thousands of products that incorporate plastics and other polymeric materials, and we believe Biofene has the potential to provide significant opportunities for development of renewable ingredients and additives for the polymer market.

In July 2011, we entered into a collaboration agreement with Kuraray to develop certain polymers from Biofene. Under the agreement, Kuraray will develop polymers from Biofene to replace or complement petroleum-derived molecules such as butadiene and isoprene in the production of specified classes of high-performing polymers. Upon successful completion of the technical development program for the first polymer, Amyris and Kuraray would enter into a supply agreement for Kuraray's exclusive use of Biofene in the manufacturing and commercialization of these polymer products.

Our synthetic biology platform is able to produce other building blocks with the potential to provide an array of new renewable polymers to serve a variety of markets. For instance, we are working with Michelin to produce renewable isoprene and acquired a muconic acid platform that allows us to expand to a broad range of plastic additives and other applications.

Transportation Fuels

We have selected diesel as our primary area of focus within the transportation fuels market because of its projected global demand growth, the lack of a scalable, competitive renewable product, and our belief that our fuel product has properties superior to those of existing renewable alternatives. In general, our renewable diesel is produced by the simple chemical step of the hydrogenation of Biofene. Hydrogenation is a common chemical process currently used in the production of numerous products, such as saturation of vegetable oils to make margarine.

In November 2011 and July 2012, we entered into amendments of our technology license, development, research and collaboration agreement with Total, and in November 2013 and December 2013 we established a joint venture with Total with respect to such programs to establish a renewable diesel development program as described in more detail below under "Total Collaboration Products." We are in the process of obtaining jet fuel certification as part of a two-year program to open up the market and launch jet fuel in partnership with Total. We are waiting approval for use of our fuel in the aviation industry by the American Society for Testing and Materials (or ASTM).

We have completed significant steps to validate our ability to produce a market-accepted diesel product. By design, our product is a hydrocarbon of similar size to many of the hydrocarbons in petroleum-sourced diesel fuel. Due to the similarity of its chemical composition to that of existing petroleum-sourced diesel, our product has the properties required of diesel fuel and thereby satisfies the ASTM D975 Table 1 specifications for petroleum-derived diesel fuel oils. The Environmental Protection Agency (or EPA), has registered our diesel for use as a 35% blend with petroleum diesel in highway vehicles and non-road equipment and we are working to obtain registration for a higher blend with petroleum diesel, as opposed to the typical 3-10% blend of other bio-diesel products with petroleum diesel. We have received required approvals with Brazilian Agência Nacional do Petróleo, Gas Natural e Biocombustíveis (or ANP) for specific uses of our fuel in Brazil and have registered our Diesel Fuel with the California Air Resources Board (or CARB) and are pursuing registration or approvals with other relevant regulatory bodies.

Our ability to enter the diesel market is also dependent upon our ability to continue to achieve the required regulatory approvals in the global markets in which we will seek to sell our diesel products. These approvals primarily involve clearance by the relevant environmental agencies in the particular jurisdiction. For instance, in 2013, the EPA registered farnesane as a new chemical substance under the Toxic Substances Control Act (or TSCA), clearing the way for us to manufacture and sell farnesane without restrictions in the United States. We must also be certified by a sufficient number of diesel engine manufacturers, vehicle manufacturers or operators of large trucking fleets so that our diesel will have an appropriately large and accessible addressable market. These certification processes include fuel analysis modeling and the testing of engines and their components to ensure that the use of our diesel fuel does not degrade performance or reduce the lifecycle of the engine or cause it to fail to meet emissions standards.

We have completed successful engine testing of our diesel fuel with Cummins Engine Company (or Cummins), and Mercedes-Benz Brasil at a blend of up to 10%, and our renewable diesel has received OEM engine warranties from Cummins, Volkswagen AG and Mercedes-Benz Brasil for demonstration purposes. We continue to work with other diesel engine manufacturers to qualify our product for use in their engines.

Total Collaboration Products

We have a license, development, research and collaboration agreement with Total that sets forth the terms for the research, development, production and commercialization of chemical and/or fuels products to be agreed on by the parties. The agreement establishes a multi-phased process through which compounds are identified, screened, selected for product feasibility studies, and then ultimately selected as a lead compound for development. To commercialize any strains and compounds that are developed, Amyris and Total expect to form one or more joint ventures, the first of which is the fuels joint venture described below. Both Amyris and Total retain certain rights to make covered products independently subject to making royalty payments to the non-producing party, and Total has certain rights to require Amyris to work on non-collaboration projects. We have retained rights to produce and commercialize products in the following markets: flavors and fragrances; cosmetics, pharmaceuticals, consumer packaged goods, food additives, and pesticides. The first programs we are focusing on with Total relate to renewable diesel and jet fuel and industrial lubricants; however, we and Total retain the right to propose product development programs under these agreements in the future.

In November 2011, we entered into an amendment of the collaboration agreement with Total with respect to development and commercialization of Biofene for diesel. This represented an expansion of the initial collaboration that the parties established in 2010, and established a global, exclusive collaboration for the development of Biofene for diesel and a framework for the creation of a joint venture to manufacture and commercialize Biofene for diesel. In July 2012 and December 2013, we entered into a series of agreements to establish a research and development program and form a joint venture to produce and commercialize Biofene-based diesel and jet fuels, which joint venture was formed in December 2013. With an exception for our fuels business in Brazil, the collaboration and joint venture establish the exclusive means for us to develop, produce and commercialize fuels from Biofene. We granted the joint venture exclusive licenses under certain of our intellectual property to make and sell joint venture products. We also granted the joint venture, in the event of a buy-out of our interest in the joint venture by Total (which Total is entitled to do under certain circumstances) a non-exclusive license to optimize or engineer yeast strains used by us to produce farnesene for the joint venture’s diesel and jet fuels.

Product Distribution and Sales

We intend to distribute and sell our products either directly, through joint ventures, or with partners, depending on the market. For most chemical applications, we intend to sell directly to specialty chemical and consumer products companies. Generally, our collaboration agreements do not include any specific purchase obligations, and sales are contingent upon achievement of technical and commercial milestones. In addition, we expect to commercialize certain products, including fuels and base oils through joint venture arrangements with Total and Cosan, respectively.

Commencing in 2008, we began developing a fuels distribution network and distribution capabilities in the U.S. through Amyris Fuels. Through mid-2012, we purchased ethanol produced by third parties and gasoline and sold both pure ethanol and reformulated ethanol-blended gasoline to wholesale customers. For 2012, Mansfield Oil Company accounted for more than 10% of our reported revenues by virtue of its purchases of ethanol and reformulated ethanol-blended gasoline from Amyris Fuels. Collaboration revenues from Total also accounted for more than 10% of our reported revenues in 2012. Customers purchased ethanol and ethanol-blended gasoline from us under short-term agreements and spot transactions, and we generally did not have any contractual commitments from customers to purchase ethanol and ethanol-blended gasoline from us over any period of time. Nearly all of our customer revenue through the third quarter of 2012 came from the sale of ethanol and reformulated ethanol-

blended gasoline, with the remainder of our revenues coming from collaborations and government grants and, more recently, sales of our renewable products. In the third quarter of 2012, we transitioned out of the ethanol and ethanol-blended gasoline business. We do not expect to be able to replace much of the revenue lost as a result of this transition, particularly in 2013, while we continue our efforts to establish a renewable products business. Renewable product sales to Nikko Chemicals Co., Ltd. (Nikko) and collaboration revenue from Firmenich, International Flavors & Fragrances Inc. (IFF), and the Defense Advanced Research Projects Agency (or DARPA) each accounted for more than 10% of our reported revenues in 2013.

Intellectual Property

Our success depends in large part upon our ability to obtain and maintain proprietary protection for our products and technologies, and to operate without infringing the proprietary rights of others. We seek to avoid the latter by monitoring patents and publications in our product areas and technologies to be aware of developments that may affect our business, and to the extent we identify such developments, evaluate and take appropriate courses of action. With respect to the former, our policy is to protect our proprietary position by, among other methods, filing for patent applications on inventions that are important to the development and conduct of our business with the U.S. Patent and Trademark Office (or the USPTO), and its foreign counterparts.

As of January 31, 2014, we had 247 issued U.S. and foreign patents and 327 pending U.S. and foreign patent applications that are owned by or licensed to us. We also use other forms of protection (such as trademark, copyright, and trade secret) to protect our intellectual property, particularly where we do not believe patent protection is appropriate or obtainable. We aim to take advantage of all of the intellectual property rights that are available to us and believe that this comprehensive approach provides us with a strong proprietary position.

Patents extend for varying periods according to the date of patent filing or grant and the legal term of patents in various countries where patent protection is obtained. The actual protection afforded by patent, which can vary from country to country, depends on the type of patent, the scope of its coverage and the availability of legal remedies in the country. See “Risk Factors-Risks Related to Our Business-Our proprietary rights may not adequately protect our technologies and product candidates.”

We also protect our proprietary information by requiring our employees, consultants, contractors and other advisers to execute nondisclosure and assignment of invention agreements upon commencement of their respective employment or engagement. Agreements with our employees also prevent them from bringing the proprietary rights of third parties to us. In addition, we also require confidentiality or material transfer agreements from third parties that receive our confidential data or materials.

Competition

We expect that our renewable products will compete with both the traditional, largely petroleum-based specialty chemical and fuels products that are currently being used in our target markets and with the alternatives to these existing products that established enterprises and new companies are seeking to produce.

Chemical Products

In the specialty chemical markets that we are initially seeking to enter, and in other chemical markets that we may seek to enter in the future, we will compete primarily with the established providers of chemicals currently used in products in these markets. Producers of these incumbent products include global oil companies, large international chemical companies and companies specializing in specific products, such as squalane or essential oils. We may also compete in one or more of these markets with products that are offered as alternatives to the traditional petroleum-based or other traditional products being offered in these markets.

Transportation Fuel Products

In the transportation fuels market, we expect to compete with independent and integrated oil refiners, advanced biofuels companies and biodiesel companies. Refiners compete with us by selling traditional fuel products and some are also pursuing hydrocarbon fuel production using non-renewable feedstocks, such as natural gas and coal, as well as processes using renewable feedstocks, such as vegetable oil and biomass. We also expect to compete with companies that are developing the capacity to produce diesel and other transportation fuels from renewable resources in other ways. These include advanced biofuels companies using specific enzymes that they have developed to convert cellulosic biomass, which is non-food plant material such as wood chips, corn stalks and sugarcane bagasse, into fermentable sugars. Similar to us, some companies are seeking to use engineered enzymes to convert sugars, in some cases from cellulosic biomass and in others from natural sugar sources, into renewable diesel and other fuels. Biodiesel companies convert vegetable oils and animal oils into diesel fuel and some are seeking to produce diesel and other transportation fuels using thermochemical methods to convert biomass into renewable fuels.

Competitive Factors

We believe the primary competitive factors in both the chemicals and fuels markets are:


•	product price;


•	product performance and other measures of quality;


•	infrastructure compatibility of products;


•	sustainability; and


•	dependability of supply.

We believe that for our chemical products to succeed in the market, we must demonstrate that our products are comparable alternatives to existing products and to any alternative products that are being developed for the same markets based on some combination of product cost, availability, performance, and consumer preference characteristics. With respect to our diesel and other transportation fuels products, we believe that our product must perform as effectively as petroleum-based fuel, or alternative fuels, and be available on a cost-competitive basis. In addition, with the wide range of renewable fuels products under development, we must be successful in reaching potential customers and convincing them that ours are effective and reliable alternatives.

Environmental and Other Regulatory Matters

Our development and production processes involve the use, generation, handling, storage, transportation and disposal of hazardous chemicals and radioactive and biological materials. We are subject to a variety of federal, state, local and international laws, regulations and permit requirements governing the use, generation, manufacture, transportation, storage, handling and disposal of these materials in the United States, Brazil and other countries where we operate or may operate or sell our products in the future. These laws, regulations and permits can require expensive fees, pollution control equipment or operational changes to limit actual or potential impact of our technology on the environment and violation of these laws could result in significant fines, civil sanctions, permit revocation or costs from environmental remediation. We believe we are currently in substantial compliance with applicable environmental regulations and permitting. However, future developments including our commencement of commercial manufacturing of one or more of our products, more stringent environmental regulation, policies and enforcement, the implementation of new laws and regulations or the discovery of unknown environmental conditions may require expenditures that could have a material adverse effect on our business, results of operations or financial condition. See “Risk Factors-Risks Relating to Our Business-We may incur significant costs complying with environmental laws and regulations, and failure to comply with these laws and regulations could expose us to significant liabilities.”

The use of genetically-modified microorganisms (or GMMs), such as our yeast strains, is subject to laws and regulations in many countries. In the United States, the EPA regulates the commercial use of GMMs as well as potential products produced from the GMMs. Various states within the United States could choose to regulate products made with GMMs as well. While the strain of genetically modified yeast that we use, S. cerevisiae , is eligible for exemption from EPA review because the EPA recognizes it as posing a low risk we must satisfy certain criteria to achieve this exemption, including but not limited to use of compliant

containment structures and safety procedures. In Brazil, GMMs are regulated by the National Biosafety Technical Commission (or the CTNBio) under its Biosafety Law No. 11.105-2005. We have obtained approval from CTNBio to generally use GMMs under specific conditions in our Campinas facilities and our production plant in Brotas for research and development purposes. In addition, we have received CTNBio approval for commercial use of a specific strain in our Brotas plant.

We expect to encounter GMM regulations in most if not all of the countries in which we may seek to make our products, however, the scope and nature of these regulations will likely be different from country to country. If we cannot meet the applicable requirements in countries in which we intend to produce our products using our yeast strains, then our business will be adversely affected. See “Risk Factors-Risks Related to Our Business-Our use of genetically-modified feedstocks and yeast strains to produce our products subjects us to risks of regulatory limitations and rejection of our products.”

Our renewable chemical products may be subject to government regulations in our target markets. In the United States, the EPA administers the requirements of the TSCA, which regulates the commercial registration, distribution, and use of many chemicals. Before an entity can manufacture or distribute significant volumes of a chemical, it needs to determine whether that chemical is listed in the TSCA inventory. If the substance is listed, then manufacture or distribution can commence immediately. If not, then in most cases a “Chemical Abstracts Service” number registration and pre-manufacture notice must be filed with the EPA, which has up to 90 days to review the filing.

Our diesel and jet fuel is subject to regulation by various government agencies. In the United States, this includes the EPA and the CARB. In Brazil, this includes ANP. To date we have obtained registration with the EPA for the use of our diesel in the United States at a 35% blend rate with petroleum diesel. In addition, ANP has authorized the use of our diesel fuel at blend rates of 10% and 30% for specific transportation fleets. In Europe, we obtained Registration, Evaluation, Authorization, and Restriction of Chemical Substances (or REACH) registration for importing/manufacturing up to 1,000 metric tons of farnesane (our diesel fuel) per year and are pursuing data validation for greater volumes. Registration with each of these bodies is required for the sale and use of our fuels within their respective jurisdictions. Jet fuel (aviation turbine fuel) validation and specifications are subject to the ASTM International industry consensus process and the Brazilian ANP national adoption process. Our jet fuel must also be validated and supported by an applicable ASTM aviation turbine fuel standard. Any failure to achieve required validation and certification for our jet fuel could impair or delay our plans to introduce a jet fuel product in 2014, which would have a material adverse impact on our renewable product revenues for the year. In addition, for us to achieve full access to the United States fuels market for our fuel products, we will need to obtain EPA and CARB (and potentially other state agencies) certifications for our feedstock pathway and production facilities, including certification of a feedstock lifecycle analysis relating to greenhouse gas emissions. Any delay in obtaining these additional certifications could impair our ability to sell our renewable fuels to refiners, importers, blenders and other parties that produce transportation fuels as they comply with federal and state requirements to include certified renewable fuels in their products. See “Risk Factors-Risks Related to Our Business-We may not be able to obtain regulatory approval for the sale of our renewable products.”

Research and Development

We devote substantial resources to our research and development efforts. As of February 28, 2014 , our research and development organization included approximately 199 employees, 65 of whom held Ph.D.s. Our technology development is currently focused primarily on improving the performance of our production strains and on developing strains that produce new molecules. To facilitate the transfer of our fermentation technology to production, we operate pilot-scale fermentation facilities in both Emeryville, California and Campinas, Brazil, and transfer strains on a regular basis. Our process consists of a number of discrete steps including:


•	identifying new target molecules


•	creating new microbial strains capable of producing the target molecule


•	increasing product yield and productivity from microbial strains through strain modification or fermentation improvements


•	increasing efficiency of product separation and purification


•	continuous translation of these steps from lab to commercial scale production.

Our research and development expenditures were approximately $56.1 million , $73.6 million , and $87.3 million for the fiscal years ended December 31, 2013, 2012 and 2011 , respectively.

Employees

As of February 28, 2014 , we had 392 full-time employees. Of these employees, 233 were in the United States and 159 were in Brazil. Except for labor union representation for Brazil-based employees based on labor code requirements in Brazil, none of our employees is represented by a labor union or is covered by a collective bargaining agreement. We have never experienced any employment-related work stoppages and consider relations with our employees to be good.

Financial Information About Geographic Areas

Financial information regarding revenues and long-lived assets by geographic area is included in Note 15, "Reporting Segments” in “Notes to Consolidated Financial Statements” included in this Form 10-K.

Business Background and Available Information

We organized our business in July 2003 as a California corporation under the name Amyris Biotechnologies, Inc. and have maintained our headquarters and research facilities in the San Francisco Bay Area since that time. In June 2010, we reincorporated in Delaware and changed our name to Amyris, Inc. We commenced research activities in 2005, focusing on the development of an alternative source of artemisinic acid for the treatment of malaria and launched research efforts for production of Biofene in 2006. In 2008, we began to sell third party ethanol to wholesale customers through our Amyris Fuels subsidiary, which generated revenue from the sale of ethanol and reformulated ethanol-blended gasoline to wholesale customers through a network of terminals in the eastern United States. We completed our planned transition out of the ethanol and ethanol-blended gasoline business in the third quarter of 2012, though we continue to maintain the Amyris Fuels subsidiary for activities related to renewable fuel sales. We first established a presence in Brazil in 2008 through the opening of laboratories in Campinas. Our corporate headquarters are located at 5885 Hollis Street, Suite 100, Emeryville, CA 94608, and our telephone number is (510) 450-0761. Our website address is www.amyris.com. The information contained in or accessible through our website or contained on other websites is not deemed to be part of this report on Form 10‑K.

We are subject to the filing requirements of the Securities Exchange Act of 1934. Therefore, we file periodic reports, proxy statements and other information with the Securities and Exchange Commission. Such reports, proxy statements and other information may be obtained by visiting the Public Reference Room of the Securities and Exchange Commission at 100 F Street, NE, Washington, D.C. 20549. You may obtain information regarding the operation of the Public Reference Room by calling the Securities and Exchange Commission at 1-800-SEC-0330. In addition, the Securities and Exchange Commission maintains a website (www.sec.gov) that contains reports, proxy and information statements, and other information regarding issuers that file electronically.

We make our annual reports on Form 10-K, quarterly reports on Form 10-Q, current reports on Form 8-K and all amendments to such reports filed or furnished pursuant to Section 13(a) or 15(d) of the Securities Exchange Act of 1934 available free of charge through a link on the Investors section of our website located at www.amyris.com (under “Financial Information-SEC Filings”) as soon as reasonably practicable after they are filed with or furnished to the Securities and Exchange Commission.

ITEM 1A. RISK FACTORS

Investing in our common stock involves a high degree of risk. You should carefully consider the risks and uncertainties described below, together with all of the other information set forth in this Annual Report on Form 10-K, which could materially affect our business, financial condition or future results. If any of the following risks actually occurs, our business, financial condition, results of operations and future prospects could be materially and adversely harmed. The trading price of our common stock could decline due to any of these risks, and, as a result, you may lose all or part of your investment.

Risks Related to Our Business

We have incurred losses to date, anticipate continuing to incur losses in the future and may never achieve or sustain profitability.

We have incurred significant losses in each year since our inception and believe that we will continue to incur losses and negative cash flow from operations into at least 2014. As of December 31, 2013 , we had an accumulated deficit of $821.4 million and had cash, cash equivalents and short term investments of $8.3 million . We have significant outstanding debt and contractual obligations related to purchase commitments, as well as capital and operating leases. As of December 31, 2013 , our debt totaled $152.1 million , net of discount of $27.9 million, of which $6.4 million matures within the next twelve months. In January 2014, we closed the issuance of an additional $34.0 million of debt pursuant to agreements entered into in 2013. In addition, our debt agreements contain various covenants, including restrictions on business that could cause us to be at risk of defaults. We expect to incur additional costs and expenses related to the continued development and expansion of our business, including construction and operation of our manufacturing facilities, contract manufacturing, research and development operations, and operation of our pilot plants and demonstration facility. There can be no assurance that we will ever achieve or sustain profitability on a quarterly or annual basis.

We have limited experience producing our products at commercial scale and may not be able to commercialize our products to the extent necessary to sustain and grow our current business.

To commercialize our products, we must be successful in using our yeast strains to produce target molecules at commercial scale and at a commercially viable cost. If we cannot achieve commercially-viable production economics for enough products to support our business plan, including through establishing and maintaining sufficient production scale and volume, we will be unable to achieve a sustainable integrated renewable products business. Virtually all of our production capacity is through a purpose-built, large-scale production plant in Brotas, Brazil. This plant commenced operations in 2013, and scaling and running the plant has been, and continues to be, a time-consuming, costly, uncertain and expensive process. Given our limited experience commissioning and operating our own manufacturing facilities and our limited financial resources, we cannot be sure that we will be successful achieving production economics that allow us to meet our plans for commercialization of various products we intend to offer. In addition, to date we have only produced Biofene at the Brotas plant. Our attempts to scale production of new molecules at the plant is subject to uncertainty and risk. For example, even to the extent we successfully complete product development in our laboratories and pilot and demonstration facilities, and at contract manufacturing facilities, we may be unable to translate such success to large-scale, purpose-built plants. If this occurs, our ability to commercialize our technology will be adversely affected and we may be unable to produce and sell any significant volumes of our products. Also, with respect to products that we are able to bring to market, we may not be able to lower the cost of production, which would adversely affect our ability to sell such products profitably.

We will require significant inflows of cash from financing and collaboration transactions to fund our anticipated operations and may not be able to obtain such financing and collaboration funding on favorable terms, if at all.

Our planned 2014 and 2015 working capital needs and our planned operating and capital expenditures for 2014 and 2015 are dependent on significant inflows of cash from existing and new collaboration partners and cash contribution from growth in renewable product sales, as well as additional funding from new joint ventures or other collaborations, and may also require additional funding from equity financings, credit facilities or loans, especially to the extent that we are unable to ramp up positive gross margin product sales or close on sufficient funding from existing and new collaboration partners. We will continue to need to fund our research and development and related activities and to provide working capital to fund production, storage, distribution and other aspects of its business. Some of our existing anticipated financing sources, such as research and development collaborations, are subject to the risk that we cannot meet milestones or are not yet subject to definitive agreements or mandatory funding commitments and, if needed, we may not be able to secure additional types of financing in a timely manner or on reasonable terms, if at all.

In 2013, we completed several equity and convertible debt financings to provide us with cash resources to pursue our business plans. In August 2013, we entered into an agreement with Total and Maxwell (Mauritius) Pte Ltd, (or Temasek), to sell up to $73.0 million in convertible promissory notes in private placements over a period of up to 24 months from the date of signing (referred to as the August 2013 Financing). The August 2013 Financing was divided into two tranches (one for $42.6 million and one for $30.4 million ), each with differing closing conditions. Of the total possible purchase price in the financing, $60.0 million was to be paid in the form of cash by Temasek ( $35.0 million in the first tranche and up to $25.0 million in the second tranche) and $13.0 million was to be paid by cancellation of outstanding convertible promissory notes held by Total in connection with its exercise of pro rata rights ($7.6 million in the first tranche and $5.4 million in the second tranche). In October 2013, the Company amended the agreement for the August 2013 Financing to include entities affiliated with FMR LLC (referred to as the Fidelity Entities) as additional investors for the first tranche in the principal amount of $7.6 million, and to proportionally increase the amount acquired by exchange and cancellation of outstanding convertible promissory notes held by Total to $14.6 million ($9.2 million in the first tranche and up to $5.4 million in the second tranche). Prior to the closing of the first tranche of the August Financing, Temasek advanced $35.0 million of financing through the purchase of a senior bridge note (referred to as the Temasek Bridge Note) due at the first closing. Also in October 2013, we completed the initial closing of the first tranche of the August 2013 Financing, issuing a total of $51.8 million in convertible promissory notes for cash proceeds of $7.6 million and cancellation of outstanding promissory notes and convertible promissory notes of $44.2 million, of which $35.0 million resulted from the cancellation of the Temasek Bridge Note. In December 2013, we agreed to sell an additional $3.0 million of senior convertible notes in the second tranche of the August 2013 Financing to funds affiliated with Wolverine Asset Management (or Wolverine) and we elected to call $25.0 million in additional funds from Temasek pursuant to its previous commitment to purchase such amount of convertible promissory notes in the second tranche. Additionally, in December 2013, we agreed to sell approximately $6.0 million of convertible promissory notes in the second tranche to Total through cancellation of the same amount of principal of previously outstanding convertible notes held by Total (in respect of Total’s preexisting contractual right to maintain its pro rata ownership position through such cancellation of indebtedness). In January 2014, we completed the offering of such convertible promissory notes in the second tranche.

The terms of the August 2013 Financing include significant potential reductions in the conversion price for the notes if we do not meet certain performance milestones and other conditions. These conditions, if triggered, could result in further reductions to the conversion price that would cause significant additional dilution to our stockholders if the notes are ultimately converted. Furthermore, if not converted, we may not have sufficient cash to repay the notes when they become due, which could result in insolvency and related issues. In addition, we were required to agree to significant covenants that have an impact on our ability to engage in certain transactions. For example, the purchase agreement for the August 2013 Financing (referred to as the August 2013 SPA) requires us to obtain the consent of a majority of the purchasers in the financing before completing any change-of-control transaction, or purchasing assets in one transaction or a series of related transactions in an amount greater than $20.0 million, in each case while the notes are outstanding. We also agreed to provide the purchasers with pro rata rights under which they could cancel up to the full amount of outstanding notes to pay for equity securities if we raise additional financing during the term of the notes, which could delay or prevent us from obtaining additional financing if the purchasers do not support it.

To the extent we obtain funding through the issuance of additional equity securities, our existing stockholders will suffer dilution. For example, in 2013, we completed private placements of our common stock that resulted in the issuance of approximately 6.6 million shares of our common stock. Also, in 2013, including the August 2013 Financing and research and development-related funding, we issued approximately $72.6 million in senior convertible promissory notes that are convertible into common stock. In June 2013 and July 2013 we issued an aggregate $30.0 million of convertible promissory notes with a conversion price of $3.08 per share pursuant to our arrangement with Total for research an development-related funding. In October 2013, we issued $51.8 million in convertible promissory notes that are convertible into common stock at an initial conversion price of $2.44 , and in December 2013, we agreed to issue approximately $34.0 million in convertible promissory notes that are convertible into common stock at an initial conversion price of $2.87, each as part of the August Financing. The placement of $34.0 million of senior unsecured convertible notes closed in January 2014. Through 2015, we may issue up to an aggregate of $21.7 million in additional unsecured senior convertible promissory notes, with a conversion price of $7.0682 per share, under the agreements with Total described below under the risk factor, “Our relationship with our strategic partner, Total, may have a substantial impact on our company.” Furthermore, under the convertible note financing approved by the stockholders of the Company in September 2013, we may issue up to an additional $3.2 million in convertible promissory notes at an initial conversion price of $2.44, and up to an additional $20.96 million in convertible promissory notes at a conversion price of $2.87. In addition, in connection with the initial closing of the August 2013 Financing, we issued a warrant to Temasek to purchase 1,000,000 shares of our common stock at an exercise price of $0.01 per share, exercisable only if Total converts certain preexisting convertible promissory notes.

In addition to dilution, to the extent we issue convertible promissory notes and similar instruments, we would become subject to various covenants, including restrictions on our business, that could cause us to be at risk of defaults. For example, the convertible notes we issued in 2012, 2013 and early 2014 contain various covenants, including restrictions on the amount of debt we are permitted to incur, a loan and security agreement we entered into in March 2014 included covenants regarding fund raising, cash

flows and revenues, and the convertible notes or other debt we may issue in connection with future debt financings could contain similar covenants.

In addition to debt and equity financing, we depend on collaboration funding to support our operating expenses. While part of this funding is committed based on existing collaboration agreements, our 2014 business plan depends on identifying and obtaining funding under additional collaborations that are not yet subject to any definitive agreement or are not yet identified. In addition, some of our existing anticipated collaboration funding is subject to our achievement of milestones or other funding conditions. If we cannot secure sufficient collaboration funding to support our operating expenses in excess of cash contributions from product sales and existing debt and equity financing, in order to raise sufficient funds to finance our ongoing operations, we may need to issue additional preferred and discounted equity, agree to onerous covenants, grant further security interests in our assets, enter into collaboration and licensing arrangements that require us to relinquish commercial rights or grant licenses on terms that are not favorable to us, or any or all of these possibilities. If we fail to secure such funding, we could be forced to curtail our operations, which would have a material adverse effect on our ability to continue with our business plans and on our status as a going concern.

If we are unable to raise additional financing, or if other expected sources of funding are delayed or not received, we would take the following actions as early as the second quarter of 2014 to support our liquidity needs through the remainder of 2014 and into 2015:


•	Effect significant headcount reductions in the United States and in Brazil, particularly with respect to both general and administrative employees and other employees not connected to critical or contracted activities.


•	Shift our focus to existing products and customers with significantly reduced investment in new product and commercial development efforts.


•	Reduce our expenditures for third party contractors, including consultants, professional advisors and other vendors.


•	Suspend operations at our pilot plants and demonstration facilities.


•	Reduce or delay uncommitted capital expenditures, including non-essential lab equipment and information technology projects.

The contingency cash plan contemplating these actions is designed to save an estimated $25.0 million to $35.0 million over the next twelve months. Implementing this plan could have a material negative impact on our ability to continue our business as currently contemplated, including, without limitation, delays or failures in its ability to:


•	Achieve planned production levels;


•	Develop and commercialize products within planned timelines or at planned scales; and


•	Continue other core activities.

Furthermore, any inability to scale-back operations as necessary, and any unexpected liquidity needs, could create pressure to implement more severe measures. Such measures could have a material adverse effect on our ability to meet contractual requirements, including obligations to maintain manufacturing operations, and increase the severity of the consequences described above.

If our major production facilities do not successfully commence or scale up operations, our customer relationships, business and results of operations may be adversely affected.

A substantial component of our planned production capacity in the near and long term depends on successful operations at our initial and planned large-scale production plants in Brazil. We are in the early stages of operating our first purpose-built, large-scale production plant in Brotas, Brazil and may complete construction of certain other facilities in the coming years. Delays or problems in the construction, start-up or operation of these facilities will cause delays in our ramp-up of production and hamper our ability to reduce our production costs. Delays in construction can occur due to a variety of factors, including regulatory requirements and our ability to fund construction and commissioning costs. Once our large-scale production facilities are built, we must successfully commission them and they must perform as we have designed them. If we encounter significant delays, cost overruns, engineering issues, contamination problems, equipment or raw material supply constraints, unexpected equipment

maintenance requirements, safety issues, work stoppage or other serious challenges in bringing these facilities online and operating them at commercial scale, we may be unable to produce our initial renewable products in the time frame we have planned. For example, we are planning to start using our plant at Brotas to produce molecules beyond Biofene. To date, we have only produced Biofene at the plant. In order to produce additional molecules at Brotas, we are required to perform thorough transition activities, and modify the design of the plant. Any modifications to the production plant could cause complications in the start-up and operations of the plant, which could result in delays or failures in production. We may also need to continue to use contract manufacturing sources more than we expect (e.g., if the modifications to the Brotas plant are not successful or have a negative impact on the plant's operations), which would reduce our anticipated gross margins and may prevent us from accessing certain markets for our products. Further, if our efforts to increase (or complete and commence, as the case may be) production at these facilities are not successful, other mill owners in Brazil or elsewhere may decide not to work with us to develop additional production facilities, demand more favorable terms or delay their commitment to invest capital in our production.

Our reliance on the large-scale production plant in Brotas, Brazil subjects us to execution and economic risks.

Our decision to focus our efforts for production capacity on the manufacturing facility in Brotas, Brazil means that we will have limited manufacturing sources for our products in 2014 and beyond. Accordingly, any failure to establish operations at that plant could have a significant negative impact on our business, including our ability to achieve commercial viability for our products. With the facility in Brotas, Brazil, we are, for the first time, operating a commercial fermentation and separation facility. We are inexperienced at operating plants and may face unexpected difficulties associated with the operation of the plant. For example, we have in the past, at certain contract manufacturing facilities, encountered significant delays and difficulties in ramping up production based on contamination in the production process, problems with plant utilities, lack of automation and related human error, issues arising from process modifications to reduce costs and adjust product specifications, and other similar challenges. Such challenges could arise in our plant in Brotas, Brazil, and we cannot be certain that we will be able to remedy them quickly or effectively enough to achieve commercially viable near-term production costs and volumes.

As part of our arrangement to build the plant in Brotas, Brazil we have an agreement with Paraíso Bioenergia to purchase from Paraíso Bioenergia sugarcane juice corresponding to a certain number of tons of sugarcane per year, along with specified water and vapor volumes. Until this annual volume is reached, we are restricted from purchasing sugarcane juice for processing in the facility from any third party, subject to limited exceptions, unless we pay the premium to Paraíso Bioenergia that we would have paid if we bought the juice from them. As such, we will be relying on Paraíso Bioenergia to supply such juice and utilities on a timely basis, in the volumes we need, and at competitive prices. If a third party can offer superior prices and Paraíso Bioenergia does not consent to our purchasing from such third party, we would be required to pay Paraíso Bioenergia the applicable premium, which would have a negative impact on our production cost. Furthermore, we agreed to pay a price for the juice that is based on the lower of the cost of two other products produced by Paraíso Bioenergia using such juice, plus a premium. Paraíso Bioenergia may not want to sell sugarcane juice to us if the price of one of the other products is substantially higher than the one setting the price for the juice we purchase. While the agreement provides that Paraíso Bioenergia would have to pay a penalty to us if it fails to supply the agreed-upon volume of juice for a given month, the penalty may not be enough to compensate us for the increased cost if third-party suppliers do not offer competitive prices. Also, if the prices of the other products produced by Paraíso Bioenergia increase, we could be forced to pay those increased prices for production without a related increase in the price at which we can sell our products, reducing or eliminating any margins we can otherwise achieve. If in the future these supply terms no longer provide a viable economic structure for the operation in Brotas, Brazil we may be required to renegotiate our agreement, which could result in manufacturing disruptions and delays.

Furthermore, as we continue to scale up production of our products, both through contract manufacturers and at our large-scale production plant in Brotas, Brazil, we may be required to store increasing amounts of our products for varying periods of time and under differing temperatures or other conditions that cannot be easily controlled, which may lead to a decrease in the quality of our products and their utility profiles and could adversely affect their value. If our stored products degrade in quality, we may suffer losses in inventory and incur additional costs in order to further refine our stored products or we may need to make new capital investments in shipping, improved storage or sales channels and related logistics.

Our joint venture with São Martinho S.A. subjects us to certain legal and financial terms that could adversely affect us.

We have various agreements with SMSA that contemplate construction of another large-scale manufacturing facility as a joint venture in Brazil. Under these agreements, we are responsible for designing and managing the construction project, and are responsible for the initial construction costs. We projected the construction costs of the project to be approximately $100.0 million . While we completed a significant portion of the construction of the plant before 2012, we delayed further construction and commissioning of the plant while we constructed and commissioned our production plant in Brotas, Brazil and we expect to continue to defer the SMA project for the near term based on economic considerations and to allow us to focus on operations at our production plant in Brotas, Brazil. We entered into an amendment to the joint venture agreement with SMSA in February 2014

which updates and documents certain preexisting business plan requirements related to the start-up of construction at the plant and sets forth, among other things, (i) the extension of the deadline for the commencement of operations at the joint venture operated plant to no later than 18 months following the construction of the plant, which shall occur no later than March 31, 2017, and (ii) the extension of an option held by SMSA to build a second large-scale farnesene production facility to no later than December 31, 2018 with the commencement of operations at such second facility to occur no later than April 1, 2019. While SMSA was obligated to contribute up to approximately R$61.8 million (approximately US$26.4 million based on the exchange rate as of December 31, 2013) to the construction of the original plant, such contributions depended on, among other things, successful commencement of operations at the plant. Notwithstanding the February 2014 amendment to the joint venture agreement, based on our shifting manufacturing priorities and uncertainty regarding financing availability, we cannot currently predict exactly when or if our facility at SMSA will be completed or commence commercial operations, which means that SMSA's anticipated contribution will continue to be delayed and may never occur. SMSA holds rights with respect to the termination and acquisition of our interests in SMA. For instance, if Amyris Brasil becomes controlled, directly or indirectly, by a competitor of SMSA, then SMSA has the right to acquire our interest in the joint venture and if SMSA becomes controlled, directly or indirectly, by a competitor of ours, then we have the right to sell our interest in the joint venture to SMSA. In either case, the purchase price is to be determined in accordance with the joint venture agreements, as amended, and we would continue to have the obligation to acquire products produced by the joint venture for the remainder of the term of the supply agreement then in effect even though we might no longer be involved in the joint venture's management.

If we are ultimately successful in establishing the plant at SMSA, the agreements governing the joint venture subject us to terms that may not be favorable to us under certain conditions. For example, we are required to purchase the output of the joint venture for the first four years at a price that guarantees the return of SMSA's investment plus a fixed surcharge rate. We may not be able to sell the output at a price that allows us to achieve anticipated, or any, level of profitability on the product we acquire under these terms. Similarly, the return that we are required to provide the joint venture for products after the first four years may have an adverse effect on the profitability we achieve from acquiring the mill's output. Additionally, we are required to purchase the output of the joint venture regardless of whether we have a customer for such output, and our results of operations and financial condition would be adversely affected if we are unable to sell the output that we are required to purchase.

Loss or termination of contract manufacturing relationships could harm our ability to meet our production goals.

As we have focused on building and commissioning our own plant and improving our production economics, we have reduced our use of contract manufacturing and have terminated relationships with some of our contract manufacturing partners. The failure to have multiple available supply options for farnesene could create a risk for us if a single source or a limited number of sources of manufacturing runs into operational issues. In addition, if we are unable to secure the services of contract manufacturers when and as needed, we may lose customer opportunities and the growth of our business may be impaired. We cannot be sure that contract manufacturers will be available when we need their services, that they will be willing to dedicate a portion of their capacity to our projects, or that we will be able to reach acceptable price and other terms with them for the provision of their production services. If we shift priorities and adjust anticipated production levels (or cease production altogether) at contract manufacturing facilities, such adjustments or cessations could also result in disputes or otherwise harm our business relationships with contract manufacturers. In addition, reducing or stopping production at one facility while increasing or starting up production at another facility generally results in significant losses of production efficiency, which can persist for significant periods of time. Also, in order for production to commence under our contract manufacturing arrangements, we generally must provide equipment, and we cannot be assured that such equipment can be ordered or installed on a timely basis, at acceptable costs, or at all. Further, in order to establish new manufacturing facilities, we need to transfer our yeast strains and production processes from lab to commercial plants controlled by third parties, which may pose technical or operational challenges that delay production or increase our costs.

Our use of contract manufacturers exposes us to risks relating to costs, contractual terms and logistics .

While we have commenced commercial production at the Brotas, Brazil plant, we continue to commercially produce, process and manufacture some specialty molecules through the use of contract manufacturers, and we anticipate that we will continue to use contract manufacturers for the foreseeable future for chemical conversion and production of end-products and, to mitigate cost and volume risks at our large-scale production facilities, for production of Biofene and other fermentation target compounds. Establishing and operating contract manufacturing facilities requires us to make significant capital expenditures, which reduces our cash and places such capital at risk. For example, based on an evaluation of our assets associated with contract manufacturing facilities and anticipated levels of use of such facilities, we recorded a loss on purchase commitments and write off of production assets of approximately $9.4 million in the year ended December 31, 2013. Also, contract manufacturing agreements contain terms that commit us to pay for capital expenditures and other costs incurred or expected to be earned by the plant operators and owners, which can result in contractual liability and losses for us even if we terminate a particular contract manufacturing arrangement or decide to reduce or stop production under such an arrangement. For example, in June 2013, we entered into a termination agreement

with a contract manufacturer that required us to make payments totaling $8.8 million in 2013, of which $3.6 million was to satisfy outstanding obligations and $5.2 million was in lieu of additional payments otherwise owed.

The locations of contract manufacturers can pose additional cost, logistics and feedstock challenges. If production capacity is available at a plant that is remote from usable chemical finishing or distribution facilities, or from customers, we will be required to incur additional expenses in shipping products to other locations. Such costs could include shipping costs, compliance with export and import controls, tariffs and additional taxes, among others. In addition, we may be required to use feedstock from a particular region for a given production facility. The feedstock available in a particular region may not be the least expensive or most effective feedstock for production, which could significantly raise our overall production cost o reduce our product's quality until we are able to optimize the supply chain.

If we are unable to reduce our production costs, we may not be able to produce our products at competitive prices and our ability to grow our business will be limited.

Currently, our costs of production are not low enough to allow us to offer many of our planned products at competitive prices relative to alternatives available in the market. Our production costs depend on many factors that could have a negative effect on our ability to offer our planned products at competitive prices, including, in particular, our ability to establish and maintain sufficient production scale and volume, and feedstock cost. For example, see "We have limited experience producing our products and commercial scale and may not be able to commercialize our products to the extent necessary to sustain and grow our current business," "Our manufacturing operations require sugar feedstock, and the ability to obtain such feedstock in sufficient quantities or in a timely manner, or at reasonable prices, may limit our ability to produce products profitably or at all," and "The price of sugarcane and other feedstocks can be volatile as a result of changes in industry policy and may increase the cost of production of our products."

We face financial risk associated with scaling up production to reduce our production costs. To reduce per-unit production costs, we must increase production to achieve economies of scale and to be able to sell our products with positive margins. However, if we do not sell production output in a timely manner or in sufficient volumes, our investment in production will harm our cash position and generate losses. Additionally, we may incur added costs in storage and we may face issues related to the decrease in quality of our stored products, which could adversely affect the value of such products. Since achieving competitive product prices generally requires increased production volumes and our manufacturing operations and cash flows from sales are in their early stages, we have had to produce and sell products at a loss in the past, and expect to continue to do so as we build our business. If we are unable to achieve adequate revenues from a combination of product sales and other sources, we may not be able to invest in production and we may not be able to pursue our business plans.

Key factors beyond production scale and feedstock cost that impact our production costs include yield, productivity, separation efficiency and chemical process efficiency. Yield refers to the amount of the desired molecule that can be produced from a fixed amount of feedstock. Productivity represents the rate at which our product is produced by a given yeast strain. Separation efficiency refers to the amount of desired product produced in the fermentation process that we are able to extract and the time that it takes to do so. Chemical process efficiency refers to the cost and yield for the chemical finishing steps that convert our target molecule into a desired product. In order to successfully enter transportation fuels and certain chemical markets, we must produce those products at significantly lower costs, which will require both substantially higher yields than we have achieved to date and other significant improvements in production efficiency, including in productivity and in separation and chemical process efficiencies. There can be no assurance that we will be able to make these improvements or reduce our production costs sufficiently to offer our planned products at competitive prices, and any such failure could have a material adverse impact on our business and prospects.

Our ability to establish substantial commercial sales of our products is subject to many risks, any of which could prevent or delay revenue growth and adversely impact our customer relationships, business and results of operations.

There can be no assurance that our products will be approved or accepted by customers, that customers will choose our products over competing products, or that we will be able to sell our products profitably at prices and with features sufficient to establish demand. The markets we have entered first are primarily those for specialty chemical products used by large consumer products or specialty chemical companies. In entering these markets, we have sold and we intend to sell our products as alternatives to chemicals currently in use, and in some cases the chemicals that we seek to replace have been used for many years. The potential customers for our molecules generally have well developed manufacturing processes and arrangements with suppliers of the chemical components of their products and may have a resistance to changing these processes and components. These potential customers frequently impose lengthy and complex product qualification procedures on their suppliers, influenced by consumer preference, manufacturing considerations such as process changes and capital and other costs associated with transitioning to alternative components, supplier operating history, established business relationships, regulatory issues, product liability and other factors, many of which are unknown to, or not well understood by, us. Satisfying these processes may take many months or years. If we are unable to convince these potential customers (and the consumers who purchase products containing such chemicals) that our products are comparable to the chemicals that they currently use or that the use of our products is otherwise to their benefits, we will not be successful in entering these markets and our business will be adversely affected.

In order for our diesel fuel or jet fuel to be accepted in various countries around the world, a significant number of diesel engine and jet engine manufacturers or operators of large trucking or jet fleets, as the case may be, must determine that the use of our fuels in their equipment will not invalidate product warranties and that they otherwise regard our diesel fuel or jet fuel as an acceptable fuel so that our diesel will have an appropriately large and accessible addressable market. In addition, we must successfully demonstrate to these manufacturers that our fuel does not degrade the performance or reduce the life cycle of their engines or cause them to fail to meet applicable emissions standards. These certification processes include fuel analysis modeling and the testing of engines and their components to ensure that the use of our diesel fuel or jet fuel does not degrade performance or reduce the lifecycle of the engine or cause them to fail to meet applicable emissions standards.

Additionally, we may be subject to product safety testing and may be required to meet certain product safety standards. Meeting these suitability or safety standards can be a time consuming and expensive process, and we may invest substantial time and resources into such qualification efforts without ultimately securing approval. To date, our diesel fuel has achieved limited approvals from certain engine manufacturers, but we cannot be assured that other engine or vehicle manufacturers or fleet operators, will approve usage of our fuels. To distribute our diesel fuel, we must also meet requirements imposed by pipeline operators and fuel distributors. If these operators impose volume limitations on the transport of our fuels, our ability to sell our fuels may be impaired. Our ability to sell a jet fuel product is subject to similar types of qualification requirements as diesel (although the jet fuel qualification process is generally more rigorous, time consuming and expensive than for diesel).

Our ability to enter the fuels market is also dependent upon our ability to continue to achieve the required regulatory approvals in the global markets in which we will seek to sell our fuel products. These approvals primarily involve clearance by the relevant environmental agencies in the particular jurisdiction and are described below under the risk factors, "Our use of genetically-modified feedstocks and yeast strains to produce our products subjects us to risks of regulatory limitations and rejection of our products," "We may not be able to obtain regulatory approval for the sale of our renewable products," and "We may incur significant costs complying with environmental laws and regulations, and failure to comply with these laws and regulations could expose us to significant liabilities."

We expect to face competition for our specialty chemical and transportation fuels products from providers of petroleum-based products and from other companies seeking to provide alternatives to these products, and if we cannot compete effectively against these companies or products we may not be successful in bringing our products to market or further growing our business after we do so.

With the emergence of many new companies seeking to produce chemicals and fuels from alternative sources, we may face increasing competition from alternative fuels and chemicals companies. As they emerge, some of these companies may be able to establish production capacity and commercial partnerships to compete with us. If we are unable to establish production and sales channels that allow us to offer comparable products at attractive prices, we may not be able to compete effectively with these companies.

We believe the primary competitive factors in both the chemicals and fuels markets are:


•	product price;


•	product performance and other measures of quality;


•	infrastructure compatibility of products;


•	sustainability; and


•	dependability of supply.

The oil companies, large chemical companies and well-established agricultural products companies with whom we compete are much larger than us, have, in many cases, well developed distribution systems and networks for their products, have valuable historical relationships with the potential customers we are seeking to serve and have much more extensive sales and marketing programs in place to promote their products. In order to be successful, we must convince customers that our products are at least as effective as the traditional products they are seeking to replace and we must provide our products on a cost-competitive basis with these traditional products and other available alternatives. Some of our competitors may use their influence to impede the development and acceptance of renewable products of the type that we are seeking to produce.

Our relationship with our strategic partner, Total, has a substantial impact on our company.

We have a license, development, research and collaboration agreement with Total, under which we may develop, produce and commercialize products with Total. Under this agreement, Total has a right of first negotiation with us with respect to exclusive commercialization arrangements that we would propose to enter into with third parties, as well as the right to purchase any of our products on terms not less favorable than those offered to or received by us from third parties in any market where Total or its affiliates have a significant market position. These rights might inhibit potential strategic partners or potential customers from entering into negotiations with us about future business opportunities. Total also has the right to terminate this agreement if we undergo a sale or change of control to certain entities, which could discourage a potential acquirer from making an offer to acquire us.

In other agreements with Total related to their original investment in our capital stock, for as long as Total owns 10% of our voting securities, it has rights to an exclusive negotiation period if our Board of Directors decides to sell our company. Total also has the right to designate one director to serve on our Board of Directors. Also, in connection with Total’s investments, our certificate

of incorporation includes a provision that excludes Total from prohibitions on business combinations between Amyris and an “interested stockholder.” These provisions could have the effect of discouraging potential acquirers from making offers to acquire us, and give Total more access to the Company than other stockholders if Total decides to pursue an acquisition.

Additionally, in connection with subsequent investments by Total, we granted Total, among other investors, a right of first investment if we propose to sell securities in a private placement financing transaction. With these rights, Total and other investors may subscribe for a portion of any new financing and require us to comply with certain notice periods, which could discourage other investors from participating, or cause delays, in our ability to close such a financing. Until June 30, 2014, Total also has a right to cancel up to approximately $9.8 million in convertible promissory notes previously issued to Total to exercise certain pro rata rights. To the extent Total exercises this right, it will reduce the cash proceeds we may realize from the relevant financing. Under agreements signed in July 2012, Total previously had the right to cancel up to $30.0 million of such convertible promissory notes, but has since, in financings that closed in December 2012, October 2013, December 2013 and January 2014, used approximately $20.2 million of such $30.0 million.

Our joint venture with Total limits our ability to independently develop and commercialize Biofene-based diesel and jet fuels.

In July 2012 and December 2013, we entered into a series of agreements to establish a research and development program and form a joint venture to produce and commercialize Biofene-based diesel and jet fuels. With an exception for our fuels business in Brazil, the collaboration and joint venture establish the exclusive means for us to develop, produce and commercialize fuels from Biofene. We granted the joint venture exclusive licenses under certain of our intellectual property to make and sell joint venture products. We also granted the joint venture, in the event of a buy-out of our interest in the joint venture by Total (which Total is entitled to do under certain circumstances described below) a non-exclusive license to optimize or engineer yeast strains used by us to produce farnesene for the joint venture’s diesel and jet fuels. As a result of these licenses, Amyris generally no longer has an independent right to make or sell Biofene fuels outside of Brazil. If, for any reason, the joint venture is not fully supported or is not successful and the joint venture does not allow us to pursue Biofene-based fuels independently, this joint venture arrangement could impair our ability to develop and commercialize such fuels, which could have a material adverse effect on our business and long term prospects. For example, these arrangements could adversely affect our ability to enter or expand in these markets on terms that would otherwise be more favorable to us independently or with third parties.

In addition to granting the joint venture exclusive licenses, we also agreed that, if we encounter certain financial hardship situations, such as bankruptcy, insolvency and debt defaults, or upon a change of control of Amyris, Total has a right to buy out our interest in the joint venture at fair market value. The agreements also provide Total with a right to buy out our interest in the joint venture in the event of a “deadlock” in negotiating agreements to establish an operational fuels joint venture following a decision to proceed with the next phase of the joint venture. In a situation where Total buys out our interest in the joint venture, it also has rights to buy our Brazil fuels business at fair market value. If Total were to exercise these rights, we would, in effect, relinquish rights to intellectual property exclusively licensed to the joint venture, and our ability to seek future revenue from Biofene in the fuels market would be adversely affected (or completely prevented). This could significantly reduce the value of our product offerings, and have a material adverse effect on our ability to grow our business in future years.

Total’s collaboration funding is in the form of convertible promissory notes.

Our agreements with Total relating to our fuels collaboration created a convertible debt financing structure for funding the research and development program. The collaboration agreements contemplated approximately $105.0 million in financing for the collaboration, of which Total has funded $83.3 million to date. Total is expected to fund up to the remaining $21.7 million, with $10.85 million to be paid by July 2014 and $10.85 million to be paid by January 2015. If Total chooses not to continue participating at certain "Go/No-Go" decision points during the program, licenses to our technology would terminate, and the notes would remain outstanding and become payable at maturity unless otherwise converted in accordance with their terms. If Total chooses to continue the collaboration and makes a final decision to proceed with the operational fuels joint venture, Total is required to buy from Amyris 50% of the preferred shares (all of which are currently held by Amyris) of a related joint venture in exchange for full settlement of principal and interest outstanding under the notes. If Total chooses to continue the collaboration and makes a final decision to proceed with the joint venture only for jet fuel, Total is required to buy from Amyris 50% of the preferred shares of the joint venture in exchanges for the settlement of 30% of the principal and interest outstanding under the notes. The remaining notes would continue to be outstanding and payable upon maturity unless otherwise converted in accordance with the terms of the notes.

We cannot be certain that Total will choose to continue funding the program or ultimately opt to participate in an operational fuels joint venture. If Total were to decide not to participate further in the collaboration or not to proceed with the operational fuels joint venture, it would not be obligated to fund any further amounts (which would reduce our anticipated near-term collaboration revenues), and, as noted above, the outstanding notes representing amounts paid by Total to date would remain outstanding and

become payable or convertible into our common stock. If Total chooses to demand repayment of amounts funded under the notes following such a decision (or a portion of such notes based on a jet fuel-only decision), we may not be able to satisfy our obligations to repay the notes by the maturity date in March 2017, which could lead to defaults and our insolvency, and Total and other creditors could pursue collections claims against us. If the notes become convertible and Total chooses to convert them, the resulting issuance of common stock would be dilutive to other stockholders.

If we do not meet technical, development and commercial milestones in our collaboration agreements, our future revenue and financial results will be adversely impacted.

We have entered into a number of agreements regarding the further development of certain of our products and, in some cases, for ultimate sale of certain products to the customer under the agreement. None of these agreements affirmatively obligates the other party to purchase specific quantities of any products at this time, and most contain important conditions that must be satisfied before additional research and development funding or product purchases would occur. These conditions include research and development milestones and technical specifications that must be achieved to the satisfaction of our collaborators, which we cannot be certain we will achieve. If we do not achieve these contractual milestones, our revenues and financial results will be adversely affected.

We are subject to risks related to our reliance on collaboration arrangements to fund development and commercialization of our products.

For most product markets we are trying to address, we either have or are seeking collaboration partners to fund the research and development, commercialization and production efforts required for the target products. Typically we provide limited exclusive rights and revenue sharing with respect to the production and sale of particular types of products in specific markets in exchange for such up-front funding. These exclusivity, revenue-sharing and other similar terms limit our ability to commercialize our products and technology, and may impact the size of our business or our profitability in ways that we do not currently envision. In addition, revenues from these types of relationships are a key part of our cash plan for 2014 and beyond. If we fail to collect expected collaboration revenues, or to identify and add sufficient additional collaborations to fund our planned operations, we may be unable to fund our operations or pursue development and commercialization of our planned products. To achieve our collaboration revenue targets from year to year, we may be forced to enter into agreements that contain less favorable terms, including broader exclusivity provisions for commercial partners and a smaller financial stake in any successful ventures resulting from collaborations.

Our manufacturing operations require sugar feedstock, and the inability to obtain such feedstock in sufficient quantities or in a timely manner, or at reasonable prices, may limit our ability to produce our products profitably, or at all.

We anticipate that the production of our products will require large volumes of feedstock. We have relied on a mixture of feedstock sources for use at our contract manufacturing operations, including cane sugar, corn-based dextrose and beet molasses. For our large-scale production facilities in Brazil, we are relying primarily on Brazilian sugarcane. We cannot predict the future availability or price of these various feedstocks, nor can we be sure that our mill partners, which we expect to supply the sugarcane feedstock necessary to produce our products in Brazil, will be able to supply it in sufficient quantities or in a timely manner. Furthermore, to the extent we are required to rely on sugar feedstock other than Brazilian sugarcane, the cost of such feedstock may be higher than we expect, increasing our anticipated production costs. Feedstock crop yields and sugar content depend on weather conditions, such as rainfall and temperature. Weather conditions have historically caused volatility in the ethanol and sugar industries by causing crop failures or reduced harvests. Excessive rainfall can adversely affect the supply of sugarcane and other sugar feedstock available for the production of our products by reducing the sucrose content and limiting growers' ability to harvest. Crop disease and pestilence can also occur from time to time and can adversely affect feedstock growth, potentially rendering useless or unusable all or a substantial portion of affected harvests. With respect to sugarcane, our initial primary feedstock, seasonal availability and price, the limited amount of time during which it keeps its sugar content after harvest, and the fact that sugarcane is not itself a traded commodity, increases these risks and limits our ability to substitute supply in the event of such an occurrence. If production of sugarcane or any other feedstock we may use to produce our products is adversely affected by these or other conditions, our production will be impaired, and our business will be adversely affected.

The price of sugarcane and other feedstocks can be volatile as a result of changes in industry policy and may increase the cost of production of our products.

In Brazil, Conselho dos Produtores de Cana, Açúcar e Álcool (Council of Sugarcane, Sugar and Ethanol Producers), or Consecana, an industry association of producers of sugarcane, sugar and ethanol, sets market terms and prices for general supply, lease and partnership agreements for sugarcane. If Consecana makes changes to such terms and prices, this could result in higher sugarcane prices and/or a significant decrease in the volume of sugarcane available for the production of our products. Furthermore,

if Consecana were to cease to be involved in this process, such prices and terms could become more volatile. Similar principles apply to pricing of other feedstocks as well. Any of these events could adversely affect our business and results of operations.

Our large-scale commercial production capacity is centered in Brazil, and our business will be adversely affected if we do not operate effectively in that country.

For the foreseeable future, we will be subject to risks associated with the concentration of essential product sourcing and operations in Brazil. The Brazilian government has changed in the past, and may change in the future, monetary, taxation, credit, tariff and other policies to influence the course of Brazil's economy. For example, the government's actions to control inflation have at times involved setting wage and price controls, adjusting interest rates, imposing taxes and exchange controls and limiting imports into Brazil. We have no control over, and cannot predict, what policies or actions the Brazilian government may take in the future. Our business, financial performance and prospects may be adversely affected by, among others, the following factors:


•	delays or failures in securing licenses, permits or other governmental approvals necessary to build and operate facilities and use our yeast strains to produce products;


•	rapid consolidation in the sugar and ethanol industries in Brazil, which could result in a decrease in competition;


•	political, economic, diplomatic or social instability in or affecting Brazil;


•	changing interest rates;


•	tax burden and policies;


•	effects of changes in currency exchange rates;


•	exchange controls and restrictions on remittances abroad;


•	inflation;


•	land reform movements;


•	changes in labor related policies;


•	export or import restrictions that limit our ability to move our products out of Brazil or interfere with the import of essential materials into Brazil;


•	changes in, or interpretations of foreign regulations that may adversely affect our ability to sell our products or repatriate profits to the United States;


•	tariffs, trade protection measures and other regulatory requirements;


•	successful compliance with United States and foreign laws that regulate the conduct of business abroad;


•	an inability, or reduced ability, to protect our intellectual property in Brazil including any effect of compulsory licensing imposed by government action; and


•	difficulties and costs of staffing and managing foreign operations.

We cannot predict whether the current or future Brazilian government will implement changes to existing policies on taxation, exchange controls, monetary strategy, labor relations, social security and the like, nor can we estimate the impact of any such changes on the Brazilian economy or our operations.

Our international operations expose us to the risk of fluctuation in currency exchange rates and rates of foreign inflation, which could adversely affect our results of operations.

We currently incur significant costs and expenses in Brazilian real and may in the future incur additional expenses in foreign currencies and derive a portion of our revenues in the local currencies of customers throughout the world. As a result, our revenues and results of operations are subject to foreign exchange fluctuations, which we may not be able to manage successfully. During

the past few decades, the Brazilian currency in particular has faced frequent and substantial exchange rate fluctuations in relation to the United States dollar and other foreign currencies. There can be no assurance that the Brazilian real will not significantly appreciate or depreciate against the United States dollar in the future. We also bear the risk that the rate of inflation in the foreign countries where we incur costs and expenses or the decline in value of the United States dollar compared to those foreign currencies will increase our costs as expressed in United States dollars. For example, future measures by the Central Bank of Brazil to control inflation, including interest rate adjustments, intervention in the foreign exchange market and actions to fix the value of the real, may weaken the United States dollar in Brazil. Whether in Brazil or otherwise, we may not be able to adjust the prices of our products to offset the effects of inflation or foreign currency appreciation on our cost structure, which could increase our costs and reduce our net operating margins. If we do not successfully manage these risks through hedging or other mechanisms, our revenues and results of operations could be adversely affected.

Our use of genetically-modified feedstocks and yeast strains to produce our products subjects us to risks of regulatory limitations and rejection of our products.

The use of GMMs, such as our yeast strains, is subject to laws and regulations in many countries, some of which are new and some of which are still evolving. Public attitudes about the safety and environmental hazards of, and ethical concerns over, genetic research and GMMs could influence public acceptance of our technology and products. In the United States, the EPA, regulates the commercial use of GMMs as well as potential products produced from the GMMs. Various states or local governments within the United States could choose to regulate products made with GMMs as well. While the strain of genetically modified yeast that we currently use for the development and anticipate using for the commercial production of our target molecules, S. cerevisiae , is eligible for exemption from EPA review because it is recognized as posing a low risk, we must satisfy certain criteria to achieve this exemption, including but not limited to use of compliant containment structures and safety procedures, and we cannot be sure that we will meet such criteria in a timely manner, or at all. If exemption of S. cerevisiae is not obtained, our business may be substantially harmed. In addition to S. cerevisiae , we may seek to use different GMMs in the future that will require EPA approval. If approval of different GMMs is not secured, our ability to grow our business could be adversely affected.

In Brazil, GMMs are regulated by CTNBio. We have obtained approval from CTNBio to use GMMs in a contained environment in our Campinas facilities for research and development purposes as well as at a contract manufacturing facility in Brazil. In addition, we have obtained initial commercial approval from CTNBio for one of our current yeast strains. As we continue to develop new yeast strains and deploy our technology at new production facilities in Brazil, we will be required to obtain further approvals from CTNBio in order to use these strains in commercial production in Brazil. We may not be able to obtain approvals from relevant Brazilian authorities on a timely basis, or at all, and if we do not, our ability to produce our products in Brazil would be impaired, which would adversely affect our results of operations and financial condition.

In addition to our production operations in the United States and Brazil, we have been party to contract manufacturing agreements with parties in other production locations around the world, including Europe. The use of GMM technology is strictly regulated in the European Union, which has established various directives for member states regarding regulation of the use of such technology, including notification processes for contained use of such technology. We expect to encounter GMM regulations in most, if not all, of the countries in which we may seek to establish production capabilities and/or conduct sales to customers or end-use consumers, and the scope and nature of these regulations will likely be different from country to country. If we cannot meet the applicable requirements in other countries in which we intend to produce products using our yeast strains, or if it takes longer than anticipated to obtain such approvals, our business could be adversely affected.

We may not be able to obtain regulatory approval for the sale of our renewable products.

Our renewable chemical products may be subject to government regulation in our target markets. In the United States, the EPA administers the TSCA, which regulates the commercial registration, distribution, and use of many chemicals. Before an entity can manufacture or distribute significant volumes of a chemical, it needs to determine whether that chemical is listed in the TSCA inventory. If the substance is listed, then manufacture or distribution can commence immediately. If not, then in most cases a “Chemical Abstracts Service” number registration and pre-manufacture notice must be filed with the EPA, which has up to 180 days to review the filing. Some of the products we produce or plan to produce, such as farnesene (i.e., Biofene), farnesane (in diesel and new jet fuel applications) and squalane, are already in the TSCA inventory. We may not be able to expediently receive approval from the EPA to list future molecules we would like to make on the TSCA registry, resulting in delays or significant increases in testing requirements. A similar program exists in the European Union, called REACH. Under this program, we need to register our new products with the European Commission, and this process could cause delays or significant costs. To the extent that other geographies, such as Brazil, may rely on TSCA or REACH (or similar laws and programs) for chemical registration in their geographies, delays with the United States or European authorities may subsequently delay entry into these markets as well.

Our diesel and jet fuel is subject to regulation by various government agencies, including the EPA, CARB and ANP. To date, we have obtained registration with the EPA for the use of our diesel fuel in the United States. at a 35% blend rate with petroleum diesel. In addition, ANP has authorized the use our diesel fuel at blend rates of 10% and 30% for specific transportation fleets. In Europe, we obtained REACH registration for importing/manufacturing up to 1,000 metric tons of our diesel fuel per year and are pursuing data validation for greater volumes. Registration with each of these bodies is required for the sale and use of our fuels within their respective jurisdictions. Jet fuel (aviation turbine fuel) validation and specifications are subject to the ASTM International industry consensus process and the Brazilian ANP national adoption process. Our jet fuel must be validated and supported by an applicable ASTM aviation turbine fuel standard. Any failure to achieve required validation and certifications for our jet fuel could impair or delay our plans to introduce a jet fuel product in 2014, which would have a material adverse impact on our renewable product revenues for the year. In addition, for us to achieve full access to the United States fuels market for our fuel products, we will need to obtain EPA and CARB (and potentially other state agencies) certifications for our feedstock pathway and production facilities, including certification of a feedstock lifecycle analysis relating to greenhouse gas emissions. Any delay in obtaining these additional certifications could impair our ability to sell our renewable fuels to refiners, importers, blenders and other parties that produce transportation fuels as they comply with federal and state requirements to include certified renewable fuels in their products.

We expect to encounter regulations in most, if not all, of the countries in which we may seek to sell our renewable chemical and fuel products (and our customers may encounter similar regulations in selling end use products o consumers), and we cannot assure you that we (or our customers) will be able to obtain necessary approvals in a timely manner or at all. If our chemical and fuel products do not meet applicable regulatory requirements in a particular country or at all, then we (or our customers) may not be able to commercialize our products and our business will be adversely affected.

Changes in government regulations, including subsidies and economic incentives, could have a material adverse effect upon our business.

The market for renewable fuels is heavily influenced by foreign, federal, state and local government regulations and policies. Changes to existing or adoption of new domestic or foreign federal, state and local legislative initiatives that impact the production, distribution or sale of renewable fuels may harm our renewable fuels business. In the United States and in a number of other countries, regulations and policies encouraging production and use of alternative fuels have been modified in the past and may be modified again in the future. Any reduction in mandated requirements for fuel alternatives and additives to gasoline or diesel may cause demand for biofuels to decline and deter investment in the research and development of renewable fuels. The market uncertainty regarding this and future standards and policies may also affect our ability to develop new renewable products or to license our technologies to third parties and to sell products to our end customers. Any inability to address these requirements and any regulatory or policy changes could have a material adverse effect on our business, financial condition and results of operations.

Concerns associated with renewable fuels, including land usage, national security interests and food crop usage, continue to receive legislative, industry and public attention. This attention could result in future legislation, regulation and/or administrative action that could adversely affect our business. Any inability to address these requirements and any regulatory or policy changes could have a material adverse effect on our business, financial condition and results of operations.

Furthermore, the production of our products will depend on the availability of feedstock, especially sugarcane. Agricultural production and trade flows are subject to government policies and regulations. Governmental policies affecting the agricultural industry, such as taxes, tariffs, duties, subsidies, incentives and import and export restrictions on agricultural commodities and commodity products, can influence the planting of certain crops, the location and size of crop production, whether unprocessed or processed commodity products are traded, the volume and types of imports and exports, and the availability and competitiveness of feedstocks as raw materials. Future government policies may adversely affect the supply of feedstocks, restrict our ability to use sugarcane or other feedstocks to produce our products, and negatively impact our future revenues and results of operations or could encourage the use of feedstocks more advantageous to our competitors which would put us at a commercial disadvantage.

We may incur significant costs complying with environmental laws and regulations, and failure to comply with these laws and regulations could expose us to significant liabilities.

We use hazardous chemicals and radioactive and biological materials in our business and such materials are subject to a variety of federal, state and local laws and regulations governing the use, generation, manufacture, storage, handling and disposal of these materials both in the United States and overseas. Although we have implemented safety procedures for handling and disposing of these materials and related waste products in an effort to comply with these laws and regulations, we cannot be sure that our safety measures will prevent accidental injury or contamination from the use, storage, handling or disposal of hazardous materials. In the event of contamination or injury, we could be held liable for any resulting damages, and any liability could exceed our insurance coverage. There can be no assurance that violations of environmental, health and safety laws will not occur in the future as a result of human error, accident, equipment failure or other causes. Compliance with applicable environmental laws and regulations may be expensive, and the failure to comply with past, present, or future laws could result in the imposition of fines, third party property damage, product liability and personal injury claims, investigation and remediation costs, the suspension of production, or a cessation of operations, and our liability may exceed our total assets. Liability under environmental laws can be joint and several, without regard to comparative fault and may be punitive in nature. Environmental laws could become more stringent over time, imposing greater compliance costs and increasing risks and penalties associated with violations, which could impair our research, development or production efforts and harm our business.

A decline in the price of petroleum and petroleum-based products may reduce demand for many of our renewable products and may otherwise adversely affect our business.

We anticipate that most of our renewable products, and in particular our fuels, will be marketed as alternatives to corresponding petroleum-based products. If the price of oil falls, we may be unable to produce products that are cost-effective alternatives to petroleum-based products. Declining oil prices, or the perception of a future decline in oil prices, may adversely affect the prices we can obtain from our potential customers or prevent potential customers from entering into agreements with us to buy our products. During sustained periods of lower oil prices we may be unable to sell some of our products, which could materially and adversely affect our operating results.

Our financial results could vary significantly from quarter to quarter and are difficult to predict.

Our revenues and results of operations could vary significantly from quarter to quarter because of a variety of factors, many of which are outside of our control. As a result, comparing our results of operations on a period-to-period basis may not be meaningful. Factors that could cause our quarterly results of operations to fluctuate include:


•	achievement, or failure, with respect to technology, product development or manufacturing milestones needed to allow us to enter identified markets on a cost effective basis;


•	delays or greater than anticipated expenses associated with the completion or commissioning of new production facilities, or the time to ramp up and stabilize production following completion of a new production facility;


•	impairment of assets based on shifting business priorities and working capital limitations;


•	disruptions in the production process at any manufacturing facility;


•	losses associated with producing our products as we ramp to commercial production levels;


•	failure to recover value added tax (or VAT) that we currently reflect as recoverable in our financial statements (e.g., due to failure to meet conditions for reimbursement of VAT under local law);


•	the timing, size and mix of sales to customers for our products;


•	increases in price or decreases in availability of feedstock;


•	the unavailability of contract manufacturing capacity altogether or at reasonable cost;


•	exit costs associated with terminating contract manufacturing relationships;


•	fluctuations in foreign currency exchange rates;


•	gains or losses associated with our hedging activities;


•	change in the fair value of derivative instruments;


•	fluctuations in the price of and demand for sugar, ethanol, and petroleum-based and other products for which our products are alternatives;


•	seasonal variability in production and sales of our products;


•	competitive pricing pressures, including decreases in average selling prices of our products;


•	unanticipated expenses associated with changes in governmental regulations and environmental, health, labor and safety requirements;


•	reductions or changes to existing fuel and chemical regulations and policies;


•	departure of executives or other key management employees resulting in transition and severance costs;


•	our ability to use our net operating loss carryforwards to offset future taxable income;


•	business interruptions such as earthquakes and other natural disasters;


•	our ability to integrate businesses that we may acquire;


•	our ability to successfully collaborate with business venture partners;


•	risks associated with the international aspects of our business; and


•	changes in general economic, industry and market conditions, both domestically and in our foreign markets.

As part of our operating plan for 2014, we are planning to keep our expenditures to be relatively consistent with prior year.

Due to the factors described above, among others, the results of any quarterly or annual period may not meet our expectations or the expectations of our investors and may not be meaningful indications of our future performance.

Loss of key personnel, including key management personnel, and/or failure to attract and retain additional personnel could delay our product development programs and harm our research and development efforts and our ability to meet our business objectives.

Our business involves complex, global operations across a variety of markets and requires a management team and employee workforce that is knowledgeable in the many areas in which we operate. As we continue to build our business, we will need to hire and retain qualified research and development, management and other personnel to succeed. The process of hiring, training and successfully integrating qualified personnel into our operations, in both the United States and Brazil, is a lengthy and expensive one. The market for qualified personnel is very competitive because of the limited number of people available with the necessary technical skills and understanding of our technology and anticipated products, particularly in Brazil. Our failure to hire and retain qualified personnel could impair our ability to meet our research and development and business objectives and adversely affect our results of operations and financial condition.

The loss of any key member of our management or key technical and operational employees, or the failure to attract or retain such employees could prevent us from developing and commercializing our products for our target markets and executing our business strategy. We also may not be able to attract or retain qualified employees in the future due to the intense competition for qualified personnel among biotechnology and other technology-based businesses, particularly in the renewable chemicals and fuels area, or due to the availability of personnel with the qualifications or experience necessary for our business. In addition, reductions to our workforce as part of cost-saving measures may make it more difficult for us to attract and retain key employees. If we do not maintain the necessary personnel to accomplish our business objectives, we may experience staffing constraints that will adversely affect our ability to meet the demands of our collaborators and customers in a timely fashion or to support our internal research and development programs and operations. In particular, our product and process development programs are dependent on our ability to attract and retain highly skilled technical and operational personnel. Competition for such personnel

from numerous companies and academic and other research institutions may limit our ability to do so on acceptable terms. All of our employees are at-will employees, which means that either the employee or we may terminate their employment at any time.

Growth may place significant demands on our management and our infrastructure.

We have experienced, and expect to continue to experience, expansion of our business as we continue to make efforts to develop and bring our products to market. We have grown from 18 employees at the end of 2005 to 392 at February 28, 2014 . Our growth and diversified operations have placed, and may continue to place, significant demands on our management and our operational and financial infrastructure. In particular, continued growth could strain our ability to:


•	manage multiple research and development programs;


•	operate multiple manufacturing facilities around the world;


•	develop and improve our operational, financial and management controls;


•	enhance our reporting systems and procedures;


•	recruit, train and retain highly skilled personnel;


•	develop and maintain our relationships with existing and potential business partners;


•	maintain our quality standards; and


•	maintain customer satisfaction.

Managing our growth will require significant expenditures and allocation of valuable management resources. If we fail to achieve the necessary level of efficiency in our organization as it grows, our business, results of operations and financial condition would be adversely impacted.

Our proprietary rights may not adequately protect our technologies and product candidates.

Our commercial success will depend substantially on our ability to obtain patents and maintain adequate legal protection for our technologies and product candidates in the United States and other countries. As of February 28, 2014 , we had 248 issued United States and foreign patents and 326 pending United States and foreign patent applications that were owned by or licensed to us. We will be able to protect our proprietary rights from unauthorized use by third parties only to the extent that our proprietary technologies and future products are covered by valid and enforceable patents or are effectively maintained as trade secrets.

We apply for patents covering both our technologies and product candidates, as we deem appropriate. However, we may fail to apply for patents on important technologies or product candidates in a timely fashion, or at all. Our existing and future patents may not be sufficiently broad to prevent others from practicing our technologies or from developing competing products or technologies. In addition, the patent positions of companies like ours are highly uncertain and involve complex legal and factual questions for which important legal principles remain unresolved. No consistent policy regarding the breadth of patent claims has emerged to date in the United States and the landscape is expected to become even more uncertain in view of recent rule changes by the USPTO, the introduction of patent reform legislation in Congress and recent decisions in patent law cases by the United States Supreme Court. In addition, we obtained certain key United States patents using a procedure for accelerated examination recently implemented by the USPTO which requires special activities and disclosures that may create additional risks related to the validity or enforceability of the United States patents so obtained. The patent situation outside of the United States is even less predictable. As a result, the validity and enforceability of patents cannot be predicted with certainty. Moreover, we cannot be certain whether:


•	we or our licensors were the first to make the inventions covered by each of our issued patents and pending patent applications;


•	we or our licensors were the first to file patent applications for these inventions;


•	others will independently develop similar or alternative technologies or duplicate any of our technologies;


•	any of our or our licensors' patents will be valid or enforceable;


•	any patents issued to us or our licensors will provide us with any competitive advantages, or will be challenged by third parties;


•	we will develop additional proprietary products or technologies that are patentable; or


•	the patents of others will have an adverse effect on our business.

We do not know whether any of our patent applications or those patent applications that we license will result in the issuance of any patents. Even if patents are issued, they may not be sufficient to protect our technology or product candidates. The patents we own or license and those that may be issued in the future may be challenged, invalidated, rendered unenforceable, or circumvented, and the rights granted under any issued patents may not provide us with proprietary protection or competitive advantages. In particular, United States patents we obtained using the USPTO accelerated examination program may introduce additional risks to the validity or enforceability of some or all of these specially-obtained United States patents if validity or enforceability are challenged. Moreover, third parties could practice our inventions in territories where we do not have patent protection or in territories where they could obtain a compulsory license to our technology where patented. Such third parties may then try to import products made using our inventions into the United States or other territories. Additional uncertainty may result from potential passage of patent reform legislation by the United States Congress, legal precedent by the United States Federal Circuit and Supreme Court as they determine legal issues concerning the scope and construction of patent claims and inconsistent interpretation of patent laws by the lower courts. Accordingly, we cannot ensure that any of our pending patent applications will result in issued patents, or even if issued, predict the breadth, validity and enforceability of the claims upheld in our and other companies' patents.

Unauthorized parties may attempt to copy or otherwise obtain and use our products or technology. Monitoring unauthorized use of our intellectual property is difficult, and we cannot be certain that the steps we have taken will prevent unauthorized use of our technology, particularly in certain foreign countries where the local laws may not protect our proprietary rights as fully as in the United States or may provide, today or in the future, for compulsory licenses. If competitors are able to use our technology, our ability to compete effectively could be harmed. Moreover, others may independently develop and obtain patents for technologies that are similar to, or superior to, our technologies. If that happens, we may need to license these technologies, and we may not be able to obtain licenses on reasonable terms, if at all, which could cause harm to our business.

We rely in part on trade secrets to protect our technology, and our failure to obtain or maintain trade secret protection could adversely affect our competitive business position.

We rely on trade secrets to protect some of our technology, particularly where we do not believe patent protection is appropriate or obtainable. However, trade secrets are difficult to maintain and protect. Our strategy for contract manufacturing and scale-up of commercial production requires us to share confidential information with our international business partners and other parties. Our product development collaborations with third parties, including with Total, require us to share confidential information, including with employees of Total who are seconded to Amyris during the term of the collaboration. While we use reasonable efforts to protect our trade secrets, our or our business partners' employees, consultants, contractors or scientific and other advisors may unintentionally or willfully disclose our proprietary information to competitors. Enforcement of claims that a third party has illegally obtained and is using trade secrets is expensive, time consuming and uncertain. In addition, foreign courts are sometimes less willing than United States courts to protect trade secrets. If our competitors independently develop equivalent knowledge, methods and know-how, we would not be able to assert our trade secrets against them.

We require new employees and consultants to execute confidentiality agreements upon the commencement of an employment or consulting arrangement with us. These agreements generally require that all confidential information developed by the individual or made known to the individual by us during the course of the individual's relationship with us be kept confidential and not disclosed to third parties. These agreements also generally provide that inventions conceived by the individual in the course of rendering services to us shall be our exclusive property. Nevertheless, our proprietary information may be disclosed, or these agreements may be unenforceable or difficult to enforce. Additionally, trade secret law in Brazil differs from that in the United States which requires us to take a different approach to protecting our trade secrets in Brazil. Some of these approaches to trade secret protection may be novel and untested under Brazilian law and we cannot guarantee that we would prevail if our trade secrets are contested in Brazil. If any of the above risks materializes, our failure to obtain or maintain trade secret protection could adversely affect our competitive business position.

Third parties may misappropriate our yeast strains.

Third parties, including contract manufacturers, sugar and ethanol mill owners, other contractors and shipping agents, often have custody or control of our yeast strains. If our yeast strains were stolen, misappropriated or reverse engineered, they could be used by other parties who may be able to reproduce the yeast strains for their own commercial gain. If this were to occur, it would be difficult for us to challenge and prevent this type of use, especially in countries where we have limited intellectual property protection or that do not have robust intellectual property law regimes.

If we are sued for infringing intellectual property rights or other proprietary rights of third parties, litigation could be costly and time consuming and could prevent us from developing or commercializing our future products.

Our commercial success depends on our ability to operate without infringing the patents and proprietary rights of other parties and without breaching any agreements we have entered into with regard to our technologies and product candidates. We cannot determine with certainty whether patents or patent applications of other parties may materially affect our ability to conduct our business. Our industry spans several sectors, including biotechnology, renewable fuels, renewable specialty chemicals and other renewable compounds, and is characterized by the existence of a significant number of patents and disputes regarding patent and other intellectual property rights. Because patent applications can take several years to issue, there may currently be pending applications, unknown to us, that may result in issued patents that cover our technologies or product candidates. We are aware of a significant number of patents and patent applications relating to aspects of our technologies filed by, and issued to, third parties. The existence of third-party patent applications and patents could significantly reduce the coverage of patents owned by or licensed to us and limit our ability to obtain meaningful patent protection. If we wish to make, use, sell, offer to sell, or import the technology or compound claimed in issued and unexpired patents owned by others, we will need to obtain a license from the owner, enter into litigation to challenge the validity of the patents or incur the risk of litigation in the event that the owner asserts that we infringe its patents. If patents containing competitive or conflicting claims are issued to third parties and these claims are ultimately determined to be valid, we may be enjoined from pursing research, development, or commercialization of products, or be required to obtain licenses to these patents, or to develop or obtain alternative technologies.

If a third-party asserts that we infringe upon its patents or other proprietary rights, we could face a number of issues that could seriously harm our competitive position, including:


•	infringement and other intellectual property claims, which could be costly and time consuming to litigate, whether or not the claims have merit, and which could delay getting our products to market and divert management attention from our business;


•	substantial damages for past infringement, which we may have to pay if a court determines that our product candidates or technologies infringe a third party's patent or other proprietary rights;


•	a court prohibiting us from selling or licensing our technologies or future products unless the holder licenses the patent or other proprietary rights to us, which it is not required to do; and


•	if a license is available from a third party, such third party may require us to pay substantial royalties or grant cross licenses to our patents or proprietary rights.

The industries in which we operate, and the biotechnology industry in particular, are characterized by frequent and extensive litigation regarding patents and other intellectual property rights. Many biotechnology companies have employed intellectual property litigation as a way to gain a competitive advantage. If any of our competitors have filed patent applications or obtained patents that claim inventions also claimed by us, we may have to participate in interference proceedings declared by the relevant patent regulatory agency to determine priority of invention and, thus, the right to the patents for these inventions in the United States These proceedings could result in substantial cost to us even if the outcome is favorable. Even if successful, an interference proceeding may result in loss of certain claims. Our involvement in litigation, interferences, opposition proceedings or other intellectual property proceedings inside and outside of the United States, to defend our intellectual property rights or as a result of alleged infringement of the rights of others, may divert management time from focusing on business operations and could cause us to spend significant resources, all of which could harm our business and results of operations.

Many of our employees were previously employed at universities, biotechnology, specialty chemical or oil companies, including our competitors or potential competitors. We may be subject to claims that these employees or we have inadvertently or otherwise used or disclosed trade secrets or other proprietary information of their former employers. Litigation may be necessary to defend against these claims. If we fail in defending such claims, in addition to paying monetary damages, we may lose valuable intellectual property rights or personnel and be enjoined from certain activities. A loss of key research personnel or their work

product could hamper or prevent our ability to commercialize our product candidates, which could severely harm our business. Even if we are successful in defending against these claims, litigation could result in substantial costs and demand on management resources.

We may need to commence litigation to enforce our intellectual property rights, which would divert resources and management's time and attention and the results of which would be uncertain.

Enforcement of claims that a third party is using our proprietary rights without permission is expensive, time consuming and uncertain. Significant litigation would result in substantial costs, even if the eventual outcome is favorable to us and would divert management's attention from our business objectives. In addition, an adverse outcome in litigation could result in a substantial loss of our proprietary rights and we may lose our ability to exclude others from practicing our technology or producing our product candidates.

The laws of some foreign countries do not protect intellectual property rights to the same extent as do the laws of the United States. Many companies have encountered significant problems in protecting and defending intellectual property rights in certain foreign jurisdictions. The legal systems of certain countries, particularly certain developing countries, do not favor the enforcement of patents and other intellectual property protection, particularly those relating to biotechnology and/or bioindustrial technologies. This could make it difficult for us to stop the infringement of our patents or misappropriation of our other intellectual property rights. Proceedings to enforce our patent rights in foreign jurisdictions could result in substantial costs and divert our efforts and attention from other aspects of our business. Moreover, our efforts to protect our intellectual property rights in such countries may be inadequate.

Our products subject us to product-safety risks, and we may be sued for product liability.

The design, development, production and sale of our products involve an inherent risk of product liability claims and the associated adverse publicity. Our potential products could be used by a wide variety of consumers with varying levels of sophistication. Although safety is a priority for us, we are not always in control of the final uses and formulations of the products we supply or their use as ingredients. Our products could have detrimental impacts or adverse impacts we cannot anticipate. Despite our efforts, negative publicity about Amyris, including product safety or similar concerns, whether real or perceived, could occur, and our products could face withdrawal, recall or other quality issues. In addition, we may be named directly in product liability suits relating to our products, even for defects resulting from errors of our commercial partners, contract manufacturers or chemical finishers. These claims could be brought by various parties, including customers who are purchasing products directly from us or other users who purchase products from our customers. We could also be named as co-parties in product liability suits that are brought against the contract manufacturers or Brazilian sugar and ethanol mills with whom we partner to produce our products. Insurance coverage is expensive, may be difficult to obtain and may not be available in the future on acceptable terms. We cannot be certain that our contract manufacturers or the sugar and ethanol producers who partner with us to produce our products will have adequate insurance coverage to cover against potential claims. Any insurance we do maintain may not provide adequate coverage against potential losses, and if claims or losses exceed our liability insurance coverage, our business would be adversely impacted. In addition, insurance coverage may become more expensive, which would harm our results of operations.

During the ordinary course of business, we may become subject to lawsuits or indemnity claims, which could materially and adversely affect our business and results of operations.

From time to time, we may in the ordinary course of business be named as a defendant in lawsuits, claims and other legal proceedings. These actions may seek, among other things, compensation for alleged personal injury, worker's compensation, employment discrimination, breach of contract, property damages, civil penalties and other losses of injunctive or declaratory relief. In the event that such actions or indemnities are ultimately resolved unfavorably at amounts exceeding our accrued liability, or at material amounts, the outcome could materially and adversely affect our reputation, business and results of operations. In addition, payments of significant amounts, even if reserved, could adversely affect our liquidity position.

If we fail to maintain an effective system of internal controls, we might not be able to report our financial results accurately or prevent fraud; in that case, our stockholders could lose confidence in our financial reporting, which would harm our business and could negatively impact the price of our stock.

Effective internal controls are necessary for us to provide reliable financial reports and prevent fraud. In addition, Section 404 of the Sarbanes-Oxley Act of 2002 requires us and our independent registered public accounting firm to evaluate and report on our internal control over financial reporting. The process of implementing our internal controls and complying with Section 404 is expensive and time consuming, and requires significant attention of management. We cannot be certain that these measures will ensure that we maintain adequate controls over our financial processes and reporting in the future. In addition, to the extent we

create joint ventures or have any variable interest entities and the financial statements of such entities are not prepared by us, we will not have direct control over their financial statement preparation. As a result, we will, for our financial reporting, depend on what these entities report to us, which could result in us adding monitoring and audit processes and increase the difficulty of implementing and maintaining adequate controls over our financial processes and reporting in the future. This may be particularly true where we are establishing such entities with commercial partners that do not have sophisticated financial accounting processes in place, or where we are entering into new relationships at a rapid pace, straining our integration capacity. Additionally, if we do not receive the information from the joint venture or variable interest entity on a timely basis, this could cause delays in our external reporting. Even if we conclude, and our independent registered public accounting firm concurs, that our internal control over financial reporting provides reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles, because of its inherent limitations, internal control over financial reporting may not prevent or detect fraud or misstatements. Failure to implement required new or improved controls, or difficulties encountered in their implementation, could harm our results of operations or cause us to fail to meet our reporting obligations. If we or our independent registered public accounting firm discover a material weakness, the disclosure of that fact, even if quickly remedied, could reduce the market's confidence in our financial statements and harm our stock price. In addition, failure to comply with Section 404 could subject us to a variety of administrative sanctions, including SEC action, ineligibility for short form resale registration, the suspension or delisting of our common stock from the stock exchange on which it is listed, and the inability of registered broker-dealers to make a market in our common stock, which would further reduce our stock price and could harm our business.

If the value of our goodwill or other intangible assets becomes impaired, it could materially reduce the value of our assets and reduce our net income for the year in which the related impairment charges occur.

We apply the applicable accounting principles set forth in the United States Financial Accounting Standards Board's Accounting Standards Codification to our intangible assets (including goodwill), which prohibits the amortization of intangible assets with indefinite useful lives and requires that these assets be reviewed for impairment at least annually. There are several methods that can be used to determine the estimated fair value of the in-process research and development acquired in a business combination. We have used the “income method,” which applies a probability weighting that considers the risk of development and commercialization, to the estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, pricing of similar products, and expected industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets will be amortized over the remaining useful life or written off, as appropriate. If the carrying amount of the assets is greater than the measures of fair value, impairment is considered to have occurred and a write-down of the asset is recorded. Any finding that the value of our intangible assets has been impaired would require us to write-down the impaired portion, which could reduce the value of our assets and reduce our net income for the year in which the related impairment charges occur. As of December 31, 2013, we had a net carrying value of approximately $9.1 million in in-process research and development and goodwill associated with our acquisition of Draths Corporation.

Our ability to use our net operating loss carryforwards to offset future taxable income may be subject to certain limitations.

In general, under Section 382 of the Internal Revenue Code (or the Code), a corporation that undergoes an “ownership change” is subject to limitations on its ability to utilize its pre-change net operating loss carryforwards (or NOLs), to offset future taxable income. If the Internal Revenue Service challenges our analysis that our existing NOLs are not subject to limitations arising from previous ownership changes, or if we undergo an ownership change, our ability to utilize NOLs could be limited by Section 382 of the Code. Future changes in our stock ownership, some of which are outside of our control, could result in an ownership change under Section 382 of the Code. Furthermore, our ability to utilize NOLs of companies that we may acquire in the future may be subject to limitations. For these reasons, we may not be able to utilize a material portion of the NOLs carryforward as of December 31, 2013, even if we attain profitability.

Loss of, or inability to secure government contract revenues could impair our business.

In early 2010, we were awarded an “Integrated Bio-Refinery” grant from the United States Department of Energy (or DOE). The terms of this grant made funds available to us through 2013 to leverage and expand our existing Emeryville, California pilot plant and support laboratories to develop United States-based production capabilities for renewable fuels and chemicals derived from sweet sorghum. In late 2010, we were selected as a sub-contractor in the National Advanced Biofuels Consortium (or NABC) Fermentation of Lignocellulosic Sugars (or FLS) grant funded by the DOE. The terms of this grant made funds available to us through 2013 to develop strains that consume C5 sugars and to demonstrate production of advanced biofuels from lignocellulosic sugars. In 2012, we entered into a Technology Investment Agreement with The Defense Advanced Research Projects Agency (or

DARPA), under which we are performing certain research and development activities funded in part by DARPA. Generally, these agreements, as amended or modified, have fixed terms and may be terminated, modified or be subject to recovery of payments by the government agency under certain conditions (such as failure to comply with detailed reporting and governance processes or failure to achieve milestones). Under these agreements, we are also subject to audits, which can result in corrective action plans and penalties up to and including termination. If DARPA terminates its agreement with us, it could reduce our revenues which could harm our business. Additionally, we anticipate securing additional government contracts as part of our business plan for 2014 and beyond. If we are unable to secure such government contracts, it could harm our business.

Our headquarters and other facilities are located in an active earthquake zone, and an earthquake or other types of natural disasters affecting us or our suppliers could cause resource shortages and disrupt and harm our results of operations.

We conduct our primary research and development operations in the San Francisco Bay Area in an active earthquake zone, and certain of our suppliers conduct their operations in the same region or in other locations that are susceptible to natural disasters. In addition, California and some of the locations where certain of our suppliers are located have experienced shortages of water, electric power and natural gas from time to time. The occurrence of a natural disaster, such as an earthquake, drought or flood, or localized extended outages of critical utilities or transportation systems, or any critical resource shortages, affecting us or our suppliers could cause a significant interruption in our business, damage or destroy our facilities, production equipment or inventory or those of our suppliers and cause us to incur significant costs or result in limitations on the availability of our raw materials, any of which could harm our business, financial condition and results of operations. The insurance we maintain against fires, earthquakes and other natural disasters may not be adequate to cover our losses in any particular case.

Risks Related to Ownership of Our Common Stock

Our stock price may be volatile.

The market price of our common stock has been, and we expect it to continue to be, subject to significant volatility, and it has declined significantly from our initial public offering price. As of February 28, 2014 , the reported closing price for our common stock on the NASDAQ Global Select Market was $4.57 per share. Market prices for securities of early stage companies have historically been particularly volatile. Such fluctuations could be in response to, among other things, the factors described in this “Risk Factors” section or elsewhere in this report, or other factors, some of which are beyond our control, such as:


•	fluctuations in our financial results or outlook or those of companies perceived to be similar to us;


•	changes in estimates of our financial results or recommendations by securities analysts;


•	changes in market valuations of similar companies;


•	changes in the prices of commodities associated with our business such as sugar, ethanol and petroleum;


•	changes in our capital structure, such as future issuances of securities or the incurrence of debt;


•	announcements by us or our competitors of significant contracts, acquisitions or strategic alliances;


•	regulatory developments in the United States, Brazil, and/or other foreign countries;


•	litigation involving us, our general industry or both;


•	additions or departures of key personnel;


•	investors' general perception of us; and


•	changes in general economic, industry and market conditions.

Furthermore, stock markets have experienced price and volume fluctuations that have affected, and continue to affect, the market prices of equity securities of many companies. These fluctuations often have been unrelated or disproportionate to the operating performance of those companies. These broad market fluctuations, as well as general economic, political and market conditions, such as recessions, interest rate changes and international currency fluctuations, may negatively affect the market price of our common stock.

In the past, many companies that have experienced volatility and sustained declines in the market price of their stock have become subject to securities class action and derivative action litigation. We are currently involved in two such lawsuits, as described in more detail below in "ITEM 3. LEGAL PROCEEDINGS", and we may be the target of this type of litigation in the future. Securities litigation against us could result in substantial costs and divert our management's attention from other business concerns, which could seriously harm our business.

The concentration of our capital stock ownership with insiders will limit the ability to influence corporate matters.

As of February 28, 2014 :


•	our executive officers and directors and their affiliates (including Total) together held approximately 40% of our outstanding common stock;


•	Total held approximately 17.7% of our outstanding common stock; and


•	the two largest holders of outstanding common stock after Total (Temasek and Biolding Investment SA (or Biolding), each of whom has a designee on our Board of Directors) together held approximately 23.2% of our outstanding common stock.

This significant concentration of share ownership may adversely affect the trading price for our common stock because investors often perceive disadvantages in owning stock in companies with controlling stockholders. Also, these stockholders, acting together, will be able to control our management and affairs and matters requiring stockholder approval, including the election of directors and the approval of significant corporate transactions, such as mergers, consolidations or the sale of substantially all of our assets. Consequently, this concentration of ownership may have the effect of delaying or preventing a change of control, including a merger, consolidation or other business combination involving us, or discouraging a potential acquirer from making a tender offer or otherwise attempting to obtain control, even if that change of control would benefit our other stockholders.

If securities or industry analysts do not publish or cease publishing research or reports about us, our business or our market, or if they change their recommendations regarding our stock adversely, our stock price and trading volume could decline.

The trading market for our common stock will be influenced by the research and reports that industry or securities analysts may publish about us, our business, our market or our competitors. If any of the analysts who cover us change their recommendation regarding our stock adversely, or provide more favorable relative recommendations about our competitors, our stock price would likely decline. If any analyst who may cover us were to cease coverage of our company or fail to regularly publish reports on us, we could lose visibility in the financial markets, which in turn could cause our stock price or trading volume to decline.

We do not expect to declare any dividends in the foreseeable future.

We do not anticipate declaring any cash dividends to holders of our common stock in the foreseeable future. In addition, certain of our equipment leases and credit facilities currently restrict our ability to pay dividends. Consequently, investors may need to rely on sales of their common stock after price appreciation, which may never occur, as the only way to realize any future gains on their investment. Investors seeking cash dividends should not purchase our common stock.

Anti-takeover provisions contained in our certificate of incorporation and bylaws, as well as provisions of Delaware law, could impair a takeover attempt.

Our certificate of incorporation and bylaws contain provisions that could delay or prevent a change in control of our company. These provisions could also make it more difficult for stockholders to elect directors and take other corporate actions. These provisions include:


•	a staggered board of directors;


•	authorizing the board of directors to issue, without stockholder approval, preferred stock with rights senior to those of our common stock;


•	authorizing the board of directors to amend our bylaws and to fill board vacancies until the next annual meeting of the stockholders;


•	prohibiting stockholder action by written consent;


•	limiting the liability of, and providing indemnification to, our directors and officers;


•	eliminating the ability of our stockholders to call special meetings; and


•	requiring advance notification of stockholder nominations and proposals.

Section 203 of the Delaware General Corporation Law prohibits, subject to some exceptions, “business combinations” between a Delaware corporation and an “interested stockholder,” which is generally defined as a stockholder who becomes a beneficial owner of 15% or more of a Delaware corporation's voting stock, for a three-year period following the date that the stockholder became an interested stockholder. We have agreed to opt out of Section 203 through our certificate of incorporation, but our certificate of incorporation contains substantially similar protections to our company and stockholders as those afforded under Section 203, except that we have agreed with Total that it and its affiliates will not be deemed to be “interested stockholders” under such protections.

In addition, we have an agreement with Total, which provides that, so long as Total holds at least 10% of our voting securities, we must inform Total of any offer to acquire us or any decision of our Board of Directors to sell our company, and we must provide Total with information about the contemplated transaction. In such events, Total will have an exclusive negotiating period of fifteen business days in the event the Board of Directors authorizes us to solicit offers to buy Amyris, or five business days in the event that we receive an unsolicited offer to purchase us. This exclusive negotiation period will be followed by an additional restricted negotiation period of ten business days, during which we are obligated to continue to negotiate with Total and will be prohibited from entering into an agreement with any other potential acquirer.

These and other provisions in our amended and restated certificate of incorporation and our amended and restated bylaws that became effective upon the completion of our initial public offering under Delaware law and in our agreement with Total could discourage potential takeover attempts, reduce the price that investors might be willing to pay in the future for shares of our common stock and result in the market price of our common stock being lower than it would be without these provisions.

EXECUTIVE OFFICERS OF THE REGISTRANT

The following table provides the names, ages and offices of each of our executive officers as of February 28, 2013:



Name	Age	Position
Executive Officers:
John Melo	47	Director, President and Chief Executive Officer
Joel Cherry, Ph.D.	53	President of Research and Development
Paulo Diniz	56	Interim Chief Financial Officer
Zanna McFerson	48	Chief Business Officer
Nicholas Khadder	40	General Counsel and Corporate Secretary

John Melo

John Melo has nearly three decades of combined experience as an entrepreneur and thought leader in the global fuels industry and technology innovation. Mr. Melo has served as our President and Chief Executive Officer and a director since January 2007 and our President since January 2008. Before joining Amyris, Mr. Melo served in various senior executive positions at BP Plc (formerly British Petroleum), one of the world’s largest energy firms, from 1997 to 2006, most recently as President of U.S. Fuels Operations from 2004 until December 2006, and previously as Chief Information Officer of the refining and marketing segment from 2001 to 2003, Senior Advisor for e-business strategy to Lord Browne, BP Chief Executive, from 2000 to 2001, and Director of Global Brand Development from 1999 to 2000. Before joining BP, Mr. Melo was with Ernst & Young, an accounting firm, from 1996 to 1997, and a member of the management teams of several startup companies, including Computer Aided Services, a management systems integration company, and Alldata Corporation, a provider of automobile repair software to the automotive service industry. Mr. Melo currently serves on the board of directors of U.S. Venture, Inc. and Renmatix Inc., and also serves as Vice Chairman of the board of directors of BayBio. Mr. Melo was formerly an appointed member to the U.S. section of the U.S.-Brazil CEO Forum.

Joel Cherry, Ph.D.

Dr. Joel Cherry has served as our President of Research and Development since July 2011 and previously as our Senior Vice President of Research Programs and Operations since November 2008. Before joining Amyris, Dr. Cherry was Senior Director of Bioenergy Biotechnology at Novozymes, a biotechnology company focusing on development and manufacture of industrial enzymes from 1992 to November 2008. At Novozymes, he served in a variety of R&D scientific and management positions, including membership in Novozymes’ International R&D Management team, and as Principal Investigator and Director of the BioEnergy Project, a U.S. Department of Energy-funded $18 million effort initiated in 2000. Dr. Cherry holds a Bachelor of Arts degree in Chemistry from Carleton College and a Doctor of Philosophy degree in Biochemistry from the University of New Hampshire.

Paulo Diniz

Paulo Diniz was named interim Chief Financial Officer in December 2013 after initially serving as the CEO of Amyris Brasil, starting in March 2011. Prior to joining Amyris, Mr. Diniz served as Chief Financial Officer of Bunge Brasil S.A., a wholly owned subsidiary of Bunge Ltd., an agribusiness and food company, from April 2009 to November 2010. From 2003 to April 2009, Mr. Diniz was Chief Financial Officer and a member of the board of directors of Cosan S.A., a renewable energy company. He received a Master of Business Administration degree from IMD in Switzerland, a Bachelor of Science degree in Production Engineering from the University of São Paulo (USP) in Brazil, and did post graduate work in human resources at INSEAD in France.

Zanna McFerson

Zanna McFerson joined us as our Chief Business Officer in March 2013. Prior to joining Amyris, Ms. McFerson was a Vice President at Cargill, Incorporated, a privately-held international producer and marketer of food, agricultural, financial and industrial products and services, where she served as Business Director, Truvia Enterprise, from August 2008 to February 2013. Previously, Ms. McFerson served as Business Director, Health and Nutrition - Truvia, at Cargill from May 2006 to July 2008. She joined Cargill in 1990 as a commodity trader and held various roles in sales, management, and new product development until joining the leadership team of Cargill Health and Nutrition in May 2005. Ms. McFerson received a Bachelor of Arts degree in Economics

from the University of Illinois and a Master of Business Administration degree from the University of Iowa. She served on the Board of Directors for the International Stevia Council, and serves on the Board of Directors of the Real Stevia Company in Stockholm, Sweden.

Nicholas Khadder

Nicholas Khadder has served as our General Counsel and Corporate Secretary since December 2013. Previously, Mr. Khadder served as our Interim General Counsel from July 2013 to December 2013, and as our Assistant General Counsel from October 2010 to July 2013. Prior to joining Amyris, Mr. Khadder served in senior corporate counsel roles at LeapFrog Enterprises, Inc., an educational entertainment company, from August 2008 to September 2010, and at Protiviti, Inc., an internal audit and risk consulting firm, from June 2005 to July 2008. Before commencing his in-house legal career, Mr. Khadder was a corporate law associate at Fenwick & West LLP from 1998 to 2005. Mr. Khadder holds a Doctor of Jurisprudence degree from Berkeley Law (the University of California, Berkeley, School of Law), and a Bachelor’s degree in English from the University of California, Berkeley.

ITEM 1B. UNRESOLVED STAFF COMMENTS

Not applicable.

ITEM 2. PROPERTIES

We lease approximately 136,000 square feet of space in two adjacent buildings in Emeryville, California, pursuant to two leases. Of this space, we use approximately 113,000 square feet for general office purposes and lab space, and approximately 23,000 square feet comprise our pilot plant. Our leases expire in May 2023 and we have an option to extend these leases for five years. We also lease approximately 19,375 square feet of space in North Carolina under a month-to-month lease. This lease relates to manufacturing operations through Glycotech, one of our variable interest entities.

Amyris Brasil leases approximately 47,000 square feet of space in Campinas, Brazil, pursuant to two leases that will expire in October 2015 and November 2016. Of this space, approximately 36,000 square feet comprise a pilot plant and demonstration facility, and the remainder is general office and lab space. Amyris Brasil has a right of first refusal to purchase the space if the landlord elects to sell it and an option to extend the lease for five additional years.

Our first large-scale Biofene production plant commenced operations in December 2012 in Brotas in the state of São Paulo, Brazil and is adjacent to an existing sugar and ethanol mill, Paraíso Bioenergia. Amyris Brasil leases approximately 800,000 square feet of space for this plant, which has six 200,000 liter production fermenters and was designed to process sugarcane juice, or its equivalent, from up to one million tons of raw sugarcane annually; this lease expires in March 2026. Amyris Brasil also leases approximately 500,000 square feet of space for a future manufacturing site; this lease expires in January 2031.

We have also secured the use of a Biofene storage tank with an aggregate capacity of 3,000 barrels or 94,500 gallons in Philadelphia. This facility provides temporary storage of our renewable farnesene prior to further processing into one of our finished products. Our current agreement expires in June 2015.

We believe that our current facilities are suitable and adequate to meet our needs and that suitable additional space will be available to accommodate the foreseeable expansion of our operations.

ITEM 3. LEGAL PROCEEDINGS

In May 2013, a securities class action complaint was filed against Amyris and our CEO, John G. Melo, in the U.S. District Court for the Northern District of California. In October 2013, the lead plaintiffs filed a consolidated amended complaint. The complaint, as amended, sought unspecified damages on behalf of a purported class that would comprise all individuals who acquired our common stock between April 29, 2011 and February 8, 2012. The complaint alleged securities law violations based on the company's commercial projections during that period. In December 2013, we filed a motion to dismiss the complaint. In March 2014, the court issued an order granting our motion to dismiss with leave to amend the complaint. We continue to believe the complaint lacks merit, and intend to defend ourselves vigorously.

In August 2013, a complaint entitled Steve Shannon, derivatively on behalf of Amyris, Inc. v. John G. Melo et al and Amyris, Inc., was filed against Amyris as nominal defendant in the United States District Court for the Northern District of California. The lawsuit seeks unspecified damages on behalf of Amyris from certain of our current and former officers, directors and employees and alleges these defendants breached their fiduciary duties to Amyris and unjustly enriched themselves by making allegedly false and misleading statements and omitting certain material facts in our securities filings. Because this purported stockholder derivative action is based on substantially the same facts as the securities class action described above, the two actions have been related and will be heard by the same judge. By stipulation of the parties, the case has been stayed until the Company either files an answer in the securities class action or the securities action is dismissed with prejudice. We do not believe the claims in the complaint have merit, and intend to defend ourselves vigorously.

We may be involved, from time to time, in legal proceedings and claims arising in the ordinary course of our business. Such matters are subject to many uncertainties and there can be no assurance that legal proceedings arising in the ordinary course of business or otherwise will not have a material adverse effect on our business, results of operations, financial position or cash flows.

ITEM 4. MINE SAFETY DISCLOSURES

Not applicable.

PART II

ITEM 5. MARKET FOR REGISTRANT’S COMMON EQUITY, RELATED STOCKHOLDER MATTERS AND ISSUER PURCHASES OF EQUITY SECURITIES

Market Information for Common Stock

Our common stock commenced trading on the NASDAQ Global Market on September 28, 2010 under the symbol “AMRS” and currently trades on the NASDAQ Global Select Market under the same symbol. The following table sets forth the high and low per share sale prices of our common stock as reported on the NASDAQ Global Select Market during each of the previous eight quarters.



	Price Range Per Share
	High		Low
Fiscal 2013
Fourth quarter	$	6.11	$	2.17
Third quarter	$	3.03	$	2.22
Second quarter	$	3.20	$	2.60
First quarter	$	4.15	$	2.56

Fiscal 2012
Fourth quarter	$	3.48	$	2.16
Third quarter	$	4.56	$	2.74
Second quarter	$	5.16	$	1.57
First quarter	$	12.29	$	4.45

Holders

As of February 27, 2014, there were approximately 104 holders of record (not including beneficial holders of stock held in street names) of our common stock.

Dividend Policy

We have never declared or paid cash dividends on our capital stock. We currently intend to retain any future earnings and do not expect to declare or pay any dividends in the foreseeable future. Any further determination to pay dividends on our capital stock will be at the discretion of our Board of Directors and will depend on our financial condition, results of operations, capital requirements and other factors that our Board of Directors considers relevant.

Securities Authorized for Issuance Under Equity Compensation Plans

See Item 12 of Part III of this Report regarding information about securities authorized for issuance under our equity compensation plans.

Performance Graph ⁽¹⁾

The following graph shows a comparison from September 28, 2010 through December 31, 2013 of cumulative total return on an assumed investment of $100.00 in cash in our common stock, the S&P SmallCap 600 Index and the NASDAQ Clean Edge Green Energy Index. Such returns are based on historical results and are not intended to suggest future performance. Data for the S&P SmallCap 600 Index and the NASDAQ Clean Edge Green Energy Index assume reinvestment of dividends.

COMPARISON OF 39 MONTH CUMULATIVE TOTAL RETURN

Among Amyris, Inc., the S&P SmallCap 600 Index, and the NASDAQ Clean Edge Green Energy Index



	9/28/2010		12/31/2010		3/31/2011		6/30/2011		9/30/2011		12/31/2011		3/31/2012		6/30/2012		9/30/2012		12/31/2012		3/31/2013		6/31/2013		9/30/2013		12/31/2013
Amyris, Inc.	$	100	$	162	$	173	$	170	$	123	$	70	$	31	$	27	$	21	$	19	$	19	$	18	$	14	$	32
S&P SmallCap 600 Index	$	100	$	116	$	124	$	124	$	99	$	116	$	129	$	124	$	130	$	133	$	148	$	153	$	169	$	185
NASDAQ Clean Edge Green Energy Index	$	100	$	109	$	112	$	102	$	66	$	64	$	72	$	62	$	59	$	63	$	74	$	94	$	108	$	119


(1)	This performance graph shall not be deemed “soliciting material” or to be “filed” with the SEC for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, or otherwise subject to the liabilities under that Section, and shall not be deemed incorporated by reference into any filing of Amyris, Inc. under the Securities Act of 1933, as amended.

Recent Sales of Unregistered Securities

Private Placements

On December 24, 2012, we sold 14,177,849 shares common stock at a price of $2.98 per share for aggregate cash proceeds of $37.2 million and cancellation of $5.0 million of an outstanding senior unsecured convertible promissory notes we previously issued to Total. The cash settlement with respect to 5,033,557 of such shares occurred on January 14, 2013.

On March 27, 2013, we sold 1,533,742 shares of common stock at a price of $3.26 per share for an aggregate cash proceeds of $5.0 million.

Promissory Notes

On June 6, 2013 and July 26, 2013, we sold $10.0 million and $20.0 million of 1.5% Senior Unsecured Convertible Notes Due 2017 for aggregate offering prices of $10.0 million and $20.0 million in cash, respectively. These notes have a March 1, 2017 maturity date and a conversion price equal to $3.08 per share of our common stock. The conversion price of these notes is subject to adjustment for proportional adjustments to outstanding common stock and under anti-dilution provisions in case of certain dividends and distributions. The holder of these notes (Total) has a right to require repayment of 101% of the principal amount of the notes in the event of a change of control in Amyris, and the notes provide for payment of unpaid interest on conversion following such a change of control if Total does not require such repayment.

On October 4, 2013, we sold a Senior Promissory Note to Temasek for a bridge loan of $35.0 million. The note was not convertible or exercisable for equity securities; however it was cancelled in exchange for a Tranche I Senior Convertible Note as described below.

On October 16, 2013, we sold approximately $51.9 million of Tranche I Senior Convertible Notes in the August Financing for an aggregate offering price of $51.9 million, including cancellation of the Temasek Bridge Note ($35.0 million), new cash proceeds of approximately $7.6 million, and cancellation by Total of previously outstanding convertible promissory notes (approximately $9.3 million). These notes are due sixty months from the date of issuance and are convertible into shares of our common stock at a conversion price equal to $2.44 per share, subject to adjustment as described below. Specifically, the notes are convertible at the option of the holder (i) at any time after 18 months from the date of the purchase agreement relating to such notes, (ii) on a change of control, and (iii) upon the occurrence of an event of default. The conversion price of the notes was subject to reduction to $2.15 if either (a) a specified company manufacturing plant fails to achieve a total production of 1,000,000 liters within a run period of 45 days prior to June 30, 2014, or we fail to achieve gross margins from product sales of at least 5% prior to June 30, 2014, or (b) we reduce the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of these new notes; provided, however, that, if both of the conditions described in clauses (a) and (b) were to occur, the conversion price of the notes could be reduced to $1.87. In addition to the conversion price adjustments set forth above, the conversion price of these notes is subject to further adjustment (i) according to proportional adjustments to outstanding common stock in case of certain dividends and distributions, (ii) according to anti-dilution provisions, and (iii) with respect to such notes held by any purchaser other than Total, in the event that Total exchanges existing convertible notes for new securities of the company in connection with future financing transactions in excess of its pro rata amount. The purchasers have a right to require repayment of 101% of the principal amount of the notes in the event of a change of control and the notes provide for payment of unpaid interest on conversion following such a change of control if the purchasers do not require such repayment.

On December 2, 2013, we issued approximately $69.0 million of 1.5% Senior Secured Convertible Notes to Total, replacing an equal amount of previously outstanding 1.5% Senior Unsecured Convertible Notes Due 2017 held by Total. The exchange was completed as part of the establishment of a joint venture, and the conversion terms of the new notes were generally identical to the terms of the notes that were cancelled, except that the new notes are secured by certain of our shares in the joint venture.

On December 24, 2013, we agreed to sell approximately $34.0 million of Tranche II Senior Convertible Notes in the August Financing for an aggregate offering price of $34.0 million, including new cash proceeds of approximately $28.0 million, and cancellation by Total of previously outstanding convertible promissory notes (approximately $6.0 million). We sold and issued these notes in January 15, 2014. The notes are due sixty months from the date of issuance and are convertible into shares of our common stock at a conversion price equal to $2.87 per share, subject to adjustment as described below. Specifically, the notes are convertible at the option of the holder (i) at any time 12 months after issuance, (ii) on a change of control, and (iii) upon the occurrence of an event of default. The conversion price of these notes is subject to adjustment (i) according to proportional adjustments to outstanding common stock in case of certain dividends and distributions, (ii) according to anti-dilution provisions, and (iii) with respect to such notes held by any purchaser other than Total, in the event that Total exchanges existing convertible notes for new securities of the company in connection with future financing transactions in excess of its pro rata amount. The

purchasers have a right to require repayment of 101% of the principal amount of the Tranche II Notes in the event of a change of control and the notes provide for payment of unpaid interest on conversion following such a change of control if the purchasers do not require such repayment.

With the exception of a placement agent used in connection with the sale of securities to one of the purchasers in the convertible note financing we closed in January 2014, no underwriters were involved in the foregoing sales of securities. These securities were issued in private transactions pursuant to Section 4(2) of the Securities Act. The recipients of these securities acquired the securities for investment purposes only and without intent to resell, were able to fend for themselves in these transactions, and were accredited investors as defined in Rule 501 of Regulation D promulgated under Section 3(b) of the Securities Act, and appropriate restrictions were set out in the agreements for, and stock certificates and notes issued in, these transactions. These security holders had adequate access, through their relationships with us, to information about us.

ITEM 6. SELECTED FINANCIAL DATA

The selected consolidated statements of operations data for the years ended December 31, 2013, 2012, 2011, 2010 and 2009 and the selected consolidated balance sheets data as of December 31, 2013, 2012, 2011, 2010 and 2009 are derived from our audited Consolidated Financial Statements, appearing elsewhere in this report. The historical results presented below are not necessarily indicative of financial results to be achieved in future periods. You should read the following selected financial data in conjunction with “Management’s Discussion Analysis of Financial Condition and Results of Operations” and our Consolidated Financial Statements and related Notes included in Item 8 of this report.



	Years Ended December 31,
	2013			2012			2011			2010			2009
	(In Thousands, Except Share and Per Share Amounts)
Consolidated Statements of Operations Data:
Revenues
Renewable product sales	$	14,428		$	10,802		$	763		$	—		$	—
Related party renewable product sales	1,380			—			—			—			—
Ethanol and ethanol-blended gasoline	—			38,836			129,074			68,664			61,689
Total product sales	15,808			49,638			129,837			68,664			61,689
Grants and collaborations revenue	22,664			14,281			17,154			11,647			2,919
Related party grants and collaborations revenue	2,647			9,775			—			—			—
Grants and collaborations revenue	25,311			24,056			17,154			11,647			2,919
Total revenues	41,119			73,694			146,991			80,311			64,608
Cost and operating expenses
Cost of products sold	38,253			77,314			155,615			70,515			60,428
Loss on purchase commitments and write off of production assets	9,366			45,854			—			—			—
Research and development	56,065			73,630			87,317			55,249			38,263
Sales, general and administrative	57,051			78,718			83,231			40,393			23,558
Restructuring and asset impairment (income) charges	—			—			—			(2,061		)	5,768
Total cost and operating expenses	160,735			275,516			326,163			164,096			128,017
Net loss from operations	(119,616		)	(201,822		)	(179,172		)	(83,785		)	(63,409		)
Other income (expense):
Interest income	162			1,472			1,542			1,540			448
Interest expense	(9,107		)	(4,926		)	(1,543		)	(1,443		)	(1,218		)
Income (loss) from change in fair value of derivative instruments	(84,726		)	1,790			—			—			—
Income (loss) from extinguishment of debt	(19,914		)	(920		)	—			—			—
Other income (expense), net	(2,553		)	(646		)	214			898			(621		)
Total other income (expense)	(116,138		)	(3,230		)	213			995			(1,391		)
Loss before income taxes	(235,754		)	(205,052		)	(178,959		)	(82,790		)	(64,800		)
Income tax benefit (provision)	847			(981		)	(552		)	—			—
Net loss	$	(234,907	)	$	(206,033	)	$	(179,511	)	$	(82,790	)	$	(64,800	)
Net (income) loss attributable to noncontrolling interest	(204		)	894			641			920			341
Net loss attributable to Amyris, Inc.	$	(235,111	)	$	(205,139	)	$	(178,870	)	$	(81,870	)	$	(64,459	)
Deemed dividend related to a beneficial conversion feature	—			—			—			(42,009		)	—
Net loss attributable to Amyris, Inc. common stockholders	$	(235,111	)	$	(205,139	)	$	(178,870	)	$	(123,879	)	$	(64,459	)
Net loss per share attributable to common stockholders, basic and diluted	$	(3.12	)	$	(3.62	)	$	(3.99	)	$	(8.35	)	$	(13.56	)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	75,472,770			56,717,869			44,799,056			14,840,253			4,753,085



	As of December 31,
	2013			2012		2011		2010		2009
	(In Thousands)
Consolidated Balance Sheets Data:
Cash, cash equivalents, investments and restricted cash	$	9,944		$	31,644	$	103,592	$	257,933	$	71,716
Working capital	(382		)	3,668		47,205		242,818		51,062
Property, plant and equipment, net	140,591			163,121		128,101		54,847		42,560
Total assets	198,864			242,834		320,111		357,453		122,159
Total indebtedness ⁽¹⁾	153,305			106,774		47,660		12,590		20,608
Convertible preferred stock warrant liability	—			—		—		—		2,740
Convertible preferred stock	—			—		—		—		179,651
Redeemable noncontrolling interest	—			—		—		—		5,506
Total equity (deficit)	(135,848		)	66,229		160,812		307,548		(113,745		)

⁽¹⁾

Total indebtedness as of December 31, 2013, 2012, 2011, 2010 and 2009 includes $1.2 million , $2.6 million , $6.3 million , $5.9 million and $7.2 million , respectively, in capital lease obligations, zero , $1.6 million , $3.1 million , $5.7 million and $4.0 million , respectively, in notes payable, $25.3 million , $26.2 million , $19.4 million , $1.0 million and $1.0 million , respectively, in loans payable, $8.8 million , $12.4 million , $18.9 million , zero and $8.3 million respectively, in credit facilities. Total indebtedness as of December 31, 2013 and 2012 also included $28.5 million and $25.0 million , respectively, in convertible notes and $89.5 million and $39.0 million , respectively in related party convertible notes. There was no convertible notes balance outstanding as of December 31, 2011, 2010 and 2009 (see Note 5, "Debt" and Note 6, "Commitments and Contingencies" to our Consolidated Financial Statements).

ITEM 7. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

Overview

Amyris is a renewable products company focused on providing sustainable alternatives to a broad range of petroleum-sourced products. We developed innovative microbial engineering and screening technologies that modify the way microorganisms process sugars. We are using our proprietary synthetic biology platform to design microbes, primarily yeast, and use them as living factories in established fermentation processes to convert plant-sourced sugars into renewable hydrocarbons. We are developing, and, in some cases, already commercializing, products from these hydrocarbons in several target industry sectors, including cosmetics, lubricants, flavors and fragrances, performance materials, and transportation fuels. We call these No Compromise products because we design them to perform comparably to or better than currently available products.

We have been applying our industrial synthetic biology platform to provide alternatives to a broad range of petroleum-sourced products. We have focused our development efforts on the production of Biofene, our brand of renewable farnesene, a long-chain, branched liquid hydrocarbon molecule. Using Biofene as a first commercial building block molecule, we are developing a wide range of renewable products for our target markets.

While our platform is able to utilize a wide variety of feedstocks, we are focusing our large-scale production plans primarily on the use of Brazilian sugarcane as our feedstock because of its abundance, low cost and relative price stability. We have also been able to produce Biofene through the use of other feedstocks such as sugar beets, corn dextrose, sweet sorghum and cellulosic sugars.

Our first purpose-built, large-scale Biofene production plant commenced operations in southeastern Brazil in December 2012. This plant is located in Brotas, in the state of São Paulo, Brazil, and is adjacent to an existing sugar and ethanol mill, Paraíso Bioenergia. We have also advanced initial construction of a second large-scale production plant in Brazil, located at the SMSA sugar and ethanol mill also in the state of São Paulo, Brazil, for which we intend to complete the construction when market developments support the start-up of that plant.

Our business strategy is focused on our commercialization efforts of specialty products while moving commodity products, including our fuels and base oil lubricants products, into joint venture arrangements with established industry leaders. We believe this approach will permit access to the capital and resources necessary to support large-scale production and global distribution

for our products. Our initial renewable products efforts have been focused on cosmetics, niche fuel opportunities, fragrance oils, and performance materials sector.

Total Relationship

In July 2012 and December 2013, we entered into a series of agreements to establish a research and development program and form a joint venture with Total to produce and commercialize Biofene-based diesel and jet fuels, and successfully formed such joint venture in December 2013. With an exception for our fuels business in Brazil, the collaboration and joint venture established the exclusive means for us to develop, produce and commercialize fuels from Biofene. We granted the joint venture exclusive licenses under certain of our intellectual property to make and sell joint venture products. We also granted the joint venture, in the event of a buy-out of our interest in the joint venture by Total (which Total is entitled to do under certain circumstances described below) a non-exclusive license to optimize or engineer yeast strains used by us to produce farnesene for the joint venture’s diesel and jet fuels. As a result of these licenses, Amyris generally no longer has an independent right to make or sell Biofene fuels outside of Brazil.

Our agreements with Total relating to our fuels collaboration created a convertible debt financing structure for funding the research and development program. The collaboration agreements contemplated approximately $105.0 million in financing for the collaboration, of which Total has funded $83.3 million to date. Total is to fund up to the remaining $21.7 million , with $10.85 million to be paid by July 2014 and $10.85 million to be paid by January 2015. If Total chooses not to continue participating at certain "Go/No-Go" decision points during the program, licenses to our technology would terminate, and the notes would remain outstanding and become payable at maturity unless otherwise converted in accordance with their terms. If Total chooses to continue the collaboration and makes a final decision to proceed with the joint venture only for jet fuel, Total is required to buy from Amyris 50% of the preferred shares of the joint venture in exchanges for the settlement of 30% of the principal and interest outstanding under the notes. The remaining notes would continue to be outstanding and payable upon maturity unless otherwise converted in accordance with the terms of the notes.

Sales and Revenue

To commercialize our initial Biofene-derived product, squalane, in the cosmetics sector for use as an emollient, we have entered into marketing and distribution agreements in Europe, Asia, and North America. As an initial step towards commercialization of Biofene-based diesel, we have entered into agreements with municipal fleet operators in Brazil. Our diesel fuel is supplied to the largest Company in Brazil's fuel distribution segment which blends our product with petroleum diesel, and sells to a number of bus fleet operators. For the industrial lubricants market, we established a joint venture with Cosan for the worldwide development, production and commercialization of renewable base oils in the lubricant sector.

Financing

In 2013, we completed multiple financings involving loans, convertible debt and equity offerings. We completed private placements of 6,567,299 shares of common stock in 2013 for aggregate proceeds of $20.0 million , of which $15.0 million was from the receipt of funds from a private placement that closed in December 2012. We raised $72.6 million in 2013 from an offering of senior unsecured convertible promissory notes pursuant to the August Financing and research and development funding from Total.

In December 2012, we completed a private placement of 14,177,849 shares of common stock for aggregate proceeds of $37.2 million and the cancellation of $5.0 million worth of outstanding senior unsecured convertible promissory notes we previously issued to Total in exchange for approximately 1,677,852 shares of common stock. Under the December 2012 purchase agreement and related documents, the purchase of a portion of the shares, representing $15.0 million of the proceeds from that transaction, was settled in January 2013. Cash received as of December 31, 2012 in the December 2012 financing, net of the note conversion and the January 2013 settlement, was $22.2 million . In January 2013, we received the $15.0 million proceeds from the private placement offering that closed in December 2012. Consequently we issued 5,033,557 shares of the 14,177,849 shares of Amyris' common stock issuable pursuant to such private placement.

In March 2013, we completed a private placement of 1,533,742 of our common stock to Biolding for aggregate proceeds of $5.0 million . This private placement represented the final tranche of Biolding's preexisting contractual obligation to fund $15.0 million upon satisfaction by us of certain criteria associated with the commissioning of our production plant in Brotas, Brazil.

In March 2013, we entered into a letter agreement with Total (referred to as the March 2013 Letter Agreement). Under the March 2013 Letter Agreement, we sold and issued a $10.0 million senior unsecured convertible note to Total with an initial conversion price of $3.08 per share in June 2013. Subsequently, in July 2013, we sold and issued a $20.0 million senior unsecured convertible note to Total with the same initial conversion price of $3.08 per share as the note sold in June 2013. The July 2013 purchase and sale completed Total's commitment to purchase $30.0 million of such notes by July 2013.

In October 2013, we completed an additional private placement of convertible promissory notes in the August 2013 Financing as described in more detail below under "Liquidity and Capital Resources.".

In December 2013, we agreed to complete an additional private placement of a portion of the second tranche of convertible promissory notes in the August 2013 Financing as described in more detail below under "Liquidity and Capital Resources." On January 15, 2014, the Company completed the offering of convertible promissory notes in the second tranche of the August 2013 Financing.

Liquidity

We have incurred significant losses since our inception and believe that we will continue to incur losses and negative cash flow from operations into at least 2014. As of December 31, 2013 , we had an accumulated deficit of $821.4 million and had cash, cash equivalents and short term investments of $8.3 million . We have significant outstanding debt and contractual obligations related to purchase commitments, as well as capital and operating leases. As of December 31, 2013 , our debt, net of discount totaled $152.1 million , of which $6.4 million matures within the next twelve months. Additionally, our debt agreements contain various covenants, including restrictions on business that could cause us to be at risk of defaults.

In addition to cash contributions from product sales and debt and equity financings, we also depend on collaboration funding to support our operating expenses. While part of this funding is committed based on existing collaboration agreements, we will need to identify and obtain funding under additional collaborations that are not yet subject to any definitive agreement or are not yet identified. In addition, some of our existing anticipated collaboration funding is subject to our achievement of milestones or other funding conditions. If we are unable to raise additional financing, or if other expected sources of funding are delayed or not received, we would take actions to support our liquidity needs that could have a material negative impact on our ability to continue our business as currently contemplated. See “Liquidity and Capital Resources” below in this section for additional detail regarding these contingency plans and their potential effects on our business.

Critical Accounting Policies and Estimates

Our discussion and analysis of our financial condition and results of operations is based upon our consolidated financial statements, which have been prepared in accordance with accounting principles generally accepted in the United States. The preparation of these consolidated financial statements requires us to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenues, expenses and related disclosures. We base our estimates and assumptions on historical experience and on various other factors that we believe to be reasonable under the circumstances. We evaluate our estimates and assumptions on an ongoing basis. The results of our analysis form the basis for making assumptions about the carrying values of assets and liabilities that are not readily apparent from other sources. Our actual results may differ from these estimates under different assumptions or conditions.

We believe the following critical accounting policies involve significant areas of management’s judgments and estimates in the preparation of our financial statements.

Revenue Recognition

We recognize revenue from the sale of farnesene-derived products, from the delivery of collaborative research services and from government grants. Through the third quarter of 2012, we sold ethanol and reformulated ethanol-blended gasoline under short-term agreements at prevailing market prices. As of September 30, 2012 we had transitioned out of that business. Revenue is recognized when all of the following criteria are met: persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, the fee is fixed or determinable and collectability is reasonably assured.

If sales arrangements contain multiple elements, we evaluate whether the components of each arrangement represent separate units of accounting. Application of revenue recognition standards requires subjective determination and requires management to make judgments about the fair values of each individual element and whether it is separable from other aspects of the contractual relationship.

For each source of revenues, we apply the above revenue recognition criteria in the following manner:

Product Sales.

Starting in the second quarter of 2011, we commenced sales of farnesene-derived products. Revenues are recognized, net of discounts and allowances, once passage of title and risk of loss have occurred, provided all other revenue recognition criteria have also been met.

Shipping and handling costs charged to customers are recorded as revenues. Shipping costs are included in cost of products sold. Such charges were not significant in any of the periods presented.

Grants and Collaborative Research Services.

Revenues from collaborative research services are recognized as the services are performed consistent with the performance requirements of the contract. In cases where the planned levels of research services fluctuate over the research term, we recognize revenues using the proportionate performance method based upon actual efforts to date relative to the amount of expected effort to be incurred by us. When up-front payments are received and the planned levels of research services do not fluctuate over the research term, revenues are recorded on a ratable basis over the arrangement term, up to the amount of cash received. When up-front payments are received and the planned levels of research services fluctuate over the research term, revenues are recorded using the proportionate performance method, up to the amount of cash received. Where arrangements include milestones that are determined to be substantive and at risk at the inception of the arrangement, revenues are recognized upon achievement of the milestone and is limited to those amounts whereby collectibility is reasonably assured.

Government grants are made pursuant to agreements that generally provide cost reimbursement for certain types of expenditures in return for research and development activities over a contractually defined period. Revenues from government grants are recognized in the period during which the related costs are incurred, provided that the conditions under which the government grants were provided have been met and only perfunctory obligations are outstanding. Under a government contract signed in June 2012, we will receive funding based on achievement of program milestones and accordingly revenues are recognized using the proportionate performance method based upon actual efforts to date relative to the amount of expected effort to be incurred, up to the amount of verified payable milestones.

Consolidations

We have interests in certain joint venture entities that are variable interest entities or VIEs. Determining whether to consolidate a variable interest entity may require judgment in assessing (i) whether an entity is a variable interest entity and (ii) if we are the entity’s primary beneficiary and thus required to consolidate the entity. To determine if we are the primary beneficiary of a VIE, we evaluate whether we have (i) the power to direct the activities that most significantly impact the VIE’s economic performance and (ii) the obligation to absorb losses or the right to receive benefits of the VIE that could potentially be significant to the VIE. Our evaluation includes identification of significant activities and an assessment of our ability to direct those activities based on governance provisions and arrangements to provide or receive product and process technology, product supply, operations services, equity funding and financing and other applicable agreements and circumstances. Our assessment of whether we are the primary beneficiary of our VIEs requires significant assumptions and judgment.

Impairment of Long-Lived Assets

We assess impairment of long-lived assets, which include property, plant and equipment and test long-lived assets for recoverability when events or changes in circumstances indicate that their carrying amount may not be recoverable. Circumstances which could trigger a review include, but are not limited to, significant decreases in the market price of the asset; significant adverse changes in the business climate or legal factors; accumulation of costs significantly in excess of the amount originally expected for the acquisition or construction of the asset; current period cash flow or operating losses combined with a history of losses or a forecast of continuing losses associated with the use of the asset; or expectations that the asset will more likely than not be sold or disposed of significantly before the end of its estimated useful life.

Recoverability is assessed based on the fair value of the asset, which is calculated as the sum of the undiscounted cash flows expected to result from the use and the eventual disposal of the asset. An impairment loss is recognized in the consolidated statements of operations when the carrying amount is determined not to be recoverable and exceeds fair value, which is determined on a discounted cash flow basis.

As a result of our impairment assessment of long-lived assets, we recorded losses on write-off of production assets of $7.7 million and $6.4 million during the year ended December 31, 2013 and 2012, respectively. There were no such losses on write off of production assets recorded in the year ended December 31, 2011.

We make estimates and judgments about future undiscounted cash flows and fair values. Although our cash flow forecasts are based on assumptions that are consistent with our plans, there is significant exercise of judgment involved in determining the cash flow attributable to a long-lived asset over its estimated remaining useful life. Significant changes in our plans in using long-lived assets, such as delays in the re-start of construction and completion of our large-scale SMA production facility, could significantly reduce our estimates of anticipated cash flows in the future. As a result, the carrying amounts of our long-lived assets could be reduced through impairment charges.

Inventories

Inventories, which consist of farnesene and farnesene-derived products are stated at the lower of cost or market. We evaluate the recoverability of our inventories based on assumptions about expected demand and net realizable value. If we determine that the cost of inventory exceeds its estimated net realizable value, we record a write-down equal to the difference between the cost of inventory and the estimated net realizable value. If actual net realizable values are lower than those projected by management, additional inventory write-downs may be required that could negatively impact our operating results. If actual net realizable values are more than those projected by management, we may have favorable operating results when products that have been previously written down are sold in the normal course of business. We also evaluate the terms of our agreements with our suppliers and establish accruals for estimated losses on adverse purchase commitments as necessary, applying the same lower of cost or market approach that is used to value inventory.

Goodwill and Intangible Assets

Goodwill represents the excess of the cost over the fair value of net assets acquired from our business combinations. Intangible assets are comprised primarily of in-process research and development (or IPR&D). We make significant judgments in relation to the valuation of goodwill and intangible assets resulting from business combinations and asset acquisitions.

There are several methods that can be used to determine the estimated fair value of the IPR&D acquired in a business combination. We have used the "income method," which applies a probability weighting that considers the risk of development and commercialization, to the estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, pricing of similar products, and expected industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets will be amortized over the remaining useful life or written off, as appropriate.

Goodwill and intangible assets with indefinite lives are assessed for impairment using fair value measurement techniques on an annual basis or more frequently if facts and circumstance warrant such a review. When required, a comparison of fair value to the carrying amount of assets is performed to determine the amount of any impairment.

We evaluate our intangible assets with finite lives for indications of impairment whenever events or changes in circumstances indicate that the carrying value may not be recoverable. Intangible assets consist of purchased licenses and permits and are amortized on a straight-line basis over their estimated useful lives. Factors that could trigger an impairment review include significant under-performance relative to historical or projected future operating results, significant changes in the manner of our use of the acquired assets or the strategy for our overall business or significant negative industry or economic trends. If this evaluation indicates that the value of the intangible asset may be impaired, we make an assessment of the recoverability of the net carrying value of the asset over its remaining useful life. If this assessment indicates that the intangible asset is not recoverable, based on the estimated undiscounted future cash flows of the technology over the remaining amortization period, we will reduce the net carrying value of the related intangible asset to fair value and may adjust the remaining amortization period. Any such impairment charge could be significant and could have a material adverse effect on our reported financial results. As a result of our impairment assessment of goodwill and intangible assets, we have not recognized any impairment charges through December 31, 2013 .

Stock-Based Compensation

Stock-based compensation cost for restricted stock units (or RSUs) is measured based on the closing fair market value of our common stock on the date of grant. Stock-based compensation cost for stock options and employee stock purchase plan rights is estimated at the grant date and offering date, respectively, based on the fair-value of our common stock using the Black-Scholes option pricing model. We amortize the fair value of the employee stock options on a straight-line basis over the requisite service period of the award, which is generally the vesting period. The measurement of nonemployee stock-based compensation is subject to periodic adjustments as the underlying equity instruments vest, and the resulting change in value, if any, is recognized in our consolidated statements of operations during the period the related services are rendered. There is inherent uncertainty in these estimates and if different assumptions had been used, the fair value of the equity instruments issued to nonemployee consultants could have been significantly different.

In future periods, our stock-based compensation expense is expected to change as a result of our existing unrecognized stock-based compensation still to be recognized and as we issue additional stock-based awards in order to attract and retain employees and nonemployee consultants.

Significant Factors, Assumptions and Methodologies Used In Determining Fair Value

We utilize the Black-Scholes option pricing model to estimate the fair value of our equity awards. The Black-Scholes option pricing model requires inputs such as the expected term of the grant, expected volatility and risk-free interest rate. Further, the forfeiture rate also affects the amount of aggregate compensation that we are required to record as an expense. These inputs are subjective and generally require significant judgment.

The fair value of employee stock options was estimated using the following weighted-average assumptions:



	Years Ended December 31,
	2013		2012	2011
Expected dividend yield	—	%	—%	—%
Risk-free interest rate	1.4	%	1.1%	2.3%
Expected term (in years)	6.1		6.0	5.8
Expected volatility	82	%	77%	86%

Expected term is derived from a comparable group of publicly listed companies that have a similar industry, life cycle, revenue, and market capitalization and the historical data on employee exercises.

Expected volatility is derived from a combination of historical volatility for our stock and the historical volatilities of a comparable group of publicly listed companies within our industry over a period equal to the expected term of our options because we do not yet have a long trading history.

Risk-free interest rate is the market yield currently available on United States Treasury securities with maturities approximately equal to the option’s expected term.

Expected dividend yield was assumed to be zero as we have not paid, and do not anticipate, declaring any cash dividends to holders of our common stock in the foreseeable future.

We estimate our forfeiture rate based on an analysis of our actual forfeitures and will continue to evaluate the appropriateness of the forfeiture rate based on actual forfeiture experience, analysis of employee turnover and other factors. Quarterly changes in the estimated forfeiture rate can have a significant effect on reported stock-based compensation expense, as the cumulative effect of adjusting the rate for all expense amortization is recognized in the period the forfeiture estimate is changed. If a revised forfeiture rate is higher than the previously estimated forfeiture rate, an adjustment is made that will result in a decrease to the stock-based compensation expense recognized in the consolidated financial statements. If a revised forfeiture rate is lower than the previously estimated forfeiture rate, an adjustment is made that will result in an increase to the stock-based compensation expense recognized in the consolidated financial statements.

We will continue to use judgment in evaluating the expected term, volatility and forfeiture rate related to our own stock-based compensation on a prospective basis and incorporating these factors into the Black-Scholes option pricing model.

Each of these inputs is subjective and generally requires significant management judgment to determine. If, in the future, we determine that another method for calculating the fair value of our stock options is more reasonable, or if another method for calculating these input assumptions is prescribed by authoritative guidance, and, therefore, should be used to estimate expected volatility or expected term, the fair value calculated for our employee stock options could change significantly. Higher volatility and longer expected terms generally result in an increase to stock-based compensation expense determined at the date of grant.

Income Taxes

We are subject to income taxes in both the United States and foreign jurisdictions, and we use estimates in determining our provisions for income taxes. We use the liability method of accounting for income taxes, whereby deferred tax assets or liability account balances are calculated at the balance sheet date using current tax laws and rates in effect for the year in which the differences are expected to affect taxable income.

Recognition of deferred tax assets is appropriate when realization of such assets is more likely than not. We recognize a valuation allowance against our net deferred tax assets if it is more likely than not that some portion of the deferred tax assets will not be fully realizable. This assessment requires judgment as to the likelihood and amounts of future taxable income by tax jurisdiction. At December 31, 2013 , we had a full valuation allowance against all of our deferred tax assets.

We apply the provisions of Financial Accounting Standards Board (or FASB) guidance on accounting for uncertainty in income taxes. We assess all material positions taken in any income tax return, including all significant uncertain positions, in all tax years that are still subject to assessment or challenge by relevant taxing authorities. Assessing an uncertain tax position begins with the initial determination of the position’s sustainability and the tax benefit to be recognized is measured at the largest amount of benefit that is greater than 50 percent likely of being realized upon ultimate settlement. As of each balance sheet date, unresolved uncertain tax positions must be reassessed, and we will determine whether (i) the factors underlying the sustainability assertion have changed and (ii) the amount of the recognized tax benefit is still appropriate. The recognition and measurement of tax benefits requires significant judgment. Judgments concerning the recognition and measurement of a tax benefit might change as new information becomes available.

Embedded Derivatives Related to Convertible Notes

Embedded derivatives that are required to be bifurcated from the underlying debt instrument (i.e. host) are accounted for and valued as a separate financial instrument. We evaluated the terms and features of our convertible notes payable and identified compound embedded derivatives (conversion options that contain “make-whole interest” provisions or down round conversion price adjustment provisions) requiring bifurcation and accounting at fair value because the economic and contractual characteristics of the embedded derivatives met the criteria for bifurcation and separate accounting due to the conversion option containing a “make-whole interest” provision, that requires cash payment for forgone interest upon a change of control and down round conversion price adjustment provisions.

We estimate the fair value of the compound embedded derivatives for the Total Notes using a Monte Carlo simulation valuation model that combines expected cash outflows with market-based assumptions regarding risk-adjusted yields, stock price volatility, probability of a change of control and the trading information of our common stock into which the notes are convertible.

We estimate the fair value of the compound embedded derivative for the Tranche I Notes using a binomial lattice model in order to estimate the fair value of the embedded derivative in the Tranche I convertible notes. A binomial lattice model generates two probable outcomes - one up and another down - arising at each point in time, starting from the date of valuation until the maturity date. A lattice model was initially used to determine if the convertible notes would be converted, called or held at each decision point. Within the lattice model, the following assumptions are made: (i) the convertible notes will be converted early if the conversion value is greater than the holding value; or (ii) the convertible notes will be called if the holding value is greater than both (a) redemption price and (b) the conversion value plus the coupon make-whole payment at the time. If the convertible notes are called, then the holder will maximize their value by finding the optimal decision between (1) redeeming at the redemption price and (2) converting the convertible notes. Using this lattice method, we fair valued the embedded derivative using the "with-and-without method", where the fair value of the convertible notes including the embedded derivative is defined as the "with", and the value of the convertible notes excluding the embedded derivative is defined as the "without". This method estimates the fair value of the embedded derivative by looking at the difference in the fair values between the convertible notes with the embedded derivative and the fair value of the convertible notes without the embedded derivative. The lattice model uses the stock price, conversion price, maturity date, risk-free interest rate, estimated stock volatility and estimated credit spread.

in the estimated value of the embedded derivatives. Conversely, a decrease (increase) in the stock price results in a decrease (increase) in the estimated fair value of the embedded derivatives. The changes in the fair value of the bifurcated compound embedded derivative is primarily related to the change in price of the underlying common stock and is reflected in our consolidated statements of operations as “Income (loss) from change in fair value of derivative instruments.”

Results of Operations

Comparison of Year Ended December 31, 2013 to Year Ended December 31, 2012

Revenues



	Years Ended December 31,				Year-to Year Change			Percentage Change
	2013		2012		Year-to Year Change			Percentage Change
	(Dollars in thousands)
Revenues
Renewable product sales	$	14,428	$	10,802	$	3,626		34	%
Related party renewable product sales	1,380		—		1,380			nm
Ethanol and ethanol-blended gasoline	—		38,836		(38,836		)	(100	)%
Total product sales	$	15,808	$	49,638	$	(33,830	)	(68	)%
Grants and collaborations revenue	22,664		14,281		8,383			59	%
Related party grants and collaborations revenue	2,647		9,775		(7,128		)	(73	)%
Total grants and collaborations revenue	25,311		24,056		1,255			5	%
Total revenues	$	41,119	$	73,694	$	(32,575	)	(44	)%

______________

nm= not meaningful

Our total revenues decreased by $32.6 million to $41.1 million in 2013 as compared to the prior year primarily due to decreased revenues from product sales. Product sales decreased by $33.8 million to $15.8 million with reductions resulting primarily from the transition out of the ethanol and ethanol-blended gasoline business during the third quarter of 2012. Renewable product sales of our farnesene-derived products increased $5.0 million in 2013 compared to the prior year primarily as a result of sales to new distributors, along with related party sales of renewable product to Novvi and Total. Grants and collaborations revenue increased in 2013 by $1.3 million to $25.3 million compared to the prior year primarily due to the increase in grants and collaborations revenue of $12.0 million , from the increase of collaborations revenue from our flavors and fragrances collaborations of $9.4 million and related party collaboration revenue from Novvi of $2.6 million , offset by the decrease in collaboration revenue from Total of $9.8 million and Cosan of $0.9 million .

Cost and Operating Expenses



	Years Ended December 31,				Year-to Year Change			Percentage Change
	2013		2012		Year-to Year Change			Percentage Change
	(Dollars in thousands)
Cost of products sold	$	38,253	$	77,314	$	(39,061	)	(51	)%
Loss on purchase commitments and write-off of production assets	9,366		45,854		(36,488		)	(80	)%
Research and development	56,065		73,630		(17,565		)	(24	)%
Sales, general and administrative	57,051		78,718		(21,667		)	(28	)%
Total cost and operating expenses	$	160,735	$	275,516	$	(114,781	)	(42	)%

Cost of Products Sold

Our cost of products sold decreased by $39.1 million to $38.3 million in 2013 . Our cost of products sold includes cost of raw materials, labor and overhead, amounts paid to contract manufacturers, period costs related to inventory write-downs resulting from applying lower cost or market inventory valuations, and costs related to scale-up in production of such products. In 2012, we began operating our own large-scale Biofene production plant located at Brotas, in the state of São Paulo, Brazil. The decrease

in cost of products sold was mainly due from our transitioning out of our ethanol and ethanol-blended gasoline business during the third quarter of 2012, resulting in a decrease of $38.6 million in the cost of products sold.

Cost of Products Sold Associated with Loss on Purchase Commitments and Write-Off of Production Assets

The loss on purchase commitments and write-off of production assets decreased by $36.5 million to $9.4 million in 2013 compared to the prior year. The decrease was mainly due to the shift of a portion of our production capacity from contract manufacturing facilities to Amyris-owned plants. Beginning in March 2012, we initiated to shift a portion of our production capacity from contract manufacturing facilities to Amyris-owned plants. As a result, we evaluated our contract manufacturing agreements and, in the first quarter of 2012 recorded a loss of $31.2 million related to facility modification costs and fixed purchase commitments. We also recorded an impairment charge of $5.5 million in the three months ended March 31, 2012 related to Amyris-owned equipment at contract manufacturing facilities, based on the excess of the carrying value of the assets over their fair value. We recognized additional charges of $1.4 million and $7.8 million , respectively, in the third and fourth quarters of 2012 associated with losses on fixed purchase commitments. We computed the loss on facility modification costs and fixed purchase commitments using the same approach that is used to value inventory-the lower of cost or market value. The computation of the loss on firm purchase commitments is subject to several estimates, including the ultimate selling price of any of our products manufactured at the relevant production facilities, and is therefore inherently uncertain. During 2013, we recorded a loss of $9.4 million related to the termination and settlement of our existing agreements with Tate & Lyle and Antibioticos.The loss of $8.4 million related to Tate & Lyle consisted of an impairment charge of $6.7 million relating to our equipment at Tate & Lyle and a $2.7 million write off of an unamortized portion of equipment costs funded by us for Tate & Lyle, offset by a $1.0 million reversal of our remaining accrual associated with our loss on fixed purchase commitments. The loss of $1.0 million related to Antibioticos, consisted of impairment charge relating to our equipment held at this location.

Research and Development Expenses

Our research and development expenses decreased by $17.6 million in 2013 over the prior year, primarily as a result of our overall cost reduction efforts and lower spending. The decreases were attributable to an $8.2 million reduction in personnel-related expenses and lower stock-based compensation expense due to lower headcount, a $2.8 million decrease in consulting and outsourced services, a $2.3 million reduction in production expenses associated with development projects, a $1.3 million decrease in laboratory supplies and equipment and a $3.0 million decrease in travel-related expenses and other overhead expenses. Research and development expenses included stock-based compensation expense of $4.3 million in 2013 compared to $6.5 million in 2012.

Sales, General and Administrative Expenses

Our sales, general and administrative expenses decreased by $21.7 million to $57.1 million in 2013 compared to the prior year, primarily as a result of our overall cost reduction efforts and lower spending. The decreases were attributable to a $14.5 million reduction in personnel-related expenses and lower stock-based compensation expense due to lower headcount, a $4.3 million decrease in consulting and outsourced services, a $0.9 million decrease in laboratory supplies and equipment, a $0.8 million reduction in production expenses associated with development projects and a decrease of $1.2. million in travel-related expenses and other overhead expenses. Sales, general and administrative expenses included stock-based compensation expense of $13.8 million and $21.0 million during 2013 and 2012 , respectively.

Other Income (Expense)



	Years Ended December 31,						Year-to Year Change			Percentage Change
	2013			2012			Year-to Year Change			Percentage Change
	(Dollars in thousands)
Other income (expense):
Interest income	$	162		$	1,472		$	(1,310	)	(89	)%
Interest expense	(9,107		)	(4,926		)	(4,181		)	85	%
Income (loss) from change in fair value of derivative instruments	(84,726		)	1,790			(86,516		)	nm
Income (loss) from extinguishment of debt	(19,914		)	(920		)	(18,994		)	nm
Other expense, net	(2,553		)	(646		)	(1,907		)	295	%
Total other income (expense)	$	(116,138	)	$	(3,230	)	$	(112,908	)	nm

______________

nm= not meaningful

Total other expense increased by approximately $112.9 million to $116.1 million in 2013 compared to the prior year. The increase in other expense of $112.9 million was primarily attributable to the increase in loss from change in fair value of derivative instruments of $86.5 million , due to a change in the fair value of the compound embedded derivative liability associated with our senior secured convertible promissory notes as a result of the changes in the inputs used in the valuation models from one reporting period to another, such as stock price and estimated stock volatility, and interest rate swap derivative liability, $19.0 million increase in loss on the extinguishment of debt related to the Temasek Bridge Loan and Total convertible notes, a $1.9 million increase in other expense, net, mainly due to an increase in realized loss on foreign currency transactions, a $1.3 million decrease in interest income due to lower cash balance compared to prior year and an increase in interest expense of $4.2 million associated with increased borrowings to fund our operations.

Comparison of Year Ended December 31, 2012 to Year Ended December 31, 2011

Revenues



	Years Ended December 31,				Year-to Year Change			Percentage Change
	2012		2011		Year-to Year Change			Percentage Change
	(Dollars in thousands)
Revenues
Renewable product sales	$	10,802	$	763	$	10,039		1,316	%
Ethanol and ethanol-blended gasoline	38,836		129,074		(90,238		)	(70	)%
Total product sales	49,638		129,837		(80,199		)	(62	)%
Grants and collaborations revenue	14,281		17,154		(2,873		)	(17	)%
Related party grants and collaborations revenue	9,775		—		9,775			nm
Total grants and collaborations revenue	24,056		17,154		6,902			40	%
Total revenues	$	73,694	$	146,991	$	(73,297	)	(50	)%

______________

nm= not meaningful

Our total revenues decreased by $73.3 million to $73.7 million in 2012 with such reduction resulting primarily from decrease in product sales. Revenue from product sales decreased by $80.2 million to $49.6 million primarily from lower sales of ethanol and reformulated ethanol-blended gasoline purchased from third parties which accounted for $90.2 million of the reduction, with a decrease in gallons sold and an increase in average selling price per gallon compared to 2011. We sold 2.3 million gallons of ethanol and 11.2 million gallons of reformulated ethanol-blended gasoline in the 2012 compared to 10.1 million gallons of ethanol and 36.4 million gallons of reformulated ethanol-blended gasoline sales in the prior year. Product sales of our farnesene-derived products increased by $10.0 million in 2012 compared to the prior year. Grants and collaborations revenue in 2012 increased by $6.9 million compared to the prior year primarily due to the revenue recognized upon the amendment of our collaboration agreement with Total which resulted in the recognition of approximately $9.8 million in collaboration revenue, partially offset by a decline in other collaboration revenue of $2.9 million.

Nearly all of our revenues in 2012 and 2011 have come from the sale of ethanol and reformulated ethanol-blended gasoline with the remainder coming from renewable products as well as from collaborations and government grants. We transitioned out of the ethanol and ethanol-blended gasoline business during the third quarter of 2012. We do not expect to be able to replace much of the revenue lost in the near term as a result of this transition, particularly in 2013 while we continue our efforts to establish a renewable products business.

Cost and Operating Expenses



	Years Ended December 31,				Year-to Year Change			Percentage Change
	2012		2011		Year-to Year Change			Percentage Change
	(Dollars in thousands)
Cost of products sold	$	77,314	$	155,615	$	(78,301	)	(50	)%
Loss on purchase commitments and write-off of production assets	45,854		—		45,854			nm
Research and development	73,630		87,317		(13,687		)	(16	)%
Sales, general and administrative	78,718		83,231		(4,513		)	(5	)%
Total cost and operating expenses	$	275,516	$	326,163	$	(50,647	)	(16	)%

______________

nm= not meaningful

Cost of products sold consists primarily of cost of purchased ethanol and reformulated ethanol-blended gasoline, terminal fees paid for storage and handling, transportation costs between terminals and changes in the fair value of derivative commodity instruments. Starting in the second quarter of 2011, our cost of products sold also included production costs of farnesene-derived products, which included cost of raw materials, amounts paid to contract manufacturers and period costs including inventory write-downs resulting from applying lower-of-cost-or-market inventory valuations. Cost of farnesene-derived products sold also includes certain costs related to the scale-up in production of such products. Our cost of products sold decreased by $78.3 million to $77.3 million in 2012 compared to the prior year. We had a decrease of $91.5 million in costs of ethanol and reformulated ethanol-blended gasoline purchased from third parties primarily due to a decline in product volume partially offset by an increase in average unit cost. This decrease in cost of products sold for ethanol and reformulated ethanol-blended gasoline was partially offset by an increase in product costs of farnesene-derived products of $13.2 million compared to the prior year as we scale up our renewable operations.

We transitioned out of our ethanol and gasoline business in the quarter ended September 30, 2012, which resulted in a reduction of cost of products sold. As we are now operating our own large-scale Biofene production plant in Brotas, in the state of São Paulo, Brazil as of December 2012, we will have a scale-up of production from this facility and the associated manufacturing costs. As we develop cost efficient manufacturing in our first production facility, we expect to seek to work selectively with other Brazilian sugar and ethanol producers to build additional facilities adjacent to their existing mills, thereby reducing the capital required to establish and scale our production operations.

Cost of Products Sold Associated with Loss on Purchase Commitments and Write-Off of Production Assets

Beginning in March 2012, we initiated a plan to shift a portion of our production capacity from contract manufacturing facilities to Amyris-owned plants that were then under construction. As a result, we evaluated our contract manufacturing agreements and, in the first quarter of 2012, recorded a loss of $31.2 million related to facility modification costs and fixed purchase commitments. We also recorded an impairment charge of $5.5 million in the three months ended March 31, 2012 related to Amyris-owned equipment at contract manufacturing facilities, based on the excess of the carrying value of the assets over their fair value. We recognized additional charges of $1.4 million and $7.8 million, respectively, in the third and fourth quarter of 2012 associated with losses on fixed purchase commitments. We computed the loss on facility modification costs and fixed purchase commitments using the same approach that is used to value inventory the lower of cost or market value. The computation of the loss on firm purchase commitments is subject to several estimates, including the ultimate selling price of any of our products manufactured at the relevant production facilities, and is therefore inherently uncertain.

Research and Development Expenses

Our research and development expenses decreased by $13.7 million in 2012 over the prior year, primarily as a result of overall lower spending. The decreases were attributable to a $5.7 million reduction in expenses associated with the completion of certain outsourced process development projects, a $2.5 million decrease in outsourced services resulting from completion of certain phases of our government grants project, $2.2 million reduction in outside consulting expenses, a $1.9 million decrease in personnel-related expenses associated with lower headcount, and a $0.9 million decrease in travel-related expenses and other overhead expenses. Research and development expenses included stock-based compensation expense of $6.5 million in 2012 compared to $6.3 million in 2011.

Sales, General and Administrative Expenses

Our sales, general and administrative expenses decreased by $4.5 million in 2012 compared to the same period of the prior year. The decrease is attributable primarily to a $7.3 million reduction in spend for consulting and professional service fees and a $0.9 million decrease in travel-related expenses partially offset by a $3.6 million increase in personnel-related expenses associated with severance and transition costs and higher stock-based compensation. Sales, general and administrative expenses included stock-based compensation expense of $21.0 million and $19.1 million during 2012 and 2011, respectively.

Other Income (Expense)



	Years Ended December 31,						Year-to Year Change			Percentage Change
	2012			2011			Year-to Year Change			Percentage Change
	(Dollars in thousands)
Other income (expense):
Interest income	$	1,472		$	1,542		$	(70	)	(5	)%
Interest expense	(4,926		)	(1,543		)	(3,383		)	219	%
Income (loss) from change in fair value of derivative instruments	1,790			—			1,790			nm
Income (loss) from extinguishment of debt	(920		)	—			(920		)	nm
Other income (expense), net	(646		)	214			(860		)	(402	)%
Total other income (expense)	$	(3,230	)	$	213		$	(3,443	)	(1,616	)%

______________

nm= not meaningful

Total other expense increased by approximately $3.4 million to $3.2 million in 2012 compared to the prior year. The increase in total other expense was related primarily to higher interest expense of $3.4 million associated with increased borrowings to fund our operations including capital expenditures for the coming year, a $0.9 million loss on the extinguishment of the $5.0 million debt associated with the December 2012 private placement, decrease in other income (expense), net for the year ended December 31, 2012 of $0.9 million from realized loss on foreign currency transactions, offset by income of $1.8 million attributable to the income from the change in fair value of the compound embedded derivative liabilities associated with our senior unsecured convertible promissory notes issued to Total of $3.1 million, offset by a $1.3 million loss recognized for the fair market value of a currency interest rate swap derivative liability. No corresponding amounts related to these transactions were recognized during the year ended December 31, 2011.

Liquidity and Capital Resources



	December 31,
	2013			2012
	(Dollars in thousands)
Working capital (deficit)	$	(382	)	$	3,668
Cash and cash equivalents and short-term investments	$	8,296		$	30,689
Debt and capital lease obligations	$	153,305		$	106,774
Accumulated deficit	$	(821,438	)	$	(586,327	)



	Years Ended December 31,
	2013			2012		2011
	(Dollars in thousands)
Net cash used in operating activities	$	(105,859	)	(150,872	)	$	(92,496	)
Net cash provided by (used in) investing activities	(10,337		)	(49,644	)	5,853
Net cash provided by financing activities	91,181			138,117		41,052

Working Capital. For the year ended December 31, 2013 , we had a working deficit of $0.4 million compared to working capital of $3.7 million for the year ended December 2012. The decrease of $4.1 million in working capital during 2013 is primarily due to cash usage to fund our operating expenses and, to a lesser extent, to service our debt obligations. This was in part offset by a reduction in accounts payable and accrued and other current liabilities of $12.1 million , a $4.4 million increase in accounts receivable and related party accounts receivable due to collaboration receivable, a $4.9 million increase in inventory. Inventory increased during the latter part of 2013 in order that we would have sufficient farnesene inventory while our Brotas plant goes through planned preventive maintenance during the first quarter of 2014.

To support production of our products in contract manufacturing and dedicated production facilities, we have incurred, and we expect to continue to incur, capital expenditures as we invest in these facilities. We plan to continue to seek external debt financing from U.S. and Brazilian sources to help fund our investment in these contract manufacturing and dedicated production facilities.

We expect to fund our operations for the foreseeable future with cash and investments currently on hand, with cash inflows from collaboration and grant funding, cash contributions from product sales, and with new debt and equity financings. Some of our anticipated financing sources, such as research and development collaborations and convertible debt financings, are subject to risk that we cannot meet milestones, are not yet subject to definitive agreements or mandatory funding commitments and, if needed, we may not be able to secure additional types of financing in a timely manner or on reasonable terms, if at all. Our planned 2014 working capital needs and our planned operating and capital expenditures for 2014 are dependent on significant inflows of cash from existing collaboration partners and from funds under existing convertible debt facilities, as well as additional funding from new collaborations, and may also require additional funding from debt or equity financings. We will continue to need to fund our research and development and related activities and to provide working capital to fund production, storage, distribution and other aspects of our business. Our operating plan contemplates capital expenditures of approximately $9.0 million in 2014.

Liquidity . We have incurred significant losses since our inception and believe that we will continue to incur losses and negative cash flow from operations into at least 2014. As of December 31, 2013 , we had an accumulated deficit of $821.4 million and had cash, cash equivalents and short term investments of $8.3 million . We have significant outstanding debt and contractual obligations related to purchase commitments, as well as capital and operating leases. As of December 31, 2013 , our debt totaled $152.1 million , of which $6.4 million matures within the next twelve months. In addition, our debt agreements contain various covenants, including restrictions on business that could cause us to be at risk of defaults.

The Company’s operating plan for 2014 contemplates significant reduction in the Company’s net cash outflows, resulting from (i) revenue growth from sales of existing and new products with positive gross margins, (ii) reduced production costs compared to prior periods as a result of manufacturing and technical developments in 2013, (iii) cash inflows from collaborations consistent with levels achieved in 2013 and (iv) operating expenses maintained at reduced levels.

If we is unable to raise additional financing, or if other expected sources of funding are delayed or not received, we would take the following actions as early as the second quarter of 2014 to support its liquidity needs through the remainder of 2014 and into 2015:


•	Effect significant headcount reductions in the United States and in Brazil, particularly with respect to both general and administrative employees and other employees not connected to critical or contracted activities.


•	Shift its focus to existing products and customers with significantly reduced investment in new product and commercial development efforts.


•	Reduce its expenditures for third party contractors, including consultants, professional advisors and other vendors.


•	Suspend operations at its pilot plants and demonstration facilities.


•	Reduce or delay uncommitted capital expenditures, including non-essential lab equipment and information technology projects.

The contingency cash plan contemplating these actions is designed to save us an estimated $25.0 million to $35.0 million over the next twelve months. Implementing this plan could have a material negative impact on our ability to continue our business as currently contemplated, including, without limitation, delays or failures in its ability to:


•	Achieve planned production levels;


•	Develop and commercialize products within planned timelines or at planned scales; and


•	Continue other core activities.

Collaboration Funding. In March 2013 , we signed a collaboration agreement with a collaboration partner that included a collaboration funding component and that resulted in an initial payment of $10 million in March 2013, and we obtained a commitment letter from Total with respect to additional convertible note funding (as described above under "Overview-Total Relationship") of which we received $10.0 million in proceeds in June 2013. We also received $20.0 million in funding through the sale of a convertible note in a private placement under an existing funding agreement with Total in July 2013. This purchase and sale completed Total's commitment to purchase $30.0 million of such notes by July 2013.

In addition to cash contributions from product sales and debt and equity financings, we depend on collaboration funding to support our operating expenses. While part of this funding is committed based on existing collaboration agreements, we will be required to identify and obtain funding under additional collaborations that are not yet subject to any definitive agreement or are not yet identified. In addition, some of our existing collaboration funding is subject to our achievement of milestones or other funding conditions.

If we cannot secure sufficient collaboration funding to support our operating expenses in excess of cash contributions from product sales and existing debt and equity financings, in order to raise sufficient funds to finance our ongoing operations, we may need to issue additional preferred and/or discounted equity, agree to onerous covenants, grant further security interests in our assets, enter into collaboration and licensing arrangements that require us to relinquish commercial rights or grant licenses on terms that are not favorable to us. If we fail to secure such funding, we could be forced to curtail our operations, which would have a material adverse effect on our ability to continue with our business plans and on our status as a going concern.

Government Contracts . In 2010, we were awarded a $24.3 million “Integrated Bio-Refinery” grant from the DOE. Under this grant, we were required to fund an additional $10.6 million in cost sharing expenses. Our obligation for this cost share was contingent on reimbursement for project costs incurred. The “Integrated Bio-Refinery” project from DOE was completed in the first quarter of 2013. Through December 31, 2013 , we had recognized the entire $24.3 million in revenue under this grant, of which $1.8 million was received in cash during the year ended December 31, 2013 .

In August 2010, we were appointed as a subcontractor to NREL under a DOE grant awarded to NREL. Under this contract, we have the right to be reimbursed for up to $3.6 million, and are required to fund an additional $1.4 million in cost sharing expenses. Through December 31, 2013 , we had recognized $3.6 million in revenue under this grant, of which $2.3 million was received in cash during the year ended December 31, 2013 .

In June 2012, we entered into a Technology Investment Agreement with DARPA, under which we are performing certain research and development activities funded in part by DARPA. The work is to be performed on a cost-share basis, where DARPA funds 90% of the work and we fund the remaining 10% (primarily by providing specified labor). The agreement provided for funding of up to approximately $7.7 million over two years based on achievement of program milestones, and, accordingly, if fully funded, we would be responsible for contributions equivalent to approximately $0.9 million . The agreement had an initial term of one year and at DARPA's option, may be renewed for an additional year. The agreement was renewed by DARPA in May 2013. Through December 31, 2013 , we had recognized $5.3 million in revenue under this agreement, of which $4.9 million was recognized during the year ended December 31, 2013 .

Convertible Note Offerings. In February 2012, we sold $25.0 million in principal amount of senior unsecured convertible promissory notes due March 1, 2017 . The notes have a 3.0% annual interest rate and are convertible into shares of our common stock at a conversion price of $7.0682 per share, subject to adjustment for proportional adjustments to outstanding common stock and anti-dilution provisions in case of dividends and distributions. The note holders have a right to require repayment of 101% of the principal amount of the notes in an acquisition of Amyris, and the notes provide for payment of unpaid interest on conversion following such an acquisition if the note holders do not require such repayment. The securities purchase agreement and notes include covenants regarding payment of interest, maintaining our listing status, limitations on debt, maintenance of corporate existence, and filing of SEC reports. The notes include standard events of default resulting in acceleration of indebtedness, including

failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the securities purchase agreement and notes, with default interest rates and associated cure periods applicable to the covenant regarding SEC reporting.

In July and September 2012, we issued $53.3 million worth of senior unsecured convertible notes to Total for an aggregate of $30.0 million in cash proceeds and our repayment of $23.3 million in previously-provided research and development funds as described in more detail in Note 5, "Debt" and Note 8, "Significant Agreements". As part of the December 2012 private placement, 1,677,852 shares of our common stock were issued in exchange for the cancellation of $5.0 million worth of an outstanding senior unsecured convertible promissory note held by Total.

In August 2013, we entered into an agreement with Total and Temasek to sell up to $73.0 million in convertible promissory notes in private placements over a period of up to 24 months from the date of signing (referred to as the August 2013 SPA and such financing is referred to as the August 2013 Financing). The August 2013 Financing was divided into two tranches (one for $42.6 million and one for $30.4 million), each with differing closing conditions. Of the total possible purchase price in the financing, $60.0 million was to be paid in the form of cash by Temasek ($35.0 million in the first tranche and up to $25.0 million in the second tranche) and $13.0 million was to be paid by cancellation of outstanding convertible promissory notes held by Total in connection with its exercise of pro rata rights ($7.6 million in the first tranche and $5.4 million in the second tranche).

In September 2013, prior to the initial closing of the August 2013 Financing, our stockholders approved the issuance in the private placement of up to $110.0 million aggregate principal amount of senior convertible promissory notes, the issuance of a warrant to purchase 1,000,000 shares of our common stock and the issuance of the common stock issuable upon conversion or exercise of such notes and warrant, which approval included the transactions contemplated by the August 2013 Financing.

In September 2013, we entered into a bridge loan agreement with an existing investor to provide additional cash availability of up to $5.0 million as needed before the initial closing of the August 2013 Financing. The bridge loan agreement provided for the sale of up to $5.0 million in principal amount of unsecured convertible notes at any time prior to October 31, 2013 following the satisfaction of certain closing conditions, including that we pay an availability fee for the bridge loan. We did not use this facility and it expired in October 2013 in accordance with its terms.

In October 2013, we sold and issued a senior secured promissory note to Temasek for a bridge loan of $35.0 million (referred to as the Temasek Bridge Note). The note was due on February 2, 2014 and accrued interest at a rate of 5.5% each four months from October 4, 2013 (with a rate of 2% per month applicable if a default occurred). The note was cancelled as payment for Temasek's purchase of a first tranche convertible note in the initial closing of the August 2013 Financing.

In October 2013, we amended the August 2013 SPA to include the Fidelity Entities in the first tranche in the principal amount of $7.6 million, and to proportionally increase the amount acquired by exchange and cancellation of outstanding convertible promissory notes by Total to $14.6 million ($9.2 million in the first tranche and up to $5.4 million in the second tranche). Also in October 2013, we completed the closing of the Tranche I Notes for cash proceeds of $7.6 million and cancellation of outstanding convertible promissory notes of $44.2 million, of which $35.0 million resulted from the cancellation of the Temasek Bridge Note. In December 2013, we agreed to place $3.0 million of senior convertible notes under the second tranche of the August 2013 Financing to funds affiliated with Wolverine Asset Management (or Wolverine) and we elected to call $25.0 million in additional funds from Temasek pursuant to its previous commitment to purchase such amount of convertible promissory notes in the second tranche. Additionally, in December 2013, we agreed to sell approximately $6.0 million of convertible promissory notes in the second tranche to Total through cancellation of the same amount of principal of previously outstanding convertible notes held by Total (in respect of Total’s preexisting contractual right to maintain its pro rata ownership position through such cancellation of indebtedness). In January 2015, we completed the offering of such convertible promissory notes in the second tranche.

Export Financing with ABC Brasil. In March 2013, we entered into an export financing agreement with Banco ABC Brasil S.A. (or ABC) for approximately $2.5 million, to fund exports through March 2014. As of December 31, 2013 , the principal amount outstanding was $2.5 million. This loan is collateralized by future exports from our subsidiary in Brazil.

In March 2014, we entered into an export financing agreement with ABC Bank for R$5.0 million (approximately US$2.2 million based on exchange rate as of March 28, 2014) for a 1 year-term to fund exports through March 2015.

Banco Pine Loans . In December 2011, we received a loan of R$35.0 million (approximately US$14.9 million based on the exchange rate as of December 31, 2013 ) from Banco Pine. Such loan was an advance on an anticipated 2012 financing from Nossa Caixa Desenvolvimento (or Nossa Caixa), the São Paulo State development bank, and Banco Pine, under which Banco Pine and Nossa Caixa would provide us with loans of up to approximately R$52.0 million (approximately $25.6 million based on the exchange rate as of December 31, 2013 ) as financing for capital expenditures relating to our manufacturing facility in Brotas. The maturity date for this loan was originally February 17, 2012; however, in February 2012, we entered into a supplemental agreement

with Banco Pine under which the parties agreed to extend the maturity date for the repayment of the original loan from February 17, 2012 to May 17, 2012, and in May 2012, we entered into an additional supplemental extending the maturity date to August 15, 2012 . This loan was repaid in July 2012.

In June 2012, we entered into a separate loan agreement with Banco Pine under which Banco Pine provided a bridge loan of R$52.0 million (approximately US$22.2 million based on the exchange rate as of December 31, 2013 ). The bridge loan was an additional advance on the anticipated Banco Pine and Nossa Caixa financing described above. The interest rate for the bridge loan was 0.4472% monthly (approximately 5.5% on an annualized basis). The principal and interest of this bridge loan matured and were required to be repaid on September 19, 2012 , subject to extension by Banco Pine. This bridge loan was repaid in July 2012.

We secured these loans to allow us to continue construction and process development at our manufacturing facility in Brotas, Brazil and we expect to seek additional loans from this bank and others in order to be able to fund the establishment of other plants in Brazil and elsewhere.

Banco Pine/Nossa Caixa Financing . In July 2012, we entered into a Note of Bank Credit and a Fiduciary Conveyance of Movable Goods agreement with each of Nossa Caixa Desenvolvimento (or Nossa Caixa) and Banco Pine S.A. (or Banco Pine). Under these instruments, we borrowed an aggregate of R$52.0 million (approximately US$22.2 million based on the exchange rate as of December 31, 2013 ) as financing for capital expenditures relating to our manufacturing facility in Brotas, Brazil. Under the loan agreements, Banco Pine agreed to lend R$22.0 million and Nossa Caixa agreed to lend R$30.0 million . The loans have a final maturity date of July 15, 2022 and bear a fixed interest rate of 5.5% per year. The loans are also subject to early maturity and delinquency charges upon occurrence of certain events including interruption of manufacturing activities at our manufacturing facility in Brotas, Brazil for more than 30 days, except during sugarcane off-season. The loans are secured by certain of our farnesene production assets at the manufacturing facility in Brotas, Brazil and we were required to provide parent guarantees to each of the lenders.

BNDES Credit Facility . In December 2011, we entered into a credit facility with Banco Nacional de Desenvolvimento Econômico e Social (or BNDES), a government-owned bank headquartered in Brazil (referred to as the BNDES Credit Facility) to finance a production site in Brazil. The BNDES Credit Facility was for R$22.4 million (approximately US$9.6 million based on the exchange rate as of December 31, 2013 ). This BNDES Credit Facility was extended as project financing for a production site in Brazil. The credit line is divided into an initial tranche for up to approximately R$19.1 million and an additional tranche of approximately R$3.3 million that becomes available upon delivery of additional guarantees. The credit line is available for 12 months from the date of the Credit Agreement for the BNDES Credit Facility, subject to extension by the lender.

The principal of loans under the BNDES Credit Facility is required to be repaid in 60 monthly installments, with the first installment due in January 2013 and the last due in December 2017. Interest was initially due on a quarterly basis with the first installment due in March 2012. From and after January 2013, interest payments will be due on a monthly basis together with principal payments. The loaned amounts carry interest of 7% per year. Additionally, a credit reserve charge of 0.1% on the unused balance from each credit installment from the day immediately after it is made available through its date of use, when it is paid.

The BNDES Credit Facility is collateralized by first priority security interest in certain of our equipment and other tangible assets totaling R$24.9 million (approximately US$10.6 million based on the exchange rate as of December 31, 2013 ). We are a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, we were required to provide a bank guarantee equal to 10% of the total approved amount ( R$22.4 million in total debt) available under the BNDES Credit Facility. For advances in the second tranche (above R$19.1 million ), we are required to provide additional bank guarantees equal to 90% of each such advance, plus additional Amyris guarantees equal to at least 130% of such advance. The BNDES Credit Facility contains customary events of default, including payment failures, failure to satisfy other obligations under the credit facility or related documents, defaults in respect of other indebtedness, bankruptcy, insolvency and inability to pay debts when due, material judgments, and changes in control of Amyris Brasil. If any event of default occurs, BNDES may terminate its commitments and declare immediately due all borrowings under the facility. As of December 31, 2013 and 2012 , the Company had R$15.3 million (approximately US$6.5 million based on the exchange rate as of December 31, 2013 ) and R$19.1 million (approximately US$9.3 million based on the exchange rate as of December 31, 2012 ), respectively, in outstanding advances under the BNDES Credit Facility.

FINEP Credit Facility. In November 2010, we entered into a credit facility with Financiadora de Estudos e Projetos (or FINEP), a state-owned company subordinated to the Brazilian Ministry of Science and Technology (referred to as the FINEP Credit Facility) to finance a research and development project on sugarcane-based biodiesel (referred to as the FINEP Project) and provided for loans of up to an aggregate principal amount of R$6.4 million (approximately US$2.7 million based on the

exchange rate as of December 31, 2013 ) which are secured by a chattel mortgage on certain equipment of Amyris as well as by bank letters of guarantee. All available credit under this facility was fully drawn.

Interest on loans drawn under the FINEP Credit Facility is fixed at 5.0% per annum. In case of default under, or non-compliance with, the terms of the agreement, the interest on loans will be dependent on the long-term interest rate as published by the Central Bank of Brazil (such rate, the TJLP). If the TJLP at the time of default is greater than 6%, then the interest will be 5.0% plus a TJLP adjustment factor otherwise the interest will be at 11.0% per annum. In addition, a fine of up to 10.0% will apply to the amount of any obligation in default. Interest on late balances will be 1.0% interest per month, levied on the overdue amount. Payment of the outstanding loan balance will be made in 81 monthly installments, which commenced in July 2012 and extends through March 2019. Interest on loans drawn and other charges are paid on a monthly basis and commenced in March 2011. As of December 31, 2013 , total outstanding loan balance under this credit facility was R$5.2 million (approximately $2.2 million based on the exchange rate as of December 31, 2013 ).

The FINEP Credit Facility contains the following significant terms and conditions:

•

We are required to share with FINEP the costs associated with the FINEP Project. At a minimum, we are required to contribute approximately R$14.5 million ( US$6.2 million based on the exchange rate as of December 31, 2013 ) of which R$11.1 million was contributed prior to the release of the second disbursement. All four disbursements were completed and we had fulfilled all of our cost sharing obligations;


•	After the release of the first disbursement, prior to any subsequent drawdown from the FINEP Credit Facility, we were required to provide bank letters of guarantee of up to R$3.3 million in aggregate (approximately US$1.4 million based on the exchange rate as of December 31, 2013 ) before receiving the second installment in December 2012. We obtained the bank letters of guarantee from ABC;


•	Amounts disbursed under the FINEP Credit Facility were required to be used towards the FINEP Project within 30 months after the contract execution.

The fair values of the notes payable, loan payable, convertible notes and credit facilities are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company that market participants would use in pricing the debt.

Hercules Loan Facility. In March 2014, we entered into a loan and security agreement with Hercules Technology Growth Capital, Inc. to make available to Amyris a loan in the aggregate principal amount of up to $25.0 million (referred to as the Hercules Loan Facility). The Hercules Loan Facility generally becomes due on May 31, 2015 and accrues interest at a rate per annum equal to the greater of either the prime rate reported in the Wall Street Journal plus 6.25% or 9.5% . The maturity date is extended to May 31, 2017 if the Company completes a financing transaction for at least $50.0 million in additional cash proceeds by September 30, 2014 . The Company may repay the loaned amounts before the maturity date if it pays an additional fee of 3% of the outstanding loans ( 1% if after the initial twelve-month period). The Company is also required to pay a 1% facility charge at the closing of the transaction, and a 10% end of term charge. In connection with the Hercules Loan Facility, Amyris agreed to certain customary representations and warranties and covenants, as well as certain covenants with respect to obtaining additional financing as described above and performance covenants related to revenues and cash flows starting with the third quarter of 2014. If the Company does not achieve the equity financing covenant, a forbearance fee of $10.0 million becomes due and is required to be paid at the end of the initial term of the facility.

Common Stock Offerings. In February 2012, we sold 10,160,325 shares of our common stock in a private placement for aggregate offering proceeds of $58.7 million .

In May 2012, we completed a private placement of 1,736,100 shares of our common stock for aggregate cash proceeds of $4.1 million .

In December 2012, we completed a private placement of 14,177,849 shares common stock for aggregate proceeds of $37.2 million , of which $22.2 million in cash was received in December 2012 and $15.0 million in cash was received in January 2013. As part of this private placement, 1,677,852 of such shares were issued to Total in exchange for the cancellation of $5.0 million worth of an outstanding senior unsecured convertible promissory note we previously issued to Total.

In March 2013, we completed a private placement of 1,533,742 of our common stock to Biolding for aggregate proceeds of $5.0 million. This private placement represented the final tranche of Biolding's preexisting contractual obligation to fund $15.0 million upon satisfaction by us of certain criteria associated with the commissioning of our production plant in Brotas, Brazil.

In March 2014, we entered into a securities purchase agreement with Kuraray Co., Ltd. under which the we agreed to sell shares of its common stock at a price equal to the greater of $2.88 per share or the average daily closing prices per share on the NASDAQ Stock Market for the three month period ending March 27, 2014 for an aggregate purchase price of $4.0 million .

Cash Flows during the Years Ended December 31, 2013, 2012, and 2011

Cash Flows from Operating Activities

Our primary uses of cash from operating activities are cost of products sold and personnel-related expenditures offset by cash received from product sales, grants and collaborative research. Cash used in operating activities was $105.9 million , $150.9 million and $92.5 million for the years ended December 31, 2013, 2012 and 2011 , respectively.

Net cash used in operating activities of $105.9 million for the year ended December 31, 2013 was related to our net loss of $234.9 million and a $23.7 million net change in our operating assets and liabilities, offset by non-cash charges of $152.8 million . Net change in operating assets and liabilities of $23.7 million primarily consisted of a $4.8 million increase in accounts receivable and related party accounts receivable from collaborations, a $5.6 million increase in inventory during the latter part of 2013 to have sufficient farnesene inventory while the Brotas plant goes through its annual planned preventive maintenance during first quarter of 2014, a $2.7 million increase in prepaid expenses and other assets, a $9.4 million decrease in accrued and other long term liabilities, a $2.6 million decrease in accounts payable and a $0.2 million decrease in deferred rent, offset by a $1.6 million decrease in deferred revenue and a $0.1 million decrease in derivative liability. Non-cash charges of $152.8 million consisted primarily of an $84.7 million change in the fair value of derivative instruments related to the embedded derivative liabilities associated with our senior secured convertible promissory notes and currency interest rate swap derivative liability, $16.6 million of depreciation and amortization expenses, $18.0 million of stock-based compensation, $3.7 million of amortization of debt discount, $19.9 million loss associated with the extinguishment of convertible debt and $9.4 million loss on purchase commitments and write-off of production assets related to a termination and settlement of our existing agreement with Tate & Lyle and Antibioticos.

Significant operating cash inflows during the year ended December 31, 2013 were derived primarily from the sale of renewable products and from collaborative research services.

Net cash used in operating activities of $150.9 million for the year ended December 31, 2012 was related to our net loss of $206.0 million and a $33.5 million net change in our operating assets and liabilities, offset by non-cash charges of $88.7 million . The net change in operating assets and liabilities of $33.5 million primarily consisted of a $35.8 million decrease in accrued and other long term liabilities, a $11.8 million decrease in accounts payable, a $1.6 million decrease in deferred revenue and a $1.3 million increase in deferred rent, offset by a $2.8 million decrease in accounts receivable, a $2.9 million decrease in inventory, an $11.2 million decrease in prepaid expenses and other assets. Non-cash charges of $88.7 million consisted primarily of $45.9 million loss on purchase commitments and write-off of production assets at contract manufacturers, $27.5 million of stock-based compensation and $14.6 million of depreciation and amortization expenses.

Net cash used in operating activities of $92.5 million for the year ended December 31, 2011 was related to our net loss of $179.5 million partially offset by non-cash charges of $37.5 million and a $49.5 million net change in our operating assets and liabilities. Net change in operating assets and liabilities of $49.5 million primarily consisted of a $53.9 million increase in accrued and other long term liabilities of which $31.9 million was due to the contingently repayable advance from Total, a $15.6 million increase in accounts payable and a $5.5 million increase in deferred revenue, partially offset by a $5.3 million increase in inventory, a $17.3 million increase in prepaid expenses and other assets, a $2.0 million increase in accounts receivable and a $1.1 million reduction in deferred rent. Non-cash charges primarily included $25.5 million of stock-based compensation and $11.1 million of depreciation and amortization expenses.

Cash Flows from Investing Activities

Our investing activities consist primarily of capital expenditures and investment activities.

Net cash used in investing activities of $10.3 million for the year ended December 31, 2013 , was a result of $8.1 million of capital expenditures and deposits on property, plant and equipment due to the construction of our first owned production facility in Brotas, Brazil, $1.5 million net purchases of short-term investments and $0.7 million of restricted cash.

Net cash used in investing activities of $49.6 million for the year ended December 31, 2012 , was a result of $56.9 million of capital expenditures and deposits on property, plant, and equipment due primarily to the construction of our first owned production facility in Brotas, Brazil and $1.0 million of restricted cash, offset by net sales of short term investments of $8.2 million .

Net cash provided by investing activities of $5.9 million for the year ended December 31, 2011 , was a result of $105.0 million in net investment securities maturities and $0.3 million in acquisition of cash in noncontrolling interest offset by a $97.0 million of capital expenditures and deposits on property, plant and equipment and a $2.9 million payment to Draths Corporation in relation to a business acquisition.

Cash Flows from Financing Activities

Net cash provided by financing activities of $91.2 million for the year ended December 31, 2013 , was a result of the net receipt of $75.5 million from debt financings, of which $65.0 million is debt financing from related parties, the receipt of $20.0 million in proceeds from sales of common stock in private placements net of issuance cost, and the receipt of $0.3 million in proceeds from option exercises. These cash inflows were offset in part by principal payments on debt of $3.3 million and principal payments on capital leases of $1.4 million .

Net cash provided by financing activities of $138.1 million for the year ended December 31, 2012 , was a result of the net receipt of $108.9 million from debt financings, of which $30.0 million is debt financing from a related party, the receipt of $84.7 million in proceeds from sales of common stock in private placements net of issuance cost, and the receipt of $0.9 million in proceeds from option exercises. These cash inflows were offset in part by principal payments on debt of $52.6 million and principal payments on capital leases of $3.7 million .

Net cash provided by financing activities was $41.1 million for the year ended December 31, 2011 , was a result of the net receipt of $38.0 million from debt financings, the receipt of $8.4 million in proceeds from option exercises, and the receipt of $3.0 million in equipment financing. These cash inflows were offset in part by principal payments on debt of $5.0 million , principal payments on capital leases of $2.8 million , and $0.5 million in costs related to the initial public offering of our common stock.

Off-Balance Sheet Arrangements

We did not have during the periods presented, and we do not currently have, any material off-balance sheet arrangements, as defined under SEC rules, such as relationships with unconsolidated entities or financial partnerships, which are often referred to as structured finance or special purpose entities, established for the purpose of facilitating financing transactions that are not required to be reflected on our consolidated financial statements.

Contractual Obligations

The following is a summary of our contractual obligations as of December 31, 2013 (in thousands):



	Total		2014		2015		2016		2017		2018		Thereafter
Principal payments on long-term debt	$	179,964	$	6,391	$	4,833	$	4,833	$	98,949	$	55,024	$	9,934
Interest payments on long-term debt, fixed rate ⁽¹⁾	46,873		2,675		2,200		1,916		5,564		33,528		990
Operating leases	65,132		6,404		6,622		6,600		6,580		6,667		32,259
Principal payments on capital leases	1,244		956		288		—		—		—		—
Interest payments on capital leases	52		50		2		—		—		—		—
Terminal storage costs	128		94		34		—		—		—		—
Purchase obligations ⁽²⁾	9,627		8,296		507		532		250		42		—
Total	$	303,020	$	24,866	$	14,486	$	13,881	$	111,343	$	95,261	$	43,183

____________________


⁽¹⁾	Does not include any obligations related to make-whole interest or downround provisions. The fixed interest rates are more fully described in Note 5, "Debt" of our consolidated financial statements.


⁽²⁾	Purchase obligations include noncancellable contractual obligations and construction commitments of $8.9 million , of which $4.0 million have been accrued as loss on purchase commitments.

This table does not reflect non-reimbursable expenses that we expect to incur in 2014 in connection with research activities under the NREL subcontract discussed above under the caption "Liquidity and Capital Resources - Government Contracts."

Additionally, this table does not reflect the expenses that we expect to incur in 2014 in connection with research activities under DARPA under which we will perform certain research and development activities funded in part by DARPA. The work is to be performed on a cost-share basis, where DARPA funds 90% of the work and we fund the remaining 10% (primarily by providing specified labor). Under the agreement, we could receive funding of up to approximately $7.7 million over two years based on achievement of program milestones, and, accordingly, we would be responsible for contributions equivalent to approximately $0.9 million .

Recent Accounting Pronouncements

The information contained in Note 2 to the Consolidated Financial Statements under the heading "Recent Accounting Pronouncements" is hereby incorporated by reference into this Part II, Item 7.

ITEM 7A. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

The market risk inherent in our market risk sensitive instruments and positions is the potential loss arising from adverse changes in: commodity market prices, foreign currency exchange rates, and interest rates as described below.

Interest Rate Risk

Our exposure to market risk for changes in interest rates relates primarily to our investment portfolio and our outstanding debt obligations. We generally invest our cash in investments with short maturities or with frequent interest reset terms. Accordingly, our interest income fluctuates with short-term market conditions. As of December 31, 2013 , our investment portfolio consisted primarily of money market funds and certificates of deposit, all of which are highly liquid investments. Due to the short-term nature of our investment portfolio, our exposure to interest rate risk is minimal. Additionally, as of December 31, 2013 , 100% of our outstanding debt is in fixed rate instruments.

Foreign Currency Risk

Most of our sales contracts are principally denominated in U.S. dollars and, therefore, our revenues are not currently subject to significant foreign currency risk. The functional currency of our wholly-owned consolidated subsidiary in Brazil is the local currency (Brazilian real) in which recurring business transactions occur. We do not use currency exchange contracts as hedges against amounts permanently invested in our foreign subsidiary. The amount we consider permanently invested in our foreign subsidiary and translated into U.S. dollars using the year end exchange rate is $145.2 million at December 31, 2013 and $76.7 million at December 31, 2012. The increase in the permanent investments in our foreign subsidiary between 2012 and 2013 is due to additional capital contributions made which includes the conversion of approximately R$89.7 million (US$39.7 million based on the exchanges rate as of December 31, 2013) of intercompany loans into equity in our wholly-owned consolidated subsidiary in Brazil which is partially offset by the depreciation of the Brazilian real versus the U.S. dollar and an increase in accumulated deficit of our wholly-owned consolidated subsidiary in Brazil. The potential loss in fair value, which would principally be recognized in Other Comprehensive Income (Loss), resulting from a hypothetical 10% adverse change in quoted Brazilian real exchange rates is $14.5 million and $7.7 million for 2013 and 2012, respectively. Actual results may differ.

We make limited use of derivative instruments, which includes currency interest rate swap agreements, to manage the Company's exposure to foreign currency exchange rate and interest rate related to the Company's Banco Pine loan. In June 2012, we entered into a currency interest rate swap arrangement with Banco Pine for R$22.0 million (approximately US$9.4 million based on the exchange rate as of December 31, 2013 ). The swap arrangement exchanges the principal and interest payments under the Banco Pine loan entered into in July 2012 for alternative principal and interest payments that are subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap has a fixed interest rate of 3.94% . This arrangement hedges the fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real.

Commodity Price Risk

Our primary exposure to market risk for changes in commodity prices currently relates to our purchases of sugar feedstocks. When possible, we manage our exposure to this risk primarily through the use of supplier pricing agreements.

ITEM 8. FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA

AMYRIS, INC.

Index to Financial Statements and Financial Statement Schedules



	Page
Consolidated Financial Statements:

Report of Independent Registered Public Accounting Firm	64

Consolidated Balance Sheets as of December 31, 2013 and 2 012	65

Consolidated Statements of Operations for the years ended December 31, 2013, 2012 an d 2011	66

Consolidated Statements of Comprehensive Loss for the years ended December 31, 2013, 2012 and 2 011	67

Consolidated Statements of Stockholders' Equity (Deficit) for the years ended December 31, 2013, 2012 and 2011	68

Consolidated Statements of Cash Flows for the years ended December 31, 2013, 2012 and 2 011	71

Notes to Consolidated Financial Statements	73

Financial Statement Schedules:

Schedule II Valuation and Qualifying Accounts for the years ended December 31, 2013, 2012 and 2011	130

Report of Independent Registered Public Accounting Firm

To the Board of Directors and Stockholders of

Amyris, Inc.:

In our opinion, the consolidated financial statements listed in the accompanying index present fairly, in all material respects, the financial position of Amyris, Inc and its subsidiaries at December 31, 2013 and December 31, 2012, and the results of their operations and their cash flows for each of the three years in the period ended December 31, 2013 in conformity with accounting principles generally accepted in the United States of America. In addition, in our opinion, the financial statement schedule listed in the accompanying index presents fairly, in all material respects, the information set forth therein when read in conjunction with the related consolidated financial statements. Also in our opinion, the Company maintained, in all material respects, effective internal control over financial reporting as of December 31, 2013, based on criteria established in Internal Control - Integrated Framework (1992) issued by the Committee of Sponsoring Organizations of the Treadway Commission (COSO). The Company's management is responsible for these financial statements and financial statement schedule, for maintaining effective internal control over financial reporting and for its assessment of the effectiveness of internal control over financial reporting, included in Management's Annual Report on Internal Control over Financial Reporting appearing under Item 9A. Our responsibility is to express opinions on these financial statements, on the financial statement schedule, and on the Company's internal control over financial reporting based on our integrated audits. We conducted our audits in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audits to obtain reasonable assurance about whether the financial statements are free of material misstatement and whether effective internal control over financial reporting was maintained in all material respects. Our audits of the financial statements included examining, on a test basis, evidence supporting the amounts and disclosures in the financial statements, assessing the accounting principles used and significant estimates made by management, and evaluating the overall financial statement presentation. Our audit of internal control over financial reporting included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, and testing and evaluating the design and operating effectiveness of internal control based on the assessed risk. Our audits also included performing such other procedures as we considered necessary in the circumstances. We believe that our audits provide a reasonable basis for our opinions.

A company's internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. A company's internal control over financial reporting includes those policies and procedures that (i) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (ii) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (iii) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company's assets that could have a material effect on the financial statements.

Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.

/s/ PricewaterhouseCoopers LLP

San Jose, California

April 1, 2014

Amyris, Inc.

Consolidated Balance Sheets

(In Thousands, Except Share and Per Share Amounts)



	December 31,
	2013			2012
Assets
Current assets:
Cash and cash equivalents	$	6,868		$	30,592
Short-term investments	1,428			97
Accounts receivable, net of allowance of $479 and $481, respectively	7,734			3,846
Related party accounts receivable	484			—
Inventories, net	10,888			6,034
Prepaid expenses and other current assets	9,518			8,925
Total current assets	36,920			49,494
Property, plant and equipment, net	140,591			163,121
Restricted cash	1,648			955
Other assets	10,585			20,112
Goodwill and intangible assets	9,120			9,152
Total assets	$	198,864		$	242,834
Liabilities and Equity (Deficit)
Current liabilities:
Accounts payable	$	6,512		$	15,392
Deferred revenue	2,222			1,333
Accrued and other current liabilities	21,221			24,410
Capital lease obligation, current portion	956			1,366
Debt, current portion	6,391			3,325
Total current liabilities	37,302			45,826
Capital lease obligation, net of current portion	287			1,244
Long-term debt, net of current portion	56,172			61,806
Related party debt	89,499			39,033
Deferred rent, net of current portion	10,191			8,508
Deferred revenue, net of current portion	5,000			4,255
Derivative liability	134,717			9,261
Other liabilities	1,544			6,672
Total liabilities	334,712			176,605
Commitments and contingencies (Note 6)
Stockholders’ equity (deficit):
Preferred stock - $0.0001 par value, 5,000,000 shares authorized, none issued and outstanding	—			—
Common stock - $0.0001 par value, 200,000,000 and 100,000,000 shares authorized as of December 31, 2013 and 2012; 76,662,812 and 68,709,660 shares issued and outstanding as of December 31, 2013 and 2012, respectively	8			7
Additional paid-in capital	706,253			666,233
Accumulated other comprehensive loss	(20,087		)	(12,807		)
Accumulated deficit	(821,438		)	(586,327		)
Total Amyris, Inc. stockholders’ equity (deficit)	(135,264		)	67,106
Noncontrolling interest	(584		)	(877		)
Total stockholders' equity (deficit)	(135,848		)	66,229
Total liabilities and stockholders' equity (deficit)	$	198,864		$	242,834

See the accompanying notes to the consolidated financial statements.

Amyris, Inc.

Consolidated Statements of Operations

(In Thousands, Except Share and Per Share Amounts)



	Years Ended December 31,
	2013			2012			2011
Revenues
Renewable product sales	$	14,428		$	10,802		$	763
Related party renewable product sales	1,380			—			—
Ethanol and ethanol-blended gasoline	—			38,836			129,074
Total product sales	15,808			49,638			129,837
Grants and collaborations revenue	22,664			14,281			17,154
Related party grants and collaborations revenue	2,647			9,775			—
Total grants and collaborations revenue	25,311			24,056			17,154
Total revenues	41,119			73,694			146,991
Cost and operating expenses
Cost of products sold	38,253			77,314			155,615
Loss on purchase commitments and write off of production assets	9,366			45,854			—
Research and development	56,065			73,630			87,317
Sales, general and administrative	57,051			78,718			83,231
Total cost and operating expenses	160,735			275,516			326,163
Loss from operations	(119,616		)	(201,822		)	(179,172		)
Other income (expense):
Interest income	162			1,472			1,542
Interest expense	(9,107		)	(4,926		)	(1,543		)
Income (loss) from change in fair value of derivative instruments	(84,726		)	1,790			—
Income (loss) from extinguishment of debt	(19,914		)	(920		)	—
Other income (expense), net	(2,553		)	(646		)	214
Total other income (expense)	(116,138		)	(3,230		)	213
Loss before income taxes	(235,754		)	(205,052		)	(178,959		)
Benefit (provision) for income taxes	847			(981		)	(552		)
Net loss	$	(234,907	)	$	(206,033	)	$	(179,511	)
Net (income) loss attributable to noncontrolling interest	(204		)	894			641
Net loss attributable to Amyris, Inc. common stockholders	$	(235,111	)	$	(205,139	)	$	(178,870	)
Net loss per share attributable to common stockholders, basic and diluted	$	(3.12	)	$	(3.62	)	$	(3.99	)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	75,472,770			56,717,869			44,799,056

See the accompanying notes to the consolidated financial statements.

Amyris, Inc.

Consolidated Statements of Comprehensive Loss

(In Thousands)



	Years Ended December 31,
	2013			2012			2011
Comprehensive loss:
Net loss	$	(234,907	)	$	(206,033	)	$	(179,511	)
Change in unrealized loss on investments	—			—			(5		)
Foreign currency translation adjustment, net of tax	(7,191		)	(6,626		)	(8,761		)
Total comprehensive loss	(242,098		)	(212,659		)	(188,277		)
Income (loss) attributable to noncontrolling interest	(204		)	894			641
Foreign currency translation adjustment attributable to noncontrolling interest	(89		)	(257		)	(30		)
Comprehensive loss attributable to Amyris, Inc.	$	(242,391	)	$	(212,022	)	$	(187,666	)

See the accompanying notes to the consolidated financial statements.

Amyris, Inc.

Consolidated Statements of Stockholders' Equity (Deficit)



	Common Stock				Additional Paid-in Capital			Accumulated Deficit			Accumulated Other Comprehensive Income (Loss)			Noncontrolling Interest			Total Equity (Deficit)
(In Thousands, Except Share and Per Share Amounts)	Shares		Amount		Additional Paid-in Capital			Accumulated Deficit			Accumulated Other Comprehensive Income (Loss)			Noncontrolling Interest			Total Equity (Deficit)
December 31, 2010	43,847,425		$	4	$	506,988		$	(202,318	)	$	2,872		$	2		$	307,548
Issuance of common stock upon exercise of stock options, net of restricted stock	1,641,439		1		8,491			—			—			—			8,492
Issuance of common stock upon net exercise of warrants	77,087		—		—			—			—			—			—
Issuance of common stock warrants in connection with equipment financing	—		—		193			—			—			—			193
Issuance of common stock in connection with Draths business acquisition	362,319		—		7,000			—			—			—			7,000
Shares issued from restricted stock unit settlement	6,005		—		—			—			—			—			—
Repurchase of common stock	(1,137	)	—		(5		)	—			—			—			(5		)
Stock-based compensation	—		—		25,492			—			—			—			25,492
Fair value of assets and liabilities assigned to noncontrolling interest	—		—		—			—			—			369			369
Change in unrealized loss on investments	—		—		—			—			(5		)	—			(5		)
Foreign currency translation adjustment, net of tax	—		—		—			—			(8,791		)	30			(8,761		)
Net loss	—		—		—			(178,870		)	—			(641		)	(179,511		)
December 31, 2011	45,933,138		$	5	$	548,159		$	(381,188	)	$	(5,924	)	$	(240	)	$	160,812

See the accompanying notes to the consolidated financial statements.

Amyris, Inc.

Consolidated Statements of Stockholders' Equity (Deficit)—(Continued)



	Common Stock				Additional Paid-in Capital			Accumulated Deficit			Accumulated Other Comprehensive Income (Loss)			Noncontrolling Interest			Total Equity (Deficit)
(In Thousands, Except Share and Per Share Amounts)	Shares		Amount		Additional Paid-in Capital			Accumulated Deficit			Accumulated Other Comprehensive Income (Loss)			Noncontrolling Interest			Total Equity (Deficit)
December 31, 2011	45,933,138		$	5	$	548,159		$	(381,188	)	$	(5,924	)	$	(240	)	$	160,812
Issuance of common stock upon exercise of stock options, net of restricted stock	1,441,676		—		1,509			—			—			—			1,509
Issuance of common stock in a private placement, net of issuance cost of $392	21,040,717		2		89,680			—			—			—			89,682
Recovery of shares from Draths escrow	(5,402	)	—		—			—			—			—			—
Shares issued from restricted stock unit settlement	299,584		—		(588		)	—			—			—			(588		)
Repurchase of common stock	(53	)	—					—			—			—			—
Stock-based compensation	—		—		27,473			—			—			—			27,473
Foreign currency translation adjustment, net of tax	—		—		—			—			(6,883		)	257			(6,626		)
Net loss	—		—		—			(205,139		)	—			(894		)	(206,033		)
December 31, 2012	68,709,660		$	7	$	666,233		$	(586,327	)	$	(12,807	)	$	(877	)	$	66,229

See the accompanying notes to the consolidated financial statements.

Amyris, Inc.

Consolidated Statements of Stockholders' Equity (Deficit)—(Continued)



	Common Stock
(In Thousands, Except Share and Per Share Amounts)	Shares	Amount		Additional Paid-in Capital			Accumulated Deficit			Accumulated Other Comprehensive Income (Loss)			Noncontrolling Interest			Total Equity (Deficit)
December 31, 2012	68,709,660	$	7	$	666,233		$	(586,327	)	$	(12,807	)	$	(877	)	$	66,229
Issuance of common stock upon exercise of stock options, net of restricted stock	777,099	—		1,489			—			—			—			1,489
Issuance of common stock in a private placement, net of issuance cost of $21	6,567,299	1		19,979												19,980
Shares issued from restricted stock unit settlement	608,754	—		(825		)	—			—			—			(825		)
Issuance of common stock warrants in connection with issuance of convertible promissory note				1,330												1,330
Stock-based compensation	—	—		18,047			—			—			—			18,047
Foreign currency translation adjustment, net of tax	—	—		—			—			(7,280		)	89			(7,191		)
Net loss	—	—		—			(235,111		)	—			204			(234,907		)
December 31, 2013	76,662,812	$	8	$	706,253		$	(821,438	)	$	(20,087	)	$	(584	)	$	(135,848	)

See the accompanying notes to the consolidated financial statements.

Amyris, Inc.

Consolidated Statements of Cash Flows

(In Thousands)



	Years Ended December 31,
	2013			2012			2011
Operating activities
Net loss	$	(234,907	)	$	(206,033	)	$	(179,511	)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	16,639			14,570			11,077
Loss on disposal of property, plant and equipment	176			370			52
Stock-based compensation	18,047			27,473			25,492
Amortization of premium on investments	—			—			630
Amortization of debt discount	3,683			838			—
Loss on extinguishment of debt	19,914			920			—
Provision for doubtful accounts	—			236			245
Loss on purchase commitments and write-off of production assets	9,366			45,854			—
Change in fair value of derivative instruments	84,726			(1,764		)	—
Other noncash expenses	211			159			40
Changes in assets and liabilities:
Accounts receivable	(4,365		)	2,837			(1,975		)
Related party accounts receivable	(484		)	—			—
Inventories, net	(5,612		)	2,919			(5,327		)
Prepaid expenses and other assets	(2,743		)	11,239			(17,250		)
Accounts payable	(2,636		)	(11,811		)	15,648
Accrued and other liabilities	(9,386		)	(35,754		)	53,894
Derivative liability	111			—			—
Deferred revenue	1,634			(1,648		)	5,542
Deferred rent	(233		)	(1,277		)	(1,053		)
Net cash used in operating activities	(105,859		)	(150,872		)	(92,496		)
Investing activities
Purchase of short-term investments	(2,795		)	(8,334		)	(67,556		)
Maturities of short-term investments	1,281			—			105,000
Sales of short-term investments	—			16,503			68,106
Change in restricted cash	(736		)	(955		)	—
Payments for business acquisitions	—			—			(2,934		)
Acquisition of cash in noncontrolling interest	—			—			344
Investment in unconsolidated joint venture	—			—			(83		)
Purchase of property, plant and equipment, net of disposals	(8,087		)	(56,832		)	(81,917		)
Deposits on property, plant and equipment	—			(26		)	(15,107		)
Net cash provided by (used in) investing activities	(10,337		)	(49,644		)	5,853
Financing activities
Proceeds from issuance of common stock, net of repurchases	309			891			8,445
Proceeds from issuance of common stock in private placements, net of issuance costs	19,980			84,682			—
Proceeds from equipment financing	—			—			3,000
Principal payments on capital leases	(1,366		)	(3,727		)	(2,835		)
Proceeds from debt issued	10,535			78,904			37,957
Proceeds from debt issued to related party	65,000			30,000			—
Principal payments on debt	(3,277		)	(52,633		)	(5,018		)
Payments of offering costs in initial public offering	—			—			(497		)
Net cash provided by financing activities	91,181			138,117			41,052
Effect of exchange rate changes on cash and cash equivalents	1,291			(2,712		)	(1,766		)
Net decrease in cash and cash equivalents	(23,724		)	(65,111		)	(47,357		)
Cash and cash equivalents at beginning of period	30,592			95,703			143,060
Cash and cash equivalents at end of period	$	6,868		$	30,592		$	95,703

Amyris, Inc.

Consolidated Statements of Cash Flows—(Continued)

(In Thousands)



	Years Ended December 31,
	2013			2012			2011
Supplemental disclosures of cash flow information:
Cash paid for interest	$	2,978		$	3,399		$	1,412
Cash paid for income taxes, net of refunds	$	—		$	—		$	—
Supplemental disclosures of noncash investing and financing activities:
Acquisitions of property, plant and equipment under accounts payable, accrued liabilities and notes payable	$	2,261		$	2,538		$	3,177
Financing of equipment	$	—		$	—		$	3,420
Warrants issued in connection with equipment financing	$	—		$	—		$	193
Warrants issued in connection with issuance of convertible promissory notes	$	1,330		$	—		$	—
Financing of insurance premium under notes payable	$	425		$	—		$	—
Receivable of proceeds for options exercised	$	355		$	—		$	—
Capitalized taxes in property, plant and equipment	$	(8,572	)	$	—		$	—
Debt issued related to an investment in joint venture	$	68		$	—		$	—
Change in unrealized gain (loss) on investments	$	—		$	—		$	(5	)
Asset retirement obligation	$	—		$	—		$	174
Issuance of common stock upon exercise of warrants	$	—		$	—		$	3,554
Issuance of common stock related to business acquisition	$	—		$	—		$	7,000
Conversion of other liability to related party debt	$	—		$	(23,300	)	$	—
Conversion of related party debt to common stock	$	—		$	5,000		$	—
Transfer of property, plant and equipment to current assets	$	—		$	—		$	886
Transfer of long term deposits to property, plant and equipment	$	—		$	12,218		$	50
Acquisition of net assets in noncontrolling interest	$	—		$	—		$	25

See the accompanying notes to the consolidated financial statements.

Amyris, Inc.

Notes to Consolidated Financial Statements

1. The Company

Amyris, Inc. (the “Company”) was incorporated in California on July 17, 2003 and reincorporated in Delaware on June 10, 2010 for the purpose of leveraging breakthroughs in synthetic biology to develop and provide renewable compounds for a variety of markets. The Company is currently building and applying its industrial synthetic biology platform to provide alternatives to select petroleum-sourced products used in specialty chemical and transportation fuel markets worldwide. The Company's first commercialization efforts have been focused on a renewable hydrocarbon molecule called farnesene (Biofene®), which forms the basis for a wide range of products varying from specialty chemical applications to transportation fuels, such as diesel. While the Company's platform is able to use a wide variety of feedstocks, the Company is focused initially on Brazilian sugarcane. In addition, the Company has entered into various contract manufacturing agreements to support commercial production. The Company has established two principal operating subsidiaries, Amyris Brasil Ltda. (formerly Amyris Brasil S.A., or Amyris Brasil) for production in Brazil, and Amyris Fuels, LLC (or Amyris Fuels). Nearly all of the Company's revenues through 2012 came from the sale of ethanol and reformulated ethanol-blended gasoline with substantially all of the remaining revenues coming from collaborations, government grants and sales of renewable products. In the third quarter of 2012, the Company transitioned out of the ethanol and reformulated ethanol-blended gasoline business. The Company does not expect to be able to replace much of the revenue lost in the near term as a result of this transition, while it continues its efforts to establish a renewable products business.

The Company's renewable products business strategy is to focus on direct commercialization of specialty products while moving established commodity products into joint venture arrangements with leading industry partners. To commercialize its products, the Company must be successful in using its technology to manufacture its products at commercial scale and on an economically viable basis (i.e., low per unit production costs). The Company is building its experience producing renewable products at commercial scale. The Company's prospects are subject to risks, expenses and uncertainties frequently encountered by companies in this stage of development.

The Company expects to fund its operations for the foreseeable future with cash and investments currently on hand, with cash inflows from collaboration and grant funding, cash contributions from product sales, and with new debt and equity financings. The Company's planned 2014 and 2015 working capital needs and its planned operating and capital expenditures are dependent on significant inflows of cash from existing collaboration partners and from funds under an existing convertible debt facility, as well as additional funding from new collaborations, and may also require additional funding from debt or equity financings. The Company will continue to need to fund its research and development and related activities and to provide working capital to fund production, storage, distribution and other aspects of its business. The Company's operating plan contemplates capital expenditures of approximately $9.0 million in 2014 and the Company expects to continue to incur costs in connection with its existing contract manufacturing arrangements.

Liquidity

The Company has incurred significant losses since its inception and believes that it will continue to incur losses and negative cash flow from operations into at least 2014. As of December 31, 2013 , the Company had an accumulated deficit of $821.4 million and had cash, cash equivalents and short term investments of $8.3 million . The Company has significant outstanding debt and contractual obligations related to purchase commitments, as well as capital and operating leases. As of December 31, 2013 , the Company's debt, net of discount of $27.9 million , totaled $152.1 million , of which $6.4 million matures within the next twelve months. In addition, the Company's debt agreements contain various covenants, including restrictions on the Company's business that could cause the Company to be at risk of defaults. Please refer to Note 5, “Debt” and Note 6, “Commitments and Contingencies” for further details regarding the Company's obligations and commitments.

In addition to cash contributions from product sales and debt and equity financings, the Company also depends on collaboration funding to support its operating expenses. While part of this funding is committed based on existing collaboration agreements, the Company will need to identify and obtain funding under additional collaborations that are not yet subject to any definitive agreement or are not yet identified. In addition, some of the Company’s existing collaboration funding is subject to achievement by the Company of milestones or other funding conditions.

If the Company cannot secure sufficient collaboration funding to support its operating expenses in excess of cash contributions from product sales and existing debt and equity financings, it may need to issue additional preferred and/or discounted equity, agree to onerous covenants, grant further security interest in its assets, enter into collaboration and licensing arrangements that require it to relinquish commercial rights, or grant licenses on terms that are not favorable. If the Company fails to secure such funding, the Company could be forced to curtail its operations, which would have a material adverse effect on the Company's ability to continue with its business plans, and the Company's status as a going concern.

If the Company is unable to raise additional financing, or if other expected sources of funding are delayed or not received, the Company would take the following actions as early as the second quarter of 2014 to support its liquidity needs through the remainder of 2014 and into 2015:


•	Effect significant headcount reductions in the United States and in Brazil, particularly with respect to both general and administrative employees and other employees not connected to critical or contracted activities.


•	Shift its focus to existing products and customers with significantly reduced investment in new product and commercial development efforts.


•	Reduce its expenditures for third party contractors, including consultants, professional advisors and other vendors.


•	Suspend operations at its pilot plants and demonstration facilities.


•	Reduce or delay uncommitted capital expenditures, including non-essential lab equipment and information technology projects.

The contingency cash plan contemplating these actions is designed to save the Company an estimated $25.0 million to $35.0 million over the next twelve months. Implementing this plan could have a material negative impact on the Company's ability to continue its business as currently contemplated, including, without limitation, delays or failures in its ability to:


•	Achieve planned production levels;


•	Develop and commercialize products within planned timelines or at planned scales; and


•	Continue other core activities.

Furthermore, any inability to scale-back operations as necessary, and any unexpected liquidity needs, could create pressure to implement more severe measures. Such measures could have a material adverse effect on the Company's ability to meet contractual requirements, including obligations to maintain manufacturing operations, and increase the severity of the consequences described above.

2. Summary of Significant Accounting Policies

Basis of Presentation

The accompanying consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (“GAAP”) and with the instructions for Form 10-K and Regulations S-X. The consolidated financial statements include the accounts of the Company and its consolidated subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation.

Principles of Consolidations

The Company has interests in joint venture entities that are variable interest entities (“VIEs”). Determining whether to consolidate a variable interest entity requires judgment in assessing (i) whether an entity is a VIE and (ii) if the Company is the entity’s primary beneficiary and thus required to consolidate the entity. To determine if the Company is the primary beneficiary of a VIE, the Company evaluates whether it has (i) the power to direct the activities that most significantly impact the VIE’s economic performance and (ii) the obligation to absorb losses or the right to receive benefits of the VIE that could potentially be significant to the VIE. The Company’s evaluation includes identification of significant activities and an assessment of its ability to direct those activities based on governance provisions and arrangements to provide or receive product and process technology, product supply, operations services, equity funding and financing and other applicable agreements and circumstances. The Company’s assessment of whether it is the primary beneficiary of its VIEs requires significant assumptions and judgment.

The consolidated financial statements of the Company include the accounts of Amyris, Inc., its subsidiaries and two consolidated VIEs with respect to which the Company is considered the primary beneficiary, after elimination of intercompany accounts and transactions. Disclosure regarding the Company’s participation in the VIEs is included in Note 7, " Joint Venture and Noncontrolling Interest."

Use of Estimates

In preparing the consolidated financial statements, management must make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities as of the date of the consolidated financial statements and the reported amounts of revenue and expenses during the reporting period. Actual results could differ from those estimates.

Concentration of Credit Risk

Financial instruments that potentially subject the Company to a concentration of credit risk consist primarily of cash and cash equivalents, short term investments and accounts receivable. The Company places its cash equivalents and investments with high credit quality financial institutions and, by policy, limits the amount of credit exposure with any one financial institution. Deposits held with banks may exceed the amount of insurance provided on such deposits. The Company has not experienced any losses on its deposits of cash and cash equivalents and short-term investments.

The Company performs ongoing credit evaluation of its customers, does not require collateral, and maintains allowances for potential credit losses on customer accounts when deemed necessary.

Customers representing 10% or greater of accounts receivable were as follows:



	December 31,
Customers	2013		2012
Customer B	27	%	*
Customer C	14	%	44	%
Customer D	*		22	%
Customer E	**		14	%
Customer F	27	%	*

______________

* No outstanding balance

** Less than 10%

Customers representing 10% or greater of revenues were as follows:



	Years Ended December 31,
Customers	2013		2012		2011
Customer A	*		13	%	11	%
Customer B	15	%	*		*
Customer C	10	%	**		**
Customer E	20	%	**		**
Customer F	12	%	**		*
Customer G	*		**		14	%
Customer H	**		13	%	*

______________

* Not a customer

** Less than 10%

Fair Value of Financial Instruments

The Company measures certain financial assets and liabilities at fair value based on the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants. Where available, fair value is based on or derived from observable market prices or other observable inputs. Where observable prices or inputs are not available, valuation models are applied. These valuation

techniques involve some level of management estimation and judgment, the degree of which is dependent on the price transparency for the instruments or market and the instruments’ complexity.

The carrying amounts of certain financial instruments, such as cash equivalents, short term investments, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities. The fair values of the notes payable, loan payable, convertible notes and credit facility are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company.

The Company estimate the fair value of the compound embedded derivatives for the convertible promissory notes to Total (refer to Note 5, "Debt" for further details) using the Monte Carlo simulation valuation model that combines expected cash outflows with market-based assumptions regarding risk-adjusted yields, stock price volatility, probability of a change of control and the trading information of the Company's common stock into which the notes are convertible.

The Company estimates the fair value of the compound embedded derivative for the Tranche I Notes using the binomial lattice model in order to estimate the fair value of the embedded derivative in the Tranche I convertible notes. A binomial lattice model generates two probable outcomes - one up and another down - arising at each point in time, starting from the date of valuation until the maturity date. A lattice model was initially used to determine if the convertible notes would be converted, called or held at each decision point. Within the lattice model, the following assumptions are made: (i) the convertible notes will be converted early if the conversion value is greater than the holding value; or (ii) the convertible notes will be called if the holding value is greater than both (a) redemption price and (b) the conversion value at the time. If the convertible notes are called, then the holder will maximize their value by finding the optimal decision between (1) redeeming at the redemption price and (2) converting the convertible notes. Using this lattice method, the Company fair valued the embedded derivatives using the "with-and-without method", where the fair value of the convertible notes including the embedded derivatives is defined as the "with", and the value of the convertible notes excluding the embedded derivatives is defined as the "without". This method estimates the fair value of the embedded derivative by looking at the difference in the fair values between the convertible notes with the embedded derivative and the fair value of the convertible notes without the embedded derivative. The lattice model uses the stock price, conversion rate, conversion price, maturity date, risk-free interest rate, estimated stock volatility and estimated credit spread.

Changes in the inputs into these valuation models have a significant impact in the estimated fair value of the embedded derivatives. For example, a decrease (increase) in the estimated credit spread for the Company results in an increase (decrease) in the estimated fair value of the embedded derivatives. Conversely, a decrease (increase) in the stock price results in a decrease (increase) in the estimated fair value of the embedded derivatives. The changes during 2013 in the fair value of the bifurcated compound embedded derivative is primarily related to the change in price of the Company's underlying common stock and is reflected in the consolidated statements of operations as “Income (loss) from change in fair value of derivative instruments.”

Cash and Cash Equivalents

All highly liquid investments purchased with an original maturity date of 90 days or less at the date of purchase are considered to be cash equivalents. Cash and cash equivalents consist of money market funds and certificates of deposit.

Accounts Receivable

The Company maintains an allowance for doubtful accounts receivable for estimated losses resulting from the inability of its customers to make required payments. The Company determines this allowance based on specific doubtful account identification and management judgment on estimated exposure. The Company writes off accounts receivable against the allowance when it determines a balance is uncollectible and no longer actively pursues collection of the receivable.

Investments

Investments with original maturities greater than 90 days that mature less than 1 year from the consolidated balance sheet date are classified as short-term investments. The Company classifies investments as short-term or long-term based upon whether such assets are reasonably expected to be realized in cash or sold or consumed during the normal cycle of business. The Company invests its excess cash balances primarily in certificates of deposit. Certificates of deposits that have maturities greater than 90 days that mature less than one year from the consolidated balance sheet date are classified as short term investments. The Company classifies all of its investments as available-for-sale and records such assets at estimated fair value in the consolidated balance sheets, with unrealized gains and losses, if any, reported as a component of accumulated other comprehensive income (loss) in stockholders’ equity (deficit). Debt securities are adjusted for amortization of premiums and accretion of discounts and such amortization and accretion are reported as a component of interest income. Realized gains and losses and declines in value that are considered to be other-than-temporary are recognized in the statements of operations. The cost of securities sold is determined

on the specific identification method. There were no significant realized gains or losses from sales of debt securities during the years ended December 31, 2013, 2012 and 2011 . As of December 31, 2013 and 2012 , the Company did not have any other-than-temporary declines in the fair value of its debt securities.

Restricted Cash

Cash accounts that are restricted to withdrawal or usage are presented as restricted cash. As of December 31, 2013 and 2012 , the Company had $1.6 million and $1.0 million , respectively, of restricted cash held by a bank in a certificate of deposit as collateral under a facility lease and bank guarantees.

Inventories

Inventories, which consist of farnesene-derived products, as well as ethanol and reformulated ethanol-blended gasoline, are stated at the lower of cost or market and categorized as finished goods, work-in-process or raw material inventories. During the quarter ended September 30, 2012, the Company sold its remaining inventory of ethanol and reformulated ethanol-blended gasoline as it transitioned out of this business. The Company evaluates the recoverability of its inventories based on assumptions about expected demand and net realizable value. If the Company determines that the cost of inventories exceeds its estimated net realizable value, the Company records a write-down equal to the difference between the cost of inventories and the estimated net realizable value. If actual net realizable values are less favorable than those projected by management, additional inventory write-downs may be required that could negatively impact the Company's operating results. If actual net realizable values are more favorable, the Company may have favorable operating results when products that have been previously written down are sold in the normal course of business. The Company also evaluates the terms of its agreements with its suppliers and establishes accruals for estimated losses on adverse purchase commitments as necessary, applying the same lower of cost or market approach that is used to value inventory. Cost is computed on a first-in, first-out basis. Inventory costs include transportation costs incurred in bringing the inventory to its existing location.

Derivative Instruments

The Company makes limited use of derivative instruments, which includes currency interest rate swap agreements to manage the Company's exposure to foreign currency exchange rate fluctuations and interest rate fluctuations related to the Company's Banco Pine S.A. loan (discussed below under Note 5, "Debt"). Through the third quarter of 2012, the Company held futures positions on the New York Mercantile Exchange and the CME/Chicago Board of Trade to mitigate the risks related to the price volatility of ethanol and reformulated ethanol-blended gasoline but, as of September 30, 2012, the Company had transitioned out of that business and no longer held such derivative instruments. The Company does not engage in speculative derivative activities, and the purpose of its activity in derivative commodity instruments is to manage the financial risk posed by physical transactions and inventory. Changes in the fair value of the derivative contracts are recognized immediately in the consolidated statements of operations.

Embedded Derivatives Related to Convertible Notes

Embedded derivatives that are required to be bifurcated from the underlying debt instrument (i.e. host) are accounted for and valued as a separate financial instrument. The Company evaluated the terms and features of the convertible notes payable and identified compound embedded derivatives (a conversion option that contains a “make-whole interest” provision and down round conversion price adjustment provisions) requiring bifurcation and accounting at fair value because the economic and contractual characteristics of the embedded derivatives met the criteria for bifurcation and separate accounting due to the conversion option containing a “make-whole interest” provision, that requires cash payment for forgone interest upon a change of control and down round conversion price adjustment provisions.

Asset Retirement Obligations

The fair value of an asset retirement obligation is recognized in the period in which it is incurred if a reasonable estimate of fair value can be made. In addition, asset retirement cost is added to the carrying amount of the associated asset and this additional carrying amount is amortized over the life of the asset. The Company’s asset retirement obligations were associated with its commitment to return property subject to an operating lease in Brazil to its original condition upon lease termination. In October 2012, this operating lease was amended which included an amendment to the terms of restitution of the property under lease. As a result of this amendment, the Company no longer has asset retirement obligations and therefore reversed the previously accrued liabilities.

As of December 31, 2013 and 2012 , the Company had no asset retirement obligations. The related leasehold improvements are being amortized to depreciation expense over the term of the lease or the useful life of the assets, whichever is shorter. Related amortization expense was zero , $0.2 million , and $0.2 million for the years ended December 31, 2013, 2012 and 2011 , respectively.

The change in the asset retirement obligation is summarized below (in thousands):



Balance at December 31, 2010	$	984
Additions	166
Foreign currency impacts and other adjustments	(133		)
Accretion expenses recorded during the period	112
Balance at December 31, 2011	$	1,129
Additions	—
Foreign currency impacts and other adjustments	(98		)
Accretion expenses recorded during the period	91
Reversals	(1,122		)
Balance at December 31, 2012	$	—

Property, Plant and Equipment, net

Property, plant and equipment, net are stated at cost less accumulated depreciation and amortization. Depreciation and amortization is computed using the straight-line method over the estimated useful lives of the related assets. Maintenance and repairs are charged to expense as incurred, and improvements and betterments are capitalized. When assets are retired or otherwise disposed of, the cost and accumulated depreciation are removed from the balance sheet and any resulting gain or loss is reflected in operations in the period realized.

Depreciation and amortization periods for the Company’s property, plant and equipment are as follows:



Machinery and equipment	7-15 years
Buildings	15 years
Computers and software	3-5 years
Furniture and office equipment	5 years
Vehicles	5 years

Buildings and leasehold improvements are amortized on a straight-line basis over the terms of the lease, or the useful life of the assets, whichever is shorter.

Computers and software includes internal-use software that is acquired to meet the Company’s needs. Amortization commences when the software is ready for its intended use and the amortization period is the estimated useful life of the software, generally 3 to 5 years. Capitalized costs primarily include contract labor and payroll costs of the individuals dedicated to the installation of internal-use software.

Impairment of Long-Lived Assets

Long-lived assets to be held and used are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of an asset may not be recoverable or the estimated useful life is no longer appropriate. If indicators of impairment exist and the undiscounted projected cash flows associated with such assets are less than the carrying amount of the asset, an impairment loss is recorded to write the asset down to their estimated fair values. Fair value is estimated based on discounted future cash flows. There were $7.7 million , $6.4 million and zero , respectively, of impairment charges recorded during the years ended December 31, 2013, 2012 and 2011 , respectively.

Goodwill and Intangible Assets

Goodwill represents the excess of the cost over the fair value of net assets acquired from business combinations. Intangible assets are comprised primarily of in-process research and development (or IPR&D). The Company makes significant judgments in relation to the valuation of goodwill and intangible assets resulting from business combinations.

There are several methods that can be used to determine the estimated fair value of the IPR&D acquired in a business combination. We used the "income method," which applies a probability weighting that considers the risk of development and commercialization, to the estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, pricing of similar products, and expected industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets will be amortized over the remaining useful life or written off, as appropriate.

The Company evaluates its intangible assets with finite lives for indications of impairment whenever events or changes in circumstances indicate that the carrying value may not be recoverable. Intangible assets consist of purchased licenses and permits and are amortized on a straight-line basis over their estimated useful lives. Amortization of intangible assets was zero , $0.4 million and $0.4 million for the years ended December 31, 2013, 2012 and 2011 , respectively. Factors that could trigger an impairment review include significant under-performance relative to expected historical or projected future operating results, significant changes in the manner of use of the acquired assets or the strategy for the Company's overall business or significant negative industry or economic trends. If this evaluation indicates that the value of the intangible asset may be impaired, we make an assessment of the recoverability of the net carrying value of the asset over its remaining useful life. If this assessment indicates that the intangible asset is not recoverable, based on the estimated undiscounted future cash flows of the technology over the remaining amortization period, we reduce the net carrying value of the related intangible asset to fair value and may adjust the remaining amortization period. Any such impairment charge could be significant and could have a material adverse effect on the Company's reported financial results. The Company has not recognized any impairment charges on its intangible assets through December 31, 2013 .

In-Process Research and Development

During 2011, the Company recorded IPR&D of $8.6 million related to the acquisition of Draths. Amounts recorded as IPR&D will begin being amortized upon first sales of the product over the estimated useful life of the technology. In accordance with authoritative guidance, as the technology has not yet been proven, the amortization of the acquired IPR&D has not begun. The Company estimates that it could take up to three years before it will have viable products resulting from the acquired technology.

Noncontrolling Interest

Changes in noncontrolling interest ownership that do not result in a change of control and where there is a difference between fair value and carrying value are accounted for as equity transactions. In April 2010, the Company entered into a joint venture with São Martinho S.A. (or SMSA), a legal successor by spin-off of Usina São Martinho S.A. The carrying value of the noncontrolling interest from this joint venture is recorded in the equity section of the consolidated balance sheets (see Note 7, "Joint Venture and Noncontrolling Interest"). In January 2011, the Company entered into a production service agreement with Glycotech, Inc. (or Glycotech). The Company has determined that the arrangement with Glycotech qualifies as a VIE. The Company determined that it is the primary beneficiary. The carrying value of the noncontrolling interest from this VIE is recorded in the equity section of the consolidated balance sheets (see Note 7, "Joint Venture and Noncontrolling Interest").

Revenue Recognition

The Company recognizes revenue from the sale of farnesene-derived products, delivery of research and development services, and from governmental grants. Revenue is recognized when all of the following criteria are met: persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, the fee is fixed or determinable, and collectibility is reasonably assured.

If sales arrangements contain multiple elements, the Company evaluates whether the components of each arrangement represent separate units of accounting.

Product Sales

Beginning in the second quarter of 2011, the Company began to sell farnesene-derived products, which were produced by contracted third parties. Through the third quarter of 2012, the Company also sold ethanol and reformulated ethanol-blended gasoline under short-term agreements at prevailing market prices. As of September 30, 2012, the Company had transitioned out of that business. Ethanol and reformulated ethanol-blended gasoline sales consisted of sales to customers through purchases from third-party suppliers in which the Company took physical control of the ethanol and reformulated ethanol-blended gasoline and accepted risk of loss. The Company's renewable product sales do not include rights of return. Returns are only accepted if the product does not meet product specifications and such nonconformity is communicated to the Company within a set number of days of delivery. The Company offers a two year standard warranty provision for squalane products sold after March 31, 2012, if the products do not meet Company-established criteria as set forth in the Company's trade terms. The Company bases its return reserve on a combination of historical rate of return for the Company's squalane products and historical returns for companies in the cosmetics industry since the Company did not have a full two years of historical return data. Revenues are recognized, net of discounts and allowances, once passage of title and risk of loss has occurred and contractually specified acceptance criteria have been met, provided all other revenue recognition criteria have also been met.

Grants and Collaborative Revenue

Revenue from collaborative research services is recognized as the services are performed consistent with the performance requirements of the contract. In cases where the planned levels of research services fluctuate over the research term, the Company recognizes revenue using the proportionate performance method based upon actual efforts to date relative to the amount of expected effort to be incurred by the Company. When up-front payments are received and the planned levels of research services do not fluctuate over the research term, revenue is recorded on a ratable basis over the arrangement term, up to the amount of cash received. When up-front payments are received and the planned levels of research services fluctuate over the research term, revenue is recorded using the proportionate performance method, up to the amount of cash received. Where arrangements include milestones that are determined to be substantive and at risk at the inception of the arrangement, revenue is recognized upon achievement of the milestone and is limited to those amounts whereby collectibility is reasonably assured.

Government grants are agreements that generally provide cost reimbursement for certain types of expenditures in return for research and development activities over a contractually defined period. Revenues from government grants are recognized in the period during which the related costs are incurred, provided that the conditions under which the government grants were provided have been met and only perfunctory obligations are outstanding. Under the Defense Advanced Research Projects Agency (or DARPA) contract signed in June 2012, the Company received funding based on achievement of program milestones. Accordingly, the Company recognized revenue using the proportionate performance method based upon actual efforts to date relative to the amount of expected effort to be incurred, up to the amount of verified payable milestones.

Cost of Products Sold

Cost of products sold includes production costs of farnesene-derived products, which include cost of raw materials, amounts paid to contract manufacturers and period costs including inventory write-downs resulting from applying lower-of-cost-or-market inventory valuation. Cost of farnesene-derived products sold also includes certain costs related to the scale-up in production of such products. Through the third quarter of 2012, cost of products sold consisted primarily of cost of purchased ethanol and reformulated ethanol-blended gasoline, terminal fees paid for storage and handling, transportation costs between terminals and changes in the fair value of derivative commodity instruments. The Company transitioned out of its ethanol and gasoline business in the quarter ended September 30, 2012.

Shipping and handling costs charged to customers are recorded as revenues. Shipping costs are included in cost of products sold. Such charges were not significant in any of the periods presented.

Costs of Start-Up Activities

Start-up activities are defined as those one-time activities related to opening a new facility, introducing a new product or service, conducting business in a new territory, conducting business with a new class of customer or beneficiary, initiating a new process in an existing facility, commencing some new operation or activities related to organizing a new entity. All the costs associated with start-up activities related to a potential facility are expensed and recorded within selling, general and administrative expenses until the facility is considered viable by management, at which time costs would be considered for capitalization based on authoritative accounting literature.

Research and Development

Research and development costs are expensed as incurred and include costs associated with research performed pursuant to collaborative agreements and government grants. Research and development costs consist of direct and indirect internal costs related to specific projects as well as fees paid to others that conduct certain research activities on the Company’s behalf.

Debt Extinguishment

The Company accounts for the income or loss from extinguishment of debt in accordance with ASC 470, "Debt", which indicates that for all extinguishment of debt, the difference between the reacquisition price and the net carrying amount of the debt being extinguished should be recognized as gain or loss when the debt is extinguished. The gain or loss from debt extinguishment is recorded in the consolidated statements of operations under "other income (expense)" as "income (loss) from extinguishment of debt".

Income Taxes

The Company accounts for income taxes under the asset and liability method, which requires, among other things, that deferred income taxes be provided for temporary differences between the tax basis of the Company’s assets and liabilities and their financial statement reported amounts. In addition, deferred tax assets are recorded for the future benefit of utilizing net operating losses and research and development credit carryforwards. A valuation allowance is provided against deferred tax assets unless it is more likely than not that they will be realized.

The Company recognizes and measures uncertain tax positions in accordance with Income Taxes subtopic 05-6 of ASC 740, which prescribes a recognition threshold and measurement process for recording uncertain tax positions taken, or expected to be taken in a tax return, in the consolidated financial statements. Additionally, the guidance also prescribes treatment for the derecognition, classification, accounting in interim periods and disclosure requirements for uncertain tax positions. The Company accrues for the estimated amount of taxes for uncertain tax positions if it is more likely than not that the Company would be required to pay such additional taxes. An uncertain tax position will not be recognized if it has a less than 50% likelihood of being sustained.

Currency Translation

The Company consider the local currency to be the functional currency of the Company’s wholly-owned subsidiary in Brazil and of the Company's joint venture. Accordingly, asset and liability accounts of those operations are translated into United States dollars using the current exchange rate in effect at the balance sheet date and equity accounts are translated into United States dollars using historical rates. The revenues and expenses are translated using the exchange rates in effect when the transactions occur. Gains and losses from foreign currency translation adjustments are included as a component of accumulated other comprehensive income (loss) in the consolidated balance sheets.

Stock-Based Compensation

The Company accounts for stock-based compensation arrangements with employees using a fair value method which requires the recognition of compensation expense for costs related to all stock-based payments including stock options. The fair value method requires the Company to estimate the fair value of stock-based payment awards on the date of grant using an option pricing model. The Company uses the Black-Scholes option pricing model to estimate the fair value of options granted, which is expensed on a straight-line basis over the vesting period. The Company accounts for restricted stock unit awards issued to employees based on the fair market value of the Company’s common stock.

The Company accounts for stock options issued to nonemployees based on the estimated fair value of the awards using the Black-Scholes option pricing model. The Company accounts for restricted stock units issued to nonemployees based on the fair market value of the Company’s common stock. The measurement of stock-based compensation is subject to periodic adjustments as the underlying equity instruments vest, and the resulting change in value, if any, is recognized in the Company’s consolidated statements of operations during the period the related services are rendered.

Comprehensive Income (Loss)

Comprehensive income (loss) represents all changes in stockholders’ equity (deficit) except those resulting from investments or contributions by stockholders. The Company’s foreign currency translation adjustments represent the components of comprehensive income (loss) excluded from the Company’s net loss and have been disclosed in the consolidated statements of comprehensive loss for all periods presented.

The components of accumulated other comprehensive loss are as follows (in thousands):



	December 31,
	2013			2012
Foreign currency translation adjustment, net of tax	$	(20,087	)	$	(12,807	)
Total accumulated other comprehensive loss	$	(20,087	)	$	(12,807	)

Net Loss Attributable to Common Stockholders and Net Loss per Share

The Company computes net loss per share in accordance with ASC 260, “Earnings per Share.” Basic net loss per share of common stock is computed by dividing the Company’s net loss attributable to Amyris, Inc. common stockholders by the weighted-average number of shares of common stock outstanding during the period. Diluted net loss per share of common stock is computed by giving effect to all potentially dilutive securities, including stock options, restricted stock units, common stock warrants, using the treasury stock method or the as converted method, as applicable. For all periods presented, basic net loss per share was the same as diluted net loss per share because the inclusion of all potentially dilutive securities outstanding was anti-dilutive. As such, the numerator and the denominator used in computing both basic and diluted net loss are the same for each period presented.

The following table presents the calculation of basic and diluted net loss per share of common stock attributable to Amyris, Inc. common stockholders (in thousands, except share and per share amounts):



	Years Ended December 31,
	2013			2012			2011
Numerator:
Net loss attributable to Amyris, Inc. common stockholders	$	(235,111	)	$	(205,139	)	$	(178,870	)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic and diluted	75,472,770			56,717,869			44,799,056
Net loss per share attributable to common stockholders, basic and diluted	$	(3.12	)	$	(3.62	)	$	(3.99	)

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock for the periods presented because including them would have been anti-dilutive:



	Years Ended December 31,
	2013	2012	2011
Period-end stock options to purchase common stock	8,409,605	8,946,592	8,377,016
Convertible promissory notes ⁽¹⁾	42,905,005	10,370,391	—
Period-end common stock subject to repurchase	—	51	7,929
Period-end common stock warrants	1,021,087	21,087	26,223
Period-end restricted stock units	2,316,437	2,550,799	375,189
Total	54,652,134	21,888,920	8,786,357

______________


⁽¹⁾	The potentially dilutive effect of convertible promissory notes were computed based on conversion ratios in effect as of December 31, 2013. A portion of the convertible promissory notes issued carries a provision for a reduction in conversion price if certain condition fails to occur, which could potentially increase the dilutive shares outstanding.

Recent Accounting Pronouncements

In December 2011, the International Accounting Standards Board and the FASB issued common disclosure requirements that are intended to enhance comparability between financial statements prepared on the basis of GAAP and those prepared in accordance with International Financial Reporting Standards. In January 2013, the FASB issued an accounting standard update to limit the scope of the new balance sheet offsetting disclosures to derivative instruments, repurchase agreements, and securities lending transactions to the extent that they are offset in the financial statement or subject to an enforceable master netting arrangement or similar arrangement. While this guidance does not change existing offsetting criteria in GAAP or the permitted balance sheet presentation for items meeting the criteria, it requires an entity to disclose both net and gross information about assets and liabilities that have been offset and the related arrangements. Required disclosures under this new guidance should be provided retrospectively for all comparative periods presented. This new guidance is effective for fiscal years beginning on or after January 1, 2013, and interim periods within those years. The adoption of this guidance did not have a material effect on the Company's consolidated financial statements.

In July 2012, the FASB issued an amended accounting standard update to simplify how entities test indefinite-lived intangible assets for impairment which improve consistency in impairment testing requirements among long-lived asset categories. The amended guidance permits an assessment of qualitative factors to determine whether it is more likely than not that the fair value of an indefinite-lived intangible asset is less than its carrying value. For assets in which this assessment concludes it is more likely than not that the fair value is more than its carrying value, then the amended guidance eliminates the requirement to perform quantitative impairment testing as outlined in the previously issued standards. The amended guidance is effective for fiscal years beginning after September 15, 2012 and early adoption was permitted. The adoption of the amended guidance did not have an impact on the Company's consolidated financial statements.

In February 2013, in connection with the accounting standard related to the presentation of the Statement of Comprehensive Income, the FASB issued an accounting standard update to improve the reporting of reclassifications out of accumulated other comprehensive income of various components. This guidance requires companies to present either parenthetically on the face of the financial statements or in the notes, significant amounts reclassified from each component of accumulated other comprehensive income and the income statement line items affected by the reclassification. This standard is effective for interim periods and fiscal years beginning after December 15, 2012. The adoption of this guidance did not have a material effect the Company's consolidated financial statements.

In July 2013, the FASB issued an amended accounting standard update on the financial statement presentation of unrecognized tax benefits. The amended guidance provides that a liability related to an unrecognized tax benefit would be presented as a reduction of a deferred tax asset for a net operating loss carryforward, a similar tax loss or a tax credit carryforward if such settlement is required or expected in the event the uncertain tax position is disallowed. The new guidance becomes effective for the Company on January 1, 2014 and will be applied prospectively to unrecognized tax benefits that exist at the effective date with retrospective applications permitted. The Company's current presentation of unrecognized tax benefits conforms with the amended guidance. Accordingly, there will be no impact to the Company resulting from the guidance.

3. Fair Value of Financial Instruments

The inputs to the valuation techniques used to measure fair value are classified into the following categories:

Level 1: Quoted market prices in active markets for identical assets or liabilities.

Level 2: Observable market-based inputs or unobservable inputs that are corroborated by market data.

Level 3: Unobservable inputs that are not corroborated by market data.

As of December 31, 2013 , the Company’s financial assets and financial liabilities are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):



	Level 1		Level 2		Level 3		Balance as of December 31, 2013
Financial Assets
Money market funds	$	398	$	—	$	—	$	398
Certificates of deposit	1,428		—		—		1,428
Total financial assets	$	1,826	$	—	$	—	$	1,826
Financial Liabilities
Loans payable	$	—	$	18,491	$	—	$	18,491
Credit facilities	—		7,571		—		7,571
Convertible notes	—		—		131,952		131,952
Compound embedded derivative liability	—		—		131,117		131,117
Currency interest rate swap derivative liability	—		3,600		—		3,600
Total financial liabilities	$	—	$	29,662	$	263,069	$	292,731

The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgments and consider factors specific to the asset or liability. The fair values of money market funds are based on fair values of identical assets. The fair values of the loans payable, convertible notes, credit facilities and currency interest rate swaps are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company. Market risk associated with the fixed and variable rate long-term debt relates to the potential reduction in fair value and negative impact to future earnings, respectively, from an increase in interest rates.

The carrying amounts of certain financial instruments, such as cash equivalents, short term investments, accounts receivable, accounts payable, accrued liabilities and notes payable, approximate fair value due to their relatively short maturities, and low market interest rates, if applicable. The fair values of the loans payable, convertible notes and credit facilities are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company.

The Company’s financial assets and financial liabilities as of December 31, 2012 are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):



	Level 1		Level 2		Level 3		Balance as of December 31, 2012
Financial Assets
Money market funds	$	15,847	$	—	$	—	$	15,847
Certificates of deposit	757		—		—		757
Total financial assets	16,604		$	—	$	—	$	16,604
Financial Liabilities
Notes payable	$	—	$	1,676	$	—	$	1,676
Loans payable	—		20,707		—		20,707
Credit facilities	—		11,503		—		11,503
Convertible notes	—		—		62,522		62,522
Compound embedded derivative liability	—		—		7,894		7,894
Currency interest rate swap derivative liability	—		1,367		—		1,367
Total financial liabilities	$	—	$	35,253	$	70,416	$	105,669

The following table provides a reconciliation of the beginning and ending balances for the convertible notes measured at fair value using significant unobservable inputs (Level 3) (in thousands):



	2013			2012
Balance at January 1	$	62,522		$	—
Additions to convertible notes	72,570			73,300
Change in fair value of convertible notes	(3,140		)	(10,778		)
Balance at December 31	$	131,952		$	62,522

Derivative Instruments

The following table provides a reconciliation of the beginning and ending balances for the compound embedded derivative liability measured at fair value using significant unobservable inputs (Level 3) (in thousands):



	2013		2012
Balance at January 1	$	7,894	$	—
Transfers in to Level 3 net of cancellation ⁽¹⁾	40,901		11,025
Total (income) loss from change in fair value of derivative liability	82,322		(3,131		)
Balance at December 31	$	131,117	$	7,894

______________

⁽¹⁾ Includes $0.8 million removal of derivative liability related to debt extinguishment.

The compound embedded derivative liability, represents the fair value of the equity conversion option and a "make-whole" provision of outstanding Total and Tranche I convertible promissory notes (see Note 5, "Debt"). There is no current observable market for this type of derivative and, as such, the Company determined the fair value of the embedded derivative using a Monte Carlo simulation valuation model for the Total Notes and the binomial lattice model for the Tranche I Notes. A Monte Carlo simulation valuation model combines expected cash outflows with market-based assumptions regarding risk-adjusted yields, stock price volatility, probability of a change of control and the trading information of the Company's common stock into which the notes are convertible. A binomial lattice model generates two probable outcomes - one up and another down - arising at each point in time, starting from the date of valuation until the maturity date. A lattice model was initially used to determine if the convertible notes would be converted, called or held at each decision point. Within the lattice model, the following assumptions are made: (i) the convertible notes will be converted early if the conversion value is greater than the holding value; or (ii) the convertible notes will be called if the holding value is greater than both (a) redemption price and (b) the conversion value at the time. If the convertible

notes are called, then the holder will maximize their value by finding the optimal decision between (1) redeeming at the redemption price and (2) converting the convertible notes. Using this lattice method, the Company valued the embedded derivative using the "with-and-without method", where the fair value of the convertible notes including the embedded derivative is defined as the "with", and the fair value of the convertible notes excluding the embedded derivative is defined as the "without". This method estimates the fair value of the embedded derivative by looking at the difference in the values between the convertible notes with the embedded derivative and the fair value of the convertible notes without the embedded derivative. The lattice model uses the stock price, conversion price, maturity date, risk-free interest rate, estimated stock volatility and estimated credit spread. The Company marks the compound embedded derivative to market due to the conversion price not being indexed to the Company's own stock. Except for the "make-whole interest" provision included in the conversion option, which is only required to be settled in cash upon a change of control at the noteholder's option, the compound embedded derivative will be settled in either cash or shares. As of December 31, 2013 , the Company has sufficient common stock available to settle the conversion option in shares.As of December 31, 2013 and 2012 , included in Derivative Liability on the consolidated balance sheet is the Company's compound embedded derivative liability of $131.1 million and $7.9 million , respectively, which represents the fair value of the equity conversion option and a "make-whole" provision relating to the outstanding senior secured convertible promissory notes issued to Total as described above.

In June 2012, the Company entered into a loan agreement with Banco Pine S.A. (or Banco Pine) under which Banco Pine provided the Company with a short term loan (referred to as the Banco Pine Bridge Loan) (see Note 5, "Debt"). At the time of the Bridge Loan, the Company also entered into a currency interest rate swap arrangement with Banco Pine with respect to the repayment of R$22.0 million (approximately US$9.4 million based on the exchange rate as of December 31, 2013 ). The swap arrangement exchanges the principal and interest payments under the Banco Pine loan of R$22.0 million entered into in July 2012 for alternative principal and interest payments that are subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap has a fixed interest rate of 3.94% . Changes in the fair value of the swap are recognized in “Income (loss) from change in fair value of derivative instruments" in the consolidated statements of operations.

Derivative instruments measured at fair value as of December 31, 2013 and 2012 , and their classification on the consolidated balance sheets and consolidated statements of operations, are presented in the following tables (in thousands except contract amounts):



	Liability as of
	December 31, 2013			December 31, 2012
Type of Derivative Contract	Quantity of Short Contracts	Fair Value		Quantity of Short Contracts	Fair Value
Currency interest rate swap, included as net liability in derivative liability	1	$	3,600	1	$	1,367



	Income Statement Classification	Years Ended December 31,
Type of Derivative Contract	Income Statement Classification	2013			2012			2011
		Gain (Loss) Recognized
Regulated fixed price futures contracts	Cost of products sold	$	—		$	(288	)	$	(2,365	)
Currency interest rate swap	Income (loss) from change in fair value of derivative instruments	$	(2,233	)	$	(1,367	)	$	—

4. Balance Sheet Components

Inventories, net

Inventories, net is comprised of the following (in thousands):



	December 31,
	2013		2012
Raw materials	$	1,796	$	1,574
Work-in-process	7,292		1,771
Finished goods	1,800		2,689
Inventories, net	$	10,888	$	6,034

Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets is comprised of the following (in thousands):



	December 31,
	2013		2012
Advances to contract manufacturers	$	7	$	784
Manufacturing catalysts	1,536		1,895
Recoverable VAT and other taxes	5,125		4,167
Other	2,850		2,079
Prepaid expenses and other current assets	$	9,518	$	8,925

Property, Plant and Equipment, net

Property, plant and equipment, net is comprised of the following (in thousands):



	December 31,
	2013			2012
Leasehold improvements	$	39,034		$	39,290
Machinery and equipment	96,585			105,162
Computers and software	8,509			8,232
Furniture and office equipment	2,535			2,467
Buildings	7,148			5,888
Vehicles	488			575
Construction in progress	41,387			45,372
	$	195,686		$	206,986
Less: accumulated depreciation and amortization	(55,095		)	(43,865		)
Property, plant and equipment, net	$	140,591		$	163,121

The Company's first, purpose-built, large-scale Biofene production plant in southeastern Brazil commenced operations in December 2012. This plant is located at Brotas in the state of São Paulo, Brazil and is adjacent to an existing sugar and ethanol mill, Paraíso Bioenergia. The Company's construction in progress consists primarily of the upfront plant design and the initial construction of a second large-scale production plant in Brazil, located at the SMSA sugar and ethanol mill (also in the state of São Paulo, Brazil).

Property, plant and equipment, net includes $3.4 million and $9.1 million of machinery and equipment under capital leases as of December 31, 2013 and 2012 , respectively. Accumulated amortization of assets under capital leases totaled $1.5 million and $4.1 million as of December 31, 2013 and 2012 , respectively.

Depreciation and amortization expense, including amortization of assets under capital leases, was $16.6 million , $14.2 million and $10.7 million for the years ended December 31, 2013, 2012 and 2011 , respectively.

The Company capitalizes interest costs incurred to construct plant and equipment. The capitalized interest is recorded as part of the depreciable cost of the asset to which it relates to and is amortized over the asset's estimated useful life. Interest cost capitalized as of December 31, 2013 and 2012 was $0.5 million and $0.6 million , respectively.

Other Assets

Other assets are comprised of the following (in thousands):



	December 31,
	2013		2012
Deposits on property and equipment, including taxes	$	1,970	$	2,363
Advances to contract manufacturers, net of current portion ⁽¹⁾	—		2,222
Recoverable taxes from Brazilian government entities	6,599		13,597
Other	2,016		1,930
Total other assets	$	10,585	$	20,112

______________


⁽¹⁾	At December 31, 2012 , the amount of $2.2 million relates to the non-current unamortized portion of equipment costs funded by the Company to a contract manufacturer. The related amortization was offset against purchases of inventory during 2013.

Accrued and Other Current Liabilities

Accrued and other current liabilities are comprised of the following (in thousands):



	December 31,
	2013		2012
Professional services	$	2,279	$	824
Accrued vacation	2,274		2,673
Payroll and related expenses	5,066		5,809
Tax-related liabilities	825		851
Deferred rent, current portion	1,111		1,448
Accrued interest ⁽¹⁾	3,176		965
Contractual obligations to contract manufacturers	4,241		9,952
Customer advances	—		970
Other ⁽¹⁾	2,249		918
Total accrued and other current liabilities	$	21,221	$	24,410

_________


⁽¹⁾	Certain reclassifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

Derivative Liability

Derivative liability is comprised of the following (in thousands):



	December 31,
	2013		2012
Fair market value of swap obligations	$	3,600	$	1,367
Fair value of compound embedded derivative liability ⁽¹⁾	131,117		7,894
Total derivative liability	$	134,717	$	9,261

______________


⁽¹⁾	The compound embedded derivative liability represents the fair value of the equity conversion features or "make-whole provision" features included in the outstanding Total and Tranche I convertible promissory notes (see Note 3, "Fair value of financial instruments" and Note 5, "Debt").

5. Debt

Debt is comprised of the following (in thousands):



	December 31,
	2013			2012
Credit facilities	$	8,767		$	12,409
Notes payable	—			1,572
Convertible notes	28,537			25,000
Related party convertible notes	89,499			39,033
Loans payable	25,259			26,150
Total debt	152,062			104,164
Less: current portion	(6,391		)	(3,325		)
Long-term debt	$	145,671		$	100,839

FINEP Credit Facility

In November 2010, the Company entered into the FINEP Credit Facility. This FINEP Credit Facility was extended to partially fund expenses related to the Company’s research and development project on sugarcane-based biodiesel (“FINEP Project”) and provided for loans of up to an aggregate principal amount of R$6.4 million (approximately US$2.7 million based on the exchange rate as of December 31, 2013 ) which is secured by a chattel mortgage on certain equipment of the Company as well as by bank letters of guarantee. All available credit under this facility was fully drawn.

Interest on loans drawn under the FINEP Credit Facility is fixed at 5% per annum. In case of default under or non-compliance with the terms of the agreement, the interest on loans will be dependent on the long-term interest rate as published by the Central Bank of Brazil (such rate, the “TJLP”). If the TJLP at the time of default is greater than 6% , then the interest will be 5% plus a TJLP adjustment factor, otherwise the interest will be at 11% per annum. In addition, a fine of up to 10% shall apply to the amount of any obligation in default. Interest on late balances will be 1% interest per month, levied on the overdue amount. Payment of the outstanding loan balance is being made in 81 monthly installments, which commenced in July 2012 and extends through March 2019. Interest on loans drawn and other charges are paid on a monthly basis and commenced in March 2011. As of December 31, 2013 and 2012 , the total outstanding loan balance under this credit facility was R$5.2 million (approximately US$2.2 million based on the exchange rate as of December 31, 2013 ) and R$6.4 million (approximately US$3.1 million based on exchange rate as of December 31, 2012 ), respectively.

The FINEP Credit Facility contains the following significant terms and conditions:

•

The Company was required to share with FINEP the costs associated with the FINEP Project. At a minimum, the Company was required to contribute from its own funds approximately R$14.5 million (approximately US$6.2 million based on the exchange rate as of December 31, 2013 ) of which R$11.1 million was contributed prior to the release of the second disbursement. All four disbursements were completed and the Company has fulfilled all of its cost sharing obligations;

•

After the release of the first disbursement, prior to any subsequent drawdown from the FINEP Credit Facility, the Company was required to provide bank letters of guarantee of up to R$3.3 million in aggregate (approximately US$1.4 million based on the exchange rate as of December 31, 2013 ). On December 17, 2012 and prior to release of the second disbursement on December 26, 2012, the Company obtained the required bank letter of guarantees from Banco ABC Brasil S.A. (or ABC);


•	Amounts disbursed under the FINEP Credit Facility were required to be used towards the FINEP Project within 30 months after the contract execution.

Revolving Credit Facility

In December 2010, the Company established a revolving credit facility with a financial institution that provided for loans and standby letters of credit of up to an aggregate principal amount of $10.0 million with a sublimit of $5.0 million on standby letters of credit. Interest on loans drawn under this revolving credit facility was equal to (i) the Eurodollar Rate plus 3.0% ; or (ii) the Prime Rate plus 0.5% . In case of default or non-compliance with the terms of the agreement, the interest on loans was Prime Rate plus 2.0% . The credit facility was collateralized by a first priority security interest in certain of the Company's present and future assets. In April 2012, the Company repaid $7.7 million of its outstanding loans under the Credit Facility. In May 2012,

the Company entered into a letter agreement with the bank amending the credit facility agreement to reduce the committed amount under the credit facility from $10.0 million to approximately $2.3 million , and the letters of credit sublimit from $5.0 million to approximately $2.3 million . The amendment also modified the current ratio covenant to require a ratio of current assets to current liabilities of at least $1.3 :1 (as compared to 2 :1 in the Credit Facility), and required the Company to maintain unrestricted cash of at least $15.0 million in its account with the Bank. In June 2012, the credit facility was terminated and, as of December 31, 2012 , no loans or letters of credit were outstanding.

BNDES Credit Facility

In December 2011, the Company entered into the BNDES Credit Facility in the amount of R$22.4 million (approximately US$9.6 million based on the exchange rate as of December 31, 2013 ). This BNDES Credit Facility was extended as project financing for a production site in Brazil. The credit line is divided into an initial tranche for up to approximately R$19.1 million reais and an additional tranche of approximately R$3.3 million that becomes available upon delivery of additional guarantees. The credit line is available for 12 months from the date of the Credit Facility, subject to extension by the lender.

The principal of the loans under the BNDES Credit Facility is required to be repaid in 60 monthly installments, with the first installment due in January 2013 and the last due in December 2017. Interest will be due initially on a quarterly basis with the first installment due in March 2012. From and after January 2013, interest payments will be due on a monthly basis together with principal payments. The loaned amounts carry interest of 7% per annum. Additionally, there is a credit reserve charge of 0.1% on the unused balance from each credit installment from the day immediately after it is made available through its date of use, when it is paid.

The BNDES Credit Facility is collateralized by a first priority security interest in certain of the Company's equipment and other tangible assets totaling R$24.9 million (approximately US$10.6 million based on the exchange rate as of December 31, 2013 ). The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company was required to provide a bank guarantee equal to 10% of the total approved amount ( R$22.4 million in total debt) available under this Credit Facility. For advances of the second tranche (above R$19.1 million ), the Company is required to provide additional bank guarantees equal to 90% of each such advance, plus additional Company guarantees equal to at least 130% of such advance. The BNDES Credit Facility contains customary events of default, including payment failures, failure to satisfy other obligations under this credit facility or related documents, defaults in respect of other indebtedness, bankruptcy, insolvency and inability to pay debts when due, material judgments, and changes in control of Amyris Brasil. If any event of default occurs, the Lender may terminate its commitments and declare immediately due all borrowings under the facility. As of December 31, 2013 and 2012 , the Company had R$15.3 million (approximately US$6.5 million based on the exchange rate as of December 31, 2013 ) and R$19.1 million (approximately US$9.3 million based on the exchange rate as of December 31, 2012 ), respectively, in outstanding advances under the BNDES Credit Facility.

Notes Payable

During the period between May 2008 and October 2008, the Company entered into notes payable agreements with the lessor of its headquarters under which it borrowed a total of $3.3 million for the purchase of tenant improvements, bearing an interest rate of 9.5% per annum and to be repaid over a period of 55 to 120 months. As of December 31, 2013 and 2012 , a principal amount of zero and $1.6 million , respectively, was outstanding under these notes payable. In June 2013, as part of the April 30, 2013 Amendment to the Company's operating lease for its headquarters, the Company recorded the elimination of these notes payable as a lease incentive and recorded approximately $1.4 million to deferred rent liability in the consolidated balance sheet. The deferred rent liability is being amortized to expense over the remaining lease term.

Convertible Notes

In February 2012, the Company completed the sale of senior unsecured convertible promissory notes in an aggregate principal amount of $25.0 million pursuant to a securities purchase agreement, between the Company and certain investment funds affiliated with Fidelity Investments Institutional Services Company, Inc. (referred to as the Fidelity Securities Purchase Agreement). The offering consisted of the sale of 3% senior unsecured convertible promissory notes with a March 1, 2017 maturity date and an initial conversion price equal to $7.0682 per share of the Company's common stock, subject to proportional adjustment for adjustments to outstanding common stock and anti-dilution provisions in case of dividends and distributions (referred to as the Fidelity Notes). As of December 31, 2013 , the Fidelity Notes were convertible into an aggregate of up to 3,536,968 shares of the Company's common stock. The note holders have a right to require repayment of 101% of the principal amount of the Fidelity Notes in an acquisition of the Company, and the notes provide for payment of unpaid interest on conversion following such an acquisition if the note holders do not require such repayment. The Fidelity Securities Purchase Agreement and Fidelity Notes include covenants regarding payment of interest, maintaining the Company's listing status, limitations on debt, maintenance of

corporate existence, and filing of SEC reports. The Fidelity Notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, material adverse effect clauses and breaches of the covenants in the Fidelity Securities Purchase Agreement and Fidelity Notes, with default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the Fidelity Notes include restrictions on the amount of debt the Company is permitted to incur. With exceptions for certain existing debt, refinancing of such debt and certain other exclusions and waivers, the Fidelity Notes provide that the Company's total outstanding debt at any time cannot exceed the greater of $200.0 million or 50% of its consolidated total assets and its secured debt cannot exceed the greater of $125.0 million or 30% of its consolidated total assets. In connection with the Company’s closing of a short-term bridge loan for $35.0 million in October 2013, holders of the Fidelity Notes waived compliance with the debt limitations outlined above as to the $35.0 million bridge loan and the August 2013 Financing. In consideration for such waiver, the Company granted to holders of the Fidelity Notes or their affiliates, the right to purchase up to an aggregate of $7.6 million worth of convertible promissory notes in the first tranche of the August 2013 Financing.

In October 2013, the Company amended the August 2013 SPA (see Note 1, "The Company") to include the Fidelity Entities in the first tranche convertible promissory notes. Pursuant to the amendment agreement the Company sold senior convertible notes with an aggregate principal amount of $7.6 million to the Fidelity Entities.The Tranche I Notes are due sixty months from the date of issuance and will be convertible into the Company’s common stock at a conversion price equal to $2.44 , subject to adjustment as described below. The Tranche I Notes are convertible at the option of the holder: (i) at any time after 18 months from the date of the August 2013 SPA, (ii) on a change of control of the Company and (iii) upon the occurrence of an event of default. The conversion price of the Tranche I Notes will be reduced to $2.15 if a specified Company manufacturing plant fails to achieve a total production of 1.0 million liters within a run period of 45 days prior to June 30, 2014, the Company fails to achieve gross margins from product sales of at least 5% prior to June 30, 2014, or the Company reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes. If either of the production and margin milestones occur, and in addition, the Company reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes, the conversion price of the Tranche I Notes will be reduced to $1.87 . Each Tranche I Note accrues interest from the date of issuance until the earlier of the date that such Tranche I Note is converted into the Company’s common stock or is repaid in full. Interest accrues at a rate of 5% per six months, compounded semiannually (with graduated interest rates of 6.5% applicable to the first 180 days and 8% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or at 6.5% for all other defaults). Interest for the first 30 months is payable in kind and added to the principal every six-months and thereafter, the Company may continue to pay interest in kind by adding to the principal every six-months or may elect to pay interest in cash. The Tranche I Notes may be prepaid by the Company after 30 months from the issuance date and initial interest payment; thereafter the Company has the option to prepay the Tranche I Notes every six months at the date of payment of the semi-annual coupon.

As of December 31, 2013 and 2012 , principal amount of $32.6 million and $25.0 million , respectively, were outstanding under these convertible notes.

Related Party Convertible Notes

In July 2012, the Company entered into an agreement with Total that expanded Total's investment in the Biofene collaboration with the Company, provided new structure for a joint venture (referred to as the Fuels JV) to commercialize the products encompassed by the diesel and jet fuel research and development program (or, the Program), and established a convertible debt structure for the collaboration funding from Total (referred to as the July 2012 Agreements).

The purchase agreement for the notes related to the funding from Total (referred to as the Total Purchase Agreement) provides for the sale of an aggregate of $105.0 million in notes as follows:

•

As part of an initial closing under the purchase agreement (which initial closing was completed in two installments), (i) on July 30, 2012 , the Company sold a 1.5% Senior Unsecured Convertible Note due March 2017 to Total in the face amount of $38.3 million , including $15.0 million in new funds and $23.3 million in previously-provided diesel research and development funding by Total, and (ii) on September 14, 2012 , the Company sold another note (in the same form) for $15.0 million in new funds from Total.


•	At a second closing under the Total Purchase Agreement (also completed in two installments) the Company sold additional notes for an aggregate of $30.0 million in new funds from Total ( $10.0 million in June 2013 and $20.0 million in July 2013).


•	The Total Purchase Agreement provides that additional notes may be sold in subsequent closings in July 2014 (for cash proceeds to the Company of $21.7 million , which would be settled in an initial installment of $10.85 million payable at such closing and a second installment of $10.85 million payable in January 2015 ).

The notes issued have a maturity date of March 1, 2017 , an initial conversion price equal to $7.0682 per share for the notes issued under the initial closing and an initial conversion price equal $3.08 per share for the notes issued under the second closing. The notes bear interest of 1.5% per annum (with a default rate of 2.5% ), accruing from the date of funding and payable at maturity or on conversion or a change of control where Total exercises the right to require the Company to repay the notes. Accrued interest is cancelled if the notes are cancelled based on a “Go” decision (see Note 8, "Significant Agreements"). The agreements contemplate that the research and development efforts under the Program may extend through 2016, with a series of “Go/No Go” decisions (see Note 8, "Significant Agreements") by Total through such date tied to funding by Total.

The notes become convertible into the Company's common stock (i) within 10 trading days prior to maturity (if they are not cancelled as described above prior to their maturity date), (ii) on a change of control of the Company, (iii) if Total is no longer the largest stockholder of the Company following a “No-Go” decision (subject to a six -month lock-up with respect to any shares of common stock issued upon conversion), and (iv) on a default by the Company. If Total makes a final “Go” decision, then the notes will be exchanged by Total for equity interests in the Fuels JV, after which the notes will not be convertible and any obligation to pay principal or interest on the notes will be extinguished. If Total makes a “No-Go” decision, outstanding notes will remain outstanding and become payable at maturity.

In connection with the December 2012 private placement described below (see Note 10, "Stockholders Equity"), Total elected to participate in the private placement by exchanging approximately $5.0 million of its $53.3 million in senior unsecured convertible promissory notes into 1,677,852 of the Company's common stock at $2.98 per share. As such, $5.0 million of the outstanding $53.3 million in senior unsecured convertible promissory notes was cancelled. The cancellation of the debt was treated as an extinguishment of debt in accordance with the guidance outlined in ASC 470-50. As a result of the exchange and cancellation of the $5.0 million debt the Company recorded a loss from extinguishment of debt of $0.9 million .

In March 2013, the Company entered into a letter agreement with Total (referred to as the March 2013 Letter Agreement) under which Total agreed to waive its right to cease its participation in the parties' fuels collaboration at the July 2013 decision point and committed to proceed with the July 2013 funding tranche of $30.0 million (subject to the Company's satisfaction of the relevant closing conditions for such funding in the Total Purchase Agreement). As consideration for this waiver and commitment, the Company agreed to:

•

Reduce the conversion price for the senior unsecured convertible promissory notes to be issued in connection with such funding from $7.0682 per share to a price per share equal to the greater of (i) the consolidated closing bid price of the Company's common stock on the date of the letter agreement, plus $0.01 , and (ii) $3.08 per share, provided that the conversion price would not be reduced by more than the maximum possible amount permitted under the rules of NASDAQ such that the new conversion price would require the Company to obtain stockholder consent; and


•	Grant Total a senior security interest in the Company's intellectual property, subject to certain exclusions and subject to release by Total when the Company and Total enter into final documentation regarding the establishment of the Fuels JV.

In addition to the waiver by Total described above, Total also agreed that, at the Company's request and contingent upon the Company meeting its obligations described above, it would pay advance installments of the amounts otherwise payable at the July 2013 closing. Specifically, if the Company requested such advance installments, subject to certain closing conditions and delivery of certifications regarding the Company's cash levels, Total was obligated to fund $10.0 million no later than May 15, 2013, and an additional $10.0 million no later than June 15, 2013 , with the remainder to be funded on the original July 2013 closing date.

In June 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $10.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above. In accordance with the March 2013 Letter Agreement, this convertible note has an initial conversion price equal to $3.08 per share of the Company's common stock. The Company did not request the May advance of $10.0 million , but did request the June advance (as described above), under which this convertible note was issued.

In July 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $20.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above. This purchase and sale completed Total's commitment to purchase $30.0 million of such notes by July 2013. In accordance with the March 2013 Letter Agreement, this convertible note has an initial conversion price equal to $3.08 per share of Company common stock.

The conversion prices of the notes issued under the Total Purchase Agreement are subject to adjustment for proportional adjustments to outstanding common stock and under anti-dilution provisions in case of certain dividends and distributions. Total has a right to require repayment of 101% of the principal amount of the notes in the event of a change of control of the Company and the notes provide for payment of unpaid interest on conversion following such a change of control if Total does not require such repayment. The purchase agreement and notes include covenants regarding payment of interest, maintenance of the Company's listing status, limitations on debt, maintenance of corporate existence, and filing of SEC reports. The notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the purchase agreement and notes, with added default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the notes include restrictions on the amount of debt the Company is permitted to incur. With exceptions for certain existing debt, refinancing of such debt and certain other exclusions and waivers, the notes provide that the Company's total outstanding debt at any time cannot exceed the greater of $200.0 million or 50% of its consolidated total assets and its secured debt cannot exceed the greater of $125.0 million or 30% of its consolidated total assets. In connection with the Company’s closing of a short-term bridge loan for $35.0 million in October 2013, Total waived compliance with the debt limitations outlined above as to the $35.0 million bridge loan and the August 2013 Financing.

In connection with the August 2013 Financing, the Company entered into the August 2013 SPA (see Note 1, "The Company") with Total and Temasek to sell up to $73.0 million in convertible promissory notes in private placements, with such notes to be sold and issued over a period of up to 24 months from the date of signing. The August 2013 SPA provided for the August 2013 Financing to be divided into two tranches (the first tranche for $42.6 million and the second tranche for $30.4 million ), each with differing closing conditions. Of the total possible purchase price in the financing, $60.0 million to be paid in the form of cash by Temasek ( $35.0 million in the first tranche and up to $25.0 million in the second tranche) and $13.0 million to be paid by the exchange and cancellation of outstanding convertible promissory notes held by Total in connection with its exercise of pro rata rights ( $7.6 million in the first tranche and $5.4 million in the second tranche). The August 2013 SPA included requirements that the Company meet certain production milestones before the second tranche would become available, obtain stockholder approval prior to completing any closing of the transaction, and issue a warrant to Temasek to purchase 1,000,000 shares of the Company's common stock at an exercise price of $0.01 per share, exercisable only if Total converts preexisting promissory notes with a certain per share conversion price. In September 2013, the Company's stockholders approved the August 2013 Financing.

In September 2013, the Company entered into a bridge loan agreement with an existing investor to provide additional cash availability of up to $5.0 million . As of December 31, 2013 , the Company had not drawn any funds from the agreement and the facility expired in October 2013 in accordance with its terms.

In October 2013, the Company sold and issued the Temasek Bridge Note to Temasek for a bridge loan of $35.0 million . The Temasek Bridge Note was due on February 2, 2014 and accrued interest at a rate of 5.5% each four months from October 4, 2013. The note was cancelled on October 16, 2013 as payment for Temasek’s purchase of the first tranche convertible note in the August 2013 Financing. As a result of the exchange and cancellation of the $35.0 million Temasek Bridge Note and the $9.2 million Total convertible note for the Tranche I Notes, the Company recorded a loss from extinguishment of debt of $19.9 million .

In October 2013, the Company amended the August 2013 SPA (see Note 1, "The Company") to include Fidelity Entities in the first tranche convertible promissory notes in the principal amount of $7.6 million , and to proportionally increase the amount acquired by exchange and cancellation of outstanding convertible promissory notes held by Total in connection with its exercise of pro rata rights to $14.6 million ( $9.2 million in the first tranche and up to $5.4 million in the second tranche). Also in October 2013, the Company completed the closing of the Tranche I Notes of the August 2013 Financing, issuing a total of $51.8 million in convertible promissory notes for cash proceeds of $7.6 million and cancellation of outstanding convertible promissory notes of $44.2 million , of which $35.0 million resulted from cancellation of the Temasek Bridge Note. The Tranche I Notes are due sixty months from the date of issuance and will be convertible into the Company’s common stock at a conversion price equal to $2.44 , subject to adjustment as described below. The Tranche I Notes are convertible at the option of the holder: (i) at any time after 18 months from the date of the August 2013 SPA, (ii) on a change of control of the Company and (iii) upon the occurrence of an event of default. The conversion price of the Tranche I Notes will be reduced to $2.15 if a specified Company manufacturing plant fails to achieve a total production of 1.0 million liters within a run period of 45 days prior to June 30, 2014, the Company fails to achieve gross margins from product sales of at least 5% prior to June 30, 2014, or the Company reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes. If either of the production and margin milestones occur, and in addition, the Company reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes, the conversion price of the Tranche I Notes will be reduced to $1.87 . Each Tranche I Note accrues interest from the date of issuance until the earlier of the date that such Tranche I Note is converted into the Company’s common stock or is repaid in full. Interest accrues at a rate of 5% per six months, compounded semiannually (with graduated interest rates of 6.5% applicable to the first 180 days and 8% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or at 6.5% for all other defaults). Interest for the first 30 months is payable in kind and added to the principal every six-months and thereafter, the Company may continue

to pay interest in kind by adding to the principal every six-months or may elect to pay interest in cash. The Tranche I Notes may be prepaid by the Company after 30 months from the issuance date and initial interest payment; thereafter the Company has the option to prepay the Tranche I Notes every six months at the date of payment of the semi-annual coupon.

The convertible promissory notes issuable in the second tranche of the August 2013 Financing (referred to as the Tranche II Notes) would be due 5 years after the date of the issuance of the first Tranche II Notes and would be subject to a conversion price equal to $2.87 , subject to adjustment as described below. Specifically, the Tranche II Notes would be convertible at the option of the holder (i) at any time 12 months after issuance, (ii) on a change of control of the Company, and (iii) upon the occurrence of an event of default. Each Tranche II Notes will accrue interest from the date of issuance until the earlier of the date that such Tranche II Notes is converted into the Company's common stock or repaid in full. Interest will accrue at a rate per annum equal to 10% , compounded annually (with graduated interest rates of 13% applicable to the first 180 days and 16% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or at a rate equal to 12% for all other defaults). Interest for the first 36 months shall be payable in kind and added to the principal every year following the issue date and thereafter, the Company may continue to pay interest in kind by adding to the principal on every year anniversary of the issue date or may elect to pay interest in cash.

In addition to the conversion price adjustments set forth above, the conversion prices of the Tranche I Notes and Tranche II Notes are subject to further adjustment (i) according to proportional adjustments to outstanding common stock of the Company in case of certain dividends and distributions, (ii) according to anti-dilution provisions, and (iii) with respect to notes held by any purchaser other than Total, in the event that Total exchanges existing convertible notes for new securities of the Company in connection with future financing transactions in excess of its pro rata amount. Notwithstanding the foregoing, holders of a majority of the principal amount of the notes outstanding at the time of conversion may waive any anti-dilution adjustments to the conversion price. The purchasers have a right to require repayment of 101% of the principal amount of the notes in the event of a change of control of the Company and the notes provide for payment of unpaid interest on conversion following such a change of control if the purchasers do not require such repayment. The August 2013 SPA, Tranche I Notes and Tranche II Notes include covenants regarding payment of interest, maintenance of the Company’s listing status, limitations on debt and on certain liens, maintenance of corporate existence, and filing of SEC reports. The notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the August 2013 SPA, Tranche I Notes and Tranche II Notes, with default interest rates and associated cure periods applicable to the covenant.

In December 2013, in connection with the execution of the Shareholders Agreement, License Agreement and related documents (collectively, referred to as the JV Documents) entered into by and among Amyris, Total and Total Amyris BioSolutions B.V. (or JVCO) relating to the establishment of JVCO (see Note 7, "Joint Venture and Noncontrolling Interest"), Amyris has agreed to (i) exchange the $69.0 million outstanding Total unsecured convertible notes and issue a replacement 1.5% senior secured convertible notes, in principal amounts equal to the principal amount of each cancelled note (the “Replacement Notes”) and (ii) to grant to Total a security interest in and lien on all Amyris’ rights, title and interest in and to Amyris’ shares in the capital of JVCO. Any Securities to be purchased and sold at the Third Closing (see Note 8, "Significant Agreements") by Total shall be 1.5% senior secured convertible notes shall have a conversion price of $7.0682 . As a consequence of executing the JV Documents and forming JVCO, the Second Amendment of the August 2013 SPA and Restated Intellectual Property Security Agreement dated as of October 16, 2013, executed by Amyris in favor of Total, Temasek, and certain entities affiliated with Fidelity Investments, under which the Company granted a security interest in all of Amyris’ intellectual property was automatically terminated effective as of December 2, 2013 upon Total’s and the Company’s joint written notice to Temasek.

In December 2013, the Company placed a $3.0 million of senior unsecured convertible notes under the second tranche of August 2013 Financing to funds affiliated with Wolverine Asset Management (or Wolverine) and elected to call $25.0 million in additional funds from Temasek pursuant to its previous commitment to purchase such amount of convertible promissory notes in the second tranche. Additionally, in December 2013, the Company agreed to sell approximately $6.0 million of convertible promissory notes in the second tranche to Total through cancellation of the same amount of principal of previously outstanding convertible notes held by Total in respect of Total’s preexisting contractual right to maintain its pro rata ownership position through such cancellation. The second tranche funding closed in the first quarter of 2014.

As of December 31, 2013 and 2012 , $89.5 million and $39.0 million , respectively, was outstanding under these convertible notes, net of debt discount of $27.9 million and $9.3 million , respectively. The debt discount is the result of the bifurcation of the equity conversion option and "make-whole" provision features associated with outstanding debt. For the year ended December 31, 2013, 2012 and 2011 , the Company recorded loss from extinguishment of debt from the exchange and cancellation of related party convertible notes of $19.9 million , $0.9 million , and zero , respectively.

Loans Payable

In December 2009, the Company entered into a loans payable agreement with the lessor of its Emeryville pilot plant under which it borrowed a total of $0.3 million , bearing an interest rate of 10.0% per annum and to be repaid over a period of 96 months. As of December 31, 2013 and 2012 , a principal amount of zero and $0.2 million , respectively, was outstanding under the loan. In June 2013, as part of the April 30, 2013 amendment entered into regarding the Company's operating lease for its headquarters, the Company recorded the elimination of this loan payable as a lease incentive and recorded approximately $0.2 million to deferred rent liability in the consolidated balance sheet. The deferred rent liability is being amortized to expense over the remaining lease term.

In December 2011, the Company entered into a loan agreement with Banco Pine under which Banco Pine provided the Company with a short term loan of R$35.0 million (approximately US$14.9 million based on the exchange rate as of December 31, 2013 ). Such loan was an advance on an anticipated July 2012 financing from Nossa Caixa Desenvolvimento, ("Nossa Caixa"), the Sao Paulo State development bank, and Banco Pine, under which Banco Pine and Nossa Caxia would provide the Company with loans of up to approximately R$52.0 million (approximately US$25.6 million based on the exchange rate as of December 31, 2013 ) as financing for capital expenditures relating to the Company's manufacturing facility in Brotas. The interest rate for the loan was 119.2% of the Brazilian interbank lending rate (approximately 12.3% on an annualized basis). The principal and interest due on the principal under the loan agreement, as amended, matured and was repaid on August 15, 2012 .

In June 2012, the Company entered into a separate loan agreement with Banco Pine under which Banco Pine provided the Company with a Banco Pine Bridge Loan of R$52.0 million (approximately US$25.6 million based on the exchange rate as of September 30, 2012 the time of loan repayment). The interest rate for the Banco Pine Bridge Loan was 0.4472% monthly (approximately 5.5% on an annualized basis). The principal and interest due under the bridge loan matured and were required to be repaid on September 19, 2012 , subject to extension by Banco Pine. At the time of this bridge loan, the Company entered into a currency interest rate swap arrangement with the lender for R$22.0 million (approximately US$9.4 million based on the exchange rate as of December 31, 2013 ). The interest rate swap arrangement exchanged the principal and interest payments under the Banco Pine Loan of R$22.0 million entered into in July 2012 for alternative principal and interest payments that were subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap had a fixed interest rate of 3.94% . In July 2012, the Company repaid the Banco Pine Bridge Loan.

In July 2012, the Company entered into a Note of Bank Credit and a Fiduciary Conveyance of Movable Goods Agreement (together, referred to as the July 2012 Bank Agreements) with each of Nossa Caixa and Banco Pine. Under the July 2012 Bank Agreements, the Company pledged certain farnesene production assets as collateral for the loans of R$52.0 million . The Company's total acquisition cost for such pledged assets was approximately R$68.0 million (approximately US$29.0 million based on the exchange rate as of December 31, 2013 ). The Company is a also a parent guarantor for the payment of the outstanding balance under these loan agreements. Under the July 2012 Bank Agreements, the Company could borrow an aggregate of R$52.0 million (approximately US$22.2 million based on the exchange rate as of December 31, 2013 ) as financing for capital expenditures relating to the Company's manufacturing facility located in Brotas, Brazil. Specifically, Banco Pine, agreed to lend R$22.0 million and Nossa Caixa agreed to lend R$30.0 million . The funds for the loans are provided by BNDES, but are guaranteed by the lenders. The loans have a final maturity date of July 15, 2022 and bear a fixed interest rate of 5.5% per year. The loans are also subject to early maturity and delinquency charges upon occurrence of certain events including interruption of manufacturing activities at the Company's manufacturing facility in Brotas, Brazil for more than 30 days, except during sugarcane off-season. For the first two years that the loans are outstanding, the Company is required to pay interest only on a quarterly basis. After August 15, 2014 , the Company is required to pay equal monthly installments of both principal and interest for the remainder of the term of the loans. As of December 31, 2013 and 2012 , a principal amount of $22.2 million and $25.4 million , respectively, was outstanding under these loan agreements.

In October 2012, the Company entered into a loans payable agreement with a lender under which it borrowed $0.6 million to pay the insurance premiums of certain schedule of policies. The loan is payable in nine monthly installments of principal and interest. Interest accrued at a rate of 3.24% per annum. The loan was settled in 2013. In October 2013, the Company entered into another loan amounting to $0.6 million to pay for the current insurance premiums under the same terms. As of December 31, 2013 and 2012 , the outstanding unpaid loan balance was $0.4 million and $0.4 million , respectively.

In March 2013, the Company entered into an export financing agreement with ABC for approximately $2.5 million a one -year-term to fund exports through March 2014. This loan is collateralized by future exports from the Company's subsidiary in Brazil. As of December 31, 2013 , the principal amount outstanding under this agreement was $2.5 million .

Letters of Credit

In June 2012, the Company entered into a letter of credit agreement for $1.0 million under which it provided a letter of credit to the landlord for its headquarters in Emeryville, California in order to cover the security deposit on the lease. This letter of credit is secured by a certificate of deposit. Accordingly, the Company has $0.9 million as restricted cash as of December 31, 2013 and 2012 .

Future minimum payments under the debt agreements as of December 31, 2013 are as follows (in thousands):



Years ending December 31:	Related Party Convertible Debt			Convertible Debt			Notes Payable		Loans Payable			Credit Facility
2014	$	—		$	760		$	—	$	5,753		$	2,552
2015	—			765			—		3,848			2,420
2016	—			760			—		3,700			2,288
2017	73,687			25,125			—		3,547			2,155
2018	72,381			12,331			—		3,396			445
Thereafter	—			—			—		10,817			107
Total future minimum payments	146,068			39,741			—		31,061			9,967
Less: amount representing interest ⁽¹⁾	(56,569		)	(11,204		)	—		(5,802		)	(1,200		)
Present value of minimum debt payments	89,499			28,537			—		25,259			8,767
Less: current portion	—			—			—		(4,333		)	(2,058		)
Noncurrent portion of debt	$	89,499		$	28,537		$	—	$	20,926		$	6,709

⁽¹⁾ Including debt discount of $27.9 million related to the embedded derivative associated with the related party convertible debt which will be accreted to interest expense under the effective interest method over the term of the convertible debt.

6. Commitments and Contingencies

Lease Obligations

The Company leases certain facilities and finances certain equipment under operating and capital leases, respectively. Operating leases include leased facilities and capital leases include leased equipment (see Note 4, "Balance Sheet Components"). The Company recognizes rent expense on a straight-line basis over the noncancellable lease term and records the difference between cash rent payments and the recognition of rent expense as a deferred rent liability. Where leases contain escalation clauses, rent abatements, and/or concessions, such as rent holidays and landlord or tenant incentives or allowances, the Company applies them in the determination of straight-line rent expense over the lease term. The Company has noncancellable operating lease agreements for office, research and development, and manufacturing space that expire at various dates, with the latest expiration in February 2031 . Rent expense under operating lease was $4.8 million , $4.9 million and $4.8 million , for the years ended December 31, 2013, 2012 and 2011 , respectively.

In December 2011, the Company executed an equipment financing agreement for $3.0 million for certain qualifying manufacturing and laboratory equipment. Pursuant to the equipment financing agreement, the Company financed the equipment with transactions representing capital leases. This sales/leaseback transaction resulted in a $1.3 million unrealized loss which is being amortized over the life of the assets under lease. Accordingly, a capital lease liability was recorded at the present value of the future lease payments of $1.2 million and $2.2 million during the years ended December 31, 2013 and 2012 , respectively. The incremental borrowing rate used to determine the present values of the future lease payments was 6.5% . The lease obligations expire on January 1, 2015 . In connection with the capital lease entered into in 2011, the Company issued a warrant to purchase shares of the Company's common stock (see Note 10, "Stockholder's Equity").

In 2007, the Company entered into an operating lease for its headquarters in Emeryville, California, with a term of ten years commencing in May 2008. As part of the operating lease agreement, the Company received a tenant improvements allowance of $11.4 million . The Company recorded the allowance as deferred rent and associated expenditures as leasehold improvements that are being amortized over the shorter of their estimated useful life or the term of the lease. In connection with the operating lease, the Company elected to defer a portion of the monthly base rent due under the lease and entered into notes payable agreements with the lessor for the purchase of certain tenant improvements. In October 2010, the Company amended its lease agreement with

the lessor of its headquarters, to lease up to approximately 22,000 square feet of research and development and office space. In return for the removal of the early termination clause in its amended lease agreement, the Company received approximately $1.0 million from the lessor in December 2010. In April 2013, the Company amended its lease agreement for its headquarters in Emeryville, California (referred to as the Lease Amendment). The Lease Amendment provided for an extension of the lease term to May 2023, a modification of the base rent and elimination of the Company's loans and notes payable to the lessor of approximately $1.6 million (see Note 5, "Debt"). In addition, per the terms of the Lease Amendment, the Company also received a rent credit of approximately $71,000 per month for the period of June 2013 through December 2013 and a rent credit of approximately $42,000 per month for the full year of 2014.

In March 2011, the Company entered into an operating lease on real property owned by Paraíso Bioenergia S.A. (“Paraíso Bioenergia”) in Brazil. In conjunction with a supply agreement (see Note 8, "Significant Agreements") with the same entity, the land is being used by the Company for its Biofene production plant in Brotas. This lease has a term of 15 years commencing in March 2011 with an estimated annual rent payment of approximately $116,000 .

In August 2011, the Company notified the lessor of its leased office facilities in Brazil of the Company's termination of its existing lease effective November 30, 2011. At the same time, the Company entered into an operating lease for new office facilities in Campinas, Brazil. The new lease has a term of 5 years commencing in November 2011 with an estimated annual rent payment of approximately $367,000 .

In October 2012, an operating lease associated with the Company's pilot plant in Brazil was amended. As a result of this amendment, the Company's operating lease was extended and the new expiration is October 2015 and included an amendment to the terms of restitution of the property under lease. As a result of this amendment, the Company no longer has asset retirement obligations and therefore reversed the previously accrued liabilities.

Future minimum payments under the Company's lease obligations as of December 31, 2013 , are as follows (in thousands):



Years ending December 31:	Capital Leases			Operating Leases		Total Lease Obligations
2014	$	1,006		$	6,404	$	7,410
2015	289			6,622		6,911
2016	—			6,600		6,600
2017	—			6,580		6,580
2018	—			6,667		6,667
Thereafter	—			32,259		32,259
Total future minimum lease payments	1,295			$	65,132	$	66,427
Less: amount representing interest	(52		)
Present value of minimum lease payments	1,243
Less: current portion	(956		)
Long-term portion	$	287

Guarantor Arrangements

The Company has agreements whereby it indemnifies its officers and directors for certain events or occurrences while the officer or director is, or was, serving at the Company’s request in such capacity. The term of the indemnification period is for the officer's or director’s lifetime. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is unlimited; however, the Company has a director and officer insurance policy that limits its exposure and enables the Company to recover a portion of any future amounts paid. As a result of its insurance policy coverage, the Company believes the estimated fair value of these indemnification agreements is minimal. Accordingly, the Company had no liabilities recorded for these agreements as of December 31, 2013 and 2012 .

The Company entered into the FINEP Credit Facility to finance a research and development project on sugarcane-based biodiesel (see Note 5, "Debt"). The FINEP Credit Facility is guaranteed by a chattel mortgage on certain equipment of the Company. The Company's total acquisition cost for the equipment under this guarantee is approximately R$6.0 million (approximately US$2.6 million based on the exchange rate as of December 31, 2013 ).

The Company entered into the BNDES Credit Facility to finance a production site in Brazil (see Note 5, "Debt").The BNDES Credit Facility is collateralized by a first priority security interest in certain of the Company's equipment and other tangible assets with a total acquisition cost of R$24.9 million (approximately US$10.6 million based on the exchange rate as of December 31, 2013 ). The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company is required to provide certain bank guarantees under the BNDES Credit Facility. Accordingly, the Company has a $0.7 million and zero as restricted cash as of December 31, 2013 and 2012, respectively.

The Company entered into loan agreements and security agreement where the Company pledged certain farnesene production assets as collateral (the fiduciary conveyance of movable goods) with each of Nossa Caixa and Banco Pine (see Note 5, "Debt"). The Company's total acquisition cost for the farnesene production assets pledged as collateral under these agreements is approximately R$68.0 million (approximately US$29.0 million based on the exchange rate as of December 31, 2013 ). The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements.

The Company has an export financing agreement for approximately $2.5 million for a one -year term to fund exports through March 2014. This loan is collateralized by future exports from the Company's subsidiary in Brazil.

Under an operating lease agreement for its office facilities in Brazil, which commenced on November 15, 2011, the Company is required to maintain restricted cash or letters of credit equal to 3 months of rent of approximately R$0.2 million (approximately US$0.1 million based on the exchange rate as of December 31, 2013 ) in the aggregate as a guarantee that the Company will meet its performance obligations under such operating lease agreement.

In October 2013, the Company entered into a letter agreement with Total relating to the Temasek Bridge Note and to the closing of the August 2013 Financing (referred to as the Amendment Agreement) (see Note 5, "Debt"). In the August 2013 Financing, the Company was required to provide the purchasers under the August 2013 SPA with a security interest in the Company’s intellectual property if Total still held such security interest as of the initial closing of the August 2013 Financing. Under the terms of a previous Intellectual Property Security Agreement by and between the Company and Total (referred to as the Security Agreement), the Company had previously granted a security interest in favor of Total to secure the obligations of the Company under certain convertible promissory notes issued and issuable to Total under the Company’s purchase agreement with Total Purchase Agreement. The Security Agreement provides that such security interest will terminate if Total and the Company enter into certain agreements relating to the formation of the Fuels JV. To get Total to (i) permit the Company to grant the security interest under the Temasek Bridge Note and the August 2013 Financing and (ii) waive a secured debt limitation contained in the outstanding convertible promissory notes held by Total (the “Total Securities”), the Company entered into the Amendment Agreement. Under the Amendment Agreement, the Company agreed to reduce, effective December 2, 2013, the conversion price for the Total Securities issued in 2012 (approximately $48.3 million of which are outstanding as of the date hereof) from $7.0682 per share to $2.20 , the market price per share of the Company’s Common Stock as of the signing of the Amendment Agreement, as determined in accordance with applicable NASDAQ rules, unless the Company and Total enter into the JV Agreements on or prior to December 2, 2013.

In December 2013, in connection with the execution of JV Documents entered into by and among Amyris, Total and JVCO relating to the establishment of the JVCO (see Note 5, "Debt" and Note 7, "Joint Venture and Noncontrolling Interest"), Amyris agreed to exchange the $69.0 million outstanding Total unsecured convertible notes and issue replacement 1.5% senior secured convertible notes, in principal amounts equal to the principal amount of each Replacement Notes and grant a security interest to Total in and lien on all Amyris’ rights, title and interest in and to Amyris’ shares in the capital of the JVCO.

Purchase Obligations

As of December 31, 2013 , the Company had $9.6 million in purchase obligations which included $8.9 million in non-cancellable contractual obligations and construction commitments, of which $4.0 million have been accrued as loss on purchase commitments.

Other Matters

Certain conditions may exist as of the date the financial statements are issued, which may result in a loss to the Company but will only be recorded when one or more future events occur or fail to occur. The Company's management assesses such contingent liabilities, and such assessment inherently involves an exercise of judgment. In assessing loss contingencies related to legal proceedings that are pending against and by the Company or unasserted claims that may result in such proceedings, the Company's management evaluates the perceived merits of any legal proceedings or unasserted claims as well as the perceived merits of the amount of relief sought or expected to be sought.

If the assessment of a contingency indicates that it is probable that a material loss has been incurred and the amount of the liability can be estimated, then the estimated liability would be accrued in the Company's financial statements. If the assessment indicates that a potential material loss contingency is not probable but is reasonably possible, or is probable but cannot be estimated, then the nature of the contingent liability, together with an estimate of the range of possible loss if determinable and material would be disclosed. Loss contingencies considered to be remote by management are generally not disclosed unless they involve guarantees, in which case the guarantee would be disclosed.

In May 2013, a securities class action complaint was filed against the Company and its CEO, John G. Melo, in the U.S. District Court for the Northern District of California. In October 2013, the lead plaintiffs filed a consolidated amended complaint. The complaint, as amended, sought unspecified damages on behalf of a purported class that would comprise all individuals who acquired the Company's common stock between April 29, 2011 and February 8, 2012. The complaint alleged securities law violations based on the Company's commercial projections during that period. In December 2013, the Company filed a motion to dismiss the complaint. In March 2014, the court issued an order granting the Company's motion to dismiss with leave to amend the complaint. The Company believes the complaint lacks merit, and intends to defend itself vigorously. Because the case is at a very early stage and no specific monetary demand has been made, it is not possible for us to estimate the potential loss or range of potential losses for the case.

In August 2013, a complaint entitled Steve Shannon, derivatively on behalf of Amyris, Inc. v. John G. Melo et al and Amyris, Inc., was filed against the Company as nominal defendant in the United States District Court for the Northern District of California. The lawsuit seeks unspecified damages on behalf of the Company from certain of its current and former officers, directors and employees and alleges these defendants breached their fiduciary duties to the Company and unjustly enriched themselves by making allegedly false and misleading statements and omitting certain material facts in the Company's securities filings. Because this purported stockholder derivative action is based on substantially the same facts as the securities class action described above, the two actions have been related and will be heard by the same judge. By stipulation of the parties, the case has been stayed until the Company either files an answer in the securities class action or the securities action is dismissed with prejudice. The Company does not believe the claims in the complaint have merit, and intends to defend itself vigorously. Because the case is at a very early stage and no specific monetary demand has been made, it is not possible to estimate the potential loss or range of potential losses for the case.

The Company is subject to disputes and claims that arise or have arisen in the ordinary course of business and that have not resulted in legal proceedings or have not been fully adjudicated. Such matters that may arise in the ordinary course of business are subject to many uncertainties and outcomes are not predictable with assurance. Therefore, if one or more of these legal disputes or claims resulted in settlements or legal proceedings that were resolved against the Company for amounts in excess of management’s expectations, the Company’s consolidated financial statements for the relevant reporting period could be materially adversely affected.

7. Joint Venture and Noncontrolling Interest

SMA Indústria Química S.A.

In April 2010, the Company established SMA Indústria Química (or SMA), a joint venture with SMSA, to build a production facility in Brazil. SMA is located at the SMSA mill in Pradópolis, São Paulo state. The joint venture agreements establishing SMA have a 20 year initial term.

SMA is managed by a three member executive committee, of which the Company appoints two members, one of whom is the plant manager who is the most senior executive responsible for managing the construction and operation of the facility. SMA is governed by a four member board of directors, of which the Company and SMSA each appoint two members. The board of directors has certain protective rights which include final approval of the engineering designs and project work plan developed and recommended by the executive committee.

The joint venture agreements require the Company would fund the construction costs of the new facility and SMSA would reimburse the Company up to RS$61.8 million (approximately US$26.4 million based on the exchange rate as of December 31, 2013 ) of the construction costs after SMA commences production. After commercialization, the Company would market and distribute Amyris renewable products produced by SMA and SMSA would sell feedstock and provide certain other services to SMA. The cost of the feedstock to SMA would be a price that is based on the average return that SMSA could receive from the production of its current products, sugar and ethanol. The Company would be required to purchase the output of SMA for the first

four years at a price that guarantees the return of SMSA’s investment plus a fixed interest rate. After this four year period, the price would be set to guarantee a break-even price to SMA plus an agreed upon return.

Under the terms of the joint venture agreements, if the Company becomes controlled, directly or indirectly, by a competitor of SMSA, then SMSA has the right to acquire the Company’s interest in SMA. If SMSA becomes controlled, directly or indirectly, by a competitor of the Company, then the Company has the right to sell its interest in SMA to SMSA. In either case, the purchase price shall be determined in accordance with the joint venture agreements, and the Company would continue to have the obligation to acquire products produced by SMA for the remainder of the term of the supply agreement then in effect even though the Company would no longer be involved in SMA’s management.

The Company has a 50% ownership interest in SMA. The Company has identified SMA as a variable interest entity (or VIE) pursuant to the accounting guidance for consolidating VIEs because the amount of total equity investment at risk is not sufficient to permit SMA to finance its activities without additional subordinated financial support, as well as because the related commercialization agreement provides a substantive minimum price guarantee. Under the terms of the joint venture agreement, the Company directs the design and construction activities, as well as production and distribution. In addition, the Company has the obligation to fund the design and construction activities until commercialization is achieved. Subsequent to the construction phase, both parties equally fund SMA for the term of the joint venture. Based on those factors, the Company was determined to have the power to direct the activities that most significantly impact SMA’s economic performance and the obligation to absorb losses and the right to receive benefits. Accordingly, the financial results of SMA are included in the Company’s consolidated financial statements and amounts pertaining to SMSA’s interest in SMA are reported as noncontrolling interests in subsidiaries.

The Company completed a significant portion of the construction of the new facility in 2012. The Company suspended construction of the facility in order to focus on completing and operating the Company's smaller production facility in Brotas, Brazil. In February 2014, the Company entered into an amendment to the joint venture agreement with SMSA which updates and documents certain preexisting business plan requirements related to the start-up of construction at the joint venture operated plant and sets forth, among other things, (i) the extension of the deadline for the commencement of operations at the joint venture operated plant to no later than 18 months following the construction of the plant, which shall occur no later than March 31, 2017, and (ii) the extension of an option held by SMSA to build a second large-scale farnesene production facility to no later than December 31, 2018 with the commencement of operations at such second facility to occur no later than April 1, 2019.

Novvi S.A.

In June 2011, the Company entered into joint venture agreements with Cosan Combustíveis e Lubrificantes S.A. and Cosan S.A. Industria e Comércio (such Cosan entities, collectively or individually, “Cosan”), related to the formation of a joint venture to focus on the worldwide development, production and commercialization of base oils made from Biofene for the automotive, commercial and industrial lubricants markets (referred to as the Original JV Agreement). The parties originally envisioned operating their joint venture through Novvi S.A., a Brazilian entity jointly owned by Cosan and Amyris Brasil.

Under the Original JV Agreement and related agreements, the Company and Cosan each owned 50% of the Novvi S.A. and each party would share equally in any costs and any profits ultimately realized by Novvi S.A. The joint venture agreement had an initial term of 20 years from the date of the Original JV Agreement, subject to earlier termination by mutual written consent or by a non-defaulting party in the event of specified defaults by the other party. The shareholders' agreement had an initial term of 10 years from the date of the agreement, subject to earlier termination if either the Company or Cosan ceases to own at least 10% of the voting stock of Novvi S.A. Since its formation, Novvi S.A. had minimal operating activities while the Company and Cosan continued to determine and finalize the strategy and operating activities for the joint venture. Upon determination by the Company and Cosan that the joint venture should be operated out of a US entity, the operating activities of Novvi S.A. ceased. The Company has identified that Novvi S.A. is a VIE and determined that the power to direct activities, which most significantly impact the economic success of the joint venture, is equally shared between the Company and Cosan. Accordingly, the Company is not the primary beneficiary and therefore accounts for its investment in Novvi S.A. under the equity method of accounting.

In March 2013, the Company, Amyris Brasil and Cosan entered into a termination agreement to terminate the Original JV Agreement. In addition, Amyris Brasil agreed to sell, its 50% ownership in Novvi S.A. for approximately R$22,000 (approximately US$9,391 based on the exchange rate as of December 31, 2013) which represented the current value of its 50% equity ownership in Novvi S.A., a now-dormant company, to Cosan. Upon the consummation of the transaction with the shares transferring from Amyris Brasil to Cosan, the Novvi S.A. shareholders agreement automatically terminated.

Novvi LLC

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In September 2011, the Company and Cosan US, Inc. (or Cosan U.S.) formed Novvi LLC, a U.S. entity that is jointly owned by the Company and Cosan U.S. (or Novvi). In March 2013, the Company and Cosan U.S. entered into agreements to (i) expand their base oils joint venture to also include additives and lubricants and (ii) operate their joint venture exclusively through Novvi. Specifically, the parties entered into an Amended and Restated Operating Agreement for Novvi (referred to as the Operating Agreement), which sets forth the governance procedures for Novvi and the joint venture and the parties' initial contribution. The Company also entered into an IP License Agreement with Novvi (referred to as the IP License Agreement) under which the Company granted Novvi (i) an exclusive (subject to certain limited exceptions for the Company), worldwide, royalty-free license to develop, produce and commercialize base oils, additives, and lubricants derived from Biofene for use in automotive and industrial lubricants markets and (ii) a non-exclusive, royalty free license, subject to certain conditions, to manufacture Biofene solely for its own products. In addition, both the Company and Cosan U.S. granted Novvi certain rights of first refusal with respect to alternative base oil and additive technologies that may be acquired by the Company or Cosan U.S. during the term of the IP License Agreement. Under these agreements, the Company and Cosan U.S. will each own 50% of Novvi and each party will share equally in any costs and any profits ultimately realized by the joint venture. Novvi is governed by a six member Board of Managers (or the Board Managers), with three managers represented by each investor. The Board of Managers appoints the officers of Novvi, who are responsible for carrying out the daily operating activities of Novvi as directed by the Board of Managers. The IP License Agreement has an initial term of 20 years from the date of the agreement, subject to standard early termination provisions such as uncured material breach or a party's insolvency. Under the terms of the Operating Agreement, Cosan U.S. is obligated to fund its 50% ownership share of Novvi in cash in the amount of $10.0 million and the Company is obligated to fund its 50% ownership share of Novvi through the granting of an IP License to develop, produce and commercialize base oils, additives, and lubricants derived from Biofene for use in the automotive, commercial and industrial lubricants markets which has been agreed upon by Cosan U.S. and Amyris valued at $10.0 million . In March 2013, the Company measured its initial contribution of intellectual property to Novvi at the Company's carrying value of the licenses granted under the IP License Agreement, which was zero. Additional funding requirements to finance the ongoing operations of Novvi are expected to happen through revolving credit or other loan facilities provided by unrelated parties (i.e. such as financial institutions); cash advances or other credit or loan facilities provided by the Company and Cosan U.S. or their affiliates; or additional capital contributions by the Company and Cosan U.S.

The Company has identified Novvi as a VIE and determined that the power to direct activities, which most significantly impact the economic success of the joint venture (i.e. continuing research and development, marketing, sales, distribution and manufacturing of Novvi products), is equally shared between the Company and Cosan U.S. Accordingly, the Company is not the primary beneficiary and therefore accounts for its investment in Novvi under the equity method of accounting. The Company will continue to reassess its primary beneficiary analysis of Novvi if there are changes in events and circumstances impacting the power to direct activities that most significantly affect Novvi's economic success. Under the equity method, the Company's share of profits and losses are included in “Other income (expense), net” in the consolidated statements of operations. For the year ended December 31, 2013 , the Company recorded no amounts for its share of Novvi's net loss as the carrying amount of the Company's investment in Novvi was zero and losses in excess of the carrying amount were offset by the accretion of the Company's share in the basis difference resulting from the parties' initial contribution. The Company recorded $2.6 million of revenue from the research and development activities that it has performed on behalf of Novvi and recognized $1.1 million in product sales from Novvi for the year ended December 31, 2013 .

Total Amyris BioSolutions B.V.

In November 2013, the Company and Total Energies Nouvelles Activités USA (formerly known as Total Gas & Power USA, SAS, or Total), formed Total Amyris BioSolutions B.V., a private company with limited liability incorporated under the laws of the Netherlands (or JVCO). The common equity of JVCO is jointly owned (50%/50%) by the Company and Total, and the preferred equity of JVCO is 100% owned by the Company. The Parties have agreed that JVCO’s purpose is limited to executing the License Agreement and maintaining such licenses under it, unless and until either (i) Total elects to go forward with either the full (diesel and jet fuel) JVCO commercialization program or the jet fuel component of the JVCO commercialization program (a “Go Decision”), (ii) Total elects to not continue its participation in the R&D Program and JVCO (a “No-Go Decision”), or (iii) Total exercises any of its rights to buy out the Company’s interest in JVCO. Following a Go Decision, the articles and shareholders’ agreement would be amended and restated to be consistent with the shareholders’ agreement contemplated by the July 2012 Agreements (see Note 5, "Debt" and Note 8, "Significant Agreements").

The JVCO has an initial capitalization of €0.1 million (approximately US$0.1 million based on the exchange rate as of December 31, 2013 ). The Company has identified JVCO as a VIE and determined that the Company is not the primary beneficiary and therefore accounts for its investment in JVCO under the equity method of accounting. Under the equity method, the Company's share of profits and losses are included in "Other income (expense), net" in the consolidated statements of operations. No later than six months prior to July 31, 2016, the Company and Total shall amend the July 2012 Agreements to reflect the corporate structure of JVCO, amend and restate the articles of association of JVCO, finalize and agree on a five-year plan and an initial

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budget, maximize economic viability and value of JVCO and enter into the Total license agreement. The Company will reevaluate its assessment in 2016 based on the specific terms of the final shareholders' agreement.

Glycotech

In January 2011, the Company entered into a production service agreement (referred to as the Glycotech Agreement) with Glycotech, Inc. (or Glycotech), under which Glycotech provides process development and production services for the manufacturing of various Company products at its leased facility in Leland, North Carolina. The Company products manufactured by Glycotech are owned and distributed by the Company. Pursuant to the terms of the production Glycotech Agreement, the Company is required to pay the manufacturing and operating costs of the Glycotech facility, which is dedicated solely to the manufacture of Amyris products. The initial term of the Glycotech Agreement was for a two year period commencing on February 1, 2011 and the Glycotech Agreement renews automatically for successive one -year terms, unless terminated by the Company. Concurrent with the Glycotech Agreement, the Company also entered into a Right of First Refusal Agreement with the lessor of the facility and site leased by Glycotech (or the ROFR Agreement). Per conditions of the ROFR Agreement, the lessor agreed not to sell the facility and site leased by Glycotech during the term of the Glycotech Agreement. In the event that the lessor is presented with an offer to sell or decides to sell an adjacent parcel, the Company has the right of first refusal to acquire it.

The Company has determined that the arrangement with Glycotech qualifies as a VIE. The Company determined that it is the primary beneficiary of this arrangement since it has the power through the management committee over which it has majority control to direct the activities that most significantly impact Glycotech's economic performance. In addition, the Company is required to fund 100% of Glycotech's actual operating costs for providing services each month while the facility is in operation under the production service agreement. Accordingly, the Company consolidates the financial results of Glycotech. As of December 31, 2013 , the carrying amounts of the consolidated VIE's assets and liabilities were not material to the Company's consolidated financial statements.

The table below reflects the carrying amount of the assets and liabilities of the two consolidated VIEs for which the Company is the primary beneficiary. As of December 31, 2013 , the assets include $21.6 million in property, plant and equipment, $3.9 million in other assets and $0.3 million in current assets. The liabilities include $0.1 million in accounts payable and accrued current liabilities and $0.1 million in loan obligations by Glycotech to its shareholders that are non-recourse to the Company. The creditors of each consolidated VIE have recourse only to the assets of that VIE.



	December 31,
(In thousands)	2013		2012
Assets	$	25,730	$	29,564
Liabilities	$	229	$	355

The change in noncontrolling interest for the years ended December 31, 2013 and 2012 is summarized below (in thousands):



	2013			2012
Balance at January 1	$	(877	)	$	(240	)
Addition to noncontrolling interest	—			—
Foreign currency translation adjustment	89			257
Loss attributable to noncontrolling interest	204			(894		)
Balance at December 31	$	(584	)	$	(877	)

8. Significant Agreements

Research and Development Activities

Total Collaboration Agreement

In June 2010, the Company entered into a technology license, development, research and collaboration agreement (referred to as the Collaboration Agreement”) with Total Gas & Power USA Biotech, Inc., an affiliate of Total S.A. (Total S.A. and its relevant affiliates, collectively, “Total”). The Collaboration Agreement sets forth the terms for the research, development, production and commercialization of certain to-be-determined chemical and/or fuel products made through the use of the

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Company’s synthetic biology platform. The Collaboration Agreement established a multiphased process through which projects are identified, screened, studied for feasibility, and ultimately selected as a project for development of an identified lead compound using an identified microbial strain. Under the terms of the Collaboration Agreement, Total funded up to the first $50.0 million in research and development costs for the selected projects; thereafter the parties share such costs equally. Amyris has agreed to dedicate the laboratory resources needed for collaboration projects. Total also plans to second employees at Amyris to work on the projects. Once a development project has commenced, the parties are obligated to work together exclusively to develop the lead compound during the project development phase. After a development project is completed, the Company and Total expect to form one or more joint ventures to commercialize any products that are developed, with costs and profits to be shared on an equal basis, provided that if Total has not achieved profits from sales of a joint venture product equal to the amount of funding it provided for development plus an agreed upon rate of return within three years of commencing sales, then Total will be entitled to receive all profits from sales until this rate of return has been achieved. Each party has certain rights to independently produce commercial quantities of these products under certain circumstances, subject to paying royalties to the other party. Total has the right of first negotiation with respect to exclusive commercialization arrangements that the Company would propose to enter into with certain third parties, as well as the right to purchase any of the Company’s products on terms no less favorable than those offered to or received by the Company from third parties in any market where Total or its affiliates have a significant market position.

The Collaboration Agreement has an initial term of twelve years and is renewable by mutual agreement by the parties for additional three year periods. Neither the Company nor Total has the right to terminate the agreement voluntarily. The Company and Total each have the right to terminate the agreement in the event the other party commits a material breach, is the subject of certain bankruptcy proceedings or challenges a patent licensed to it under the Collaboration Agreement. Total also has the right to terminate the Collaboration Agreement in the event the Company undergoes a sale or change of control to certain entities. If the Company terminates the Collaboration Agreement due to a breach, bankruptcy or patent challenge by Total, all licenses the Company has granted to Total terminate except licenses related to products for which Total has made a material investment and licenses related to products with respect to which binding commercialization arrangements have been approved, which will survive subject, in most cases, to the payment of certain royalties by Total to the Company. Similarly, if Total terminates the Collaboration Agreement due to a breach, bankruptcy or patent challenge by the Company, all licenses Total has granted to the Company terminate except licenses related to products for which the Company has made a material investment, certain grant-back licenses and licenses related to products with respect to which binding commercialization arrangements have been approved, which will survive subject, in most cases, to the payment of certain royalties to Total by the Company. On expiration of the Collaboration Agreement, or in the event the Collaboration Agreement is terminated for a reason other than a breach, bankruptcy or patent challenge by one party, licenses applicable to activities outside the collaboration generally continue with respect to intellectual property existing at the time of expiration or termination subject, in most cases, to royalty payments. There are circumstances under which certain of the licenses granted to Total will survive on a perpetual, royalty-free basis after expiration or termination of the Collaboration Agreement. Generally these involve licenses to use the Company’s synthetic biology technology and core metabolic pathway for purposes of either independently developing further improvements to marketed collaboration technologies or products or the processes for producing them within a specified scope agreed to by the Company and Total prior to the time of expiration or termination, or independently developing early stage commercializing products developed from collaboration compounds that met certain performance criteria prior to the time the agreement expired or was terminated and commercializing products related to such compounds. After the Collaboration Agreement expires, the Company may be obligated to provide Total with ongoing access to Amyris laboratory facilities to enable Total to complete research and development activities that commenced prior to termination.

In June 2010, concurrent with the Collaboration Agreement, the Company issued 7,101,548 shares of Series D preferred stock to Total for aggregate proceeds of approximately $133.0 million at a per share price of $18.75 , which was lower than the per share fair value of common stock as determined by management and the Board of Directors. Due to the fact the Collaboration Agreement and the issuance of shares to Total occurred concurrently, the terms of both the Collaboration Agreement and the issuance of preferred stock were evaluated to determine whether their separately stated pricing was equal to the fair value of services and preferred stock. The Company determined that the fair value of Series D preferred stock was $22.68 at the time of issuance, and therefore, the Company measured the preferred stock initially at its fair value with a corresponding reduction in the consideration for the services under the Collaboration Agreement. As revenue from the Collaboration Agreement will be generated over a period of time based on the performance requirements, the Company recorded the difference between the fair value and consideration received for the Series D preferred stock of $27.9 million as a Deferred Charge Asset within "Other Assets" on the balance sheet at the time of issuance which will be recognized as a reduction to revenue in proportion to the total estimated revenue under the collaboration agreement. As of December 31, 2013 and 2012 , the Company has recognized a cumulative reduction of $27.9 million and $27.9 million , respectively, against the deferred charge asset.

As a result of recording the Series D preferred stock at its fair value, the effective conversion price was greater than the fair value of common stock as determined by management and the Board of Directors. Therefore, no beneficial conversion feature

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was recorded at the time of issuance. The Company further determined that the conversion option with a contingent reduction in the conversion price upon a qualified IPO was a potential contingent beneficial feature and, as a result, the Company calculated the intrinsic value of such conversion option upon occurrence of the qualified IPO. The Company determined that a contingent beneficial conversion feature existed and the Company recorded a charge within the equity section of its balance sheet, which impacted earnings per share for the year ended December 31, 2010, based upon the price at which shares were offered to the public in the IPO in relation to the adjustment provisions provided for the Series D preferred stock.

In connection with Total’s equity investment, the Company agreed to appoint a person designated by Total to serve as a member of the Company’s Board of Directors in the class subject to the latest reelection date, and to use reasonable efforts, consistent with the Board of Directors’ fiduciary duties, to cause the director designated by Total to be re-nominated by the Board of Directors in the future. These membership rights terminate upon the earlier of Total holding less than half of the shares of common stock originally issuable upon conversion of the Series D preferred stock or a sale of the Company.

The Company also agreed with Total that, so long as Total holds at least 10% of the Company’s voting securities, the Company will notify Total if the Company’s Board of Directors seeks to cause the sale of the Company or if the Company receives an offer to be acquired. In the event of such decision or offer, the Company must provide Total with all information given to an offering party and certain other information, and Total will have an exclusive negotiating period of fifteen business days in the event the Board of Directors authorizes the Company to solicit offers to buy the Company, or five business days in the event that the Company receives an unsolicited offer to be acquired. This exclusive negotiation period will be followed by an additional restricted negotiation period of ten business days, during which the Company will be obligated to negotiate with Total and will be prohibited from entering into an agreement with any other potential acquirer. Total has also entered into a standstill agreement pursuant to which it agreed for a period of three years not to acquire in excess of the greater of 20% of the number of shares of Series D preferred stock purchased by Total (during the initial two years) or 30% (during the third year) of the Company’s common stock without the prior consent of the Company's Board of Directors, except that, among other things, if another person acquires more than Total’s then current holdings of the Company’s common stock, then Total may acquire up to that amount plus one share.

In November 2011, the Company and Total entered into an amendment of their Technology License, Development, Research and Collaboration Agreement (referred to as the Amendment). The Amendment provided for an exclusive strategic collaboration for the development of renewable diesel products and contemplated that the parties would establish a joint venture (or the JV) for the production and commercialization of such renewable diesel products on an exclusive, worldwide basis. In addition, the Amendment contemplated providing the JV with the right to produce and commercialize certain other chemical products on a non-exclusive basis. The amendment further provided that definitive agreements to form the JV had to be in place by March 31, 2012 or such other date as agreed to by the parties or the renewable diesel program, including any further collaboration payments by Total related to the renewable diesel program, would terminate. In the second quarter of 2012, the parties extended the deadline to June 30, 2012, and, through June 30, 2012 the parties were engaged in discussions regarding the structure of future payments related to the program, until the amendment was superseded by a further amendment in July 2012.

Pursuant to the Amendment, Total agreed to fund the following amounts: (i) the first $30.0 million in research and development costs related to the renewable diesel program which have been incurred since August 1, 2011, which amount would be in addition to the $50.0 million in research and development funding contemplated by the Collaboration Agreement, and (ii) for any research and development costs incurred following the JV formation date that were not covered by the initial $30.0 million , an additional $10.0 million in 2012 and up to an additional $10.0 million in 2013, which amounts would be considered part of the $50.0 million contemplated by the Collaboration Agreement. In addition to these payments, Total further agreed to fund 50% of all remaining research and development costs for the renewable diesel program under the Amendment.

In July 2012 , the Company entered into the July 2012 Agreements with Total that expanded Total's investment in the biofene collaboration to encompass certain joint venture products for use in diesel and jet fuel on a worldwide basis and provide a new structure for the research and development program and formation of the joint venture (or the Fuels JV), to commercialize the products encompassed by the diesel and jet fuel research and development program (the “Program”) and change the structure of the funding from Total to include a convertible debt mechanism (see Note 5, "Debt"). As a part of the July 2012 Agreements, Total's royalty option contingency related to diesel was removed and the jet fuel collaboration was combined with the expanded biofene collaboration. As a result, $46.5 million of payments received from Total that had been recorded as an advance from the collaborator were no longer contingently repayable. Of this amount, $23.3 million was treated as a repayment by the Company and included as part of the senior unsecured convertible promissory note issued to Total in July 2012 and the remaining $23.2 million was recorded as a contract to perform research and development services, which was offset by the reduction of the capitalized deferred charge asset of $14.4 million resulting in the Company recording revenue from a related party of $8.9 million in 2012.

Under the July 2012 Agreements, the Company controls operations and execution of the Program subject to strategic and ultimate decision-making authority by a management committee composed of Company and Total representatives, and Total

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participates in the ultimate Fuels JV, or receives rights to recover its investment if, at a series of decision points, it decides not to proceed with the project. The agreements contemplate that the parties would grant exclusive manufacturing and commercial licenses to the Fuels JV for the Fuels JV products when the Fuels JV is formed (subject to requirements for the Company to grant the license to Total in the event the Fuels JV is not formed because of a deadlock, followed by an election by the Company to sell to Total the assets it otherwise would have contributed to the Fuels JV, or earlier under certain circumstances), and that the Company would retain the right to make and sell products other than the Fuels JV products. Under the agreements, the Fuels JV licenses would be consistent with the principle that development, production and commercialization of the Fuels JV products in Brazil will remain with the Company unless Total elects, after formation of the Fuels JV, to have such business contributed to the Fuels JV. The agreements also provide that certain Fuels JV non-exclusive products that were contemplated by the November 2011 amendment to the collaboration agreement are no longer to be included in the Fuels JV, but that the parties will explore potential development and commercialization of such products at a later date.

The agreements contemplate that the research and development efforts under the Program may extend through 2016, with a series of “Go/No Go” decisions by Total through such date tied to funding by Total. Each funding tranche involves the issuance of senior unsecured convertible promissory notes by the Company to Total (see Note 5, "Debt"). The agreements provided for cash funding by Total of $15.0 million in July 2012 and an additional $15.0 million in September 2012 . Such funding occurred in July and September as contemplated by the agreements. Further, Total funded $30.0 million in July 2013 , and, if it chooses to proceed with the Program, will fund an additional $10.85 million in July 2014 and $10.85 million in January 2015 (referred to as the Third Closing). Thirty days following the earlier of the completion of the research and development program or December 31, 2016, Total has a final opportunity to decide whether or not to proceed with the Program.

At either of the decision points tied to the funding described above (in July 2013 or July 2014), if Total decides not to continue to fund the Program (or, at any funding date does not provide funding based on (i) the Company's failure to satisfy a closing condition under the purchase agreement for the notes, or (ii) Total's breach of the purchase agreement), the notes previously issued under the purchase agreement would remain outstanding and become payable by the Company at the maturity date in March 2017, the Program and associated agreements would terminate, all Company rights granted for use in farnesene-based diesel and farnesene-based jet fuel would revert to the Company, and no Fuels JV would be formed to commercialize the Fuels JV products.

In the final “Go/No Go” decision described above, Total may elect to (i) go forward with the full Program (diesel and jet fuel) (a “Go” decision), (ii) not continue its participation in the full Program, or (iii) go forward only with the jet fuel component of the Program, with the following outcomes:


•	For a “Go” decision by Total with respect to the whole Program, the parties would form the Fuels JV and the notes would be cancelled.


•	For a “No-Go” decision by Total with respect to the whole Program, the consequences would be as described in the paragraph above regarding a decision by Total not to continue to fund the Program.

•

For a decision by Total to proceed with the jet fuel component of the Program and not the diesel component of the Program, 70% of the principal amount outstanding under the notes would remain outstanding and become payable by the Company and 30% of the outstanding principal of such notes would be cancelled, the diesel product would no longer be included in the collaboration, the Fuels JV would not receive rights to products for use in diesel fuels, and the Fuels JV would be formed by the parties to commercialize products for use in jet fuels.

The agreements contemplate that the parties will finalize the structure for the Fuels JV as set forth in the agreements and that the Fuels JV, if and when it is formed, would, subject to the conditions described below and absent other agreement, be owned equally ( 50% / 50% ) by the Company and Total. Under the agreements, the parties will, prior to the projected completion date, enter into a shareholders' agreement governing the Fuels JV, agree on the budget and business plan for the Fuels JV, and form the Fuels JV. In addition, following a final “Go” decision, the parties would enter into the Fuels JV license agreements, contribution agreements and other agreements required to establish the Fuels JV and enable it to operate.

Within thirty days prior to the final “Go” decision, Total may declare a “deadlock” if the parties fail to come to agreement on various matters relating to the formation of the Fuels JV, at which point Total may (i) elect to declare a “No-Go” decision, which has the consequences described above, or (ii) initiate a process whereby the fair value of the proposed Fuels JV would be determined and the Company would then have the option to: (i) elect to sell to Total the assets that the Company would have been required to contribute to the Fuels JV for an amount equal to 50% of such fair value; (ii) proceed with the formation of the Fuels JV (accepting Total's position with respect to the funding requirement of the Fuels JV) and becoming a 50% owner of the Fuels JV; or (iii) proceed with the formation of the Fuels JV (accepting Total's position with respect to the funding requirements of the

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Fuels JV), and then sell all or a portion of its 50% interest in the Fuels JV to Total for a price equal to the fair value multiplied by the percentage ownership of the Fuels JV sold to Total.

The agreements provide that the Company would initially retain its ability to develop its diesel and jet fuel business in Brazil, and that Total has an option to require the Company to contribute its Brazil diesel and jet fuel business to the Fuels JV at a price determined pursuant to the agreements. Such option terminates if the Fuels JV is not formed or if Total subsequently buys out the Company's Fuels JV contribution. Furthermore, the option is limited to the jet fuel business if Total opts out of the diesel component of the Program as described above.

Under the agreements, Total has a right to participate in future equity or convertible debt financings of the Company through December 31, 2013 to preserve its pro rata ownership of the Company and thereafter in limited circumstances. The purchase price for the first $30.0 million of purchases under this pro rata right would be paid by cancellation of outstanding notes held by Total.

In connection with the purchase agreement and sale of the Notes, the Company entered into a registration rights agreement. Under such agreement, the Company is obligated to file a registration statement on Form S-3 with the SEC registering the resale of all of the shares of the Company's common stock issuable upon conversion of the notes within twenty days prior to the maturity date of the notes or within 30 days following optional conversion. In addition, the Company is obligated to have the registration statement declared effective within 70 - 100 days following the filing depending on whether the Company receives comments from the SEC. If the registration statement filing is delayed or the registration statement is not declared effective within the foregoing time frames, the Company is required to make certain monthly payments to the Total.

As a result, $46.5 million of payments received from Total that had been recorded as an advance from the collaborator were no longer contingently repayable. Of this amount, $23.3 million was treated as a repayment by the Company and included as part of the senior unsecured convertible promissory note issued to Total in July 2012 and the remaining $23.2 million was recorded as a contract to perform research and development services, which was offset by the reduction of the capitalized deferred charge asset of $14.4 million resulting in the Company recording revenue from a related party of $8.9 million .

In December 2012, Total elected to participate in a private placement of the Company's common stock by exchanging approximately $5.0 million of its $53.3 million in senior unsecured convertible promissory notes into 1,677,852 shares of the Company's common stock at $2.98 per share. As such, $5.0 million of the outstanding $53.3 million in senior unsecured convertible debt was cancelled.

In March 2013, the Company entered into the March 2013 Letter Agreement under which Total agreed to waive its right and to cease its participation in the fuels collaboration at the July 2013 decision point and committed to proceed with the July 2013 funding tranche of $30.0 million (subject to the Company's satisfaction of the relevant closing conditions for such funding in the Total Purchase Agreement). As consideration for this waiver and commitment, the Company agreed to:

•


•	Grant Total a senior security interest in the Company's intellectual property, subject to certain exclusions and subject to release by Total when the Company and Total enter into final documentation regarding the establishment of the Fuels JV.

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In July 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $20.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above (see Note 5, "Debt"). This purchase and sale completed Total's commitment to purchase $30.0 million of such notes by July 2013. In accordance with the March 2013 Letter Agreement, this convertible note has an initial conversion price equal to $3.08 per share of Company common stock.

In connection with the August 2013 Financing, the Company entered into the August 2013 SPA (see Note 1, "The Company" and Note 5, "Debt") with Total and Temasek to sell up to $73.0 million in convertible promissory notes in private placements, with such notes to be sold and issued over a period of up to 24 months from the date of signing. The August 2013 SPA provided for the August 2013 Financing to be divided into two tranches (the first tranche for $42.6 million and the second tranche for $30.4 million ), each with differing closing conditions. Of the total possible purchase price in the financing, $60.0 million to be paid in the form of cash by Temasek ( $35.0 million in the first tranche and up to $25.0 million in the second tranche) and $13.0 million to be paid by the exchange and cancellation of outstanding convertible promissory notes held by Total in connection with its exercise of pro rata rights ( $7.6 million in the first tranche and $5.4 million in the second tranche). The August 2013 SPA included requirements that the Company meet certain production milestones before the second tranche would become available, obtain stockholder approval prior to completing any closing of the transaction, and issue a warrant to Temasek to purchase 1,000,000 shares of the Company's common stock at an exercise price of $0.01 per share, exercisable only if Total converts preexisting promissory notes with a certain per share conversion price. In September 2013, the Company's stockholders approved the August 2013 Financing.

In October 2013, the Company amended the August 2013 SPA (referred to as the Amendment No. 1 to SPA) (see Note 1, "The Company") to include Fidelity Entities in the Tranche I Notes in the principal amount of $7.6 million , and to proportionally increase the amount acquired by exchange and cancellation of outstanding convertible notes held by Total through pro rata rights to $14.6 million ( $9.2 million in the Tranche I and up to $5.4 million in the Tranche II). Also in October 2013, the Company completed the closing of the first tranche of the August 2013 Financing, issuing a total of $51.8 million in convertible promissory notes (the “Tranche I Notes”) for cash proceeds of $7.6 million and cancellation of outstanding convertible promissory notes of $44.2 million , of which $35.0 million resulted from cancellation of the Temasek Bridge Note (see Note 5, "Debt"). The Tranche I Notes are due sixty months from the date of issuance and will be convertible into the Company’s common stock at a conversion price equal to $2.44 , subject to adjustment as described below. The Tranche I Notes are convertible at the option of the holder: (i) at any time after 18 months from the date of the August 2013 SPA, (ii) on a change of control of the Company and (iii) upon the occurrence of an event of default. The conversion price of the Tranche I Notes will be reduced to $2.15 if a specified Company manufacturing plant fails to achieve a total production of 1.0 million liters within a run period of 45 days prior to June 30, 2014, the Company fails to achieve gross margins from product sales of at least 5% prior to June 30, 2014, or the Company reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes. If either of the production and margin milestones occur, and in addition, the Company reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes, the conversion price of the Tranche I Notes will be reduced to $1.87 . Each Tranche I Note accrues interest from the date of issuance until the earlier of the date that such Tranche I Note is converted into the Company’s common stock or is repaid in full. Interest accrues at a rate of 5% per six months, compounded semiannually (with graduated interest rates of 6.5% applicable to the first 180 days and 8% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or at 6.5% for all other defaults). Interest for the first 30 months is payable in kind and added to the principal every six-months and thereafter, the Company may continue to pay interest in kind by adding to the principal every six-months or may elect to pay interest in cash. The Tranche I Notes may be prepaid by the Company after 30 months from the issuance date and initial interest payment; thereafter the Company has the option to prepay the Tranche I Notes every six months at the date of payment of the semi-annual coupon.

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In December 2013, the Company executed the JV Documents among Amyris, Total and JVCO relating to the establishment of the JVCO (see Note 7, "Joint Venture and Noncontrolling Interest"), Amyris has agreed to (i) exchange the $69.0 million outstanding Total 1.5% Senior Unsecured Convertible Note and issue a replacement 1.5% senior secured convertible notes, in principal amounts equal to the principal amount of each cancelled note (the “Replacement Notes”) and (ii) to grant to Total a security interest in and lien on all Amyris’ rights, title and interest in and to Amyris’ shares in the capital of the JVCO. Any Securities to be purchased and sold at the Third Closing by Total shall be 1.5% senior secured convertible notes shall have a conversion price of $7.0682 . As a consequence of executing the JV Documents and forming JVCO, the Second Amendment of the August 2013 SPA and Restated Intellectual Property Security Agreement dated as of October 16, 2013, executed by Amyris in favor of Total, Temasek, and certain entities affiliated with Fidelity Investments, under which the Company granted a security interest in all of Amyris’ intellectual property was automatically terminated effective as of December 2, 2013 upon Total’s and the Company’s joint written notice to Temasek. Also, in December 2013, Amyris and Total executed the Amended and Restated Master Framework Agreement which amends and restates the Master Framework Agreement dated July 30, 2012 and amended on March 24, 2013.

In December 2013, the Company, Total, Temasek, Fidelity Entities and Wolverine amended the August 2013 SPA and Amendment No. 1 to SPA (referred to as Amendment No. 2 to SPA). Under the Amendment No. 2 to the SPA the Company placed a $3.0 million of senior unsecured convertible notes under the second tranche of August 2013 Financing to funds affiliated with Wolverine Asset Management and elected to call $25.0 million in additional funds from Temasek pursuant to its previous commitment to purchase such amount of convertible promissory notes in the second tranche. Additionally, the Company agreed to sell approximately $6.0 million of convertible promissory notes in the second tranche to Total through cancellation of the same amount of principal of previously outstanding convertible notes held by Total (in respect of Total’s preexisting contractual right to maintain its pro rata ownership position through such cancellation. The second tranche funding closed in the first quarter of 2014.

Collaboration Partner Joint Development and License Agreement

In April 2013, the Company entered into a joint development and license agreement with a collaboration partner. Under the terms of the multi-year agreement, the collaboration partner and the Company will jointly develop certain fragrance ingredients. The collaboration partner will have exclusive rights to these fragrance ingredients for applications in the flavors and fragrances field, and the Company will have exclusive rights in other fields. The collaboration partner and the Company will share in the economic value derived from these ingredients. The joint development and license agreement provided for up to $6.0 million in funding based upon the achievement of certain technical milestones which are considered substantive by the Company during the first phase of the collaboration. For the year ended December 31, 2013 , the Company recorded $6.0 million of revenue from the

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joint development and license agreement with the collaboration partner. As of December 31, 2013 , $1.5 million was recorded in deferred revenue.

Collaboration Partner Master Collaboration and Joint Development Agreement

In November 2010, the Company entered into a Master Collaboration and Joint Development Agreement with a collaboration partner. Under the agreements, the collaboration partner will fund technical development at the Company to produce an ingredient for the flavors and fragrances (or F&F) market. The Company will manufacture the ingredient and the collaboration partner will market it, and the parties will share in any resulting economic value. The agreement also grants exclusive worldwide F&F commercialization rights to the collaboration partner for the ingredient. Under further agreements, the collaboration partner has an option to collaborate with the Company to develop additional ingredients. These agreements continue in effect until the later of the expiration or termination of the development agreements or the supply agreements. The Company is also eligible to receive potential total payments of $6.0 million upon the achievement of certain performance milestones towards which the Company will be required to make a contributory performance. These milestones are accounted for under the guidance in the FASB accounting standard update related to revenue recognition under the milestone method. The Company concluded that these milestone payments are substantive.

In March 2013, the Company entered into a Master Collaboration Agreement with the collaboration partner to establish a collaboration for the development and commercialization of multiple renewable F&F compounds. Under this agreement, except for rights granted under preexisting collaboration relationships, the Company granted the collaboration partner exclusive access for such compounds to specified Company intellectual property for the development and commercialization of F&F products in exchange for research and development funding and a profit sharing arrangement. The agreement superseded and expand the prior collaboration agreement between the Company and collaboration partner.

The agreement provides annual, up-front funding to the Company by the collaboration partner of $10.0 million for each of the first three years of the collaboration. The initial payment of $10.0 million was received by the Company on March 2013. The agreement contemplates additional funding by the collaboration partner of up to $5.0 million under three potential milestone payments, as well as additional funding by the collaboration partner on a discretionary basis.

In addition, the agreement contemplates that the parties will mutually agree on a supply price for each compound and share product margins from sales of each compound on a 70/30 basis ( 70% for the collaboration partner) until the collaboration partner receives $15.0 million more than the Company in the aggregate, after which the parties will share 50/50 in the product margins on all compounds. The Company also agreed to pay a one-time success bonus of up to $2.5 million to the collaboration partner's for outperforming certain commercialization targets. The collaboration partner eligibility to receive the one -time success bonus commences upon the first sale of the collaboration partner's product.

The agreement does not impose any specific research and development commitments on either party after year six, but if the parties mutually agree to perform development after year six, the agreement provides that the parties will fund it equally.

Under the agreement, the parties jointly select target compounds, subject to final approval of compound specifications by the collaboration partner. During the development phase, the Company is required to provide labor, intellectual property and technology infrastructure and the collaboration partner is required to contribute downstream polishing expertise and market access. The agreement provides that the Company will own research and development and strain engineering intellectual property, and the collaboration partner will own blending and, if applicable, chemical conversion intellectual property. Under certain circumstances such as the Company's insolvency, the collaboration partner gains expanded access to the Company's intellectual property. Following development of F&F compounds under the agreement, the agreement contemplates that Company will manufacture the initial target molecules for the compounds and the collaboration partner will perform any required downstream polishing and distribution, sales and marketing.

For the years ended December 31, 2013, 2012 and 2011 the Company recorded $8.2 million , $4.8 million and $5.2 million , respectively, of revenue from the collaboration agreement with the collaboration partner.

Michelin Collaboration Agreement

In September 2011, the Company entered into a collaboration agreement with Manufacture Francaise des Pneumatiques Michelin (“Michelin”). Under the terms of the collaboration agreement, the Company and Michelin will collaborate on the development, production and worldwide commercialization of isoprene or isoprenol, generally for tire applications, using the Company's technology. Under the agreement, Michelin has agreed to pay an upfront payment to the Company of $5.0 million , subject to a reimbursement provision under which the Company would have to repay $1.0 million if it fails to achieve specified

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future technical milestones. The agreement provides that, subject to achievement of technical milestones, Michelin can notify the Company of its desired date for initial delivery, and the parties will either collaborate to establish a production facility or use an existing Company facility for production. The agreement also includes a term sheet for a supply agreement that would be negotiated at the time the decision regarding production facilities is made. The agreement has an initial term that will expire upon the earlier of 42 months from the effective date and the completion of a development work plan. As of December 31, 2013 , the Company recorded the upfront payment of $5.0 million from Michelin as deferred revenue.

Manufacturing Agreements

The Company entered into contract manufacturing agreements with various contract manufacturing partners to utilize their manufacturing facilities to produce Amyris products.

In March 2012, the Company initiated a plan to shift a portion of its production capacity from contract manufacturing facilities to a Company-owned plant that was then under construction. As a result, the Company evaluated its contract manufacturing agreements and recorded a loss of $31.2 million related to the write-off of $10.0 million in facility modification costs and the recognition of $21.2 million of fixed purchase commitments in the three months ended March 31, 2012. The Company recognized an additional charge of $1.4 million and $7.8 million , respectively, in the third and fourth quarters of 2012 associated with loss on fixed purchase commitments. The Company computed the loss on facility modification costs and fixed purchase commitments using the same lower of cost or market approach that is used to value inventory. The computation of the loss on fixed purchase commitments is subject to several estimates, including cost to complete and the ultimate selling price of any Company products manufactured at the relevant production facilities, and is therefore inherently uncertain. The Company also recorded a loss on write-off of production assets of $5.5 million related to Amyris-owned production equipment at contract manufacturing facilities in the quarter ended March 31, 2012.

Total loss on purchase commitments and write-off of production assets for the year ended December 31, 2013 was $9.4 million . The Company will continue to evaluate the potential for losses in future periods based on updated production and sales price assumptions.

Tate & Lyle

In November 2010, the Company entered into a Contract Manufacturing Agreement (referred to as the Contract Manufacturing Agreement) with Tate & Lyle Ingredients Americas, Inc. (or Tate & Lyle), an affiliate of Tate & Lyle PLC. Tate & Lyle commenced production operations in the fourth quarter of 2011. At December 31, 2013 and 2012 , the Company has recorded zero and $0.8 million , respectively, in prepaid and other current assets and zero and $2.2 million , respectively, in other noncurrent assets pertaining to the unamortized portion of equipment costs funded by the Company to Tate & Lyle (see Note 4, "Balance Sheet Components"). The related amortization is being offset against purchases of inventory from this contract manufacturer.

The Contract Manufacturing Agreement had secured manufacturing capacity for farnesene through 2016 at Tate & Lyle’s facility in Decatur, Illinois. The Contract Manufacturing Agreement included a base monthly payment and a variable payment based on production volume at the Tate & Lyle facility. With the Company’s commencement of production at its farnesene facility located in Brazil, the Company determined that the Contract Manufacturing Agreement was no longer desired from a cost and operational perspective. The Company had no production at the Tate & Lyle facility since the first quarter of 2013.

In June 2013, the Company and Tate & Lyle entered into a Termination Agreement to terminate the parties’ November 2010 Contract Manufacturing Agreement. The Termination Agreement resolves all outstanding issues that had arisen in connection with the Company’s relationship with Tate & Lyle.

Pursuant to the Termination Agreement, the Company is required to make four payments to Tate & Lyle, totaling approximately $8.8 million , of which $3.6 million is to satisfy outstanding obligations and $5.2 million is in lieu of additional payments otherwise owed under the Contract Manufacturing Agreement. These four payments are due under the Termination Agreement between July 17, 2013 and December 16, 2013, and are deemed to be in full satisfaction of all amounts otherwise owed under the Contract Manufacturing Agreement. Under the Termination Agreement, no further payments will be owed for the remaining term of the Contract Manufacturing Agreement (i.e., through 2016). As a result, the Company recorded a loss of $8.4 million which is included in the loss on purchase commitments and write-off of production assets and consisted of an impairment charge of $6.7 million relating to Company-owned equipment at the Tate & Lyle facility, a $2.7 million write off of an unamortized portion of equipment costs funded by the Company for Tate & Lyle, offset by a reversal of $1.0 million provision for loss on fixed purchase commitments. As of December 31, 2013 , the Company had no outstanding liability under the Termination Agreement.

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Paraíso Bioenergia

In March 2011, the Company entered into a supply agreement with Paraíso Bioenergia, a renewable energy company producing sugar, ethanol and electricity headquartered in São Paulo State, Brazil. Under the agreement, the Company constructed a fermentation and separation capacity to produce its products and Paraíso Bioenergia provides supply of sugar cane juice and other utilities. The Company retains the full economic benefits enabled by the sale of Amyris renewable products over the lower of sugar or ethanol alternatives. In conjunction with the supply agreement, the Company also entered into an operating lease on a land owned by Paraíso Bioenergia. The real property is being used by the Company for its production site in Brotas, Brazil.

Per the terms of the supply agreement, in the event that Paraíso is presented with an offer to sell or decides to sell the real property, the Company has the right of first refusal to acquire it. If the Company fails to exercise its right of first refusal the purchaser of the real property will need to comply with the specific obligations of Paraíso Bioenergia to the Company under the lease agreement.

Albemarle

In July 2011, the Company entered into a contract manufacturing agreement with Albemarle Corporation (or Albemarle), which will provide toll manufacturing services at its facility in Orangeburg, South Carolina. Under this agreement, Albemarle will manufacture lubricant base oils from Biofene, which will be owned and distributed by the Company or a Company-designated commercial partner. The initial term of this agreement is from July 31, 2011 through December 31, 2012. Albemarle is required to modify its facility, including installation and qualification of equipment and instruments necessary to perform the toll manufacturing services under the agreement. The Company reimbursed Albemarle $10.0 million for all capital expenditures related to the facility modification, which was accounted for as a prepaid asset. All equipment or facility modifications acquired or made by Albemarle will be owned by Albemarle, subject to Albemarle's obligation to transfer title to, and ownership of, certain assets to the Company within 30 days after termination of the agreement, at the Company's discretion and sole expense. In March 2012, the Company recorded a loss of $7.8 million related to the write-off of the facility modification costs, described above.

In addition, the Company paid a one-time, non-refundable performance bonus of $5.0 million if Albemarle delivers to the Company certain quantity of the lubricant base stock by December 31, 2011 or $2.0 million if Albemarle delivers the same quantity by January 31, 2012. Based on Albermarle's performance as of December 31, 2011, the Company concluded that Albermarle had earned the bonus which is payable in two payments. The Company paid Albemarle $2.5 million during the year ended December 31, 2012 and $2.5 million during the year ended December 31, 2013 .

In February 2012, the Company entered into an amended and restated agreement with Albemarle, which superseded the original contract manufacturing agreement with Albemarle. The term of the new agreement continues through December 31, 2019. The agreement includes certain obligations for the Company to pay fixed costs totaling $7.5 million , of which $3.5 million and $4.0 million are payable in 2012 and 2014, respectively. In the three months ended March 31, 2012, the Company recorded a corresponding loss related to these fixed purchase commitments, as described above. As of December 31, 2013 , the Company have a $4.0 million outstanding liability payable to Albermarle.

9. Goodwill and Intangible Assets

The following table presents the components of the Company's intangible assets (in thousands):



		December 31, 2013							December 31, 2012
	Useful Life in Years	Gross Carrying Amount		Accumulated Amortization			Net Carrying Value		Gross Carrying Amount		Accumulated Amortization			Net Carrying Value
In-process research and development	Indefinite	$	8,560	$	—		$	8,560	$	8,560	$	—		$	8,560
Acquired licenses and permits	2	772		(772		)	—		772		(740		)	32
Goodwill	Indefinite	560		—			560		560		—			560
		$	9,892	$	(772	)	$	9,120	$	9,892	$	(740	)	$	9,152

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The following table presents the activity of intangible assets for the year ended December 31, 2013 (in thousands):



	December 31, 2012									December 31, 2013
	Net Carrying Value		Additions		Adjustments		Amortization			Net Carrying Value
In-process research and development	$	8,560	$	—	$	—	$	—		$	8,560
Acquired licenses and permits	32		—		—		(32		)	—
Goodwill	560		—		—		—			560
	$	9,152	$	—	$	—	$	(32	)	$	9,120

The intangible assets acquired through the Draths Corporation acquisition in October 2011 of in-process research and development of $8.6 million and goodwill of $0.6 million are treated as indefinite lived intangible assets until completion or abandonment of the projects, at which time the assets will be amortized over the remaining useful life or written-off, as appropriate. If the carrying amount of the assets is greater than the measures of fair value, impairment is considered to have occurred and a write-down of the asset is recorded. Any finding that the value of its intangible assets has been impaired would require the Company to write-down the impaired portion, which could reduce the value of its assets and reduce (increase) its net income (loss) for the year in which the related impairment charges occur. As of December 31, 2013 and 2012, no impairment of the goodwill and intangible assets was recorded.

Acquired licenses and permits are amortized using a straight-line method over its estimated useful life. Amortization expense for this intangible was $32,170 , $0.4 million and $0.4 million for the year ended December 31, 2013, 2012 and 2011 , respectively. As of December 31, 2013 , acquired licenses and permits were fully amortized.

10. Stockholders’ Equity

Private Placement

February 2012 Private Placement

In February 2012, the Company completed a private placement of 10,160,325 shares of its common stock at a price of $5.78 per share for aggregate proceeds of $58.7 million . In connection with this private placement, the Company entered into an agreement with an investor to purchase additional shares of the Company's Common Stock for an additional $15.0 million by March 2013 upon satisfaction by the Company of criteria associated with the commissioning of the Company's production plant in Brotas, Brazil. This additional investment provided by the investor through a $10.0 million investment in a private placement completed by the Company in December 2012 and subsequently, through a $5.0 million investment in a private placement completed by the Company in March 2013.

May 2012 Private Placement

In May 2012, the Company completed a private placement of 1,736,100 shares of it's common stock at a price of $2.36 per share for aggregate proceeds of $4.1 million .

December 2012 Private Placement

In December 2012, the Company completed a private placement of 14,177,849 shares of its common stock at a price of $2.98 per share for aggregate proceeds of $37.2 million and the cancellation of $5.0 million worth of outstanding senior unsecured convertible promissory notes previously issued to Total by the Company. The Company issued 1,677,852 shares to Total in exchange for this note cancellation. Net cash received for this private placement as of December 31, 2012 was $22.2 million and the remaining $15.0 million of proceeds was received in January 2013. In connection with this, the Company entered into a letter of agreement with an investor under which the Company acknowledged that the investor's initial investment of $10.0 million in December 2012 represented partial satisfaction of the investor's preexisting contractual obligation to fund $15.0 million by March 31, 2013 upon satisfaction by the Company of criteria associated with the commissioning of the Company's production plant in Brotas, Brazil.

In January 2013, the Company received $15.0 million in proceeds from the private placement offering that closed in December 2012. Consequently, the Company issued 5,033,557 shares of the 14,177,849 shares of the Company's common stock .

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March 2013 Private Placement

In March 2013, the Company completed a private placement of 1,533,742 shares of its common stock at a price of $3.26 per share for aggregate proceeds of $5.0 million . This private placement represented the final tranche of an investor’s preexisting contractual obligation to fund $15.0 million upon satisfaction by the Company of certain criteria associated with the commissioning of a production plant in Brotas, Brazil.

Evergreen Shares for 2010 Equity Plan and 2010 ESPP

In January 2013, the Company's Board of Directors (or Board) approved an increase to the number of shares available for issuance under the Company's 2010 Equity Incentive Plan (or Equity Plan) and the 2010 Employee Stock Purchase Plan (or ESPP). These shares represent an automatic annual increase in the number of shares available for issuance under the Equity Plan and the ESPP of 3,435,483 and 687,096 , respectively, equal to 5% and 1% , respectively of 68,709,660 shares, the total outstanding shares of the Company’s common stock as of December 31, 2012. This automatic increase was effective as of January 1, 2013. Shares available for issuance under the Equity Plan and ESPP were initially registered on a registration statement on Form S-8 filed with the Securities and Exchange Commission on October 1, 2010 (Registration No. 333-169715). The Company filed registration statements on Form S-8 on March 28, 2013 and May 20, 2013 with respect to the shares added by the automatic increase on January 1, 2013.

Common Stock

As of December 31, 2012, the Company was authorized to issue 100,000,000 shares of common stock pursuant to the Company’s amended and restated certificate of incorporation. On May 9, 2013, the Company amended and restated its certificate of incorporation and increased its authorized number of shares of common stock to 200,000,000 . Holders of the Company’s common stock are entitled to dividends as and when declared by the Board of Directors, subject to the rights of holders of all classes of stock outstanding having priority rights as to dividends. There have been no dividends declared to date. The holder of each share of common stock is entitled to one vote.

Preferred Stock

Pursuant to the Company’s amended and restated certificate of incorporation, the Company is authorized to issue 5,000,000 shares of preferred stock. The Board of Directors has the authority, without action by its stockholders, to designate and issue shares of preferred stock in one or more series and to fix the rights, preferences, privileges and restrictions thereof. Prior to the closing of the Company’s IPO, the Company had four series of convertible preferred stock outstanding, including Series D preferred stock issued to Total (see Note 8, "Significant Agreements"). As of December 31, 2013 and December 31, 2012 , the Company had zero convertible preferred stock outstanding.

Common Stock Warrants

In December 2011, in connection with a capital lease agreement, the Company issued warrants to purchase 21,087 shares of the Company's common stock at an exercise price of $10.67 per share. The Company estimated the fair value of these warrants as of the issuance date to be $0.2 million and recorded these warrants as other assets and were amortized subsequently over the term of the lease. The fair value was based on the contractual term of the warrants of 10 years, risk free interest rate of 2% , expected volatility of 86% and zero expected dividend yield. These warrants remain unexercised and outstanding as of December 31, 2013 .

In October 2013, in connection with the issuance of the Temasek Tranche I convertible promissory notes (see Note 5, "Debt"), the Company issued contingently exercisable warrants to purchase 1,000,000 shares of the Company's common stock at an exercise price of $0.01 per share. The Company estimated the fair value of these warrants as of the issuance date at $1.3 million and recorded these warrants as debt issuance cost to be amortized over the term of the note. The fair-value was calculated using a Monte Carlo simulation valuation model based on the contractual term of the warrants of 3.4 years, risk free interest rate of 0.77% , expected volatility of 45% and zero expected dividend yield. These warrants remain unexercised and outstanding as of December 31, 2013 .

Each of these warrants includes a cashless exercise provision which permits the holder of the warrant to elect to exercise the warrant without paying the cash exercise price, and receive a number of shares determined by multiplying (i) the number of shares for which the warrant is being exercised by (ii) the difference between the fair market value of the stock on the date of exercise and the warrant exercise price, and dividing such by (iii) the fair market value of the stock on the date of exercise. During the years ended December 31, 2013 and 2012 , no warrants were exercised through the cashless exercise provision.

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As of December 31, 2013 and 2012 , the Company had 1,021,087 and 21,087 of unexercised common stock warrants, respectively.

11. Stock-Based Compensation Plans

2010 Equity Incentive Plan

The Company's 2010 Equity Incentive Plan (or 2010 Equity Plan) became effective on September 28, 2010 and will terminate in 2020. Pursuant to the 2010 Equity Plan, any shares of the Company’s common stock (i) issued upon exercise of stock options granted under the Company's 2005 Stock Option/Stock Issuance Plan (or the 2005 Plan) that cease to be subject to such option and (ii) issued under the 2005 Plan that are forfeited or repurchased by the Company at the original purchase price will become part of the 2010 Equity Plan. Subsequent to the effective date of the 2010 Equity Plan, an additional 1,730,807 shares that were forfeited under the 2005 Plan were added to the shares reserved for issuance under the 2010 Equity Plan.

The number of shares reserved for issuance under the 2010 Equity Plan increase automatically on January 1 ^st of each year starting with January 1, 2011, by a number of shares equal to 5% percent of the Company’s total outstanding shares as of the immediately preceding December 31 ^st . The Company’s Board of Directors or the Leadership Development and Compensation Committee of the Board of Directors is able to reduce the amount of the increase in any particular year. The 2010 Equity Plan provides for the granting of common stock options, restricted stock awards, stock bonuses, stock appreciation rights, restricted stock units and performance awards. It allows for time-based or performance-based vesting for the awards. Options granted under the 2010 Equity Plan may be either incentive stock options (or ISOs) or non-statutory stock options (or NSOs). ISOs may be granted only to Company employees (including officers and directors who are also employees). NSOs may be granted to Company employees, non-employee directors and consultants. The Company will be able to issue no more than 30,000,000 shares pursuant to the grant of ISOs under the 2010 Equity Plan. Options under the 2010 Equity Plan may be granted for periods of up to ten years. All options issued to date have had a ten year life. Under the plan, the exercise price of any ISOs and NSOs may not be less than 100% of the fair market value of the shares on the date of grant. The exercise price of any ISOs and NSOs granted to a 10% stockholder may not be less than 110% of the fair value of the underlying stock on the date of grant. The options granted to date generally vest over four to five years.

As of December 31, 2013 , options to purchase 6,334,836 shares of the Company's common stock granted from the 2010 Equity Plan were outstanding and 4,351,596 shares of the Company’s common stock remained available for future awards that may be granted from the 2010 Equity Plan. The options outstanding as of December 31, 2013 had a weighted-average exercise price of approximately $7.04 per share.

2005 Stock Option/Stock Issuance Plan

In 2005, the Company established its 2005 Plan which provided for the granting of common stock options, restricted stock units, restricted stock and stock purchase rights awards to employees and consultants of the Company. The 2005 Plan allowed for time-based or performance-based vesting for the awards. Options granted under the 2005 Plan were ISOs or NSOs. ISOs were granted only to Company employees (including officers and directors who are also employees). NSOs were granted to Company employees, non-employee directors, and consultants.

All options issued under the 2005 Plan have had a ten year life. The exercise prices of ISOs and NSOs granted under the 2005 Plan were not less than 100% of the estimated fair value of the shares on the date of grant, as determined by the Board of Directors. The exercise price of an ISO and NSO granted to a 10% stockholder could not be less than 110% of the estimated fair value of the underlying stock on the date of grant as determined by the Board of Directors. The options generally vested over 5 years.

As of December 31, 2013 , options to purchase 2,014,769 shares of the Company’s common stock granted from the 2005 Stock Option/Stock Issuance Plan remained outstanding and, as a result of the adoption of the 2010 Equity Incentive Plan discussed above, zero shares of the Company’s common stock remained available for issuance under the 2005 Plan. The options outstanding under the 2005 Plan as of December 31, 2013 had a weighted-average exercise price of approximately $8.59 per share.

No income tax benefit has been recognized relating to stock-based compensation expense and no tax benefits have been realized from exercised stock options or release of restricted stock units.

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2010 Employee Stock Purchase Plan

The 2010 Employee Stock Purchase Plan (referred to as the 2010 ESPP) became effective on September 28, 2010. The 2010 ESPP is designed to enable eligible employees to purchase shares of the Company’s common stock at a discount. Each offering period is for one year and consists of two six-month purchase periods. Each twelve-month offering period generally commences on May 16 ^th and November 16 ^th , each consisting of two six-month purchase periods. The purchase price for shares of common stock under the 2010 ESPP is the lesser of 85% of the fair market value of the Company’s common stock on the first day of the applicable offering period or the last day of each purchase period. A total of 168,627 shares of common stock were initially reserved for future issuance under the 2010 Employee Stock Purchase Plan. During the first eight years of the life of the 2010 ESPP, the number of shares reserved for issuance increases automatically on January 1 ^st of each year, starting with January 1, 2011, by a number of shares equal to 1% of the Company’s total outstanding shares as of the immediately preceding December 31 ^st . Pursuant to the automatic increase provision, an additional 687,096 shares were reserved for issuance during the year ended December 31, 2013 for a cumulative total of 1,584,895 additional shares reserved for issuance under the automatic increase provision. The Company’s Board of Directors or the Leadership Development and Compensation Committee of the Board of Directors is able to reduce the amount of the increase in any particular year. No more than 10,000,000 shares of the Company’s common stock may be issued under the 2010 ESPP and no other shares may be added to this plan without the approval of the Company’s stockholders.

During the year ended December 31, 2013 , 472,039 shares of the Company's common stock were purchased under the 2010 ESPP. At December 31, 2013 , 401,757 shares of the Company’s common stock remained available for issuance under the 2010 ESPP.

Stock Option Activity

The Company’s stock option activity and related information for the year ended December 31, 2013 was as follows:



		Number Outstanding		Weighted- Average Exercise Price		Weighted-Average Remaining Contractual Life (Years)	Aggregate Intrinsic Value
							(in thousands)
Outstanding - December 31, 2012		8,946,592		$	9.07	7.5	$	954
	Options granted	2,989,919		$	2.82
	Options exercised	(305,060	)	$	1.89
	Options cancelled	(3,221,846	)	$	8.34
Outstanding - December 31, 2013		8,409,605		$	7.39	7.4	$	12,393
Vested and expected to vest after December 31, 2013		7,879,704		$	7.58	7.3	$	11,290
Exercisable at December 31, 2013		3,999,486		$	9.70	5.9	$	3,822

The aggregate intrinsic value of options exercised under all option plans was $0.6 million , $2.7 million and $28.7 million for the years ended December 31, 2013, 2012 and 2011 , respectively, determined as of the date of option exercise.

The Company’s restricted stock units (or RSU) and restricted stock activity and related information for the year ended December 31, 2013 was as follows:



	RSUs		Weighted-Average Grant-Date Fair Value		Weighted Average Remaining Contractual Life (Years)
Outstanding - December 31, 2012	2,550,799		$	7.92	1.3
Awarded	1,222,250		$	2.85	—
Vested	(889,619	)	$	5.08	—
Forfeited	(566,993	)	$	3.57	—
Outstanding - December 31, 2013	2,316,437		$	4.30	0.88
Expected to vest after December 31, 2013	2,121,306		$	4.30	0.81

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The following table summarizes information about stock options outstanding as of December 31, 2013 :



	Options Outstanding				Options Exercisable
Exercise Price	Number of Options	Weighted- Average Remaining Contractual Life (Years)	Weighted-Average Exercise Price		Number of Options	Weighted-Average Exercise Price
$0.10—$2.75	848,011	8.1	$	2.54	189,629	$	2.15
$2.76—$2.79	1,046,855	8.1	$	2.78	166,250	$	2.76
$2.81—$2.89	960,500	9.4	$	2.87	137	$	2.85
$2.94—$3.23	892,138	9.0	$	3.04	255,031	$	3.07
$3.55—$3.83	45,655	8.6	$	3.57	42,402	$	3.55
$3.86—$3.86	967,500	8.0	$	3.86	426,760	$	3.86
$3.93—$4.06	895,456	4.3	$	3.94	835,039	$	3.94
$4.31—$11.20	854,569	5.8	$	6.73	733,001	$	6.39
$11.51—$18.22	842,905	6.9	$	16.08	577,767	$	16.09
$19.61—$30.17	1,056,016	6.8	$	23.57	773,470	$	23.38
$0.10—$30.17	8,409,605	7.4	$	7.39	3,999,486	$	9.70

Stock-Based Compensation Expense

Stock-based compensation expense related to options and restricted stock units granted to employees and nonemployees was allocated to research and development expense and sales, general and administrative expense as follows (in thousands):



	Years Ended December 31,
	2013		2012		2011
Research and development	$	4,281	$	6,451	$	6,345
Sales, general and administrative	13,766		21,022		19,147
Total stock-based compensation expense	$	18,047	$	27,473	$	25,492

Employee Stock–Based Compensation

During the years ended December 31, 2013, 2012 and 2011 , the Company granted options to purchase 2,849,919 shares, 3,589,593 shares, and 2,677,249 shares of its common stock, respectively, to employees with weighted-average grant date fair values of $1.98 , $2.28 , and $18.41 per share, respectively. Compensation expense of $13.1 million , $20.2 million , and $19.2 million was recorded for the years ended December 31, 2013, 2012 and 2011 , respectively, for stock-based options granted to employees. As of December 31, 2013, 2012 and 2011 , there were unrecognized compensation costs of $15.0 million , $51.2 million , and $54.7 million , respectively, related to these stock options. The Company expects to recognize those costs over a weighted-average period of 2.7 years as of December 31, 2013 . Future option grants will increase the amount of compensation expense to be recorded in these periods.

In August 2012, the Company's CEO exercised outstanding options to purchase 668,730 shares of the Company's common stock and sold the shares to certain members of the Company's Board of Directors or their affiliates through a private sale at a price of $3.70 , which was greater than the fair market value of the stock at the date of sale. The Company recorded $0.4 million in stock-based compensation expense as an excess of the sale price over the fair market value of shares in this transaction during the year ended December 31, 2012.

During the years ended December 31, 2013, 2012 and 2011 , 1,222,250 , 2,956,900 and 352,301 of restricted stock units, respectively, were granted to employees with a weighted-average service-inception date fair value of $2.85 , $3.46 and $29.85 per unit, respectively. The Company recognized a total of $4.1 million , $6.3 million and $3.6 million , respectively, in December 31, 2013, 2012 and 2011 in stock-based compensation expense for restricted stock units granted to employees. As of December 31, 2013, 2012 and 2011 , there were unrecognized compensation costs of $3.6 million , $7.8 million and $6.0 million , respectively, related to these restricted stock units.

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During the years ended December 31, 2013, 2012 and 2011 , the Company also recognized stock-based compensation expense related to its 2010 ESPP of $0.6 million , $0.8 million , and $1.9 million , respectively.

Compensation expense was recorded for stock-based awards granted to employees based on the grant date estimated fair value (in thousands):



	Years Ended December 31,
	2013		2012		2011
Research and development	$	4,278	$	6,442	$	6,306
Sales, general and administrative	13,453		20,887		18,288
Total stock-based compensation expense	$	17,731	$	27,329	$	24,594

Employee stock-based compensation expense recognized for the years ended December 31, 2013 and 2012 included $1.0 million and $0.9 million , respectively, related to option modifications. As part of separation agreements with certain former senior employees, the Company agreed to accelerate the vesting of options for 458,424 and 825,523 shares of common stock and extend the exercise period for certain grants in the years ended December 31, 2013 and 2012 , respectively. The stock-based compensation expense for the year ended December 31, 2012 , includes the impact of a repricing of stock options in June 2012 under which certain non-executive employees received a one-time reduction in the exercise price for such options with per share exercise prices per share higher than $24.00 held by U.S. employees of Amyris and the new exercise price for such options was $16.00 , the Company's initial public offering price. The total amount of the stock-based compensation associated with repricing was immaterial to the consolidated financial statements.

In the quarter ended June 30, 2011, the Company commenced sales of farnesene-derived products which were produced by contracted third parties. Accordingly, the Company did not have any dedicated production headcount so there is no stock-based compensation expense recorded in cost of products sold.

Stock-based compensation cost for RSUs is measured based on the closing fair market value of the Company's common stock on the date of grant. Stock-based compensation cost for stock options and employee stock purchase plan rights is estimated at the grant date and offering date, respectively, based on the fair-value using the Black-Scholes option pricing model. The fair value of employee stock options is being amortized on a straight-line basis over the requisite service period of the awards. The fair value of employee stock options was estimated using the following weighted-average assumptions:



	Years Ended December 31,
	2013		2012		2011
Expected dividend yield	—	%	—	%	—	%
Risk-free interest rate	1.4	%	1.1	%	2.3	%
Expected term (in years)	6.1		6.0		5.8
Expected volatility	82	%	77	%	86	%

Expected Dividend Yield —The Company has never paid dividends and does not expect to pay dividends.

Risk-Free Interest Rate —The risk-free interest rate was based on the market yield currently available on United States Treasury securities with maturities approximately equal to the option’s expected term.

Expected Term —Expected term represents the period that the Company’s stock-based awards are expected to be outstanding. The Company’s assumptions about the expected term have been based on that of companies that have similar industry, life cycle, revenue, and market capitalization and the historical data on employee exercises.

Expected Volatility —The expected volatility is based on a combination of historical volatility for the Company's stock and the historical stock volatilities of several of the Company’s publicly listed comparable companies over a period equal to the expected terms of the options, as the Company does not have a long trading history.

Forfeiture Rate —The Company estimates its forfeiture rate based on an analysis of its actual forfeitures and will continue to evaluate the adequacy of the forfeiture rate based on actual forfeiture experience, analysis of employee turnover behavior, and other factors. The impact from a forfeiture rate adjustment will be recognized in full in the period of adjustment, and if the actual

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number of future forfeitures differs from that estimated by the Company, the Company may be required to record adjustments to stock-based compensation expense in future periods.

Each of the inputs discussed above is subjective and generally requires significant management and director judgment.

Nonemployee Stock–Based Compensation

During the years ended December 31, 2013, 2012 and 2011 , the Company granted nonemployee options to purchase 140,000 , 3,000 and 15,000 shares of its common stock, respectively, to nonemployees in exchange for services. Compensation expense of $0.1 million , $86,000 and $0.8 million was recorded for the years ended December 31, 2013, 2012 and 2011 , respectively, for stock-based options granted to nonemployees. The nonemployee options were valued using the Black-Scholes option pricing model.

During the years ended December 31, 2013, 2012 and 2011 , zero , 10,000 and 32,855 restricted stock units, respectively, were granted to nonemployees and a total of $0.1 million , $58,000 and $0.1 million , respectively, in stock-based compensation expense was recognized by the Company for the years ended December 31, 2013, 2012 and 2011 .

The fair value of nonemployee stock options was estimated using the following weighted-average assumptions:



	Years Ended December 31,
	2013		2012		2011
Expected dividend yield	—	%	—	%	—	%
Risk-free interest rate	1.3	%	1.4	%	2.1	%
Expected term (in years)	4.8		7.0		7.8
Expected volatility	81	%	77	%	86	%

12. Employee Benefit Plan

The Company established a 401(k) Plan to provide tax deferred salary deductions for all eligible employees. Participants may make voluntary contributions to the 401(k) Plan up to 90% of their eligible compensation, limited by certain Internal Revenue Service restrictions. As of December 31, 2013 the Company does not match employee contributions.

13. Related Party Transactions

February 2012 Private Placement

In February 2012, the Company completed a private placement of 10,160,325 shares of its common stock at a price of $5.78 per share for aggregate proceeds of $58.7 million pursuant to a securities purchase agreement, among the Company and existing certain investors, including Total and Temasek, each a beneficial owner of more than 5% of the Company's existing common stock at the time of the transaction. In addition, members of the Board and certain parties related to such directors participated in the offering.

May 2012 Private Placement

In May 2012, the Company completed a private placement of 1,736,100 shares of it's common stock at a price of $2.36 per share for aggregate proceeds of $4.1 million pursuant to a series of Common Stock Purchase Agreements, among the Company and members of the Board and certain parties related to such directors.

March 2013 Private Placement

In March 2013, the Company completed a private placement of 1,533,742 shares of its common stock to an existing stockholder, Biolding Investment SA (or Biolding), at a price of $3.26 per share for aggregate proceeds of $5.0 million . This private placement represented the final tranche of Biolding's preexisting contractual obligation to fund $15.0 million upon satisfaction by the Company of certain criteria associated with the commissioning of a production plant in Brotas, Brazil.

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Related Party Financings

In July 2012, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $38.3 million , including $15.0 million in new funds and repayment by Amyris of $23.3 million in previously-provided diesel research and development funding by Total with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above under “Related Party Convertible Notes” in Note 5, “Debt."

In September 2012, the Company sold and issued 1.5% Senior Unsecured Convertible Note to Total in the face amount of $15.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above under “Related Party Convertible Notes” in Note 5, “Debt."

In December 2012, in connection with the December 2012 private placement described in Note 10, "Stockholders Equity", Total elected to participate in the private placement by exchanging approximately $5.0 million of its $53.3 million in senior unsecured convertible promissory notes into 1,677,852 of the Company's common stock at $2.98 per share. As such, $5.0 million of the outstanding $53.3 million in senior unsecured convertible promissory notes was cancelled (see Note 5, "Debt").

In August 2013, the Company entered into a securities purchase agreement by and among the Company, Total and Temasek, each a beneficial owner of more than 5% of the Company's existing common stock at the time of the transaction, for a private placement of convertible promissory notes in an aggregate principal amount of $73.0 million (see Note 1, "The Company"). The initial closing of the August 2013 Financing was completed in October 2013 (see Note 5, "Debt").

In September 2013, the Company entered into a bridge loan agreement with an existing investor to provide additional cash availability of up to $5.0 million as needed before the initial closing of the August 2013 Financing. The Company did not use this facility and it expired in October 2013 in accordance with its terms.

In October 2013, the Company sold and issued a senior secured promissory note to Temasek for a bridge loan of $35.0 million . The note was due on February 2, 2014 and accrued interest at a rate of 5.5% each four months from October 4, 2013 (with a rate of 2% per month if a default occurred). The note was cancelled as payment for the investor’s purchase of the first tranche convertible note in the August 2013 Financing. The note was cancelled on October 16, 2013 as payment for Temasek’s purchase of the first tranche convertible note in the August 2013 Financing (see Note 5, "Debt").

In October 2013, the Company completed the closing of the first tranche of the August 2013 Financing, which resulted to the exchange and cancellation of the $35.0 million Temasek Bridge Note and the $9.2 million Total convertible note, as a result of the exchange and cancellation the Company recorded a loss from extinguishment of debt of $19.9 million (see Note 5, "Debt").

In December 2013, the Company agreed to exchange the $69.0 million outstanding Total unsecured convertible notes and issue a replacement 1.5% senior secured convertible notes, in principal amounts equal to the principal amount of each cancelled note (see Note 5, "Debt").

In December 2013, the Company agreed to issue to Temasek $25.0 million of the second tranche of convertible promissory notes for cash. Total purchased approximately $6.0 million of the the second tranche of convertible promissory notes through cancellation of the same amount of principal of previously outstanding convertible promissory notes held by Total (in respect of Total’s preexisting contractual right to maintain its pro rata ownership position through such cancellation). Such financing transactions closed in January 2014 (see Note 5, "Debt" and Note 16, "Subsequent Events").

As of December 31, 2013 and 2012 , $89.5 million and $39.0 million , respectively, was outstanding under these convertible notes, net of debt discount of $27.9 million and $9.3 million , respectively. For the years ended December 31, 2013, 2012 and 2011 , the Company recorded loss from extinguishment of debt from the exchange and cancellation of related party convertible notes of $19.9 million , $0.9 million , and zero , respectively (see Note 5, "Debt").

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Derivative liability related to the related party convertible notes as of December 31, 2013 and 2012 are $131.1 million and $7.9 million , respectively. The Company for the year ended December 31, 2013 recognized an $82.3 million loss from change in fair value of the derivative instruments and a $3.1 million income from change in fair value of the derivative instruments for the year ended December 31, 2012 , respectively, related to these derivative liabilities (see Note 3, "Fair Value of Financial Instruments").

Related Party Revenue

The Company recognized related party revenue from Novvi for the year ended December 31, 2013 , of $1.1 million from product sales and $2.6 million of revenue from the research and development activities that it has performed on behalf of Novvi. The related party accounts receivables from Novvi as of December 31, 2013 , was $0.3 million .

The Company recognized related party revenue from Total for the year ended December 31, 2013 , of $0.2 million from product sales and as a result of the July 2012 agreements with Total, the Company recognized related party collaboration revenue from Total for the year ended December 31, 2012 , of $9.8 million associated with the diesel and jet fuel research and development program. The related party accounts receivables from Total as of December 31, 2013 , was $0.2 million .

Joint Venture

In November 2013, the Company and Total Energies Nouvelles Activités USA (formerly known as Total Gas & Power USA, SAS), formed Total Amyris BioSolutions B.V., a private company with limited liability incorporated under the laws of the Netherlands (or JVCO). The common equity of JVCO is jointly owned ( 50% /50%) by the Company and Total, and the preferred equity of JVCO is 100% owned by the Company. The Parties have agreed that JVCO’s purpose is limited to executing the License Agreement and maintaining such licenses under it, unless and until either (i) Total elects to go forward with either the full (diesel and jet fuel) JVCO commercialization program or the jet fuel component of the JVCO commercialization program (a “Go Decision”), (ii) Total elects to not continue its participation in the R&D Program and JVCO (a “No-Go Decision”), or (iii) Total exercises any of its rights to buy out the Company’s interest in JVCO. Following a Go Decision, the Articles and Shareholders’ Agreement would be amended and restated to be consistent with the shareholders’ agreement contemplated by the July 2012 Agreements (see Note 7, "Joint Venture and Noncontrolling Interest").

14. Income Taxes

For the years ended December 31, 2013, 2012 and 2011 , the Company recorded a benefit from income taxes of $0.8 million and a provision for income taxes of $1.0 million and $0.6 million , respectively. In the year ended December 31, 2013, the recorded tax benefit was associated with the conversion of certain loans to equity, which reduces the accrual of the interest from the Company's subsidiary and will correspondingly eliminate the withholding tax obligation. The provision for income taxes for the years ended December 31, 2012 and 2011, generally relates to accrued withholding taxes that would be due in connection with the payment of interest on intercompany loans. Other than the above mentioned provision for income tax, no additional provision for income taxes has been made, net of the valuation allowance, due to cumulative losses since the commencement of operations.

The components of loss before income taxes and minority interests are as follows for the years ended December 31, 2013, 2012 and 2011 (in thousands):



	Years Ended December 31,
	2013			2012			2011
United States	$	(216,583	)	$	(146,028	)	$	(140,153	)
Foreign	(19,171		)	(59,024		)	(38,806		)
Loss before income taxes	$	(235,754	)	$	(205,052	)	$	(178,959	)

The components of the provision for (benefit from) income taxes are as follows for the years ended December 31, 2013, 2012 and 2011 (in thousands):

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	Years Ended December 31,
	2013			2012		2011
Current:
Federal	$	—		$	—	$	—
State	—			—		—
Foreign	(847		)	981		727
Total current provision (benefit)	(847		)	981		727
Deferred:
Federal	—					(150		)
State	—			—		(25		)
Foreign	—			—		—
Total deferred provision (benefit)	—			—		(175		)
Total provision for income taxes	$	(847	)	$	981	$	552

A reconciliation between the statutory federal income tax and the Company’s effective tax rates as a percentage of loss before income taxes is as follows:



	Years Ended December 31,
	2013		2012		2011
Statutory tax rate	(34.0	)%	(34.0	)%	(34.0	)%
State tax rate, net of federal benefit	(0.7	)%	(0.3	)%	(4.4	)%
Stock-based compensation	0.1	%	0.2	%	0.6	%
Federal R&D credit	(0.8	)%	—	%	(0.8	)%
Derivative liability	13.9	%	1.3	%	—	%
Other	(0.6	)%	0.2	%	(0.7	)%
Foreign losses	(1.4	)%	(5.8	)%	(5.4	)%
Change in valuation allowance	23.1	%	38.8	%	45.0	%
Effective income tax rate	(0.4	)%	0.4	%	0.3	%

Temporary differences and carryforwards that gave rise to significant portions of deferred taxes are as follows (in thousands):



	December 31,
	2013			2012			2011
Net operating loss carryforwards	$	167,354		$	145,324		$	103,390
Fixed assets	822			—			—
Research and development credits	11,654			7,259			5,937
Foreign Tax Credit	935			1,782			801
Accruals and reserves	17,893			15,997			12,150
Stock-based compensation	17,521			15,882			11,351
Capitalized start-up costs	15,133			16,070			22,974
Capitalized research and development costs	45,968			26,850			—
Other	6,741			7,649			2,904
Total deferred tax assets	284,021			236,813			159,507
Fixed assets	—			(525		)	(2,742		)
Total deferred tax liabilities	—			(525		)	(2,742		)
Net deferred tax asset prior to valuation allowance	284,021			236,288			156,765
Less: Valuation allowance	(284,021		)	(236,288		)	(156,765		)
Net deferred tax assets (liabilities)	$	—		$	—		$	—

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Recognition of deferred tax assets is appropriate when realization of such assets is more likely than not. Based upon the weight of available evidence, especially the uncertainties surrounding the realization of deferred tax assets through future taxable income, the Company believes it is not yet more likely than not that the net deferred tax assets will be fully realizable. Accordingly, the Company has provided a full valuation allowance against its net deferred tax assets as of December 31, 2013 . The valuation allowance increased $47.7 million , $79.5 million , and $80.7 million , during the years ended December 31, 2013, 2012 and 2011 , respectively.

As of December 31, 2013 , the Company had federal and state net operating loss carryforwards of approximately $440.4 million and $198.3 million , respectively, available to reduce future taxable income, if any. Approximately $25.8 million and $12.8 million of the federal and state net operating loss carryforwards, respectively, resulted from exercises of employee stock options and vesting of restricted stock units and have not been included in the Company’s gross deferred tax assets. In accordance with ASC 718, such unrealized tax benefits will be accounted for as a credit to additional paid-in capital if and when realized through a reduction in income taxes payable.

The Company also has federal research and development credits of $6.7 million and California research and development credit carryforwards of $7.5 million , respectively, at December 31, 2013 .

The Tax Reform Act of 1986 and similar state provisions limit the use of net operating loss and credit carryforwards in certain situations where equity transactions result in a change of ownership as defined by Internal Revenue Code Section 382. In the event the Company has experienced an ownership change, as defined, utilization of its federal and state net operating loss and credit carryforwards could be limited. If not utilized, the federal net operating loss carryforward begins expiring in 2025, and the California net operating loss carryforward begins expiring in 2015. The federal research and development credit carryforwards will expire starting in 2024 if not utilized. The California tax credits can be carried forward indefinitely.

In January 2013, the American Taxpayer Relief Act of 2012 (referred to as the ATRA) was enacted. Under prior law, a taxpayer was entitled to a research tax credit for qualifying amounts incurred through December 31, 2011. The ATRA extends the research credit for two years for qualified research expenditures incurred through the end of 2013. The extension of the research credit is retroactive and includes amounts incurred after 2011. The benefit of the reinstated credit did not impact the income statement in the period of enactment, which is the first quarter of 2013, as the research and development credit carryforwards are offset by a full valuation allowance.

Effective January 1, 2007, the Company adopted the accounting guidance on uncertainties in income taxes. A reconciliation of the beginning and ending amounts of unrecognized tax benefits since the adoption of accounting guidance on uncertainty in income taxes is as follows:



Balance at December 31, 2011	$	3,103
Increases in tax positions for prior period	82
Increases in tax positions during current period	733
Balance at December 31, 2012	$	3,918
Increases in tax positions for prior period	469
Increases in tax positions during current period	1,693
Balance at December 31, 2013	$	6,080

The Company’s policy is to include interest and penalties related to unrecognized tax benefits within the provision for taxes. The Company determined that no accrual for interest and penalties was required as of December 31, 2013 .

As of December 31, 2013 , the Company’s total unrecognized tax benefits were $6.1 million , of which none of the tax benefits, if recognized, would affect the effective income tax rate due to the valuation allowance that currently offsets deferred tax assets. The Company does not anticipate the total amount of unrecognized income tax benefits will significantly increase or decrease in the next 12 months.

The Company’s primary tax jurisdiction is the United States. For United States federal and state tax purposes, tax years 2003 and forward remain open and subject to tax examination by the appropriate federal or state taxing authorities. Brazil tax years 2008 through the current remain open and subject to examination.

As of December 31, 2013 , the US Internal Revenue Service (the "IRS") has completed its audit of the Company for tax year 2008 which concluded that there were no adjustments resulting from the audit. While the statutes are closed for tax year 2008, the

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US federal tax carryforwards (net operating losses and tax credits) may be adjusted by the IRS in the year in which the carryforward is utilized.

15. Reporting Segments

The chief operating decision maker for the Company is the chief executive officer. The chief executive officer reviews financial information presented on a consolidated basis, accompanied by information about revenue by geographic region, for purposes of allocating resources and evaluating financial performance. The Company has one business activity comprised of research and development and sales of fuels and farnesene-derived products and there are no segment managers who are held accountable for operations, operating results or plans for levels or components below the consolidated unit level. Accordingly, the Company has determined that it has a single reportable segment and operating segment structure.

Revenues by geography are based on the location of the customer. The following tables set forth revenue and long-lived assets by geographic area (in thousands):

Revenues



	Years Ended December 31,
	2013		2012		2011
United States	$	21,235	$	49,111	$	141,098
Brazil	4,071		3,786		141
Europe	10,340		16,461		5,695
Asia	5,473		4,336		57
Total	$	41,119	$	73,694	$	146,991

Long-Lived Assets



	December 31,
	2013		2012
United States	$	54,015	$	70,273
Brazil	85,891		90,982
Europe	685		1,866
Total	$	140,591	$	163,121

16. Subsequent Events

Tranche II Notes

In January 2014, the Company sold and issued, for face value, approximately $34.0 million of senior convertible promissory notes in a closing under the August 2013 SPA , as amended by Amendment No. 1 to Securities Purchase Agreement in October 2013 and Amendment No. 2 to Securities Purchase Agreement and Tranche I Note Amendment in December 2013.

In January 2014, Temasek purchased $25.0 million of the Tranche II Notes for cash and certain funds affiliated with Wolverine Asset Management, LLC purchased $3.0 million of the Tranche II Notes for cash. Total purchased approximately $6.0 million of the Tranche II Notes through cancellation of the same amount of principal of previously outstanding convertible promissory notes held by Total (in respect to Total's preexisting contractual right to maintain its pro rata ownership position through such cancellation). The Tranche II Notes are due sixty months from the date of issuance and become convertible into shares of Common Stock of the Company at a conversion price equal to $2.87 , which represents a trailing 60-day weighted-average closing price of the Common Stock on the NASDAQ Stock Market through August 7, 2013, subject to adjustment as described below. Specifically, the Tranche II Notes become convertible at the option of the holder (i) at any time 12 months after issuance, (ii) on a change of control of the Company, and (iii) upon the occurrence of an event of default. Each Tranche II Note accrues interest from the date of issuance until the earlier of the date that such Tranche II Note is converted into Common Stock or repaid in full. Interest accrues at a rate per annum equal to 10% , compounded annually (with graduated interest rates of 13% applicable to the first 180 days and 16% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or at 12% for all other defaults). Interest for the first 36 months shall be payable in kind and added to principal every year following the issue date and

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thereafter, the Company may continue to pay interest in kind by adding to principal on every year anniversary of the issue date or may elect to pay interest in cash. The conversion price of the Tranche II Notes is subject to adjustment (i) according to proportional adjustments to outstanding Common Stock in the case of certain dividends and distributions, (ii) according to anti-dilution provisions, and (iii) with respect to Tranche II Notes held by any purchase other than Total, in the event that Total exchanges existing convertible notes for new securities of the Company in connection with future financing transactions in excess of its pro rata amount. The holders of the Tranche II Notes have a right to require repayment of 101% of the principal amount of the Tranche II Notes in the event of a change in control of the Company and the Tranche II Notes provide for payment of unpaid interest on conversion following such a change of control if the holders do not require such repayment.

SMA Indústria Química S.A.

In February 2014, the Company, Amyris Brasil and SMSA entered into an amendment dated January 27, 2014 of the joint venture agreement that the parties originally entered into on April 2010 (see Note 7, "Joint venture and noncontrolling interest"). The amendment to the joint venture agreement with SMSA updates and documents certain preexisting business plan requirements related to the start-up of construction at the joint venture operated plant and sets forth, among other things, (i) the extension of the deadline for the commencement of operations at the joint venture operated plant to no later than 18 months following the construction of the plant, which shall occur no later than March 31, 2017, and (ii) the extension of an option held by SMSA to build a second large-scale farnesene production facility to no later than December 31, 2018 with the commencement of operations at such second facility to occur no later than April 1, 2019.

Export Financing with ABC

In March, 2014, the Company entered into an export financing agreement with ABC Bank for R$5.0 million (approximately US$2.2 million based on exchange rate as of the date the parties entered into the agreement) for a 1 year-term to fund exports through March 2015 .

Kuraray Securities Purchase Agreement

On March 28, 2014 , the Company and Kuraray Co., Ltd. (or Kuraray) entered into a securities purchase agreement under which the Company agreed to sell shares of its common stock at a price equal to the greater of $2.88 per share or the average daily closing prices per share on the NASDAQ Stock Market for the three month period ending March 27, 2014 for an aggregate purchase price of $4.0 million . The Company and Kuraray also agreed to amend their prexisting collaboration agreement to expand and extend their collaboration with respect to high performance polymers.

Hercules Loan Facility

On March 29, 2014 , the Company and Hercules Technology Growth Capital, Inc. entered into a loan and security agreement to make available to Amyris a loan in the aggregate principal amount of up to $25.0 million (referred to as the Hercules Loan Facility), and the Company borrowed the full amount available under the facility. Loans under the facility are secured by various liens, including a lien on certain Company intellectual property. The Hercules Loan Facility generally becomes due on May 31, 2015 and accrues interest at a rate per annum equal to the greater of either the prime rate reported in the Wall Street Journal plus 6.25% or 9.5% . The maturity date is extended to May 31, 2017 if the Company completes a financing transaction for at least $50.0 million in additional cash proceeds by September 30, 2014 . The Company may repay the loaned amounts before the maturity date if it pays an additional fee of 3% of the outstanding loans ( 1% if after the initial twelve-month period). The Company is also required to pay a 1% facility charge at the closing of the transaction, and a 10% end of term charge. In connection with the Hercules Loan Facility, Amyris agreed to certain customary representations and warranties and covenants, as well as certain covenants with respect to obtaining additional financing as described above and performance covenants related to revenues and cash flows starting with the third quarter of 2014. If the Company does not achieve the equity financing covenant, a forbearance fee of $10.0 million becomes due and is required to be paid at the end of the initial term of the facility.

March 2014 Letter Agreement with Total

On April 1, 2014, the Company and Total entered into a letter agreement dated as of March 29, 2014 (referred to as March 2014 Letter Agreement) to amend the Amended and Restated Master Framework Agreement entered into as of December 2, 2013 (included as part of JV Documents). Under the March 2014 Letter Agreement, the Company agreed to (i) amend the conversion price of the Third Closing from $7.0682 to $4.11 (or the “New Conversion Price”) subject to stockholder approval at our 2014 annual meeting (to the extent required by applicable law or regulation), (ii) extend the period during which Total may exchange for other Company securities certain outstanding convertible promissory notes issued under the July 2012 Agreements from June

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30, 2014 to the later of December 31, 2014 and the date on which Amyris shall have raised $75.0 million of equity and convertible debt financing (excluding any convertible promissory notes issued pursuant to the Total Purchase Agreement), (iii) eliminate the Company’s ability to qualify, in a disclosure letter to Total, certain of the representations and warranties that the Company must make at the closing of any sale of the Third Closing, and (iv) provide Total with monthly reporting on the Company’s cash, cash equivalents and short-term investments. In consideration of these agreements, Total agreed to waive its right not to consummate the closing of the issuance of the Remaining Notes if it decides not to proceed with the collaboration and makes a "No-Go" decision with respect thereto, subject to the Company obtaining stockholder approval of the issuance of the Third Closing at the New Conversion Price.

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SUPPLEMENTARY FINANCIAL DATA

Selected Quarterly Financial Data (unaudited)

The following table presents selected unaudited consolidated financial data for each of the eight quarters in the two-year periods ended December 31, 2013 . In the Company’s opinion, this unaudited information has been prepared on the same basis as the audited information and includes all adjustments (consisting of only normal recurring adjustments) necessary for a fair statement of the financial information for the periods presented. Net loss per share—basic and diluted, for the four quarters of each fiscal year may not sum to the total for the fiscal year because of the different number of shares outstanding during each period.



	Quarter
	First			Second			Third			Fourth
	(In thousands, except share and per share amounts)
Year Ended December 31, 2013
Total revenues	$	7,869		$	10,849		$	7,004		$	15,397
Product sales	$	2,983		$	4,185		$	4,144		$	4,496
Gross profit (loss) from product sales	$	(5,977	)	$	(4,668	)	$	(4,184	)	$	(7,616	)
Net loss attributable to common stockholders	$	(32,614	)	$	(38,876	)	$	(24,199	)	$	(139,422	)
Net loss per share—basic and diluted	$	(0.44	)	$	(0.51	)	$	(0.32	)	$	(1.83	)
Shares used in calculation—basic and diluted	73,306,860			75,959,228			76,205,853			76,377,574
Year Ended December 31, 2012
Total revenues	$	29,469		$	19,263		$	19,108		$	5,854
Product sales	$	26,307		$	15,580		$	4,728		$	3,023
Gross profit (loss) from product sales	$	(17,504	)	$	(8,056	)	$	284		$	(2,400	)
Net loss attributable to common stockholders	$	(94,548	)	$	(46,806	)	$	(20,293	)	$	(43,492	)
Net loss per share—basic and diluted	$	(1.88	)	$	(0.81	)	$	(0.34	)	$	(0.72	)
Shares used in calculation—basic and diluted	50,214,192			57,442,834			58,964,226			60,187,256

ITEM 9. CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING AND FINANCIAL DISCLOSURE

Not applicable.

ITEM 9A. CONTROLS AND PROCEDURES

Disclosure Controls and Procedures

Our management, with the participation of our chief executive officer and chief financial officer, evaluated the effectiveness of our disclosure controls and procedures pursuant to Rule 13a-15 under the Securities Exchange Act of 1934, as amended (Exchange Act), as of the end of the period covered by this Annual Report on Form 10-K. Based on this evaluation, our chief executive officer (CEO) and chief financial officer (CFO) concluded that, as of December 31, 2013 , our disclosure controls and procedures are designed and are effective to provide reasonable assurance that information we are required to disclose in reports that we file or submit under the Exchange Act is recorded, processed, summarized, and reported within the time periods specified in the SEC's rules and forms, and that such information is accumulated and communicated to our management, including our CEO and CFO, as appropriate, to allow timely decisions regarding required disclosure.

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Our management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures.

Management’s Annual Report on Internal Control over Financial Reporting

Our management is responsible for establishing and maintaining adequate internal control over financial reporting. Internal control over financial reporting is a process designed by, or under the supervision of, our chief executive officer and chief financial officer, and effected by our Board of Directors, management and other personnel, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles and includes those policies and procedures that:


•	Pertain to the maintenance of records that accurately and fairly reflect in reasonable detail the transactions and dispositions of the assets of our company;


•	Provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that our receipts and expenditures are being made only in accordance with authorizations of our management and directors; and


•	Provide reasonable assurances regarding prevention or timely detection of unauthorized acquisition, use or disposition of our assets that could have a material adverse effect on our financial statements.

Our management assessed our internal control over financial reporting as of December 31, 2013, the end of our fiscal year. Management based its assessment on criteria established in "Internal Control-Integrated Framework" (1992) issued by the Committee of Sponsoring Organizations of the Treadway Commission . Based on management's assessment of our internal control over financial reporting, management concluded that, as of December 31, 2013, our internal control over financial reporting was effective. The effectiveness of the Company's internal control over financial reporting as of December 31, 2013 has been audited by PricewaterhouseCoopers LLP, an independent registered public accounting firm, as stated in their report which appears herein.

Internal control over financial reporting has inherent limitations. Internal control over financial reporting is a process that involves human diligence and compliance and is subject to lapses in judgment and breakdowns resulting from human failures. Internal control over financial reporting also can be circumvented by collusion or improper management override. Because of such limitations, there is a risk that material misstatements will not be prevented or detected on a timely basis by internal control over financial reporting. However, these inherent limitations are known features of the financial reporting process. Therefore, it is possible to design into the process safeguards to reduce, though not eliminate, this risk.

Changes in Internal Control over Financial Reporting

There were no changes in our internal control over financial reporting identified in management’s evaluation pursuant to Rules 13a-15(d) or 15d-15(d) of the Exchange Act during our fourth fiscal quarter ended December 31, 2013 that materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

ITEM 9B. OTHER INFORMATION

Not applicable.

127

PART III

Certain information required by Part III is omitted from this Annual Report on Form 10-K and is incorporated herein by reference from our definitive proxy statement, relating to our 2013 annual meeting of stockholders, pursuant to Regulation 14A of the Exchange Act, also referred to in this Form 10-K as our 2014 Proxy Statement, which we expect to file with the SEC no later than April 30, 2014.

ITEM 10. DIRECTORS, EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE

The information appearing in our 2014 Proxy Statement under the following headings is incorporated herein by reference:


•	Proposal 1—Election of Directors


•	Corporate Governance


•	Section 16(a) Beneficial Ownership Reporting Compliance

The information under the heading “Executive Officers of the Registrant” in Item 1(a) of this Annual Report on Form 10-K is also incorporated by reference in this section.

We have adopted a Code of Business Conduct and Ethics that applies to all directors, officers and employees of Amyris as required by NASDAQ governance rules and as defined by applicable SEC rules. Our Code of Business Conduct and Ethics includes a section entitled “Code of Ethics for Chief Executive Officer and Senior Financial Officers,” providing additional principles for ethical leadership and a requirement that such individuals foster a culture throughout Amyris that helps ensure the fair and timely reporting of our financial results and condition. Our Code of Business Conduct and Ethics is available on the corporate governance section of our website at “http://investors.amyris.com/governance.cfm.” Stockholders may also obtain a print copy of our Code of Business Conduct and Ethics and our Corporate Governance Guidelines by writing to the Secretary of Amyris at 5885 Hollis Street, Suite 100, Emeryville, California 94608. If we make any substantive amendments to our Code of Business Conduct and Ethics or grant any waiver from a provision of the Internal Revenue Code to any executive officer or director, we will promptly disclose the nature of the amendment or waiver on the corporate governance section of our website at “http://investors.amyris.com/governance.cfm.”

ITEM 11. EXECUTIVE COMPENSATION

The information appearing in our 2014 Proxy Statement under the following headings is incorporated herein by reference:


•	Executive Compensation


•	Director Compensation


•	Compensation Committee Interlocks and Insider Participation

ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERS

The information appearing in our 2014 Proxy Statement under the following headings is incorporated herein by reference:


•	Security Ownership of Certain Beneficial Owners and Management


•	Equity Compensation Plan Information

ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS, AND DIRECTOR INDEPENDENCE

The information appearing in our 2014 Proxy Statement under the following headings is incorporated herein by reference:


•	Transactions with Related Persons


•	Proposal 1—Election of Directors—Independence of Directors


•	Proposal 1—Election of Directors—Committees of the Board

128

ITEM 14. PRINCIPAL ACCOUNTING FEES AND SERVICES

The information appearing in our 2014 Proxy Statement under the proposal entitled “Ratification of Appointment of Independent Registered Public Accounting Firm” is incorporated herein by reference.

PART IV

ITEM 15. EXHIBITS, FINANCIAL STATEMENT SCHEDULES


(a)	The following documents are filed as part of this report on Form 10-K:

(1) Financial Statements. Reference is made to the Index to the registrant’s Financial Statements under Item 8 in Part II of this Form 10-K.

(2) Financial Statement Schedules. The following consolidated financial statement schedule of the registrant is filed as part of this report on Form 10-K and should be read in conjunction with the Consolidated Financial Statements of Amyris, Inc.

129

SCHEDULE II

VALUATION AND QUALIFYING ACCOUNTS

FOR THE YEARS ENDED DECEMBER 31, 2013, 2012 and 2011

(in thousands)



	Balance at Beginning of Period		Additions		Write-off/ Adjustments		Balance at End of Period
Deferred Tax Assets Valuation Allowance:
Year ended December 31, 2013	$	236,288	$	47,733	$	—	$	284,021
Year ended December 31, 2012	$	156,765	$	79,523	$	—	$	236,288
Year ended December 31, 2011	$	76,071	$	80,694	$	—	$	156,765



	Balance at Beginning of Period		Additions		Write-off/ Adjustments			Balance at End of Period
Allowance for Doubtful Accounts:
Year ended December 31, 2013	$	481			$	(2	)	$	479
Year ended December 31, 2012	$	245	$	236	$	—		$	481
Year ended December 31, 2011	$	—	$	245	$	—		$	245

Schedules not listed above are omitted because they are not required, they are not applicable or the information is already included in the consolidated financial statements or notes thereto.

(3) Exhibits. Reference is made to the exhibits listed in the index to exhibits in Item 15(b) below.

130


(b)	Exhibits.

The following table lists the exhibits filed as part of this report on Form 10-K. In some cases, these exhibits are incorporated into this report by reference to exhibits to our other filings with the Securities and Exchange Commission. Where an exhibit is incorporated by reference, we have noted the type of form filed with the Securities and Exchange Commission, the file number of that form, the date of the filing, and the number of the exhibit referenced in that filing.



Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
3.01	Restated Certificate of Incorporation	10-Q	001-34885	November 10, 2010	3.01
3.02	Restated Bylaws	10-Q	001-34885	November 10, 2010	3.02
4.01	Form of Stock Certificate	S-1	333-166135	July 6, 2010	4.01
4.02	Amended and Restated Investors’ Rights Agreement, dated June 21, 2010, among registrant and its security holders listed therein	S-1	333-166135	June 23, 2010	4.02
4.03	First Amendment to Amended and Restated Investors' Rights Agreement, dated February 23, 2012, among registrant and registrant's security holders listed therein	S-3	333-180005	March 9, 2012	4.06
4.04	Amendment No. 2 to Amended and Restated Investors' Rights Agreement, dated December 24, 2012, among registrant and registrant's security holders listed therein	10-K	001-34885	March 28, 2013	4.04
4.05	Amendment No. 3 to Amended and Restated Investors' Rights Agreement, dated March 27, 2013, among registrant and registrant's security holders listed therein	10-Q	001-34885	June 9, 2013	4.02
4.06	Amendment No. 4 to Amended and Restated Investors' Rights Agreement, dated October 16, 2013, among registrant and registrant's security holders listed therein					X
4.07	Amendment No. 5 to Amended and Restated Investors' Rights Agreement, dated December 24, 2013, among registrant and registrant's security holders listed therein					X
4.08	Warrant to Purchase Stock, dated December 23, 2011, issued to ATEL Ventures, Inc.	10-K	001-34885	February 28, 2012	4.07
4.09 ^d	Warrant to Purchase Stock, Dated October 16, 2013, issued to Maxwell (Mauritius) Pte Ltd.					X
4.10	Side Letter, dated June 21, 2010, between registrant and Total Gas & Power USA, SAS	S-1	333-166135	June 23, 2010	4.19
4.11	Agreement, dated February 23, 2012, among registrant, Maxwell (Mauritius) Pte Ltd, Naxyris SA, Biolding Investment SA and Sualk Capital Ltd.	10-Q	001-34885	May 9, 2012	4.02
4.12	Securities Purchase Agreement, dated February 24, 2012, among registrant and certain investment funds affiliated with Fidelity Investments Institutional Services Company, Inc. listed therein (each, a Fidelity Purchaser)	S-3	333-180005	March 9, 2012	4.02
4.13	Form of Unsecured Senior Convertible Promissory Note issued by registrant to the Fidelity Purchasers in the amounts set forth next to each Fidelity Purchaser's name on Schedule I of Exhibit 4.09 hereof	S-3	333-180005	March 9, 2012	4.03
4.14	Registration Rights Agreement, dated February 27, 2012, among registrant and the Fidelity Purchasers	S-3	333-180005	March 9, 2012	4.04
4.15 ^a	Form of Common Stock Purchase Agreement among registrant and certain investors	10-Q	001-34885	August 8, 2012	4.01

131



Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
4.16	Securities Purchase Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	4.01
4.17 ^b	1.5% Senior Unsecured Convertible Notes, dated July 30, 2012, September 14, 2012 and December 24, 2012, respectively, issued by registrant to Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	4.02	b
4.18	Registration Rights Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	4.03
4.19 ^c	Securities Purchase Agreement, dated December 24, 2012, between registrant and certain investors listed therein	10-K	001-34885	March 28, 2013	4.16
4.20 ^c	Follow-On Investment Agreement, dated December 24, 2012, between registrant and Biolding Investment SA	10-K	001-34885	March 28, 2013	4.17
4.21	Securities Purchase Agreement, dated March 27, 2013, between registrant and Biolding Investment SA	10-Q	001-34885	June 9, 2013	4.01
4.22	1.5% Senior Unsecured Convertible Note, dated June 6, 2013, issued by registrant to Total Energies Nouvelles Activités USA (f.k.a. Total Gas & Power USA, SAS)	10-Q	001-34885	August 9, 2013	4.01
4.23	Securities Purchase Agreement, dated August 8, 2013, between registrant, Maxwell (Mauritius) Pte Ltd and Total Energies Nouvelles Activités USA (f.k.a Total Gas & Power USA, SAS)	10-Q	001-34885	November 5, 2013	4.01
4.24 ^d	Amendment No. 1 to Securities Purchase Agreement, dated October 16, 2013, between registrant and other parties named therein					X
4.25	Amendment No. 2 to Securities Purchase Agreement and Tranche I Note Amendment Agreement dated December 24, 2013, between registrant and other parties therein					X
10.01	Form of Indemnity Agreement between registrant and its directors and officers	S-1	333-166135	June 23, 2010	10.01
10.02	Assistance Agreement, dated December 30, 2009, as modified by Assistance Agreement dated March 26, 2010, between registrant and the U.S. Department of Energy, together with schedules and supplements thereto	S-1	333-166135	April 16, 2010	10.09
10.03	Modification No. 2, dated April 19, 2010, to Assistance Agreement between registrant and the U.S. Department of Energy	S-1	333-166135	May 25, 2010	10.13
10.04	Modification Nos. 3-8 to Assistance Agreement between registrant and the U.S. Department of Energy	10-K	001-34885	March 28, 2013	10.10

132



10.05 ^c	Modification No.9, dated January 9, 2013, to Assistance Agreement between registrant and the U.S. Department of Energy	10Q		June 9, 2013	10.01
10.06 ^c	Technology Investment Agreement, dated June 11, 2012, between registrant and The Defense Advanced Research Projects Agency (DARPA)	10-Q	001-34885	August 8, 2012	10.08
10.07 ^d	Modification to Technology Investment Agreement dated November 4, 2013 between registrant and The Defense Advanced Research Project Agency (DARPA)					X

133



Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
10.08 ^ce	Agreement for Credit Opening, dated November 16, 2011, between Amyris Brasil Ltda. and Banco Nacional de Desenvolvimento Econômico e Social - BNDES	10-K	001-34885	February 28, 2012	10.11
10.09 ^c	Corporate Guarantee, dated November 28, 2011, issued by registrant to Banco Nacional de Desenvolvimento Econômico e Social - BNDES	10-K	001-34885	February 28, 2012	10.12
10.10 ^e	Bank Credit Agreement, dated December 21, 2011, between Amyris Brasil Ltda. and Banco Pine S.A.	10-K	001-34885	February 28, 2012	10.13
10.11 ^e	Addendum to the Banking Credit Form, dated February 17, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	May 9, 2012	10.02
10.12 ^e	Addendum to the Banking Credit Form, dated May 17, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	August 8, 2012	10.02
10.13 ^e	Note of Bank Credit, dated June 21, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	August 8, 2012	10.03
10.14 ^ce	Global Derivatives Contract (swap agreement), dated June 15, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	August 8, 2012	10.04
10.15 ^ce	Note of Bank Credit, dated July 13, 2012, between Amyris Brasil Ltda. and Nossa Caixa Desenvolvimento	10-Q	001-34885	November 9, 2012	10.01
10.16 ^ce	Note of Bank Credit, dated July 13, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	November 9, 2012	10.02
10.17 ^e	Fiduciary Conveyance of Movable Goods Agreement, dated July 13, 2012, among Amyris Brasil Ltda., Nossa Caixa Desenvolvimento and Banco Pine S.A.	10-Q	001-34885	November 9, 2012	10.03
10.18	Corporate Guarantee, dated July 13, 2012, issued by registrant to Nossa Caixa Desenvolvimento	10-Q	001-34885	November 9, 2012	10.04
10.19	Corporate Guarantee, dated July 13, 2012, issued by registrant to Banco Pine S.A.	10-Q	001-34885	November 9, 2012	10.05
10.20 ^c	Joint Venture Agreement dated April 14, 2010 among registrant, Amyris Brasil S.A. and Usina São Martinho S.A.	S-1	333-166135	August 31, 2010	10.14
10.21 ^c	Shareholders’ Agreement dated April 14, 2010 among registrant, Amyris Brasil S.A. and Usina São Martinho S.A.	S-1	333-166135	May 25, 2010	10.17
10.22 ^d	Articles of Association of Total Amyris BioSolutions B.V.					X
10.23 ^d	Shareholders Agreement dated December 2, 2013					X
10.24 ^d	License Agreement dated December 2, 2013 between registrant and Total Amyris BioSolutions B.V.					X

134



10.25 ^d	Pledge of Shares dated December 2, 2013 among registrant, Total Energies Nouvelles Activités USA and Total Amyris BioSolutions B.V.	X
10.26 ^d	Escrow Agreement dated December 2, 2013 among registrant, Total Energies Nouvelles Activités USA and Stichting Total Amyris BioSolutions	X
10.27 ^d	1.5% Senior Secured Convertible Note dated December 2, 2013 issued by registrant to Total Energies Nouvelles Activités USA	X

135



Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
10.28	Letter Agreement re: Waiver of Debt Covenants dated December 24, 2013 between registrant and Total Energies Nouvelles Activités USA					X
10.29 ^d	Amended and Restated Master Framework Agreement, dated December 2, 2013, between Amyris and Total Gas & Power USA, SAS					X
10.30	Letter Agreement dated December 2, 2013 relating to the Senior Secured Convertible Notes and the 1.5% Senior Unsecured Convertible Notes due 2017 between the registrant and Total Energies Nouvelles Activités USA					X
10.31	Letter Agreement dated October 4, 2013 between registrant and Total Energies Nouvelles Activités USA					X
10.32	Amendment dated December 1, 2013 to Letter Agreement dated October 4, 2013 between registrant and Total Energies Nouvelles Activités USA					X
10.33	Securities Purchase Agreement, dated August 8, 2013, between registrant, Maxwell (Mauritius) Pte Ltd and Total Energies Nouvelles Activités USA (f.k.a. Total Gas & Power USA, SAS)	10-Q	001-34885	November 5, 2013	4.01
10.34	Voting Agreement, dated August 8, 2013, among registrant and registrant's security holders named therein	10-Q	001-34885	November 5, 2013	4.02
10.35	Securities Purchase Agreement, dated September 20, 2013, between registrant and Naxyris S.A.	10-Q	001-34885	November 5, 2013	4.03
10.36 ^c	Technology License, Development, Research and Collaboration Agreement, dated June 21, 2010, between registrant and Total Gas & Power USA Biotech, Inc.	S-1	333-16135	September 20, 2010	10.46

136



10.37	Letter agreement, dated January 11, 2011, between registrant and Total Gas & Power USA Biotech, Inc.	10-Q	001-34885	May 11, 2011	10.01
10.38 ^c	First Amendment to Technology License, Development, Research and Collaboration Agreement, dated November 23, 2011, between Amyris and Total Gas & Power USA SAS	10-K/A	001-34885	May 2, 2012	10.19
10.39 ^c	Master Framework Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	10.06
10.40 ^c	Second Amendment to the Technology License, Development, Research and Collaboration Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	10.07
10.41 ^c	Joint Venture Implementation Agreement dated June 3, 2011 among Amyris, Inc., Amyris Brasil S.A., Cosan Combustíveis e Lubrificantes S.A. and Cosan S.A. Indústria e Comércio	10-Q	001-34885	August 11, 2011	10.01

137



Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
10.42 ^c	Shareholders' Agreement, dated June 3, 2011, among Amyris Brasil S.A., Cosan Combustíveis e Lubrificantes S.A. and Novvi S.A.	10-Q	001-34885	August 11, 2011	10.02
10.43 ^ce	Agreement for the Supply of Sugarcane Juice and Other Utilities, dated March 18, 2011, between Amyris Brasil Ltda. and Paraíso Bioenergia S.A.	10-Q	001-34885	May 9, 2012	10.06
10.44 ^ce	Lease Agreement, dated March 18, 2011, between Amyris Brasil Ltda. and Paraíso Bioenergia S.A.	10-K	001-34885	March 28, 2013	10.37
10.45 ^ce	Addendum to Lease Agreement, dated April 28, 2011, between Amyris Brasil Ltda. and Paraíso Bioenergia S.A.	10-K	001-34885	March 28, 2013	10.38
10.46	Lease, dated August 22, 2007, between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.17
10.47	First Amendment, dated March 10, 2008, to Lease between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.18
10.48	Second Amendment, dated April 25, 2008, to Lease between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.19
10.49	Third Amendment, dated July 31, 2008, to Lease between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.20
10.50	Fourth Amendment, dated November 14, 2009, to Lease between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.21
10.51	Fifth Amendment, dated October 15, 2010, to Lease between registrant and ES East, LLC	10-K	001-34885	March 14, 2011	10.17
10.52	Sixth Amendment, dated April 30, 2013, to Lease between registrant and ES East, LLC (as successor-in-interest to ES East Associates, LLC)	10-Q	001-34885	August 9, 2013	10.02

138



10.53	Lease dated April 25, 2008 between registrant and EmeryStation Triangle, LLC	S-1	333-166135	April 16, 2010	10.22
10.54	Letter, dated April 25, 2008, amending Lease between registrant and EmeryStation Triangle, LLC	S-1	333-166135	April 16, 2010	10.23
10.55	Second Amendment, dated February 5, 2010, to Lease between registrant and EmeryStation Triangle, LLC	S-1	333-166135	April 16, 2010	10.24
10.56	Third Amendment, dated May 1, 2013, to Lease between registrant and EmeryStation Triangle, LLC	10-Q	001-34885	August 9, 2013	10.03
10.57	Pilot Plant Expansion Right Letter dated December 22, 2008 between registrant and EmeryStation Triangle, LLC	S-1	333-166135	April 16, 2010	10.25
10.58	Lease Agreement, dated August 10, 2011, between Amyris Brasil Ltda. and Techno Park Empreendimentos e Administração Imobiliária Ltda.	10-K	001-34885	February 28, 2012	10.32
10.59	First Amendment to Lease Agreement, dated July 31, 2013, between Amyris Brasil Ltda. and Techno Park Empreendimentos e Administração Imobiliária	10-Q	001-34885	November 5, 2013	10.01
10.60	Private Instrument of Non-Residential Real Estate Lease Agreement, dated March 31, 2008, as amended, between Lucio Tomasiello and Amyris Brasil S.A.	S-1	333-166135	April 16, 2010	10.26
10.61 ^ce	Third Amendment to the Private Instrument of Non Residential Real Estate Lease Agreement, dated October 1, 2012, between Lucio Tomasiello and Amyris Brasil Ltda.	10-K	001-34885	March 28, 2013	0.01051
10.62 ^f	Offer Letter dated September 27, 2006 between registrant and John Melo	S-1	333-16135	April 16, 2010	10.27
10.63 ^f	Amendment, dated December 18, 2008, between registrant and John Melo	S-1	333-16135	April 16, 2010	10.28



Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
10.64 ^f	Offer letter, dated January 17, 2008, between registrant and Paulo Diniz	S-1	333-16135	April 16, 2010	10.31
10.65 ^f	Offer letter, dated March 23, 2012, between registrant and Steven R. Mills	S-1	001-34885	May 9, 2012	10.05
10.66 ^df	Consulting Agreement, dated December 6, 2013, between registrant and Steven R. Mills					X
10.67 ^f	Offer letter, dated November 9, 2009, between registrant and Peter Boynton	10-Q	001-34885	August 11, 2011	10.05
10.68 ^f	Offer letter, dated September 30, 2008, between registrant and Joel Cherry	S-1	333-166135	April 16, 2010	10.29
10.69 ^f	Offer letter, dated March 30, 2011, between registrant and Gary Loeb	10-Q	001-34885	June 9, 2013	10.07
10.70 ^f	Amendment to offer letter, dated May 31 2012, between registrant and Gary Loeb	10-Q	001-34885	June 9, 2013	10.08
10.71 ^f	Offer letter, dated July 29, 2010, between registrant and Mark Patel	10-Q	001-34885	June 9, 2013	10.09
10.72 ^f	Offer Letter, dated January 24, 2005, between registrant and Tamara Tompkins	S-1	333-16135	April 16, 2010	10.35
10.73 ^f	Amendment, dated January 15, 2009, between registrant and Tamara Tompkins	S-1	333-16135	April 16, 2010	10.36

139

140



10.74 ^f	Separation agreement, dated May 1, 2012, between registrant and Tamara Tompkins	10-Q	001-34885	August 8, 2012	10.12
10.75 ^f	2005 Stock Option/Stock Issuance Plan	10-Q	001-34885	November 9, 2011	10.02
10.76 ^f	Form of Notice of Grant of Stock Option under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.38
10.77 ^f	Form of Notice of Grant of Stock Option (non-Exempt) under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.39
10.78 ^f	Form of Notice of Grant of Stock Option (non-US) under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.40
10.79 ^f	Form of Stock Option Agreement under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.41
10.80 ^f	Form of Stock Option Agreement (non-US) under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.42
10.81 ^f	Form of Stock Purchase Agreement under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.43
10.82 ^f	Form of Stock Purchase Agreement (non-US) under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.44
10.83 ^f	2010 Equity Incentive Plan and forms of award agreements thereunder	S-1	333-16135	June 23, 2010	10.46

141

Insert Title Here

Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
10.84 ^f	2010 Employee Stock Purchase Plan and forms of award agreements thereunder	S-1	333-16135	September 20, 2010	10.45
10.85	Master Collaboration Agreement, dated March 13, 2013, between registrant and Firmenich SA	10-Q	001-34885	June 9, 2013	10.02
10.86	Letter agreement, dated March 24, 2013, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	June 9, 2013	10.03
10.87	Amended and Restated Operating Agreement, dated March 26, 2013, among registrant, Cosan US, Inc. and Novvi LLC	10-Q	001-34885	June 9, 2013	10.04
10.88	Termination of the Joint Venture Implementation Agreement, dated March 26, 2013, among registrant, Amyris Brasil Ltda., Cosan Lubrificantes e Especialidades S.A. and Cosan S.A. Indústria E Comércio	10-Q	001-34885	June 9, 2013	10.05
10.89	IP License Agreement, dated as of March 26, 2013, between registrant and Novvi LLC	10-Q	001-34885	June 9, 2013	10.06
10.90	Settlement Agreement, Termination Agreement and Mutual Release, dated June 25, 2013, between registrant and Tate & Lyle Ingredients Americas LLC	10-Q	001-34885	August 9, 2013	10.04
10.91	Modification Agreement, dated September 16, 2013, between registrant and Tate & Lyle Ingredients Americas LLC					X

142

Insert Title Here

10.92	Amyris, Inc. Executive Severance Plan, effective November 6, 2013	X
10.93 ^fg	Compensation arrangements between registrant and its non-employee directors	g
10.94 ^fh	Compensation arrangements between registrant and its executive officers	h
21.01	List of subsidiaries	X
23.01	Consent of PricewaterhouseCoopers LLP, independent registered public accounting firm	X
24.01	Power of Attorney (see signature page to this Form 10-K)	X
31.01	Certification of Chief Executive Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002	X
31.02	Certification of Chief Financial Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002	X
32.01 ⁱ	Certification of Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002	X
32.02 ⁱ	Certification of Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002	X

143



Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
101 ^j	The following materials from registrant's Annual Report on Form 10-K for the fiscal year ended December 31, 2013, formatted in XBRL (Extensible Business Reporting Language): (i) the Consolidated Statements of Operations; (ii) the Consolidated Balance Sheets; (iii) the Consolidated Statements of Comprehensive Income; (iv) the Consolidated Statements of Convertible Preferred Stock, Redeemable Noncontrolling Interest and Equity (Deficit); (v) the Consolidated Statements of Cash Flows; and (vi) Notes to Consolidated Financial Statements					X



a	Substantially identical Common Stock Purchase Agreements, each dated May 18, 2012, were entered into with five separate investors. Registrant has filed the form of such Common Stock Purchase Agreements, which is substantially identical in all material respects to all of such Common Stock Purchase Agreements, except as to the parties thereto and the number of shares.
b	Registrant issued substantially identical 1.5% Senior Unsecured Convertible Notes (or the Notes) to Total Gas & Power USA, SAS on separate dates. Registrant has filed the first of the Notes (number R-1), and has included, with such exhibit, a schedule (updated Schedule A to Exhibit 4.02) identifying each of the Notes and setting forth the material details in which the other Note(s) differ from the filed Note (i.e., the dates of issuance and the amounts of the Notes).
c	Portions of this exhibit, which have been granted confidential treatment by the Securities and Exchange Commission, have been omitted.
d	Portions of this exhibit have been omitted pending a determination by the Securities and Exchange Commission as to whether these portions should be granted confidential treatment.
e	Translation to English from Portuguese or Dutch, as applicable, in accordance with Rule 12b-12(d) of the regulations promulgated by the Securities and Exchange Commission under the Securities Exchange Act of 1934, as amended (or the Exchange Act).
f	Indicates management contract or compensatory plan or arrangement.
g	Description contained under the heading "Director Compensation" in registrant's definitive proxy materials filed with the Securities and Exchange Commission on April 12, 2012 is incorporated herein by reference.
h	Descriptions contained under the heading "Executive Compensation" in registrant's definitive proxy materials filed with the Securities and Exchange Commission on April 16, 2013.
i	This certification shall not be deemed “filed” for purposes of Section 18 of the Exchange Act or otherwise subject to the liability of that Section, nor shall it be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act.
j	Pursuant to applicable securities laws and regulations, registrant is deemed to have complied with the reporting obligation relating to the submission of interactive data files in such exhibits and is not subject to liability under any anti-fraud provisions of the federal securities laws as long as registrant has made a good faith attempt to comply with the submission requirements and promptly amends the interactive data files after becoming aware that the interactive data files fails to comply with the submission requirements. These interactive data files are deemed not filed or part of a registration statement or prospectus for purposes of sections 11 or 12 of the Securities Act, are deemed not filed for purposes of section 18 of the Exchange Act and otherwise are not subject to liability under these sections.


(c)	Financial statements and schedules.

Reference is made to Item 15(a) above.

144

145

SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized in the city of Emeryville, County of Alameda, State of California on April 1, 2014.



Dated: April 1, 2014	Amyris, Inc.

	/s/ JOHN G. MELO
	John G. Melo
	President and Chief Executive Officer
	(Principal Executive Officer)

POWER OF ATTORNEY

KNOW ALL MEN BY THESE PRESENTS, that each person whose signature appears below constitutes and appoints John Melo and Paulo Diniz as his or her true and lawful attorneys-in-fact and agents, with full power of substitution and resubstitution, for him or her and in his or her name, place and stead, in any and all capacities, to sign any and all amendments to this Report on Form 10-K, and to file the same, with all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents full power and authority to do and perform each and every act and thing requisite and necessary to be done in connection therewith, as fully to all intents and purposes as he might or could do in person, hereby ratifying and confirming all that said attorneys-in-fact and agents, or their substitute or substitutes, may lawfully do or cause to be done by virtue hereof.

Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the Registrant and in the capacities and on the dates indicated.

146



Signature	Title	Date


/s/ JOHN MELO John Melo	Director, President and Chief Executive Officer (Principal Executive Officer)	April 1, 2014

/s/ PAULO DINIZ Paulo Diniz	Interim Chief Financial Officer (Principal Financial Officer)	April 1, 2014

/s/ KAREN WEAVER Karen Weaver	Vice President, Corporate Controller (Principal Accounting Officer)	April 1, 2014

/s/ PHILIPPE BOISSEAU Philippe Boisseau	Director	April 1, 2014

/s/ NAM-HAI CHUA Nam-Hai Chua	Director	April 1, 2014

/s/ JOHN DOERR John Doerr	Director	April 1, 2014

/s/ GEOFFREY DUYK Geoffrey Duyk	Director	April 1, 2014

/s/ ARTHUR LEVINSON Arthur Levinson	Director	April 1, 2014

/s/ CAROL PIWNICA Carole Piwnica	Director	April 1, 2014

/s/ FERNANDO REINACH Fernando Reinach	Director	April 1, 2014

__________________________________ HH Sheikh Abdullah bin Khalifa Al Thani	Director	April 1, 2014

/s/ R. NEIL WILLIAMS R. Neil Williams	Director	April 1, 2014

147

EXHIBIT INDEX



Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
3.01	Restated Certificate of Incorporation	10-Q	001-34885	November 10, 2010	3.01
3.02	Restated Bylaws	10-Q	001-34885	November 10, 2010	3.02
4.01	Form of Stock Certificate	S-1	333-166135	July 6, 2010	4.01
4.02	Amended and Restated Investors’ Rights Agreement, dated June 21, 2010, among registrant and its security holders listed therein	S-1	333-166135	June 23, 2010	4.02
4.03	First Amendment to Amended and Restated Investors' Rights Agreement, dated February 23, 2012, among registrant and registrant's security holders listed therein	S-3	333-180005	March 9, 2012	4.06
4.04	Amendment No. 2 to Amended and Restated Investors' Rights Agreement, dated December 24, 2012, among registrant and registrant's security holders listed therein	10-K	001-34885	March 28, 2013	4.04
4.05	Amendment No. 3 to Amended and Restated Investors' Rights Agreement, dated March 27, 2013, among registrant and registrant's security holders listed therein	10-Q	001-34885	June 9, 2013	4.02
4.06	Amendment No. 4 to Amended and Restated Investors' Rights Agreement, dated October 16, 2013, among registrant and registrant's security holders listed therein					X
4.07	Amendment No. 5 to Amended and Restated Investors' Rights Agreement, dated December 24, 2013, among registrant and registrant's security holders listed therein					X
4.08	Warrant to Purchase Stock, dated December 23, 2011, issued to ATEL Ventures, Inc.	10-K	001-34885	February 28, 2012	4.07
4.09 ^d	Warrant to Purchase Stock, Dated October 16, 2013, issued to Maxwell (Mauritius) Pte Ltd.					X
4.10	Side Letter, dated June 21, 2010, between registrant and Total Gas & Power USA, SAS	S-1	333-166135	June 23, 2010	4.19
4.11	Agreement, dated February 23, 2012, among registrant, Maxwell (Mauritius) Pte Ltd, Naxyris SA, Biolding Investment SA and Sualk Capital Ltd.	10-Q	001-34885	May 9, 2012	4.02
4.12	Securities Purchase Agreement, dated February 24, 2012, among registrant and certain investment funds affiliated with Fidelity Investments Institutional Services Company, Inc. listed therein (each, a Fidelity Purchaser)	S-3	333-180005	March 9, 2012	4.02
4.13	Form of Unsecured Senior Convertible Promissory Note issued by registrant to the Fidelity Purchasers in the amounts set forth next to each Fidelity Purchaser's name on Schedule I of Exhibit 4.09 hereof	S-3	333-180005	March 9, 2012	4.03
4.14	Registration Rights Agreement, dated February 27, 2012, among registrant and the Fidelity Purchasers	S-3	333-180005	March 9, 2012	4.04
4.15 ^a	Form of Common Stock Purchase Agreement among registrant and certain investors	10-Q	001-34885	August 8, 2012	4.01

148



Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
4.16	Securities Purchase Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	4.01
4.17 ^b	1.5% Senior Unsecured Convertible Notes, dated July 30, 2012, September 14, 2012 and December 24, 2012, respectively, issued by registrant to Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	4.02	b
4.18	Registration Rights Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	4.03
4.19 ^c	Securities Purchase Agreement, dated December 24, 2012, between registrant and certain investors listed therein	10-K	001-34885	March 28, 2013	4.16
4.20 ^c	Follow-On Investment Agreement, dated December 24, 2012, between registrant and Biolding Investment SA	10-K	001-34885	March 28, 2013	4.17
4.21	Securities Purchase Agreement, dated March 27, 2013, between registrant and Biolding Investment SA	10-Q	001-34885	June 9, 2013	4.01
4.22	1.5% Senior Unsecured Convertible Note, dated June 6, 2013, issued by registrant to Total Energies Nouvelles Activités USA (f.k.a. Total Gas & Power USA, SAS)	10-Q	001-34885	August 9, 2013	4.01
4.23	Securities Purchase Agreement, dated August 8, 2013, between registrant, Maxwell (Mauritius) Pte Ltd and Total Energies Nouvelles Activités USA (f.k.a Total Gas & Power USA, SAS)	10-Q	001-34885	November 5, 2013	4.01

149



4.24 ^d	Amendment No. 1 to Securities Purchase Agreement, dated October 16, 2013, between registrant and other parties named therein					X
4.25	Amendment No. 2 to Securities Purchase Agreement and Tranche I Note Amendment Agreement dated December 24, 2013, between registrant and other parties therein					X
10.01	Form of Indemnity Agreement between registrant and its directors and officers	S-1	333-166135	June 23, 2010	10.01
10.02	Assistance Agreement, dated December 30, 2009, as modified by Assistance Agreement dated March 26, 2010, between registrant and the U.S. Department of Energy, together with schedules and supplements thereto	S-1	333-166135	April 16, 2010	10.09
10.03	Modification No. 2, dated April 19, 2010, to Assistance Agreement between registrant and the U.S. Department of Energy	S-1	333-166135	May 25, 2010	10.13
10.04	Modification Nos. 3-8 to Assistance Agreement between registrant and the U.S. Department of Energy	10-K	001-34885	March 28, 2013	10.10
10.05 ^c	Modification No.9, dated January 9, 2013, to Assistance Agreement between registrant and the U.S. Department of Energy	10Q		June 9, 2013	10.01
10.06 ^c	Technology Investment Agreement, dated June 11, 2012, between registrant and The Defense Advanced Research Projects Agency (DARPA)	10-Q	001-34885	August 8, 2012	10.08
10.07 ^d	Modification to Technology Investment Agreement dated November 4, 2013 between registrant and The Defense Advanced Research Project Agency (DARPA)					X

150



Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
10.08 ^ce	Agreement for Credit Opening, dated November 16, 2011, between Amyris Brasil Ltda. and Banco Nacional de Desenvolvimento Econômico e Social - BNDES	10-K	001-34885	February 28, 2012	10.11
10.09 ^c	Corporate Guarantee, dated November 28, 2011, issued by registrant to Banco Nacional de Desenvolvimento Econômico e Social - BNDES	10-K	001-34885	February 28, 2012	10.12
10.10 ^e	Bank Credit Agreement, dated December 21, 2011, between Amyris Brasil Ltda. and Banco Pine S.A.	10-K	001-34885	February 28, 2012	10.13
10.11 ^e	Addendum to the Banking Credit Form, dated February 17, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	May 9, 2012	10.02
10.12 ^e	Addendum to the Banking Credit Form, dated May 17, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	August 8, 2012	10.02
10.13 ^e	Note of Bank Credit, dated June 21, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	August 8, 2012	10.03
10.14 ^ce	Global Derivatives Contract (swap agreement), dated June 15, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	August 8, 2012	10.04
10.15 ^ce	Note of Bank Credit, dated July 13, 2012, between Amyris Brasil Ltda. and Nossa Caixa Desenvolvimento	10-Q	001-34885	November 9, 2012	10.01
10.16 ^ce	Note of Bank Credit, dated July 13, 2012, between Amyris Brasil Ltda. and Banco Pine S.A.	10-Q	001-34885	November 9, 2012	10.02
10.17 ^e	Fiduciary Conveyance of Movable Goods Agreement, dated July 13, 2012, among Amyris Brasil Ltda., Nossa Caixa Desenvolvimento and Banco Pine S.A.	10-Q	001-34885	November 9, 2012	10.03
10.18	Corporate Guarantee, dated July 13, 2012, issued by registrant to Nossa Caixa Desenvolvimento	10-Q	001-34885	November 9, 2012	10.04
10.19	Corporate Guarantee, dated July 13, 2012, issued by registrant to Banco Pine S.A.	10-Q	001-34885	November 9, 2012	10.05
10.20 ^c	Joint Venture Agreement dated April 14, 2010 among registrant, Amyris Brasil S.A. and Usina São Martinho S.A.	S-1	333-166135	August 31, 2010	10.14
10.21 ^c	Shareholders’ Agreement dated April 14, 2010 among registrant, Amyris Brasil S.A. and Usina São Martinho S.A.	S-1	333-166135	May 25, 2010	10.17
10.22 ^d	Articles of Association of Total Amyris BioSolutions B.V.					X
10.23 ^d	Shareholders Agreement dated December 2, 2013					X
10.24 ^d	License Agreement dated December 2, 2013 between registrant and Total Amyris BioSolutions B.V.					X
10.25 ^d	Pledge of Shares dated December 2, 2013 among registrant, Total Energies Nouvelles Activités USA and Total Amyris BioSolutions B.V.					X

151



10.26 ^d	Escrow Agreement dated December 2, 2013 among registrant, Total Energies Nouvelles Activités USA and Stichting Total Amyris BioSolutions	X
10.27 ^d	1.5% Senior Secured Convertible Note dated December 2, 2013 issued by registrant to Total Energies Nouvelles Activités USA	X

152



Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
10.28	Letter Agreement re: Waiver of Debt Covenants dated December 24, 2013 between registrant and Total Energies Nouvelles Activités USA					X
10.29 ^d	Amended and Restated Master Framework Agreement, dated December 2, 2013, between Amyris and Total Gas & Power USA, SAS					X
10.30	Letter Agreement dated December 2, 2013 relating to the Senior Secured Convertible Notes and the 1.5% Senior Unsecured Convertible Notes due 2017 between the registrant and Total Energies Nouvelles Activités USA					X
10.31	Letter Agreement dated October 4, 2013 between registrant and Total Energies Nouvelles Activités USA					X
10.32	Amendment dated December 1, 2013 to Letter Agreement dated October 4, 2013 between registrant and Total Energies Nouvelles Activités USA					X
10.33	Securities Purchase Agreement, dated August 8, 2013, between registrant, Maxwell (Mauritius) Pte Ltd and Total Energies Nouvelles Activités USA (f.k.a. Total Gas & Power USA, SAS)	10-Q	001-34885	November 5, 2013	4.01
10.34	Voting Agreement, dated August 8, 2013, among registrant and registrant's security holders named therein	10-Q	001-34885	November 5, 2013	4.02
10.35	Securities Purchase Agreement, dated September 20, 2013, between registrant and Naxyris S.A.	10-Q	001-34885	November 5, 2013	4.03
10.36 ^c	Technology License, Development, Research and Collaboration Agreement, dated June 21, 2010, between registrant and Total Gas & Power USA Biotech, Inc.	S-1	333-16135	September 20, 2010	10.46

153



10.37	Letter agreement, dated January 11, 2011, between registrant and Total Gas & Power USA Biotech, Inc.	10-Q	001-34885	May 11, 2011	10.01
10.38 ^c	First Amendment to Technology License, Development, Research and Collaboration Agreement, dated November 23, 2011, between Amyris and Total Gas & Power USA SAS	10-K/A	001-34885	May 2, 2012	10.19
10.39 ^c	Master Framework Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	10.06
10.40 ^c	Second Amendment to the Technology License, Development, Research and Collaboration Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	10.07
10.41 ^c	Joint Venture Implementation Agreement dated June 3, 2011 among Amyris, Inc., Amyris Brasil S.A., Cosan Combustíveis e Lubrificantes S.A. and Cosan S.A. Indústria e Comércio	10-Q	001-34885	August 11, 2011	10.01

154



Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
10.42 ^c	Shareholders' Agreement, dated June 3, 2011, among Amyris Brasil S.A., Cosan Combustíveis e Lubrificantes S.A. and Novvi S.A.	10-Q	001-34885	August 11, 2011	10.02
10.43 ^ce	Agreement for the Supply of Sugarcane Juice and Other Utilities, dated March 18, 2011, between Amyris Brasil Ltda. and Paraíso Bioenergia S.A.	10-Q	001-34885	May 9, 2012	10.06
10.44 ^ce	Lease Agreement, dated March 18, 2011, between Amyris Brasil Ltda. and Paraíso Bioenergia S.A.	10-K	001-34885	March 28, 2013	10.37
10.45 ^ce	Addendum to Lease Agreement, dated April 28, 2011, between Amyris Brasil Ltda. and Paraíso Bioenergia S.A.	10-K	001-34885	March 28, 2013	10.38
10.46	Lease, dated August 22, 2007, between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.17
10.47	First Amendment, dated March 10, 2008, to Lease between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.18
10.48	Second Amendment, dated April 25, 2008, to Lease between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.19
10.49	Third Amendment, dated July 31, 2008, to Lease between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.20
10.50	Fourth Amendment, dated November 14, 2009, to Lease between registrant and ES East Associates, LLC	S-1	333-166135	April 16, 2010	10.21
10.51	Fifth Amendment, dated October 15, 2010, to Lease between registrant and ES East, LLC	10-K	001-34885	March 14, 2011	10.17
10.52	Sixth Amendment, dated April 30, 2013, to Lease between registrant and ES East, LLC (as successor-in-interest to ES East Associates, LLC)	10-Q	001-34885	August 9, 2013	10.02
10.53	Lease dated April 25, 2008 between registrant and EmeryStation Triangle, LLC	S-1	333-166135	April 16, 2010	10.22

155



10.54	Letter, dated April 25, 2008, amending Lease between registrant and EmeryStation Triangle, LLC	S-1	333-166135	April 16, 2010	10.23
10.55	Second Amendment, dated February 5, 2010, to Lease between registrant and EmeryStation Triangle, LLC	S-1	333-166135	April 16, 2010	10.24
10.56	Third Amendment, dated May 1, 2013, to Lease between registrant and EmeryStation Triangle, LLC	10-Q	001-34885	August 9, 2013	10.03
10.57	Pilot Plant Expansion Right Letter dated December 22, 2008 between registrant and EmeryStation Triangle, LLC	S-1	333-166135	April 16, 2010	10.25
10.58	Lease Agreement, dated August 10, 2011, between Amyris Brasil Ltda. and Techno Park Empreendimentos e Administração Imobiliária Ltda.	10-K	001-34885	February 28, 2012	10.32
10.59	First Amendment to Lease Agreement, dated July 31, 2013, between Amyris Brasil Ltda. and Techno Park Empreendimentos e Administração Imobiliária	10-Q	001-34885	November 5, 2013	10.01
10.60	Private Instrument of Non-Residential Real Estate Lease Agreement, dated March 31, 2008, as amended, between Lucio Tomasiello and Amyris Brasil S.A.	S-1	333-166135	April 16, 2010	10.26
10.61 ^ce	Third Amendment to the Private Instrument of Non Residential Real Estate Lease Agreement, dated October 1, 2012, between Lucio Tomasiello and Amyris Brasil Ltda.	10-K	001-34885	March 28, 2013	0.01051
10.62 ^f	Offer Letter dated September 27, 2006 between registrant and John Melo	S-1	333-16135	April 16, 2010	10.27
10.63 ^f	Amendment, dated December 18, 2008, between registrant and John Melo	S-1	333-16135	April 16, 2010	10.28



Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith

156



10.64 ^f	Offer letter, dated January 17, 2008, between registrant and Paulo Diniz	S-1	333-16135	April 16, 2010	10.31
10.65 ^f	Offer letter, dated March 23, 2012, between registrant and Steven R. Mills	S-1	001-34885	May 9, 2012	10.05
10.66 ^df	Consulting Agreement, dated December 6, 2013, between registrant and Steven R. Mills					X
10.67 ^f	Offer letter, dated November 9, 2009, between registrant and Peter Boynton	10-Q	001-34885	August 11, 2011	10.05
10.68 ^f	Offer letter, dated September 30, 2008, between registrant and Joel Cherry	S-1	333-166135	April 16, 2010	10.29
10.69 ^f	Offer letter, dated March 30, 2011, between registrant and Gary Loeb	10-Q	001-34885	June 9, 2013	10.07
10.70 ^f	Amendment to offer letter, dated May 31 2012, between registrant and Gary Loeb	10-Q	001-34885	June 9, 2013	10.08
10.71 ^f	Offer letter, dated July 29, 2010, between registrant and Mark Patel	10-Q	001-34885	June 9, 2013	10.09
10.72 ^f	Offer Letter, dated January 24, 2005, between registrant and Tamara Tompkins	S-1	333-16135	April 16, 2010	10.35
10.73 ^f	Amendment, dated January 15, 2009, between registrant and Tamara Tompkins	S-1	333-16135	April 16, 2010	10.36
10.74 ^f	Separation agreement, dated May 1, 2012, between registrant and Tamara Tompkins	10-Q	001-34885	August 8, 2012	10.12
10.75 ^f	2005 Stock Option/Stock Issuance Plan	10-Q	001-34885	November 9, 2011	10.02
10.76 ^f	Form of Notice of Grant of Stock Option under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.38
10.77 ^f	Form of Notice of Grant of Stock Option (non-Exempt) under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.39

157



10.78 ^f	Form of Notice of Grant of Stock Option (non-US) under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.40
10.79 ^f	Form of Stock Option Agreement under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.41
10.80 ^f	Form of Stock Option Agreement (non-US) under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.42
10.81 ^f	Form of Stock Purchase Agreement under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.43
10.82 ^f	Form of Stock Purchase Agreement (non-US) under registrant’s 2005 Stock Option/Stock Issuance Plan	S-1	333-16135	April 16, 2010	10.44
10.83 ^f	2010 Equity Incentive Plan and forms of award agreements thereunder	S-1	333-16135	June 23, 2010	10.46
10.84 ^f	2010 Employee Stock Purchase Plan and forms of award agreements thereunder	S-1	333-16135	September 20, 2010	10.45
10.85	Master Collaboration Agreement, dated March 13, 2013, between registrant and Firmenich SA	10-Q	001-34885	June 9, 2013	10.02
10.86	Letter agreement, dated March 24, 2013, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	June 9, 2013	10.03
10.87	Amended and Restated Operating Agreement, dated March 26, 2013, among registrant, Cosan US, Inc. and Novvi LLC	10-Q	001-34885	June 9, 2013	10.04
10.88	Termination of the Joint Venture Implementation Agreement, dated March 26, 2013, among registrant, Amyris Brasil Ltda., Cosan Lubrificantes e Especialidades S.A. and Cosan S.A. Indústria E Comércio	10-Q	001-34885	June 9, 2013	10.05

158



Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
10.89	IP License Agreement, dated as of March 26, 2013, between registrant and Novvi LLC	10-Q	001-34885	June 9, 2013	10.06
10.90	Settlement Agreement, Termination Agreement and Mutual Release, dated June 25, 2013, between registrant and Tate & Lyle Ingredients Americas LLC	10-Q	001-34885	August 9, 2013	10.04
10.91	Modification Agreement, dated September 16, 2013, between registrant and Tate & Lyle Ingredients Americas LLC					X
10.92	Amyris, Inc. Executive Severance Plan, effective November 6, 2013					X
10.93 ^fg	Compensation arrangements between registrant and its non-employee directors					g
10.94 ^fh	Compensation arrangements between registrant and its executive officers					h
21.01	List of subsidiaries					X
23.01	Consent of PricewaterhouseCoopers LLP, independent registered public accounting firm					X
24.01	Power of Attorney (see signature page to this Form 10-K)					X
31.01	Certification of Chief Executive Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002					X

159



31.02	Certification of Chief Financial Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002	X
32.01 ⁱ	Certification of Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002	X
32.02 ⁱ	Certification of Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002	X
101 ^j	The following materials from registrant's Annual Report on Form 10-K for the fiscal year ended December 31, 2013, formatted in XBRL (Extensible Business Reporting Language): (i) the Consolidated Statements of Operations; (ii) the Consolidated Balance Sheets; (iii) the Consolidated Statements of Comprehensive Income; (iv) the Consolidated Statements of Convertible Preferred Stock, Redeemable Noncontrolling Interest and Equity (Deficit); (v) the Consolidated Statements of Cash Flows; and (vi) Notes to Consolidated Financial Statements	X

160



a	Substantially identical Common Stock Purchase Agreements, each dated May 18, 2012, were entered into with five separate investors. Registrant has filed the form of such Common Stock Purchase Agreements, which is substantially identical in all material respects to all of such Common Stock Purchase Agreements, except as to the parties thereto and the number of shares.
b	Registrant issued substantially identical 1.5% Senior Unsecured Convertible Notes (or the Notes) to Total Gas & Power USA, SAS on separate dates. Registrant has filed the first of the Notes (number R-1), and has included, with such exhibit, a schedule (updated Schedule A to Exhibit 4.02) identifying each of the Notes and setting forth the material details in which the other Note(s) differ from the filed Note (i.e., the dates of issuance and the amounts of the Notes).
c	Portions of this exhibit, which have been granted confidential treatment by the Securities and Exchange Commission, have been omitted.
d	Portions of this exhibit have been omitted pending a determination by the Securities and Exchange Commission as to whether these portions should be granted confidential treatment.
e	Translation to English from Portuguese or Dutch, as applicable, in accordance with Rule 12b-12(d) of the regulations promulgated by the Securities and Exchange Commission under the Securities Exchange Act of 1934, as amended (or the Exchange Act).
f	Indicates management contract or compensatory plan or arrangement.
g	Description contained under the heading "Director Compensation" in registrant's definitive proxy materials filed with the Securities and Exchange Commission on April 12, 2012 is incorporated herein by reference.
h	Descriptions contained under the heading "Executive Compensation" in registrant's definitive proxy materials filed with the Securities and Exchange Commission on April 16, 2013.
i	This certification shall not be deemed “filed” for purposes of Section 18 of the Exchange Act or otherwise subject to the liability of that Section, nor shall it be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act.
j	Pursuant to applicable securities laws and regulations, registrant is deemed to have complied with the reporting obligation relating to the submission of interactive data files in such exhibits and is not subject to liability under any anti-fraud provisions of the federal securities laws as long as registrant has made a good faith attempt to comply with the submission requirements and promptly amends the interactive data files after becoming aware that the interactive data files fails to comply with the submission requirements. These interactive data files are deemed not filed or part of a registration statement or prospectus for purposes of sections 11 or 12 of the Securities Act, are deemed not filed for purposes of section 18 of the Exchange Act and otherwise are not subject to liability under these sections.

161

AMYRIS, INC.

AMENDMENT NO. 2 TO AMENDED AND RESTATED INVESTORS' RIGHTS AGREEMENT

This Amendment No. 2 to the Amended and Restated Investors' Rights Agreement (this “ Amendment ”) is made and entered into as of December 24, 2012, by and among Amyris, Inc., a Delaware corporation (the “ Company ”), the Investors and the Common Holders.

RECITALS

WHEREAS, the Company, the Investors and the Common Holders are parties to that certain Amended and Restated Investors' Rights Agreement dated June 21, 2010 (the “ Rights Agreement ”). Capitalized terms used in this Amendment and not otherwise defined herein have the meanings ascribed to them in the Rights Agreement.

WHEREAS, the Company, certain Investors and certain Common Holders are parties to that certain Amendment No. 1 to Amended and Restated Investors' Rights Agreement, dated as of February 23, 2012 (“ Amendment No. 1 ”), pursuant to which the Rights Agreement was amended and certain parties were added.

WHEREAS, the Company, the Investors and the Common Holders desire to make certain additional amendments to the Rights Agreement.

WHEREAS, pursuant to Section 3.7 of the Rights Agreement, the Rights Agreement may be amended with the written consent of the (i) Company, and (ii) the holders of a majority of the Registrable Securities currently outstanding (together, the “ Requisite Majority ”).

WHEREAS, the undersigned parties constitute the Requisite Majority.

NOW, THEREFORE, the parties hereby agree as follows:

1. AMENDMENT OF SECTION 1.1(c) OF THE RIGHTS AGREEMENT . Section 1.1(c) of the Rights Agreement shall be deleted in its entirety and replaced with the following:

2. AMENDMENT OF SECTION 1.1(f) OF THE RIGHTS AGREEMENT . Section 1.1(f) of the Rights Agreement shall be deleted in its entirety and replaced with the following:

“The term “Registrable Securities” means: (i) any Common Stock issued or issuable upon conversion of the Preferred Stock of the Company, (ii) other than with respect to Sections 1.2, 1.12, 1.13 and Section 2 hereof, any Common Stock of the Company held by the Common Holders, (iii) the Common Shares, as defined in that certain Stock Transfer Agreement, dated December 24, 2009, by and among the Company, certain holders of the Company's Preferred Stock and certain holders of the Company's Common Stock, (iv) shares of Common Stock issued pursuant to that certain Securities Purchase Agreement dated February 22, 2012 by and among the Company and the February Purchasers, (v) shares of Common Stock issued pursuant to that certain Securities Purchase Agreement dated December 24, 2012 by and among the Company and the December Purchasers, (vi) any Common Stock of the Company issued as (or issuable upon the conversion or exercise of any warrant, right or other security that is issued as) a dividend or other distribution with respect to, or in exchange for, or in replacement of, the securities set forth in subsection (i), (ii), (iii), (iv) or (v) hereof, excluding, however, any Registrable Securities which (A) have previously been registered or which have been sold to the public either pursuant to a registration statement or Rule 144, (B) which have been sold in a private transaction in which the transferor's rights under this Agreement are not assigned, or (C) held by a Holder (together with its affiliates) if, as reflected on the Company's list of stockholders, such Holder (together with its affiliates) holds less than 1% of the Company's outstanding Common Stock (treating all shares of Preferred Stock on an as converted basis)”

3. FULL FORCE AND EFFECT . Except as expressly modified by this Amendment, the terms of the Rights Agreement shall remain in full force and effect.

4. GOVERNING LAW . This Amendment shall be governed by and construed under the internal laws of the State of California as applied to agreements among California residents entered into and to be performed entirely within California, without reference to principles of conflict of laws or choice of laws.

5. INTEGRATION . This Amendment and the Rights Agreement and the documents referred to herein and therein and the exhibits and schedules thereto, constitute the entire agreement and understanding of the parties with respect to the subject matter hereof, and supersede all prior understandings and agreements, whether oral or written, between or among the parties hereto with respect to the specific subject matter hereof.

6. COUNTERPARTS; FACSIMILE . This Amendment may be executed in two (2) or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. This Amendment may be executed and delivered by facsimile, or by email in portable document format (.pdf) and delivery of the signature page by such method will be deemed to have the same effect as if the original signature had been delivered to the other parties.

[Remainder of Page Intentionally Left Blank]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

COMPANY:

AMYRIS, INC.

By: /s/ John Melo

John Melo, Chief Executive Officer

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTOR:

By: /s/ Christoph Piel /s/ Jacques Reckinger

Name: Christoph Piel Jacques Reckinger

Title: Director

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

TPG BIOTECHNOLOGY PARTNERS II, L.P.

By: TPG Biotechnology GenPar II, L.P., its general partner

By: TPG Biotechnology GenPar II Advisors, LLC, its general partner

By: /s/ Ronald Cami

Name: Ronald Cami

Title: Vice President

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTOR:

MAXWELL (MAURITIUS) PTE LTD

By: /s/ Fidah Alsagoff

Name: Fidah Alsagoff

Title: Authorised Signatory

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTOR:

SUALK CAPITAL LTD

By: /s/ Fernando Reinach

Name: Fernando Reinach

Title: Director

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTOR:

KPCB HOLDINGS, INC., AS NOMINEE

By: /s/ Paul M. Vronsky

Name: Paul M. Vronsky

Title: General Counsel

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTOR:

FORIS VENTURES, LLC

By: /s/ Barbara S. Hager

Name: Barbara S. Hager

Title: Manager

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTOR:

TOTAL GAS & POWER USA, SAS

By: /s/ Arnaud Chaperon

Name: Arnaud Chaperon

Title: President

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

By: /s/ Sheikh Abdullah bin Khalifa Al Thani

Name: Biolding Investment SA -

Sheikh Abdullah bin Khalifa Al Thani

Title: Director

[Signature Page to Amendment No. 2 to Amyris, Inc. Amended and Restated Investors' Rights Agreement]

AMYRIS, INC.

AMENDMENT NO. 4 TO AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT

This Amendment No. 4 to the Amended and Restated Investors’ Rights Agreement (this “ Amendment ”) is made and entered into as of October 16, 2013, by and among Amyris, Inc., a Delaware corporation (the “ Company ”), the Investors and the Common Holders.

RECITALS

WHEREAS, the Company, the Investors and the Common Holders are parties to that certain Amended and Restated Investors’ Rights Agreement dated June 21, 2010 (the “ Rights Agreement ”). Capitalized terms used in this Amendment and not otherwise defined herein have the meanings ascribed to them in the Rights Agreement.

WHEREAS, the Company, certain Investors and certain Common Holders are parties to that certain Amendment No. 1 to Amended and Restated Investors’ Rights Agreement, dated as of February 23, 2012 (“ Amendment No. 1 ”), pursuant to which the Rights Agreement was amended and certain parties were added thereto.

WHEREAS, the Company, certain Investors and certain Common Holders are parties to that certain Amendment No. 2 to Amended and Restated Investors’ Rights Agreement, dated as of December 24, 2012 (“ Amendment No. 2 ”), pursuant to which the Rights Agreement was amended and certain parties were added thereto.

WHEREAS, the Company, certain Investors and certain Common Holders are parties to that certain Amendment No. 3 to Amended and Restated Investors’ Rights Agreement, dated as of March 27, 2013 (“ Amendment No. 3 ”), pursuant to which the Rights Agreement was amended and certain parties were added thereto.

WHEREAS, the Company, the Investors and the Common Holders desire to make certain additional amendments to the Rights Agreement.

WHEREAS, the undersigned parties constitute the Requisite Majority.

NOW, THEREFORE, the parties hereby agree as follows:

1. AMENDMENT OF SECTION 1.1(c) OF THE RIGHTS AGREEMENT . Section 1.1(c) of the Rights Agreement shall be deleted in its entirety and replaced with the following:

Registrable Securities or any assignee thereof in accordance with Section 1.13 hereof, (iii) each “Purchaser” as such term is defined in that certain Securities Purchase Agreement dated as of February 22, 2012 by and among the Company and the purchasers identified therein (each, a “ February Purchaser ”), (iv) each “Purchaser” as such term is defined in that certain Securities Purchase Agreement dated December 24, 2012 by and among the Company and purchasers identified therein (each, a “ December Purchaser ”), (v) each “Purchaser” as such term is defined in that certain Securities Purchase Agreement dated March 27, 2013 by and among the Company and purchasers identified therein (each, a “ March Purchaser ”),” and (vi) each “Purchaser” as such term is defined in that certain Securities Purchase Agreement dated August 8, 2013, as the same may be amended from time to time, (the “ August 2013 Purchase Agreement ”) by and among the Company and purchasers identified therein (each, an “ August Note Purchaser ”) and (vii) the holder of that certain warrant to purchase shares of Common Stock of the Company to be issued pursuant to Section 6.1(l) of the August Purchase Agreement (the “ Temasek Warrant ”).”

2. AMENDMENT OF SECTION 1.1(f) OF THE RIGHTS AGREEMENT . Section 1.1(f) of the Rights Agreement shall be deleted in its entirety and replaced with the following:

“The term “Registrable Securities” means: (i) any Common Stock issued or issuable upon conversion of the Preferred Stock of the Company, (ii) other than with respect to Sections 1.2, 1.12, 1.13 and Section 2 hereof, any Common Stock of the Company held by the Common Holders, (iii) the Common Shares, as defined in that certain Stock Transfer Agreement, dated December 24, 2009, by and among the Company, certain holders of the Company’s Preferred Stock and certain holders of the Company’s Common Stock, (iv) shares of Common Stock issued pursuant to that certain Securities Purchase Agreement dated as of February 22, 2012 by and among the Company and the February Purchasers, (v) shares of Common Stock issued pursuant to that certain Securities Purchase Agreement dated December 24, 2012 by and among the Company and the December Purchasers, (vi) shares of Common Stock issued pursuant to that certain Securities Purchase Agreement dated March 27, 2013 by and among the Company and the March Purchasers, (vii) Common Stock issued or issuable upon conversion of the convertible promissory notes issued to the August Note Purchasers pursuant to the August 2013 Purchase Agreement; (viii) Common Stock issued or issuable upon conversion of the Temasek Warrant (ix) any Common Stock of the Company issued as (or issuable upon the conversion or exercise of any warrant, right or other security that is issued as) a dividend or other distribution with respect to, or in exchange for, or in replacement of, the securities set forth in subsection (i), (ii), (iii), (iv), (v), (vi),(vii) or (viii) hereof, excluding, however, any Registrable Securities which (A) have previously been registered or which have been sold to the public either pursuant to a registration statement or Rule 144, (B) which have been sold in a private transaction in which the transferor’s rights under this Agreement are not assigned, or (C) held by a Holder (together with its affiliates) if, as reflected on the Company’s list of stockholders, such Holder (together with its affiliates) holds less than 1% of the Company’s outstanding Common Stock (treating all shares of Preferred Stock on an as converted basis).”

3. ADDITION OF PARTIES TO RIGHTS AGREEMENT . Effective upon the execution of this Amendment, each August Note Purchaser shall become a party to the Rights Agreement as an “Investor”, and in connection therewith they shall each execute a counterpart signature page to the Rights Agreement in substantially the form attached hereto as Exhibit A .

4. FULL FORCE AND EFFECT . Except as expressly modified by this Amendment, the terms of the Rights Agreement shall remain in full force and effect.

5. GOVERNING LAW . This Amendment shall be governed by and construed under the internal laws of the State of California as applied to agreements among California residents entered into and to be performed entirely within California, without reference to principles of conflict of laws or choice of laws.

6. INTEGRATION . This Amendment and the Rights Agreement and the documents referred to herein and therein and the exhibits and schedules thereto, constitute the entire agreement and understanding of the parties with respect to the subject matter hereof, and supersede all prior understandings and agreements, whether oral or written, between or among the parties hereto with respect to the specific subject matter hereof.

7. COUNTERPARTS; FACSIMILE . This Amendment may be executed in two (2) or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. This Amendment may be executed and delivered by facsimile, or by email in portable document format (.pdf) and delivery of the signature page by such method will be deemed to have the same effect as if the original signature had been delivered to the other parties.

[Remainder of Page Intentionally Left Blank]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

COMPANY:

AMYRIS, INC.

By: /s/ John Melo

John Melo, Chief Executive Officer

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

NAXYRIS S.A.



By: /s/ Christopher Piel Name: Christopher Piel Title: Director	/s/ Jacques Reckinger Jacques Reckinger Director

[SIGNATURE PAGE TO AMENDMENT NO. 4 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

MAXWELL (MAURITIUS) PTE LTD

By: /s/

Name: ROHIT SIPAHIMALANI

Title: Authorized Signatory

[SIGNATURE PAGE TO AMENDMENT NO. 4 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

KPCB HOLDINGS, INC., AS NOMINEE

By: /s/ Paul M. Vronsky

Name: Paul M. Vronsky

Title: General Counsel

[SIGNATURE PAGE TO AMENDMENT NO. 4 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

FORIS VENTURES, LLC

By: /s/ Barbara Hagen

Name: Barbara Hagen

Title: Manager

[SIGNATURE PAGE TO AMENDMENT NO. 4 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

BIOLDING INVESTMENT SA

By: /s/ Abdulla Al Thani

Name: Abdulla Al Thani

Title:

[SIGNATURE PAGE TO AMENDMENT NO. 4 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

TOTAL ENERGIES NOUVELLES ACTIVITЙS USA

(F.K.A. TOTAL GAS & POWER USA, SAS)

By: /s/ Jean Francois Abrighi de Casanova

Name: Jean Francois Abrighi de Casanova

Title: Attorney in Fact

[SIGNATURE PAGE TO AMENDMENT NO. 4 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

TPG BIOTECHNOLOGY PARTNERS II, L.P.

By: TPG Biotechnology GenPar II, L.P.,

its general partner

By: TPG Biotechnology GenPar II Advisors, LLC,

its general partner

By: /s/ Ronald Cami

Name: Ronald Cami

Title: Vice President

TPG BIOTECHNOLOGY PARTNERS III, L.P.

By: TPG Biotechnology GenPar III, L.P.,

its general partner

By: TPG Biotechnology GenPar III, LLC.,

its general partner

By: /s/ Ronald Cami

Name: Ronald Cami

Title: Vice President

[SIGNATURE PAGE TO AMENDMENT NO. 4 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

SUALK CAPITAL LTD

By: /s/ Fernando O. Reinach

Name: Fernando O. Reinach

Title: Director

[SIGNATURE PAGE TO AMENDMENT NO. 4 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

EXHIBIT A

Counterpart Signature Page

IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the date first above written.

INVESTORS:

Pyramis Lifecycle Large Cap Stock Commingled Pool

By: Pyramis Global Advisors Trust Company, as Trustee

By: /s/ Richard Synrod

Name: Richard Synrod

Title: Director

[SIGNATURE PAGE TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT, AS AMENDED]

IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the date first above written.

INVESTORS:

Variable Insurance Products Fund III: Growth & Income Portfolio

By: /s/ Adrien Deberghes

Name: Adrien Deberghes

Title: Deputy Treasurer

[SIGNATURE PAGE TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT, AS AMENDED]

IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the date first above written.

INVESTORS:

Fidelity Securities Fund: Fidelity Growth & Income Portfolio

By: /s/ Adrien Deberghes

Name: Adrien Deberghes

Title: Deputy Treasurer

[SIGNATURE PAGE TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT, AS AMENDED]

IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the date first above written.

INVESTORS:

Fidelity Commonwealth Trust: Fidelity Large Cap Stock Fund

By: /s/ Adrien Deberghes

Name: Adrien Deberghes

Title: Deputy Treasurer

[SIGNATURE PAGE TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT, AS AMENDED]

IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the date first above written.

INVESTORS:

Fidelity Hastings Street Trust: Fidelity Series Growth & Income Fund

By: /s/ Adrien Deberghes

Name: Adrien Deberghes

Title: Deputy Treasurer

[SIGNATURE PAGE TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT, AS AMENDED]

IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the date first above written.

INVESTORS:

Fidelity Hastings Street Trust: Fidelity Advisor Series Growth & Income Fund

By: /s/ Adrien Deberghes

Name: Adrien Deberghes

Title: Deputy Treasurer

[Signature Page to Amyris, Inc. Amended and Restated Investors’ Rights Agreement, As Amended]

[SIGNATURE PAGE TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT, AS AMENDED]

AMYRIS, INC.

AMENDMENT NO. 5 TO AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT

This Amendment No. 5 to the Amended and Restated Investors’ Rights Agreement (this “ Amendment ”) is made and entered into as of December 24, 2013, by and among Amyris, Inc., a Delaware corporation (the “ Company ”), the Investors and the Common Holders.

RECITALS

WHEREAS, the Company, certain Investors and certain Common Holders are parties to that certain Amendment No. 4 to Amended and Restated Investors’ Rights Agreement, dated as of October 16, 2013 (“ Amendment No. 4 ”), pursuant to which the Rights Agreement was amended and certain parties were added thereto.

WHEREAS, the Company, the Investors and the Common Holders desire to make certain additional amendments to the Rights Agreement.

WHEREAS, pursuant to Section 3.7 of the Rights Agreement, the Rights Agreement may be amended with the written consent of the (i) Company and (ii) the holders of a majority of the Registrable Securities currently outstanding (together, the “ Requisite Majority ”).

WHEREAS, the undersigned parties constitute the Requisite Majority.

NOW, THEREFORE, the parties hereby agree as follows:

1. AMENDMENT OF SECTION 1.1(c) OF THE RIGHTS AGREEMENT . Section 1.1(c) of the Rights Agreement shall be deleted in its entirety and replaced with the following:

“The term “ Holder ” means (i) any Investor having purchased more than 5% of the Preferred Stock sold by the Company, (ii) except with respect to Sections 1.2, 1.12, 1.13 and Section 2 hereof, the Common Holders owning or having the right to acquire Registrable Securities or any assignee thereof in accordance with Section 1.13 hereof, (iii) each “Purchaser” as such term is defined in that certain Securities Purchase Agreement dated as of February 22, 2012 by and among the Company and the purchasers identified therein (each, a “ February 2012 Purchaser ”), (iv) each “Purchaser” as such term is defined in that certain Securities Purchase Agreement dated December 24, 2012 by and among the Company and purchasers identified therein (each, a “ December 2012 Purchaser ”), (v) each “Purchaser” as such term is defined in that certain Securities Purchase Agreement dated March 27, 2013 by and among the Company and purchasers identified therein (each, a “ March 2013 Purchaser ”), (vi) each “Purchaser” as such term is defined in that certain Securities Purchase Agreement dated August 8, 2013, as amended by Amendment No. 1 to Securities Purchase Agreement dated as of October 16, 2013 (such agreement as amended by Amendment No. 1 to Securities Purchase Agreement the “ August/October 2013 Purchase Agreement ”) by and among the Company and purchasers identified therein (each, an “ August/October 2013 Note Purchaser ”), (vii) the holder of that certain warrant to purchase shares of Common Stock of the Company issued pursuant to Section 6.1(l) of the August/October 2013 Purchase Agreement (the “ Temasek Warrant ”) and (viii) each “Purchaser” as such term is defined in that certain Amendment No. 2 to Securities Purchase Agreement dated December 23, 2013 (the “ December 2013 Purchase Agreement Amendment ”) by and among the Company and purchasers identified therein (each, a “ December 2013 Note Purchaser ”).”

2. AMENDMENT OF SECTION 1.1(f) OF THE RIGHTS AGREEMENT . Section 1.1(f) of the Rights Agreement shall be deleted in its entirety and replaced with the following:

Stock issued or issuable upon conversion of the Temasek Warrant (ix) Common Stock issued or issuable upon conversion of the convertible promissory notes issued to the December 2013 Note Purchasers pursuant to the December 2013 Purchase Agreement, and (x) any Common Stock of the Company issued as (or issuable upon the conversion or exercise of any warrant, right or other security that is issued as) a dividend or other distribution with respect to, or in exchange for, or in replacement of, the securities set forth in subsections (i) through (x) above, excluding, however, any Registrable Securities which (A) have previously been registered or which have been sold to the public either pursuant to a registration statement or Rule 144, (B) which have been sold in a private transaction in which the transferor’s rights under this Agreement are not assigned, or (C) held by a Holder (together with its affiliates) if, as reflected on the Company’s list of stockholders, such Holder (together with its affiliates) holds less than 1% of the Company’s outstanding Common Stock (treating all shares of Preferred Stock on an as converted basis).”

3. ADDITION OF PARTIES TO RIGHTS AGREEMENT . Effective upon the execution of this Amendment, each December 2013 Note Purchaser who is not already a party to the Rights Agreement as an “Investor” shall become a party to the Rights Agreement as an “Investor”, and in connection therewith they shall each execute a counterpart signature page to the Rights Agreement in substantially the form attached hereto as Exhibit A .

4. FULL FORCE AND EFFECT . Except as expressly modified by this Amendment, the terms of the Rights Agreement shall remain in full force and effect.

[Remainder of Page Intentionally Left Blank]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

COMPANY:

AMYRIS, INC.

By: /s/ John G. Melo

John G. Melo, President and Chief Executive Officer

[SIGNATURE PAGE TO AMENDMENT NO. 5 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

NAXYRIS S.A.



By: /s/ Christopher Piel Name: Christopher Piel Title: Director	/s/ Jacques Reckinger Jacques Reckinger Director

[SIGNATURE PAGE TO AMENDMENT NO. 5 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

KPCB HOLDINGS, INC., AS NOMINEE

By: /s/ Paul M. Vronsky

Name: Paul M. Vronsky

Title: General Counsel

[SIGNATURE PAGE TO AMENDMENT NO. 5 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

FORIS VENTURES, LLC

By: /s/ Barbara Hagen

Name:

Title:

[SIGNATURE PAGE TO AMENDMENT NO. 5 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

BIOLDING INVESTMENT SA

By: /s/ Abdulla Al Thani

Name:

Title:

[SIGNATURE PAGE TO AMENDMENT NO. 5 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

TOTAL ENERGIES NOUVELLES ACTIVITЙS USA

(F.K.A. TOTAL GAS & POWER USA, SAS)

By: /s/ Bernard Clement

Name: Bernand Clement

Title: President

[SIGNATURE PAGE TO AMENDMENT NO. 5 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

Pyramis Lifecycle Large Cap Stock Commingled Pool

By: /s/ Lynn M. Farroad

Name: Lynn M. Farroad

Title: Director

Variable Insurance Products Fund III: Growth & Income Portfolio

By: /s/ Stacie M. Smith

Name: Stacie M. Smith

Title: Deputy Treasurer

Fidelity Securities Fund: Fidelity Growth & Income Portfolio

By: /s/ Stacie M. Smith

Name: Stacie M. Smith

Title: Deputy Treasurer

Fidelity Commonwealth Trust: Fidelity Large Cap Stock Fund

By: /s/ Stacie M. Smith

Name: Stacie M. Smith

Title: Deputy Treasurer

Fidelity Hastings Street Trust: Fidelity Series Growth & Income Fund

By: /s/ Stacie M. Smith

Name: Stacie M. Smith

Title: Deputy Treasurer

Fidelity Hastings Street Trust: Fidelity Advisor Series Growth & Income Fund

By: /s/ Stacie M. Smith

Name: Stacie M. Smith

Title: Deputy Treasurer

[SIGNATURE PAGE TO AMENDMENT NO. 5 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

INVESTORS:

MAXWELL (MAURITIUS) PTE LTD

By: /s/ Rohit Sipahimalani

Name: Rohit Sipahimalani

Title: Managing Member

[SIGNATURE PAGE TO AMENDMENT NO. 5 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT]

EXHIBIT A

Counterpart Signature Page

IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the date first above written.

INVESTORS:

WOLVERINE FLAGSHIP FUND TRADING LIMITED

By: Wolverine Asset Management, LLC,

its Investment Manager

By: /s/ Ken Nadel

Name: Ken Nadel

Title: Chief Operating Officer

[Signature Page to Amyris, Inc. Amended and Restated Investors’ Rights Agreement, As Amended]



CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES ACT’), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AND PURSUANT TO THE PROVISIONS OF ARTICLE 5 BELOW, MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED UNLESS AND UNTIL REGISTERED UNDER SAID SECURITIES ACT AND APPLICABLE STATE SECURITIES LAW OR, IN THE OPINION OF LEGAL COUNSEL IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER OF THESE SECURITIES, SUCH OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION IS EXEMPT FROM REGISTRATION.

WARRANT TO PURCHASE STOCK

Company: Amyris, Inc., a Delaware corporation

Number of Shares: 1,000,000

Class of Stock: Common Stock

Warrant Price: $0.01 per share

Issue Date: October 16, 2013

Expiration Date: The 10th anniversary after the Issue Date


Credit Facility:	This Warrant is issued in connection with the Securities Purchase Agreement between Company, Maxwell (Mauritius) Pte Ltd and certain other investors dated as of August 8, 2013, as amended from time to time (the “Purchase Agreement”).

THIS WARRANT CERTIFIES THAT, for good and valuable consideration, MAXWELL (MAURITIUS) PTE LTD (together with any registered holder from time to time of this Warrant or any holder of the shares issuable or issued upon exercise of this Warrant “Holder”) is entitled to purchase the number of fully paid and nonassessable shares of the class of securities (the “Shares”) of the Company at the Warrant Price, all as set forth above and as adjusted pursuant to Article 2 of this Warrant, subject to the provisions and upon the terms and conditions set forth in this Warrant.

ARTICLE 1 EXERCISE .

1.1 Conditions to Exercise . Holder may not exercise this Warrant unless and until Total Energies Nouvelles Activités USA (or its assignee) (“Total”) converts any of the Total Notes (as defined in the Tranche I Senior Convertible Notes to be issued by the Company pursuant to the Purchase Agreement) issued pursuant to the Second Closing (as defined in that certain Securities Purchase Agreement dated July 30, 2012 by and between the Company and Total) that had a conversion price of $3.08 as of August 8, 2013 (the “2013 Notes”) into shares of the Company’s Common Stock (the “Exercise Condition”). Upon satisfaction of the Exercise Condition and thereafter, this Warrant shall be exercisable for that number of Shares (subject to adjustment as provided herein) equal to the product of (i) the Number of Shares multiplied by (ii) the quotient of the aggregate principal amount of the 2013 Notes so converted divided by U.S. $30,000,000. The number of shares and the Warrant Price are subject to adjustment as provided herein, and all references to “Shares” and “Warrant Price” herein shall be deemed to include any such adjustment or series of adjustments.

1.2 Method of Exercise . Holder may exercise this Warrant by delivering a duly completed and executed Notice of Exercise in substantially the form attached as Appendix 1 to the principal office of the Company. Unless Holder is exercising the conversion right set forth in Article 1.3, Holder shall also deliver to the Company a check, wire transfer (to an account designated by the Company), or other form of payment acceptable to the Company for the aggregate Warrant Price for the Shares being purchased.

1.3 Conversion Right . In lieu of exercising this Warrant as specified in Article 1.2, Holder may from time to time convert this Warrant, in whole or in part, into a number of Shares determined by dividing (a) the aggregate fair market value of the Shares or other securities for which the Warrant is then being converted (which shall be no more than the number of Shares for which the Warrant is then exercisable under Article 1.1) minus the aggregate Warrant Price of such Shares by (b) the fair market value of one Share. The fair market value of the Shares shall be determined pursuant to Article 1.4.

1.4 Fair Market Value . The fair market value of each Share shall be the average for the five business days immediately prior to the date of determination thereof of the last reported sale price regular way on each such day, or, in the case no such sale takes place on any such day, the average of the reported closing bid and asked prices regular way of the shares of Common Stock on such day, in each case as quoted on The NASDAQ Stock Market or such other principal securities exchange or inter-dealer quotation system on which the shares of Common Stock are then traded.

1.5 Delivery of Certificate and New Warrant . Promptly after Holder exercises or converts this Warrant, and, if applicable, the Company receives payment of the aggregate Warrant Price, the Company shall deliver to Holder certificates for the Shares acquired and, if this Warrant has not been fully exercised or converted and has not expired, a new Warrant representing the Shares not so acquired. Holder shall be deemed to own and have all of the rights associated with any Shares or other securities or property to which it is entitled pursuant to this Warrant upon the exercise or conversion of the Warrant in accordance with this Article 1.

1.6 Replacement of Warrants . On receipt of evidence reasonably satisfactory to the Company of the loss, theft, destruction or mutilation of this Warrant and in the case of loss, theft or destruction, on delivery of an indemnity agreement reasonably satisfactory in form and amount to the Company or, in the case of mutilation on surrender and cancellation of this Warrant, the Company shall execute and deliver, in lieu of this Warrant, a new warrant of like tenor.

1.7 Treatment of Warrant Upon Acquisition of Company .

1.7.1 “ Acquisition ”. For the purpose of this Warrant, “Acquisition” shall mean the occurrence of any of the following: (i) the consolidation of the Company with, or the merger of the Company with or into, another “person” (as such term is used in Rule 13d-3 and Rule 13d5 of the Exchange Act), or the sale, lease, transfer, conveyance or other disposition, in one or a series of related transactions, of all or substantially all of the assets of the Company and its Subsidiaries taken as a whole, or the consolidation of another “person” with, or the merger of another “person” into, the Company, other than in each case pursuant to a transaction in which

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the “persons” that “beneficially owned” (as such term is defined in Rule 13d-3 and Rule 13d-5 under the Exchange Act), directly or indirectly, the Voting Shares (as defined below) of the Company immediately prior to the transaction “beneficially own”, directly or indirectly, Voting Shares representing at least a majority of the total voting power of all outstanding classes of voting stock of the surviving or transferee person; (ii) the adoption by the Company of a plan relating to the liquidation or dissolution of the Company; (iii) the consummation of any transaction (including, without limitation, any merger or consolidation) the result of which is that any “person” becomes the “beneficial owner” directly or indirectly, of more than 50% of the Voting Shares of the Company (measured by voting power rather than number of shares); or (iv) the first day on which a majority of the members of the Board of Directors does not consist of Continuing Directors (as defined in the Purchase Agreement). For the purposes of this Article 1.7.1, “Voting Shares” of any person shall mean capital shares or capital stock of such person which ordinarily has voting power for the election of directors (or persons performing similar functions) of such person, whether at all times or only so long as no senior class of securities has such voting power by reason of any contingency.

1.7.2 Treatment of Warrant at Acquisition . In the event of an Acquisition, either (a) Holder shall exercise or convert his Warrant in full with respect to all remaining Shares for which the Warrant is then exercisable and such exercise or conversion will be deemed effective immediately prior to the consummation of such Acquisition or (b) if Holder elects not to exercise or convert the Warrant, this Warrant will expire upon the consummation of such Acquisition. The Company shall provide Holder with written notice of the foregoing (together with such reasonable information as Holder may request in connection with such contemplated Acquisition giving rise to such notice), which is to be delivered to Holder not less than ten (10) days prior to the closing of the proposed Acquisition.

ARTICLE 2 ADJUSTMENTS TO THE SHARES .

2.1 Stock Dividends, Splits, Etc . If the Company declares or pays a dividend on the Shares payable in common stock of the Company, or other securities, then upon exercise of this Warrant, for each Share acquired, Holder shall receive, without cost to Holder, the total number and kind of shares of common stock of the Company to which Holder would have been entitled had Holder owned the Shares of record as of the date the dividend occurred. If the Company subdivides the Shares by reclassification or otherwise into a greater number of shares or takes any other action which increases the amount of stock for which this Warrant is exercisable, the number of Shares subject to the Warrant shall be proportionately increased and the Warrant Price shall be proportionately decreased. If the outstanding shares are combined or consolidated, by reclassification or otherwise, into a lesser number of shares, the Warrant Price shall be proportionately increased and the number of Shares subject to the Warrant shall be proportionately decreased.

2.2 Reclassification, Exchange, Combinations or Substitution . Upon any reclassification, exchange, substitution, or other event that results in a change of the number and/or class of the securities issuable upon exercise or conversion of this Warrant (other than an Acquisition which is subject to the provisions of Article 1.7), Holder shall be entitled to receive, upon exercise or conversion of this Warrant the number and kind of securities and property that Holder would have received for the Shares if this Warrant had been exercised immediately

27121/00010/DOCS/2977604.7

before such reclassification, exchange, substitution, or other event. The Company or its successor shall promptly issue to Holder an amendment to this Warrant setting forth the number and kind of such new securities or other property issuable upon exercise or conversion of this Warrant as a result of such reclassification, exchange, substitution or other event that results in a change of the number and/or class of securities issuable upon exercise or conversion of this Warrant. The amendment to this Warrant shall provide for adjustments which shall be as nearly equivalent as may be practicable to the adjustments provided for in this Article 2 including, without limitation, adjustments to the Warrant Price and to the number of securities or property issuable upon exercise of the new Warrant. The provisions of this Article 2.2 shall similarly apply to successive reclassifications, exchanges, substitutions, or other events.

2.3 No Impairment . Without the consent of the Holder, the Company shall not by amendment of its Certificate of Incorporation or through a reorganization, transfer of assets, consolidation, merger, dissolution, issue, or sale of securities or any other voluntary action, avoid or seek to avoid the observance or performance of any of the terms to be observed or performed under this Warrant by the Company, but shall at all times in good faith assist in carrying out of all the provisions of this Article 2 and in taking all such action as may be necessary or appropriate to protect Holder’s rights under this Article against impairment.

2.4 Fractional Shares . No fractional Shares shall be issuable upon exercise or conversion of this Warrant and the number of Shares to be issued shall be rounded down to the nearest whole Share. If a fractional share interest arises upon any exercise or conversion of the Warrant, the Company shall eliminate such fractional share interest by paying Holder in cash equivalent to the amount computed by multiplying the fractional interest by the fair market value of a full Share.

2.5 Certificate as to Adjustments . Upon each adjustment of the Warrant Price, the Company shall promptly notify Holder in writing, and, at the Company’s expense, promptly compute such adjustment, and furnish Holder with a certificate of its Chief Financial Officer, Corporate Secretary or a senior financial officer setting forth such adjustment and the facts upon which such adjustment is based. The Company shall, upon written request, furnish Holder a certificate setting forth the Warrant Price in effect upon the date thereof and the series of adjustments leading to such Warrant Price.

ARTICLE 3 REPRESENTATIONS AND COVENANTS OF THE COMPANY .

3.1 Representations and Warranties . The Company represents and warrants and covenants to the Holder as follows: all Shares which may be issued upon the exercise of the purchase right represented by this Warrant, and all securities, if any, issuable upon conversion of the Shares, shall, upon issuance, be duly authorized, validly issued, fully paid and nonassessable, and free of any liens and encumbrances except for restrictions on transfer provided for herein or under applicable federal and state securities laws. The Company will at all times reserve and keep available, out of its authorized but unissued share of Common Stock, solely for the purpose of providing the exercise or conversion of this Warrant, the aggregate number of Shares issuable upon exercise or conversion of this Warrant. The Company will use its reasonable best efforts to ensure that the Shares may be issued without violation of any law or regulation applicable to the

27121/00010/DOCS/2977604.7

Company or of any requirement of any securities exchange applicable to the Company on which the Shares are listed or traded.

3.2 No Stockholder Rights . Except as provided in this Warrant, and other than with regard to shares of the Company’s common stock acquired by Holder other than pursuant to the exercise of this Warrant, the Holder will not have any rights as a stockholder of the Company until the exercise of this Warrant.

3.3 Charges, Taxes and Expenses . Issuance of certificates for Shares to the Holder upon the exercise or conversion of this Warrant shall be made without charge to the Holder for any issue or transfer tax or other incidental expense in respect of the issuance of such certificates, all of which taxes and expenses shall be paid by the Company.

ARTICLE 4 REPRESENTATIONS, WARRANTIES OF THE HOLDER . The Holder represents and warrants to the Company as follows:

4.1 Purchase for Own Account . This Warrant and the securities to be acquired upon exercise or conversion of this Warrant by the Holder will be acquired for investment for the Holders account, not as a nominee or agent, and not with a view to the public resale or distribution within the meaning of the Securities Act of 1933 (the “Securities Act”) and the Holder has no present intention, and upon exercise or conversion will have no intention, of selling or engaging in any public distribution of the same except pursuant to a registration or exemption. Holder also represents that the Holder has not been formed for the specific purpose of acquiring this Warrant or the Shares.

4.2 Disclosure of Information . The Holder has received or has had full access to all the information it considers necessary or appropriate to make an informed investment decision with respect to the acquisition of this Warrant and its underlying securities. The Holder further has had an opportunity to ask questions and receive answers from the Company regarding the terms and conditions of the offering of this Warrant and its underlying securities and to obtain additional information (to the extent the Company possessed such information or could acquire it without unreasonable effort or expense) necessary to verify any information furnished to the Holder or to which the Holder has access.

4.3 Investment Experience . The Holder understands that the purchase of this Warrant and its underlying securities involves substantial risk. The Holder has experience as an investor in securities of companies in the development stage and acknowledges that the Holder can bear the economic risk of such Holder’s investment in this Warrant and its underlying securities and has such knowledge and experience in financial or business matters that the Holder is capable of evaluating the merits and risks of its investment in this Warrant and its underlying securities and/or has a preexisting personal or business relationship with the Company and certain of its officers, directors or controlling persons of a nature and duration that enables the Holder to be aware of the character, business acumen and financial circumstances of such persons.

4.4 Accredited Investor Status . The Holder is an “accredited investor” within the meaning of Regulation D promulgated under the Securities Act.

27121/00010/DOCS/2977604.7

4.5 The Securities Act . The Holder understands that this Warrant and the Shares issuable upon exercise or conversion hereof have not been registered under the Securities Act in reliance upon a specific exemption therefrom, which exemption depends upon, among other things, the bona fide nature of the Holder’s investment intent as expressed herein. The Holder understands that this Warrant and the Shares issued upon any exercise or conversion hereof must be held indefinitely unless subsequently registered under the Securities Act and qualified under applicable state securities laws, or unless exemption from such registration and qualification are otherwise available. The Holder further understands that settlement of this Warrant is to be made in Shares and, for the elimination of doubt, the fact that the Shares delivered on exercise of this Warrant will not be registered under the Securities Act (as defined below) will not in any way require the Company to settle this Warrant otherwise than in Shares, including without limitation, that there is no circumstance that would require the Company to settle this Warrant in cash.

ARTICLE 5 MISCELLANEOUS .

5.1 Term . Following the occurrence of the conversion described in Article 1.1, this Warrant will be exercisable in whole or in part at any time and from time to time on or before the Expiration Date.

5.2 Legends . This Warrant and the Shares (and the securities issuable, directly or indirectly, upon conversion of the Shares, if any) shall be imprinted with a legend in substantially the following form:

5.3 Compliance with Securities Laws on Transfer . This Warrant and the Shares issuable upon exercise of this Warrant (and the securities issuable, directly or indirectly, upon conversion of the Shares, if any) may not be transferred or assigned in whole or in part without compliance with applicable federal and state securities laws by the transferor and the transferee (including, without limitation, the delivery of investment representation letters and legal opinions reasonably satisfactory to the Company, as reasonably requested by the Company). The Company shall not require Holder to provide an opinion of counsel if the transfer is to any affiliate of the Holder, provided that any such transferee is an “accredited investor” as defined in Regulation D under the Securities Act; provided, however, in any such transfer the transferee shall agree to be bound by the terms of this Warrant as if an original holder hereof.

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5.4 Notices . All notices and other communications from the Company to the Holder, or vice versa, shall be deemed delivered and effective when given personally or mailed by first-class registered or certified mail, postage prepaid, at such address as may have been furnished to the Company or the Holder, as the case may be (or on the first business day after transmission by facsimile), in writing by the Company or such Holder from time to time. Effective upon receipt of the fully executed Warrant, all notices to the Holder shall be addressed as follows until the Company receives notice of a change of address in connection with a transfer or otherwise:

MAXWELL (MAURITIUS) PTE LTD

60 B Orchard Road #06-18

Tower 2, The Atrium @ Orchard

Singapore 238891

Facsimile: [*]

Notice to the Company shall be addressed as follows until the Holder receives notice of a change

in address:

AMYRIS, INC.

5885 Hollis Street, Suite 100

Emeryville, CA 94608

Attn: General Counsel

Facsimile: [*]

With a copy (which shall not constitute notice) to:

Fenwick & West LLP

801 California Street

Mountain View, CA 94041

Attn: [*]

Facsimile: [*]

5.5 Waiver . This Warrant and any term hereof may be changed, waived, discharged or terminated only by an instrument in writing signed by the parties against which enforcement of such change, waiver, discharge or termination is sought.

5.6 Automatic Conversion upon Expiration . In the event that, upon the Expiration Date, the fair market value of one Share as determined in accordance with Article 1.4 above is greater than the Warrant Price in effect on such date and the Exercise Condition has occurred prior to such date, then this Warrant shall automatically be deemed on and as of such date to be converted pursuant to Article 1.3 above as to all Shares (or such other securities) for which it shall not previously have been exercised or converted, and the Company shall promptly deliver a certificate representing the Shares (or such other securities) issued upon such conversion to the Holder.

5.7 Counterparts . This Warrant may be executed in counterparts, all of which together shall constitute one and the same agreement.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

27121/00010/DOCS/2977604.7

5.8 Amendment . This Warrant may be amended and the observance of any term of this Warrant may be waived only with the written consent of the Company and the Holder.

5.9 Binding Effect . This Warrant shall be binding upon any successors or assigns of the Company.

5.10 Governing Law . This Warrant, and the provisions, rights, obligations, and conditions set forth herein, and the legal relations between the parties hereto, including all disputes and claims, whether arising in contract, tort, or under statute, shall be governed by and construed in accordance with the laws of the State of Delaware without giving effect to its conflict of law provisions.

5.9 Dispute Resolution . This Warrant shall be subject to the dispute resolution provisions of the Purchase Agreement, as such provisions are outlined in Section 9.6 thereof.

[Balance of Page Intentionally Left Blank]

27121/00010/DOCS/2977604.7

"COMPANY"

AMYRIS, INC.

By: /s/

John Melo, Chief Executive Officer

AGREED AND ACKNOWLEDGED:

"HOLDER"

MAXWELL (MAURITIUS) PTE LTD

(Signature)

(Print Name)

(Title)

[Signature Page to Amyris, Inc. Warrant]

"COMPANY"

AMYRIS, INC.

By:

John Melo, Chief Executive Officer

AGREED AND ACKNOWLEDGED:

"HOLDER"

MAXWELL (MAURITIUS) PTE LTD

/s/

(Signature)

ROHIT SIPAHIMALANI

(Print Name)

Authorized Signatory

(Title)

[Signature Page to Amyris, Inc. Warrant]

APPENDIX 1

NOTICE OF EXERCISE

1. Holder elects to purchase ____________ shares of the Common Stock of AMYRIS, INC. pursuant to the terms of the attached Warrant, and tenders payment of the purchase price of the shares in full.

[or]

1. Holder elects to convert the attached Warrant into Shares/cash [strike one] in the manner specified in the Warrant. This conversion is exercised for ____________________ of the Shares covered by the Warrant.

[Strike paragraph that does not apply.]

2. Please issue a certificate or certificates representing the shares in the name specified below:

Holders Name

(Address)

3. By its execution below and for the benefit of the Company, Holder hereby restates each of the representations and warranties in Article 4 of the Warrant as the date hereof.

HOLDER:

By:

Name:

Title:

(Date):

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Schedule A

(see Exhibit 4.02 Quarterly Report on Form 10-Q as filed on November 9, 2012)

Notes Issued by Registrant



Note Number	Date of Note	Amount	Conversion Price	Comments
R-1	July 30, 2012	$38,300,000	$7.0682	Note No. R-1 was cancelled pursuant to Securities Purchase Agreement dated December 24, 2012 (Exhibit 4.16 Annual Report on Form 10-K for fiscal 2012 as filed on March 2013). The new issued Note is No. R-3.
R-2	September 14, 2012	$15,000,000	$7.0682
R-3	December 24, 2012	$33,300,001.04	$7.0682

CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

SECURITIES PURCHASE AGREEMENT

This SECURITIES PURCHASE AGREEMENT (this “ Agreement ”) is made and entered into as of December 24, 2012, by and between Amyris, Inc., a Delaware corporation (the “ Company ”), and the individuals or entities listed on Schedule I hereto (each, a “ Purchaser ,” and collectively, the “ Purchasers ”).

Preliminary Statement

The Purchasers desire to purchase, and the Company desires to offer and sell to the Purchasers, shares of the Company's common stock, par value $0.0001 per share (“ Common Stock ”).

Agreement

The parties, intending to be legally bound, agree as follows:

ARTICLE 1

SALE OF SHARES

Each Purchaser will purchase from the Company the number of shares of Common Stock set forth next to such Purchaser's name on Schedule I hereto (such shares, the “ Shares ”) at a price of U.S. $2.98 per Share in cash or by cancellation or conversion of indebtedness of the Company to such applicable Purchaser. The total purchase price payable by each Purchaser for the Shares that such Purchaser is hereby agreeing to purchase is set forth next to such Purchaser's name on Schedule I hereto (the “ Total Purchase Price ”). The sale and purchase of the Shares to each Purchaser shall constitute a separate sale and purchase hereunder.

ARTICLE 2

CLOSING; DELIVERY

2.1. Closing . The closing (“ Closing ”) of the transactions contemplated hereby shall be held at the offices of Fenwick & West LLP, 801 California Street, Mountain View, California 94041 within one business day following the date on which the last of the conditions set forth in Articles 6 and 7 have been satisfied or waived in accordance with this Agreement but in no event later than December 26, 2012 (such date, the “ Closing Date ”), or at such other time and place as the Company and the Purchasers mutually agree upon.

2.2. Delivery . At the Closing, the Company shall execute and deliver to the Purchasers this Agreement, the Amendment No. 2 to Amended and Restated Investors' Rights Agreement in the form attached hereto as Exhibit A (the “ Rights Agreement Amendment ”) and the other documents referenced in Article 6 . At the Closing, each Purchaser (a) shall pay the Company the applicable Total Purchase Price in immediately available funds or by cancellation or conversion of indebtedness of the Company to Purchaser, (b) if applicable, shall initiate irrevocable payment instructions to its paying bank to make the payment (an “ Irrevocable Payment Instruction ”) to the Company of the applicable Total Purchase Price in immediately available funds, or (c) if applicable, shall provide to the Company a side letter in the form

attached hereto as Schedule 2.2 (a “ Payment Commitment Letter ”) which shall provide that such applicable Purchaser irrevocably commits to make payment to the Company with respect to the Shares being purchased by such Purchaser hereunder as soon as reasonably practicable but in any event no later than January 14, 2013. At the Closing, or, if applicable, upon receipt of the applicable Total Purchase Price from a Purchaser who makes an Irrevocable Payment Instruction or provides a Payment Commitment Letter at the Closing, the Company shall deliver to each Purchaser a single stock certificate representing the number of Shares purchased by such Purchaser, or deliver irrevocable instructions to the Company's transfer agent to deliver such certificate to a Purchaser who has delivered an Irrevocable Payment Instruction or a Payment Commitment Letter upon the Company's receipt of the Total Purchase Price from such Purchaser, as set forth next to such Purchaser's name on Schedule I hereto, such stock certificate to be registered in the name of such Purchaser, or in such nominee's or nominees' name(s) as designated by such Purchaser in writing in the form of the Purchaser Suitability Questionnaire of the Purchaser attached hereto as (i) for Purchasers who are natural Persons, Exhibit B , or (ii) for Purchasers who are entities, Exhibit C (each, as applicable, the “ Purchaser Suitability Questionnaire ”), against payment of the purchase price therefor by wire transfer of immediately available funds to such account or accounts as the Company shall designate in writing to Purchaser at least two days prior to the Closing Date or by cancellation or conversion of indebtedness of the Company to such applicable Purchaser. Each Purchaser purchasing Shares through conversion or cancellation of indebtedness agrees that each convertible promissory note held by such Purchaser is cancelled as of the Closing and all principal and interest outstanding thereunder shall be converted as reflected on Schedule I as of the Closing Date; provided that to the extent only a portion of the principal and interest outstanding thereunder shall be converted as reflected on Schedule I as of the Closing Date, then the Company shall issue a new convertible promissory note to such Purchaser reflecting the remaining principal and interest outstanding under such original convertible promissory note after giving effect to the conversion contemplated hereby.

ARTICLE 3

REPRESENTATIONS AND WARRANTIES OF THE COMPANY

The Company represents, warrants and covenants to each Purchaser, except as set forth in the disclosure letter supplied by the Company to the Purchasers dated as of the date hereof, which exceptions shall be deemed to be part of the representations and warranties made hereunder as provided therein, as follows:

3.1. Organization and Standing . The Company and each of its subsidiaries is duly incorporated, validly existing, and in good standing under the laws of the jurisdiction of its organization. Each of the Company and its subsidiaries has all requisite power and authority to own and operate its respective properties and assets and to carry on its respective business as presently conducted and as proposed to be conducted. The Company and each of its subsidiaries is qualified to do business as a foreign entity in every jurisdiction in which the failure to be so qualified would have, or would reasonably be expected to have, a material adverse effect, individually or in the aggregate, upon the business, properties, tangible and intangible assets, liabilities, operations, prospects, financial condition or results of operation of the Company and its subsidiaries or the ability of the Company or any of its subsidiaries to perform their respective obligations under the Transaction Agreements (as defined below) (a “ Material Adverse Effect ”).

3.2. Subsidiaries . As used in this Agreement, references to any “subsidiary” of a specified Person shall refer to an Affiliate controlled by such Person directly, or indirectly through one or more intermediaries, as such terms are used in and construed under Rule 405 under the Securities Act (which, for the avoidance of doubt, shall include the Company's controlled joint ventures, including shared-controlled joint ventures). The Company's subsidiaries, as of the date hereof, are listed on Exhibit 21.01 to the Company's Annual Report on Form 10-K for the year ended December 31, 2011 and, except as Previously Disclosed (as defined in Section 3.9) are the only subsidiaries, direct or indirect, of the Company as of the date hereof. All the issued and outstanding shares of each subsidiary's capital stock have been duly authorized and validly issued, are fully paid and nonassessable, have been issued in compliance with all federal and state securities laws, were not issued in violation of or subject to any preemptive rights or other rights to subscribe for or purchase securities, and, except as Previously Disclosed, are owned by the Company or a Company subsidiary free and clear of all liens, encumbrances and equities and claims. As used herein, “ Person ” shall mean any individual, corporation, limited liability company, partnership, joint venture, association, joint-stock company, trust, unincorporated organization or government or any agency or political subdividion thereof, and an “ Affiliate ” means, with respect to any Person, any other Person that directly or indirectly controls, is controlled by, or is under common control with, such Person.

3.3. Power . The Company has all requisite power to execute and deliver this Agreement, to sell and issue the Shares hereunder, and to carry out and perform its obligations under the terms of this Agreement, the Rights Agreement Amendment and any ancillary agreements and instruments to be entered into by the Company hereunder (together, the “ Transaction Agreements ”).

3.4. Authorization . The execution, delivery, and performance of the Transaction Agreements by the Company has been duly authorized by all requisite action on the part of the Company and its officers, directors and stockholders, and the Transaction Agreements constitute the legal, valid, and binding obligations of the Company enforceable in accordance with their terms, except (a) as limited by applicable bankruptcy, insolvency, reorganization, moratorium, and other laws of general application affecting enforcement of creditors' rights generally, and (b) as limited by laws relating to the availability of specific performance, injunctive relief or other equitable remedies (together, the “ Enforceability Exceptions ”).

3.5. Consents and Approvals . Except for any Current Report on Form 8-K or Notice of Exempt Offering of Securities on Form D to be filed by the Company in connection with the transactions contemplated hereby, the Company is not required to give any notice to, make any filing with, or obtain any authorization, consent, or approval of any government or governmental agency in order to consummate the transactions contemplated by the Transaction Agreements. Assuming the accuracy of the representations of each Purchaser in the Purchaser Suitability Questionnaire of such Purchaser, as applicable, no consent, approval, authorization or other order of, or registration, qualification or filing with, any court, regulatory body, administrative agency, self-regulatory organization, stock exchange or market (including The NASDAQ Stock Market), or other governmental body is required for the execution and delivery of these Transaction Agreements, the valid issuance, sale and delivery of the Shares to be sold pursuant to this Agreement other than such as have been made or obtained, or for any securities filings required to be made under federal or state securities laws applicable to the offering of the Shares.

3.6. Non-Contravention . The execution and delivery of the Transaction Agreements, the issuance, sale and delivery of the Shares to be sold by the Company under this Agreement, the performance by the Company of its obligations under the Transaction Agreements and/or the consummation of the transactions contemplated thereby will not (a) conflict with, result in the breach or violation of, or constitute (with or without the giving of notice or the passage of time or both) a violation of, or default under, (i) any bond, debenture, note or other evidence of indebtedness, or under any lease, license, franchise, permit, indenture, mortgage, deed of trust, loan agreement, joint venture or other agreement or instrument to which the Company or any subsidiary is a party or by which it or its properties may be bound or affected, (ii) the Company's Restated Certificate of Incorporation, as amended and as in effect on the date hereof (the “ Certificate of Incorporation ”), the Company's Bylaws, as amended and as in effect on the date hereof (the “ Bylaws ”), or the equivalent document with respect to any subsidiary, as amended and as in effect on the date hereof, or (iii) any statute or law, judgment, decree, rule, regulation, ordinance or order of any court or governmental or regulatory body (including The NASDAQ Stock Market), governmental agency, arbitration panel or authority applicable to the Company, any of its subsidiaries or their respective properties, except in the case of clauses (i) and (iii) for such conflicts, breaches, violations or defaults that would not be likely to have, individually or in the aggregate, a Material Adverse Effect, or (b) result in the creation or imposition of any lien, encumbrance, claim, security interest or restriction whatsoever upon any of the material properties or assets of the Company or any of its subsidiaries or an acceleration of indebtedness pursuant to any obligation, agreement or condition contained in any material bond, debenture, note or any other evidence of indebtedness or any material indenture, mortgage, deed of trust or any other agreement or instrument to which the Company or any if its subsidiaries is a party or by which the Company or any of its subsidiaries is bound or to which any of the property or assets of the Company is subject. For purposes of this Section 3.6, the term “material” shall apply to agreements, understandings, instruments, contracts or proposed transactions to which the Company is a party or by which it is bound involving obligations (contingent or otherwise) of, or payments to, the Company in excess of $100,000 in a consecutive 12-month period.

3.7. Shares . The Shares are duly authorized and when issued pursuant to the terms of this Agreement will be validly issued, fully paid, and nonassessable, and will be free of any liens or encumbrances with respect to the issuance thereof; provided , however , that the Shares shall be subject to restrictions on transfer under state or federal securities laws as set forth in this Agreement, or as otherwise may be required under state or federal securities laws as set forth in this Agreement at the time a transfer is proposed. The issuance and delivery of the Shares is not subject to preemptive, co-sale, right of first refusal or any other similar rights of the stockholders of the Company or any other Person, or any liens or encumbrances or result in the triggering of any anti-dilution or other similar rights under any outstanding securities of the Company.

3.8. No Registration . Assuming the accuracy of each of the representations and warranties of each Purchaser herein and in the Purchaser Suitability Questionnaire, the issuance by the Company of the Shares is exempt from registration under the Securities Act of 1933, as amended (the “ Securities Act ”).

3.9. Reporting Status . The Company is subject to the reporting requirements of the Securities Exchange Act of 1934, as amended (the “ Exchange Act ”), and has, in a timely manner, filed all documents and reports that the Company was required to file pursuant to

Section I.A.3.b of the General Instructions to Form S-3 promulgated under the Securities Act in order for the Company to be eligible to use Form S-3 for the two years preceding the Closing Date or such shorter time period as the Company has been subject to such reporting requirements (the foregoing materials, together with any materials filed by the Company under the Exchange Act, whether or not required, collectively, the “ SEC Documents ”). The SEC Documents complied as to form in all material respects with requirements of the Securities Act and Exchange Act and the rules and regulations of the U.S. Securities and Exchange Commission (the “ SEC ”) promulgated thereunder (collectively, the “ SEC Rules ”), and none of the SEC Documents and the information contained therein, as of their respective filing dates, contained any untrue statement of a material fact or omitted to state a material fact required to be stated therein or necessary in order to make the statements therein, in light of the circumstances under which they were made, not misleading. As used in this Agreement, “ Previously Disclosed ” means information set forth in or incorporated by reference into the SEC Documents filed with the SEC on or after February 28, 2012 but prior to the date hereof (except for risks and forward-looking information set forth in the “Risk Factors” section of the applicable SEC Documents or in any forward-looking statement disclaimers or similar statements that are similarly non-specific and are predictive or forward-looking in nature).

3.10. Contracts . Each indenture, contract, lease, mortgage, deed of trust, note agreement, loan or other agreement or instrument of a character that is required to be described or summarized in the SEC Documents or to be filed as an exhibit to the SEC Documents under the SEC Rules (collectively, the “ Material Contracts ”) is so described, summarized or filed. The Material Contracts to which the Company or its subsidiaries are a party have been duly and validly authorized, executed and delivered by the Company and constitute the legal, valid and binding agreements of the Company or its subsidiaries, as applicable, enforceable by and against the Company or its subsidiaries, as applicable, in accordance with their respective terms, subject to the Enforceability Exceptions.

3.11. Capitalization . Immediately prior to the Closing, the authorized capital stock of the Company consists of (a) 100,000,000 shares of Common Stock, $0.0001 par value per share, 59,555,333 shares of which are issued and outstanding as of the date hereof, and (b) 5,000,000 shares of Preferred Stock, $0.0001 par value per share, of which no shares are issued and outstanding as of the date hereof. All subscriptions, warrants, options, convertible securities, and other rights (contingent or other) to purchase or otherwise acquire equity securities of the Company issued and outstanding as of the date hereof, or material contracts, commitments, understandings, or arrangements by which the Company or any of its subsidiaries is or may be obligated to issue shares of capital stock, or securities or rights convertible or exchangeable for shares of capital stock, are as set forth in the SEC Documents. The issued and outstanding shares of the Company's capital stock have been duly authorized and validly issued, are fully paid and nonassessable, have been issued in compliance with all applicable federal and state securities laws, and were not issued in violation of or subject to any preemptive rights or other rights to subscribe for or purchase securities. Except as Previously Disclosed, no holder of the Company's capital stock is entitled to preemptive or similar rights. There are no bonds, debentures, notes or other indebtedness having general voting rights (or convertible into securities having such rights) of the Company issued and outstanding. Except as Previously Disclosed, there are no agreements or arrangements under which the Company or any of its subsidiaries is obligated to register the sale of any of their securities under the Securities Act. The Company has made available to the

Purchasers, a true, correct and complete copy of the Company's Certificate of Incorporation and Bylaws.

3.12. Legal Proceedings . Except as Previously Disclosed, there is no action, suit or proceeding before any court, governmental agency or body, domestic or foreign, now pending or, to the knowledge of the Company, threatened against the Company or its subsidiaries wherein an unfavorable decision, ruling or finding would reasonably be expected to, individually or in the aggregate, (i) materially adversely affect the validity or enforceability of, or the authority or ability of the Company to perform its obligations under, this Agreement or (ii) have a Material Adverse Effect. The Company is not a party to or subject to the provisions of any injunction, judgment, decree or order of any court, regulatory body, administrative agency or other governmental agency or body that might have, individually or in the aggregate, a Material Adverse Effect.

3.13. No Violations . Neither the Company nor any of its subsidiaries is in violation of its respective certificate of incorporation, bylaws or other organizational documents, or to its knowledge, is in violation of any statute or law, judgment, decree, rule, regulation, ordinance or order of any court or governmental or regulatory body (including The NASDAQ Stock Market), governmental agency, arbitration panel or authority applicable to the Company or any of its subsidiaries, which violation, individually or in the aggregate, would be reasonably likely to have a Material Adverse Effect. Neither the Company nor any of its subsidiaries is in default (and there exists no condition which, with or without the passage of time or giving of notice or both, would constitute a default) in the performance of any bond, debenture, note or any other evidence of indebtedness in any indenture, mortgage, deed of trust or any other material agreement or instrument to which the Company or any of its subsidiaries is a party or by which the Company or any of its subsidiaries is bound or by which the properties of the Company are bound, which would be reasonably likely to have a Material Adverse Effect. There has not been, and to the knowledge of the Company, there is not pending or contemplated, any investigation by the SEC involving the Company or any current or former director or officer of the Company and the Company is not an “ineligible issuer” pursuant to Rules 164, 405 and 433 under the Securities Act. The Company has not received any comment letter from the SEC relating to any SEC Documents which has not been finally resolved. The SEC has not issued any stop order or other order suspending the effectiveness of any registration statement filed by the Company under the Exchange Act or the Securities Act.

3.14. Governmental Permits; FDA Matters.

(a) Permits . The Company and its subsidiaries possess all necessary franchises, licenses, certificates and other authorizations from any foreign, federal, state or local government or governmental agency, department or body that are currently necessary for the operation of their respective businesses as currently conducted, except where such failure to possess would not reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect. Neither the Company nor any of its subsidiaries has received any notice of proceedings relating to the revocation or modification of any such permit which, if the subject of an unfavorable decision, ruling or finding, could reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect.

(b) EPA and FDA Matters . As to each of the manufacturing processes, intermediate products and research or commercial products of the Company and each of its subsidiaries, including, without limitation, products or compounds currently under research and/or development by the Company, subject to the jurisdiction of the United States Environmental Protection Agency (“ EPA ”) under the Toxic Substances Control Act and regulations thereunder (“ TSCA ”) or the Food and Drug Administration (“ FDA ”) under the Federal Food, Drug and Cosmetic Act and the regulations thereunder (“ FDCA ”) (each such product, a “ Life Science Product ”), such Life Science Product is being researched, developed, manufactured, tested, distributed and/or marketed in compliance in all material respects with all applicable requirements under the FDCA and TSCA and similar laws and regulations applicable to such Life Science Product, including those relating to investigational use, premarket approval, good manufacturing practices, labeling, advertising, record keeping, filing of reports and security. The Company has not received any notice or other communication from the FDA, EPA or any other federal, state or foreign governmental entity (i) contesting the premarket approval of, the uses of or the labeling and promotion of any Life Science Product or (ii) otherwise alleging any violation by the Company of any law, regulation or other legal provision applicable to a Life Science Product. Neither the Company, nor any officer, employee or agent of the Company has made an untrue statement of a material fact or fraudulent statement to the FDA or other federal, state or foreign governmental entity performing similar or equivalent functions or failed to disclose a material fact required to be disclosed to the FDA or such other federal, state or foreign governmental entity.

3.15. Listing Compliance . The Company is in compliance with the requirements of The NASDAQ Stock Market LLC (“ The NASDAQ Stock Market ”) for continued listing of the Common Stock thereon and has no knowledge of any facts or circumstances that could reasonably lead to delisting of its Common Stock from The NASDAQ Stock Market. The Company has taken no action designed to, or likely to have the effect of, terminating the registration of the Common Stock under the Exchange Act or the listing of the Common Stock on The NASDAQ Stock Market, nor has the Company received any notification that the SEC or The NASDAQ Stock Market is contemplating terminating such registration or listing. The transactions contemplated by the Transaction Agreements will not contravene the rules and regulations of The NASDAQ Stock Market. The Company will comply with all requirements of The NASDAQ Stock Market with respect to the issuance of the Shares, including the filing of any listing notice with respect to the issuance of the Shares.

3.16. Intellectual Property .

(a) The Company and/or its subsidiaries owns or possesses, free and clear of all encumbrances, all legal rights to all intellectual property and industrial property rights and rights in confidential information, including all (i) patents, patent applications, invention disclosures, and all related continuations, continuations-in-part, divisional, reissues, re-examinations, substitutions and extensions thereof, (ii) trademarks, trademark rights, service marks, service mark rights, corporate names, trade names, trade name rights, domain names, logos, slogans, trade dress, design rights, and other similar designations of source or origin, together with the goodwill symbolized by and of the foregoing, (iii) trade secrets and all other confidential information, ideas, know-how, inventions, proprietary processes, formulae, models, and other methodologies, (iv) copyrights, (v) computer programs (whether in object code,

subject code or other form), algorithms, databases, compilations and data, technology supporting the foregoing, and all related documentation, (vi) licenses to any of the foregoing, and (vii) all applications and registrations of the foregoing, and (viii) all other similar proprietary rights (collectively, “ Intellectual Property ”) used or held for use in, or necessary for the conduct of their businesses as now conducted and as proposed to be conducted, and neither the Company nor any of its subsidiaries (i) has received any communications alleging that either the Company or any of its subsidiaries has violated, infringed or misappropriated or, by conducting their businesses as now conducted and as proposed to be conducted, would violate, infringe or misappropriate any of the Intellectual Property of any other Person, (ii) knows of any basis for any claim that the Company or any of its subsidiaries has violated, infringed or misappropriated, or, by conducting their businesses as now conducted and as proposed to be conducted, would violate, infringe or misappropriate any of the Intellectual Property of any other Person, and (iii) knows of any third-party infringement, misappropriation or violation of any Company or any Company subsidiary's Intellectual Property. The Company has taken and takes reasonable security measures to protect the secrecy, confidentiality and value of its Intellectual Property, including requiring all Persons with access thereto to enter into appropriate non-disclosure agreements. To the knowledge of the Company, there has not been any disclosure of any material trade secret of the Company or a Company subsidiary (including any such information of any other Person disclosed in confidence to the Company) to any other Person in a manner that has resulted or is likely to result in the loss of trade secret in and to such information. Except as Previously Disclosed, and except as would not reasonably be expected to have, individually or in the aggregate, a Material Adverse Effect, there are no outstanding options, licenses or agreements, claims, encumbrances or shared ownership interests of any kind relating to the Company's or its subsidiaries' Intellectual Property, nor is the Company or its subsidiaries bound by or a party to any options, licenses or agreements of any kind with respect to the Intellectual Property of any other Person.

(b) To the Company's knowledge, none of the employees of the Company or its subsidiaries are obligated under any contract (including, without limitation, licenses, covenants or commitments of any nature or contracts entered into with prior employers), or subject to any judgment, decree or order of any court or administrative agency, that would interfere with the use of his or her best efforts to promote the interests of the Company or its subsidiaries or would conflict with their businesses as now conducted and as proposed to be conducted. Neither the execution nor delivery of the Transaction Agreements will conflict with or result in a breach of the terms, conditions or provisions of, or constitute a default under any contract, covenant or instrument under which the Company or its subsidiaries or any of the employees of the Company or its subsidiaries is now obligated, and neither the Company nor its subsidiaries will need to use any inventions that any of its employees, or Persons it currently intends to employ, have made prior to their employment with the Company or its subsidiaries, except for inventions that have been assigned or licensed to the Company or its subsidiaries as of the date hereof. Each current and former employee or contractor of the Company or its subsidiaries that has developed any Intellectual Property owned or purported to be owned by the Company or its subsidiaries has executed and delivered to the Company a valid and enforceable Invention Assignment and Confidentiality Agreement that (i) assigns to the Company or such subsidiaries all right, title and interest in and to any Intellectual Property rights arising from or developed or delivered to the Company or such subsidiaries in connection with such Person's work for or on behalf of the Company or such subsidiaries, and (ii) provides reasonable

protection for the trade secrets, know-how and other confidential information (1) of the Company or such subsidiaries and (2) of any third party that has disclosed same to the Company or such subsidiaries. To the knowledge of the Company, no current or former employee, officer, consultant or contractor is in default or breach of any term of any employment, consulting or contractor agreement, non-disclosure agreement, assignment agreement, or similar agreement. Except as Previously Disclosed, to the knowledge of the Company, no present or former employee, officer, consultant or contractor of the Company has any ownership, license or other right, title or interest, directly or indirectly, in whole or in part, in any Intellectual Property that is owned or purported to be owned, in whole or part, by the Company or its subsidiaries.

3.17. Financial Statements . The consolidated financial statements of the Company and its subsidiaries and the related notes thereto included in the SEC Documents (the “ Financial Statements ”) comply in all material respects with applicable accounting requirements and the rules and regulations of the SEC with respect thereto as in effect at the time of filing and present fairly, in all material respects, the financial position of the Company and its subsidiaries as of the dates indicated and the results of its operations and cash flows for the periods therein specified subject, in the case of unaudited statements, to normal year-end audit adjustments. Except as set forth in such Financial Statements (or the notes thereto), such Financial Statements (including the related notes) have been prepared in accordance with U.S. generally accepted accounting principles applied on a consistent basis throughout the periods therein specified (“ GAAP ”). Except as set forth in the Financial Statements, neither the Company nor its subsidiaries has any material liabilities other than liabilities and obligations that have arisen in the ordinary course of business and which would not be required to be reflected in financial statements prepared in accordance with GAAP.

3.18. Accountants . PricewaterhouseCoopers LLP, which has expressed its opinion with respect to the consolidated financial statements contained in the Company's Annual Report on Form 10-K for the year ended December 31, 2011, are registered independent public accountants as required by the Exchange Act and the rules and regulations promulgated thereunder (and by the rules of the Public Company Accounting Oversight Board). The Company believes based on the Company's current cash plan, as disclosed to the Purchasers and that the Company intends to adopt, that at the time of the filing of the Company's Annual Report on Form 10-K for the year ended December 31, 2012 (the “ 2012 10-K ”), the Company will have sufficient cash on hand to fund the Company's operations for at least twelve months thereafter. The Company shall use its best efforts to ensure that the opinion of PricewaterhouseCoopers LLP with respect to the consolidated financial statements contained in the 2012 10-K do not contain any “going concern” opinions.

3.19. Internal Accounting Controls . The Company maintains a system of internal accounting controls sufficient to provide reasonable assurances that (i) transactions are executed in accordance with management's general or specific authorizations; (ii) transactions are recorded as necessary to permit preparation of financial statements in conformity with GAAP and to maintain accountability for assets; (iii) access to assets is permitted only in accordance with management's general or specific authorization; and (iv) the recorded accountability for assets is compared with existing assets at reasonable intervals and appropriate action is taken with respect to any differences. The Company has disclosure controls and procedures (as defined in Rules 13a-14 and 15d-14 under the Exchange Act) that are effective and designed to ensure

that (i) information required to be disclosed in the reports that it files or submits under the Exchange Act is recorded, processed, summarized and reported, within the time periods specified by the SEC Rules, and (ii) such information is accumulated and communicated to the Company's management, including its principal executive officer and principal financial officer, to allow timely decisions regarding required disclosure. The Company is otherwise in compliance in all material respects with all applicable provisions of the Sarbanes-Oxley Act of 2002, as amended and the rules and regulations promulgated thereunder.

3.20. Off-Balance Sheet Arrangements . There is no transaction, arrangement or other relationship between the Company or its subsidiaries and an unconsolidated or other off-balance sheet entity that is required to be disclosed by the Company in its Exchange Act filings and is not so disclosed or that otherwise would be reasonably likely to have, individually or in the aggregate, a Material Adverse Effect. There are no such transactions, arrangements or other relationships with the Company that may create contingencies or liabilities that are not otherwise disclosed by the Company in its Exchange Act filings.

3.21. No Material Adverse Change . Except as set forth in (i) the SEC Documents in each case, filed or made through and including the date hereof, since June 30, 2012, or (ii) the written transcript of the Company's webcast conference call held at 5:00 p.m. E.S.T. on November 6, 2012 previously made available to the Purchasers and/or their respective counsel:

(a) there has not been any event, occurrence or development that, individually or in the aggregate, has had or that could reasonably be expected to result in a Material Adverse Effect,

(b) the Company has not incurred any liabilities (contingent or otherwise) other than (1) trade payables and accrued expenses incurred in the ordinary course of business consistent with past practice and (2) liabilities not required to be reflected in the Company's financial statements pursuant to GAAP or not required to be disclosed in filings made with the SEC,

(c) the Company has not declared or made any dividend or distribution of cash or other property to its stockholders or purchased, redeemed or made any agreements to purchase or redeem any shares of its capital stock other than routine withholding in accordance with the Company's existing stock-based plan,

(d) the Company has not altered its method of accounting or the identity of its auditors, except as Previously Disclosed,

(e) the Company has not issued any equity securities except pursuant to the Company's existing stock based plans or as otherwise Previously Disclosed; and

(f) there has not been any loss or damage (whether or not insured) to the physical property of the Company or any of its subsidiaries.

The Company is not as of the date hereof, and after giving effect to the transactions contemplated hereby to occur at the Closing, will not be Insolvent (as defined below). For purposes of this Section, “ Insolvent ” means, with respect to any Person, (i) the

present fair saleable value of such Person's assets is less than the amount required to pay such Person's total indebtedness, (ii) such Person is unable to pay its debts and liabilities, subordinated, contingent or otherwise, as such debts and liabilities become absolute and matured, (iii) such Person intends to incur or believes that it will incur debts that would be beyond its ability to pay as such debts mature or (iv) such Person has unreasonably small capital with which to conduct the business in which it is engaged as such business is now conducted and is currently proposed to be conducted.

3.22. No Manipulation of Stock . Neither the Company nor any of its subsidiaries, nor to the Company's knowledge, any of their respective officers, directors, employees, Affiliates or controlling Persons has taken and will not, in violation of applicable law, take, any action designed to or that might reasonably be expected to, directly or indirectly, cause or result in stabilization or manipulation of the price of the Common Stock.

3.23. Insurance . The Company and its subsidiaries are insured by insurers of recognized financial responsibility against such losses and risks and in such amounts as are prudent and customary in the businesses in which the Company and its subsidiaries are engaged. The Company and its subsidiaries will continue to maintain such insurance or substantially similar insurance, which covers the same risks at the same levels as the existing insurance with insurers which guarantee the same financial responsibility as the current insurers, and neither the Company nor any subsidiary has any reason to believe that it will not be able to renew its existing insurance coverage as and when such coverage expires or to obtain similar coverage from similar insurers as may be necessary to continue its business without a significant increase in cost.

3.24. Properties . The Company and its subsidiaries have good and marketable title to all the properties and assets (both tangible and intangible) described as owned by them in the consolidated financial statements included in the SEC Documents, free and clear of all liens, mortgages, pledges, or encumbrances of any kind except (i) those, if any, reflected in such consolidated financial statements (including the notes thereto), or (ii) those that are not material in amount and do not adversely affect the use made and proposed to be made of such property by the Company or its subsidiaries. The Company and each of its subsidiaries hold their leased properties under valid and binding leases. The Company and each of its subsidiaries own or lease all such properties as are necessary to its operations as now conducted.

3.25. Tax Matters . The Company and its subsidiaries have filed all Tax Returns, and these Tax Returns are true, correct, and complete in all material respects. The Company and each subsidiary (i) have paid all Taxes that are due from the Company or such subsidiary for the periods covered by the Tax Returns or (ii) have duly and fully provided reserves adequate to pay all Taxes in accordance with GAAP. No agreement as to indemnification for, contribution to, or payment of Taxes exists between the Company or any subsidiary, on the one hand, and any other Person, on the other, including pursuant to any Tax sharing agreement, lease agreement, purchase or sale agreement, partnership agreement or any other agreement not entered into in the ordinary course of business. Neither the Company nor any of its subsidiaries has any liability for Taxes of any Person (other than the Company or any of its subsidiaries) under Treasury Regulation Section 1.1502-6 (or any similar provision of any state, local or foreign law), or as a transferee or successor, by contract or otherwise. Since the date of the Company's most recent

Financial Statements, the Company has not incurred any liability for Taxes other than in the ordinary course of business consistent with past practice. Neither the Company nor its subsidiaries has been advised (a) that any of its Tax Returns have been or are being audited as of the date hereof, or (b) of any deficiency in assessment or proposed judgment to its Taxes. Neither the Company nor any of its subsidiaries has knowledge of any Tax liability to be imposed upon its properties or assets as of the date of this Agreement that is not adequately provided for. The Company has not distributed stock of another corporation, or has had its stock distributed by another corporation, in a transaction that was governed, or purported or intended to be governed, in whole or in part, by Section 355 of the Internal Revenue Code (i) in the two years prior to the date of this Agreement or (ii) in a distribution that could otherwise constitute part of a “plan” or “series of related transactions” (within the meaning of Section 355(e) of the Internal Revenue Code) in conjunction with the purchase of the Shares. “ Tax ” or “ Taxes ” means any foreign, federal, state or local income, gross receipts, license, payroll, employment, excise, severance, stamp, occupation, premium, property, windfall, profits, environmental, customs, capital stock, franchise, employees' income withholding, foreign or domestic withholding, social security, unemployment, disability, real property, personal property, sales, use, transfer, value added, alternative or add-on minimum or other similar tax, governmental fee, governmental assessment or governmental charge, including any interest, penalties or additions to Taxes or additional amounts with respect to the foregoing. “ Tax Returns ” means all returns, reports, or statements required to be filed with respect to any Tax (including any elections, notifications, declarations, schedules or attachments thereto, and any amendment thereof) including any information return, claim for refund, amended return or declaration of estimated Tax.

3.26. Investment Company Status . The Company is not, and immediately after receipt of payment for the Shares will not be, an “investment company,” an “affiliated person” of, “promoter” for or “principal underwriter” for, or an entity “controlled” by an “investment company,” within the meaning of the Investment Company Act of 1940, as amended, or the rules and regulations promulgated thereunder.

3.27. Transactions With Affiliates and Employees . Except as Previously Disclosed, none of the officers or directors of the Company or its subsidiaries and, to the knowledge of the Company, none of the employees of the Company or its subsidiaries is presently a party to any transaction with the Company or any subsidiary (other than for services as employees, officers and directors required to be disclosed under Item 404 of Regulation S-K under the Exchange Act).

3.28. Foreign Corrupt Practices . Neither the Company nor its subsidiaries or Affiliates, any director or officer, nor to the knowledge of the Company, any agent, employee or other Person acting on behalf of the Company or its subsidiaries has, in the course of its actions for, or on behalf of, the Company or any of its subsidiaries (a) used any corporate funds for any unlawful contribution, gift, entertainment or other unlawful expenses relating to political activity, (b) made or promised to make any direct or indirect unlawful payment to any foreign or domestic government official or employee (including any officer or employee of a government or government-owned or controlled entity or of a public international organization, or any Person acting in an official capacity for or on behalf of any of the foregoing, or of any political party or part official or candidate for political office (each such Person, a “ Government Official ”)) from corporate funds, (c) violated or is in violation of any provision of the U.S. Foreign Corrupt

Practices Act of 1977, as amended or (d) made or promised to make any unlawful bribe, rebate, payoff, influence payment, kickback or other unlawful payment to any foreign or domestic Government Official.

3.29. Money Laundering Laws . The operations of the Company and its subsidiaries are and have been conducted at all times in compliance with applicable financial record-keeping and reporting requirements of the Currency and Foreign Transactions Reporting Act of 1970, as amended, and the Bank Secrecy Act, as amended by Title III of the Uniting and Strengthening America by Providing Appropriate Tools Required to Intercept and Obstruct Terrorism Act of 2001 (Title III of Pub. L. 107-56 (signed into law on October 26, 2001)), applicable money laundering statutes and applicable rules and regulations thereunder (collectively, the “ Money Laundering Laws ”), and no action, suit or proceeding by or before any court or governmental agency, authority or body or any arbitrator involving the Company or any of its subsidiaries with respect to the Money Laundering Laws is pending or, to the Company's knowledge, threatened.

3.30. OFAC . Neither the Company, any director or officer, nor, to the Company's knowledge, any agent, employee, subsidiary or Affiliate of the Company is currently subject to any U.S. sanctions administered by the Office of Foreign Assets Control of the U.S. Treasury Department (“ OFAC ”); and the Company will not directly or indirectly use the proceeds of the offering, or lend, contribute or otherwise make available such proceeds to any subsidiary, joint venture partner or other Person, for the purpose of financing the activities of any Person currently subject to any U.S. sanctions administered by OFAC.

3.31. Environmental Laws . The Company and its subsidiaries (i) are in compliance with any and all applicable foreign, federal, state and local laws and regulations relating to the protection of human health and safety, the environment or hazardous or toxic substances or wastes, pollutants or contaminants (“ Environmental Laws ”), (ii) have received all permits, licenses or other approvals required of them under applicable Environmental Laws to conduct their respective businesses and (iii) are in compliance with all terms and conditions of any such permit, license or approval, except where such noncompliance with Environmental Laws, failure to receive required permits, licenses or other approvals or failure to comply with the terms and conditions of such permits, licenses or approvals would not, singly or in the aggregate, have a Material Adverse Effect on the Company and its subsidiaries, taken as a whole. There are no costs or liabilities associated with Environmental Laws (including, without limitation, any capital or operating expenditures required for clean-up, closure of properties or compliance with Environmental Laws or any permit, license or approval, any related constraints on operating activities and any potential liabilities to third parties) which would, singly or in the aggregate, have a Material Adverse Effect on the Company and its subsidiaries, taken as a whole.

3.32. Employee Relations . Neither the Company nor any of its subsidiaries is a party to any collective bargaining agreement or employs any member of a union. Neither the Company nor any of its subsidiaries is engaged in any unfair labor practice. There is (i) (x) no unfair labor practice complaint pending or, to the Company's knowledge, threatened against the Company or any of its subsidiaries before the National Labor Relations Board, and no grievance or arbitration proceeding arising out of or under collective bargaining agreements is pending or threatened, (y) no strike, labor dispute, slowdown or stoppage pending or, to the Company's knowledge, threatened against the Company or any of its subsidiaries and (z) no union representation dispute

currently existing concerning the employees of the Company or any of its subsidiaries, and (ii) to the Company's knowledge, (x) no union organizing activities are currently taking place concerning the employees of the Company or any of its subsidiaries and (y) there has been no violation of any federal, state, local or foreign law relating to discrimination in the hiring, promotion or pay of employees or any applicable wage or hour laws. No executive officer of the Company (as defined in Rule 501(f) promulgated under the Securities Act) has notified the Company that such officer intends to leave the Company or otherwise terminate such officer's employment with the Company. No executive officer of the Company, to the knowledge of the Company, is, or is now expected to be, in violation of any material term of any employment contract, confidentiality, disclosure or proprietary information agreement, non-competition agreement, or any other agreement or any restrictive covenant, and the continued employment of each such executive officer does not subject the Company or any of its subsidiaries to any liability with respect to any of the foregoing matters.

3.33. ERISA . The Company and its subsidiaries are in compliance in all material respects with all presently applicable provisions of the Employee Retirement Income Security Act of 1974, as amended, including the regulations and published interpretations thereunder (herein called “ ERISA ”); no “reportable event” (as defined in ERISA) has occurred with respect to any “pension plan” (as defined in ERISA) for which the Company or any of its subsidiaries would have any liability; the Company has not incurred and does not expect to incur liability under (i) Title IV of ERISA with respect to termination of, or withdrawal from, any “pension plan”; or (ii) Sections 412 or 4971 of the Internal Revenue Code of 1986, as amended, including the regulations and published interpretations thereunder (the “ Code ”); and each “Pension Plan” for which the Company would have liability that is intended to be qualified under Section 401(a) of the Code is so qualified in all material respects and nothing has occurred, whether by action or by failure to act, which would cause the loss of such qualification.

3.34. Obligations of Management . To the Company's knowledge, each officer and key employee of the Company or its subsidiaries is currently devoting substantially all of his or her business time to the conduct of the business of the Company or its subsidiaries, respectively. The Company is not aware that any officer or key employee of the Company or its subsidiaries is planning to work less than full time at the Company or its subsidiaries, respectively, in the future. To the Company's knowledge, no officer or key employee is currently working or plans to work for a competitive enterprise, whether or not such officer or key employee is or will be compensated by such enterprise. To the Company's knowledge, no officer or Person currently nominated to become an officer of the Company or its subsidiaries is or has been subject to any judgment or order of, the subject of any pending civil or administrative action by the SEC or any self-regulatory organization .

3.35. Integration; Other Issuances of Shares . Neither the Company nor its subsidiaries or any Affiliates, nor any Person acting on its or their behalf, has issued any shares of Common Stock or shares of any series of preferred stock or other securities or instruments convertible into, exchangeable for or otherwise entitling the holder thereof to acquire shares of Common Stock which would be integrated with the sale of the Shares to the Purchasers for purposes of the Securities Act or of any applicable stockholder approval provisions, including, without limitation, under the rules and regulations of The NASDAQ Stock Market, nor will the Company or its subsidiaries or Affiliates take any action or steps that would require registration of any of

the Shares under the Securities Act or cause the offering of the Shares to be integrated with other offerings if any such integration would cause the issuance of the Shares hereunder to fail to be exempt from registration under the Securities Act as provided in Section 3.8 above or cause the transactions contemplated hereby to contravene the rules and regulations of The NASDAQ Stock Market. The Company is eligible to register the Shares for resale by the Purchasers using Form S-3 promulgated under the Securities Act.

3.36. No General Solicitation . Neither the Company nor its subsidiaries or any Affiliates, nor any Person acting on its or their behalf, has offered or sold any of the Shares by any form of general solicitation or general advertising.

3.37. No Brokers' Fees . The Company has not incurred any liability for any finder's or broker's fee or agent's commission in connection with the execution and delivery of this Agreement or the consummation of the transactions contemplated hereby.

3.38. Registration Rights . Except as set forth in (i) the Amended and Restated Investors' Rights Agreement dated June 21, 2010, by and among the Company and the parties listed on Exhibits A through G thereof, as amended by Amendment No. 1 to Amended and Restated Investors' Rights Agreement dated February 23, 2012, and as further amended by the Rights Agreement Amendment (as amended, the “ Rights Agreement ”); (ii) the Registration Rights Agreement, dated February 27, 2012, by and among the Company and the several purchasers signatory thereto; and (iii) the Registration Rights Agreement, dated July 30, 2012, by and between the Company and Total Gas & Power USA, SAS, the Company has not granted or agreed to grant to any Person any rights (including “piggy-back” registration rights) to have any securities of the Company registered with the SEC or any other governmental authority that have not been satisfied or waived.

3.39. Application of Takeover Protections . There is no control share acquisition, business combination, poison pill (including any distribution under a rights agreement) or other similar anti-takeover provision under the Company's charter documents or the laws of its state of incorporation that is or could become applicable to any of the Purchasers as a result of the Purchaser and the Company fulfilling their obligations or exercising their rights under the Transaction Agreements, including, without limitation, as a result of the Company's issuance of the Shares and the Purchasers' ownership of the Shares.

3.40. Disclosure . The Company understands and confirms that the Purchasers will rely on the foregoing representations in effecting transactions in the Shares. All disclosure furnished by or on behalf of the Company to the Purchasers in connection with this Agreement regarding the Company, its business and the transactions contemplated hereby is true and correct in all material respects and does not contain any untrue statement of a material fact or omit to state any material fact necessary in order to make the statements made therein, in light of the circumstances under which they were made, not misleading. The Company acknowledges and agrees that no Purchasers make or have made any representations or warranties with respect to the transactions contemplated hereby other than those set forth in Article 4 hereto. Other than (a) side letters contemplated by Section 6(h) hereof, (b) Payment Commitment Letters contemplated by Section 2.2(c) hereof, (c) that certain letter agreement with Biolding Investment SA in the form attached hereto as Schedule 3.40 (the “ Biolding Letter ”) and (d) letter agreements regarding

waivers of rights by any of the Purchasers, the Company has not entered into any letter agreement with a Purchaser hereunder in connection with the transactions contemplated hereby.

ARTICLE 4

REPRESENTATIONS AND WARRANTIES OF THE PURCHASER

Each Purchaser, as to itself only and not with respect to any other Purchaser, represents, warrants and covenants to the Company with respect to this purchase as follows:

4.1 Organization . The Purchaser is duly organized, validly existing, and in good standing under the laws of the jurisdiction of its organization.

4.2. Power . The Purchaser has all requisite power to execute and deliver this Agreement and to carry out and perform its obligations under the terms of this Agreement.

4.3. Authorization . The execution, delivery, and performance of this Agreement by the Purchaser has been duly authorized by all requisite action, and this Agreement constitutes the legal, valid, and binding obligation of the Purchaser enforceable in accordance with its terms, except (a) as limited by applicable bankruptcy, insolvency, reorganization, moratorium, and other laws of general application affecting enforcement of creditors' rights generally, and (b) as limited by laws relating to the availability of specific performance, injunctive relief or other equitable remedies.

4.4. Consents and Approvals . The Purchaser need not give any notice to, make any filing with, or obtain any authorization, consent, or approval of any government or governmental agency in order to consummate the transactions contemplated by this Agreement.

4.5. Non-Contravention . Neither the execution and the delivery of this Agreement, nor the consummation of the transactions contemplated hereby, will violate in any material respect any constitution, statute, regulation, rule, injunction, judgment, order, decree, ruling, charge, or other restriction of any government, governmental agency, or court to which the Purchaser is subject. No approval, waiver, or consent by the Purchaser under any instrument, contract, or agreement to which the Purchaser or any of its Affiliates is a party is necessary to consummate the transactions contemplated hereby.

4.6. Purchase for Investment Only . The Purchaser is purchasing the Shares for the Purchaser's own account for investment purposes only and not with a view to, or for resale in connection with, any “distribution” in violation of the Securities Act. By executing this Agreement, the Purchaser further represents that it does not have any contract, undertaking, agreement, or arrangement with any Person to sell, transfer, or grant participation to such Person or to any third Person, with respect to any of the Shares. The Purchaser understands that the Shares have not been registered under the Securities Act or any applicable state securities laws by reason of a specific exemption therefrom that depends upon, among other things, the bona fide nature of the investment intent as expressed herein.

4.7 Disclosure of Information . The Purchaser has had an opportunity to review the Company's filings under the Securities Act and the Exchange Act (including risks factors set forth therein) and the Purchaser represents that it has had an opportunity to ask questions and

receive answers from the Company to evaluate the financial risk inherent in making an investment in the Shares. The Purchaser has not been offered the opportunity to purchase the Shares by means of any general solicitation or general advertising.

4.8. Risk of Investment . The Purchaser realizes that the purchase of the Shares will be a highly speculative investment and the Purchaser may suffer a complete loss of its investment. The Purchaser understands all of the risks related to the purchase of the Shares. By virtue of the Purchaser's experience in evaluating and investing in private placement transactions of securities in companies similar to the Company, the Purchaser is capable of evaluating the merits and risks of the Purchaser's investment in the Company and has the capacity to protect the Purchaser's own interests.

4.9. Advisors . The Purchaser has reviewed with its own tax advisors the federal, state, and local tax consequences of this investment and the transactions contemplated by this Agreement. The Purchaser acknowledges that it has had the opportunity to review the Transaction Agreements and the transactions contemplated thereby with the Purchaser's own legal counsel.

4.10. Finder . The Purchaser is not obligated and will not be obligated to pay any broker commission, finders' fee, success fee, or commission in connection with the transactions contemplated by this Agreement.

4.11. Restricted Shares . The Purchaser understands that the Shares must be held indefinitely unless subsequently registered under the Securities Act or unless an exemption from registration is otherwise available. Moreover, the Purchaser understands that, except as set forth in the Rights Agreement, the Company is under no obligation to register the Shares. The Purchaser is aware of Rule 144 promulgated under the Securities Act (“ SEC Rule 144 ”) that permits limited resales of securities purchased in a private placement subject to the satisfaction of certain conditions.

4.12. Legend . It is understood by the Purchaser that each certificate representing the Shares shall be endorsed with a legend substantially in the following form:

“THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR APPLICABLE STATE SECURITIES LAWS. THE SECURITIES MAY NOT BE OFFERED FOR SALE, SOLD, TRANSFERRED OR ASSIGNED (I) IN THE ABSENCE OF (A) AN EFFECTIVE REGISTRATION STATEMENT FOR THE SECURITIES UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR (B) AN OPINION OF COUNSEL (WHICH COUNSEL SHALL BE SELECTED BY THE HOLDER), IN A FORM REASONABLY ACCEPTABLE TO THE COMPANY, THAT REGISTRATION IS NOT REQUIRED UNDER SAID ACT OR (II) UNLESS SOLD PURSUANT TO RULE 144 UNDER SAID ACT. NOTWITHSTANDING THE FOREGOING, THESE SECURITIES MAY BE PLEDGED IN CONNECTION WITH A BONA FIDE MARGIN

ACCOUNT OR OTHER LOAN OR FINANCING ARRANGEMENT SECURED BY THE SECURITIES.”

Subject to Section 7.3, the Company need not register a transfer of Shares unless the conditions specified in the foregoing legend are satisfied. Subject to Section 7.3, the Company may also instruct its transfer agent not to register the transfer of any of the Shares unless the conditions specified in the foregoing legend are satisfied.

4.13. Investor Qualification . The Purchaser is an “accredited investor” as defined in Rule 501(a) of Regulation D under the Securities Act. The Purchaser acknowledges that it has completed the Purchaser Suitability Questionnaire. The Purchaser has truthfully set forth in the Purchaser Suitability Questionnaire the factual basis or reason for qualification as an “accredited investor” as defined in Rule 501(a) of Regulation D under the Securities Act and such information remains true and correct as of the date hereof. The Purchaser agrees to furnish any additional information that the Company deems reasonably necessary in order to verify the answers set forth in the Purchaser Suitability Questionnaire.

ARTICLE 5

CONDITIONS TO COMPANY'S OBLIGATIONS AT THE CLOSING.

The Company's obligation to complete the sale and issuance of the Shares and deliver the Shares to each Purchaser, individually, at the Closing shall be subject to the following conditions to the extent not waived by the Company:

(a) Receipt of Payment . The Company shall have received payment (or confirmation that an Irrevocable Payment Instruction has been made, or a Payment Commitment Letter has been delivered, with respect to such payment), by wire transfer of immediately available funds or by cancellation or conversion of indebtedness of the Company to Purchaser, in the full amount of the Total Purchase Price for the number of Shares being purchased by such Purchaser at the Closing as set forth next to such Purchaser's name on Schedule I hereto.

(b) Representations and Warranties . The representations and warranties made by such Purchaser in Section 4 hereof shall be true and correct in all material respects as of, and as if made on, the date of this Agreement and as of the Closing.

(c) Receipt of Executed Documents . Such Purchaser shall have duly executed and delivered to the Company the Rights Agreement Amendment and the Purchaser Suitability Questionnaire.

ARTICLE 6

CONDITIONS TO PURCHASERS' OBLIGATIONS AT THE CLOSING

Each Purchaser's obligation to accept delivery of the Shares and to pay for the Shares shall be subject to the following conditions to the extent not waived by such Purchaser:

(a) Delivery . The Company shall have complied with its obligations set forth under Section 2.2 to (i) provide, with respect to each Purchaser, a single stock certificate for each Purchaser representing the number of Shares purchased by such Purchaser, (ii) to have instructed

the transfer agent to deliver such certificate upon the receipt of the Total Purchase Price from a Purchaser that has delivered an Irrevocable Payment Instruction and to have provided such Purchaser a portable document format (pdf) copy of the stock certificate at the time of the Closing; provided that such pdf copy of the stock certificate will be held by such Purchaser in escrow until the Company has been notified by its bank that it has received by wire transfer such Purchaser's applicable Total Purchase Price, or (iii) to have instructed the transfer agent to deliver such certificate upon the receipt of the Total Purchase Price from a Purchaser that has delivered a Payment Commitment Letter; provided that once such Purchaser provides the Company with an Irrevocable Payment Instruction then the Company shall provide such Purchaser a portable document format (pdf) copy of the stock certificate at such time; provided that such pdf copy of the stock certificate will be held by such Purchaser in escrow until the Company has been notified by its bank that it has received by wire transfer such Purchaser's applicable Total Purchase Price.

(b) Representations and Warranties . The representations and warranties made by the Company in Section 3 hereof shall be true and correct in all respects as of, and as if made on, the date of this Agreement and as of the Closing.

(c) Receipt of Rights Agreement Amendment . The Company shall have executed and delivered to each Purchaser the Rights Agreement Amendment.

(d) Legal Opinion . The Purchasers shall have received an opinion of Fenwick & West LLP, counsel to the Company, substantially in the form set forth in Exhibit D hereto.

(e) Certificate . Each Purchaser shall have received a certificate signed by the Company's Chief Executive Officer and Chief Financial Officer to the effect that the representations and warranties of the Company in Section 3 hereof are true and correct in all respects as of, and as if made on, the date of this Agreement and as of the Closing and that the Company has satisfied in all material respects all of the conditions set forth in this Agreement.

(f) Good Standing . The Company is validly existing as a corporation in good standing under the laws of Delaware as evidenced by a certificate of the Secretary of State of the State of Delaware, a copy of which was provided to the Purchasers.

(g) Waiver of Standstill Obligations . To the extent that any Purchaser is prohibited from purchasing Shares hereunder pursuant to the terms of any existing agreement entered into with the Company, the Company shall deliver to such Purchaser a waiver in form reasonably acceptable to Purchaser that permits such Purchaser to purchase Shares pursuant to this Agreement.

(h) Receipt of Minimum Funds . The Company shall have received (i) payments from the Purchasers in consideration of the Shares being sold pursuant to this Agreement, and (ii) with respect to any Purchasers who have not made any payment to the Company in consideration of the Shares to be purchased by such Purchaser, confirmation that such Purchaser has (x) made an Irrevocable Payment Instruction, such confirmation to either be in the form of (A) a federal reference number or other similar written evidence that a wire has been initiated, or (B) a side letter in the form attached hereto as Schedule 6(h) , or (y) delivered a Payment

Commitment Letter to the Company; provided that the payments received under clause (i) above and the payments to be received pursuant to any Irrevocable Payment Instruction or Payment Commitment Letter delivered to the Company pursuant to clause (ii) above shall total at least $42,249,991.06 in the aggregate excluding any payments being made by conversion of indebtedness of the Company to Purchaser (the “ Minimum Payment Amount ”); provided that upon execution of the Biolding Letter by the Company and Biolding Investment SA the Minimum Payment Amount shall be reduced to $37,249,991.06.

(i) Secretary's Certificate . A certificate, executed by the Secretary of the Company and dated as of the Closing Date, as to (A) the resolutions approving the issuance of the Shares as adopted by an Independent Committee of the Board of Directors and/or the Company's Board of Directors in a form reasonably acceptable to such Purchaser, (B) the certificate of incorporation, and (C) the bylaws, each as in effect as of the Closing Date.

(j) Board Approval . The terms and conditions of the issuance of the Shares and the Transaction Agreements shall have been approved by an Independent Committee of the Board of Directors and/or a majority of the disinterested directors of the Board of Directors, as applicable.

(k) Approvals . The Company shall have obtained all governmental, regulatory or third party consents and approvals, if any, necessary for the sale of the Shares, including, without limitation, from The NASDAQ Stock Market.

ARTICLE 7

OTHER AGREEMENTS OF THE PARTIES

7.1 Securities Laws Disclosure; Publicity . Promptly after the Closing Date, the Company shall issue a press release (the “ Press Release ”) reasonably acceptable to the Purchasers disclosing all material terms of the transactions contemplated hereby. On or before 5:30 p.m., New York City time, on the fourth trading day immediately following the execution of this Agreement, the Company will file a Current Report on Form 8-K with the SEC describing the terms of the Transaction Agreements.

7.2. Form D . The Company agrees to timely file a Form D with respect to the Shares as required under Regulation D and to provide a copy thereof to the Purchaser (provided that the posting of the Form D on the SEC's EDGAR system shall be deemed delivery of the Form D for purposes of this Agreement).

7.3. Removal of Legend and Transfer Restrictions . The Company hereby covenants with the Purchasers to, no later than three trading days following the delivery by the Purchaser to the Company of a legended certificate representing Shares (endorsed or with stock powers attached, signatures guaranteed, and otherwise in form necessary to affect the reissuance and/or transfer), in connection with the transfer or sale of all or a portion of the Shares pursuant to (1) an effective registration statement that is effective at the time of such sale or transfer, (2) a transaction exempt from the registration requirements of the Securities Act in which the Company receives an opinion of counsel reasonably satisfactory to the Company that the Shares are freely transferable and that the legend is no longer required on such stock certificate, or (3) an exemption from registration pursuant to SEC Rule 144, deliver or cause the Company's

transfer agent to deliver to the transferee of the Shares or to the Purchaser, as applicable, a new stock certificate representing such Shares that is free from all restrictive and other legends. The Company acknowledges that the remedy at law for a breach of its obligations under this Section 7.3 may be inadequate and agrees, in the event of a breach or threatened breach by the Company of the provisions of this Section 7.3 with respect to any Purchaser, the Purchaser shall be entitled, in addition to all other available remedies, to an order and/or injunction restraining any breach and requiring immediate issuance and transfer, without the necessity of showing economic loss and without any bond or other security being required.

7.4. Use of Proceeds . The Company agrees to use the proceeds of the offering for bona fide general corporate purposes and to provide working capital.

7.5. Subsequent Equity Sales . The Company shall not, and shall use its commercially reasonable efforts to ensure that no Affiliate of the Company shall, sell, offer for sale or solicit offers to buy or otherwise negotiate in respect of any security (as defined in Section 2 of the Securities Act) that will be integrated with the offer or sale of the Shares in a manner that would require the registration under the Securities Act of the sale of the Shares to the Purchasers, or that will be integrated with the offer or sale of the Shares for purposes of the rules and regulations of any trading market such that it would require stockholder approval prior to the closing of such other transaction unless stockholder approval is obtained before the closing of such subsequent transaction.

7.6. Listing . The Company shall promptly take any action required to maintain the listing of all of the Shares, once they have been issued, upon each national securities exchange and automated quotation system, if any, upon which shares of Common Stock are then listed (subject to official notice of issuance) and shall maintain, so long as any other shares of Common Stock shall be so listed, such listing of all Shares from time to time issuable under the terms of the Transaction Agreements. The Company shall take all actions within its control to comply with the reporting requirements of the Exchange Act and each applicable national securities exchange and automated quotation system on which the Common Stock is listed. The Company shall make and keep public information available, as those terms are understood and defined in SEC Rule 144, for so long as required in order to permit the resale of the Shares pursuant to SEC Rule 144 and to file period reports with the SEC whether or not required to do so. The Company shall not take any action which would be reasonably expected to result in the delisting or suspension of the Common Stock on The NASDAQ Stock Market.

ARTICLE 8

MISCELLANEOUS

8.1. Survival . The representations, warranties and covenants contained herein shall survive the execution and delivery of this Agreement and the sale of the Shares.

8.2. Indemnification .

(a) Indemnification of Purchasers . The Company agrees to indemnify and hold harmless each Purchaser and its Affiliates and their respective directors, officers, trustees,

members, managers, employees and agents, and their respective successors and assigns, from and against any and all losses, claims, damages, liabilities and expenses (including without limitation reasonable attorney fees and disbursements and other expenses reasonably incurred in connection with investigating, preparing or defending any action, claim or proceeding, pending or threatened and the costs of enforcement thereof) (collectively, “ Losses ”) to which such Person may become subject as a result of any breach of representation, warranty, covenant or agreement made by or to be performed on the part of the Company under this Agreement, and will reimburse any such Person for all such Losses as they are incurred by such Person.

(b) Conduct of Indemnification Proceedings . Any Person entitled to indemnification hereunder shall (i) give prompt notice to the Company of any claim with respect to which it seeks indemnification and (ii) permit the Company to assume the defense of such claim with counsel reasonably satisfactory to the indemnified party; provided that any Person entitled to indemnification hereunder shall have the right to employ separate counsel and to participate in the defense of such claim, but the fees and expenses of such counsel shall be at the expense of such Person unless (a) the Company has agreed to pay such fees or expenses, or (b) the Company shall have failed to assume the defense of such claim and employ counsel reasonably satisfactory to such Person or (c) in the reasonable judgment of any such Person, based upon written advice of its counsel, a conflict of interest exists between such Person and the Company with respect to such claims (in which case, if the Person notifies the Company in writing that such Person elects to employ separate counsel at the expense of the Company, the Company shall not have the right to assume the defense of such claim on behalf of such Person); and provided , further , that the failure of any indemnified party to give notice as provided herein shall not relieve the Company of its obligations hereunder, except to the extent that such failure to give notice shall materially adversely affect the Company in the defense of any such claim or litigation. It is understood that the Company shall not, in connection with any proceeding in the same jurisdiction, be liable for fees or expenses of more than one separate firm of attorneys at any time for all such indemnified parties. The Company will not, except with the consent of the indemnified party, which consent shall not be unreasonably withheld, conditioned or delayed, consent to entry of any judgment or enter into any settlement that does not include as an unconditional term thereof the giving by the claimant or plaintiff to such indemnified party of a release from all liability in respect of such claim or litigation. No indemnified party will, except with the consent of the Company, consent to entry of any judgment or enter into any settlement.

8.3. Assignment; Successors and Assigns . This Agreement may not be assigned by either party without the prior written consent of the other party; provided , that this Agreement may be assigned by any Purchaser to the valid transferee of any security purchased hereunder if such security remains a “restricted security” under the Securities Act. This Agreement and all provisions thereof shall be binding upon, inure to the benefit of, and are enforceable by the parties hereto and their respective successors and permitted assigns.

8.4. Notices . All notices, requests, and other communications hereunder shall be in writing and will be deemed to have been duly given and received (a) when personally delivered, (b) when sent by facsimile upon confirmation of receipt, (c) one business day after the day on which the same has been delivered prepaid to a nationally recognized courier service, or (d) five business days after the deposit in the United States mail, registered or certified, return receipt requested, postage prepaid, in each case addressed to, as to the Company, Amyris, Inc., 5885

Hollis Street, Suite 100, Emeryville, CA 94608, Attn: General Counsel, facsimile number: (510) 740-7416, with a copy to Fenwick & West LLP, 801 California Street, Mountain View, CA 94041, Attn: Dan Winnike, Esq., facsimile number: (650) 938-5200, and as to the Purchaser at the address and facsimile number set forth below the Purchaser's signature on the signature pages of this Agreement. Any party hereto from time to time may change its address, facsimile number, or other information for the purpose of notices to that party by giving notice specifying such change to the other parties hereto. Each Purchaser and the Company may each agree in writing to accept notices and other communications to it hereunder by electronic communications pursuant to procedures reasonably approved by it; provided that approval of such procedures may be limited to particular notices or communications.

8.5. Governing Law . This Agreement, and the provisions, rights, obligations, and conditions set forth herein, and the legal relations between the parties hereto, including all disputes and claims, whether arising in contract, tort, or under statute, shall be governed by and construed in accordance with the laws of the State of Delaware without giving effect to its conflict of law provisions.

8.6. Dispute Resolution .

8.6.1 Escalation . Prior to commencing any arbitration in connection with any dispute, controversy or claim arising out of relating to this Agreement or the breach, termination or validity thereof (“ Dispute ”), the parties shall first engage in the procedures set forth in this Section 8.6.1. Such Dispute shall first be referred by written notice of the Dispute (the “ Dispute Notice ”) from any party to its executive officers and to the executive officers of each party that the party sending the Dispute Notice has the Dispute with (the “ Executive Officers ”) and the Executive Officers shall attempt to resolve such Dispute within ten (10) days after a party sent the Dispute Notice to the Executive Officers by meeting (either in person or by video teleconference, unless otherwise mutually agreed) at a mutually acceptable time, and thereafter as often as they reasonably deem necessary, to exchange relevant information and to attempt to resolve the Dispute. If the Dispute has not been resolved within thirty (30) days after the Dispute Notice has been sent by a party to its Executive Officers and to the Executive Officers of the other party or parties, then either the party that has sent the Dispute Notice, or the party or parties that have received the Dispute Notice may, by written notice to the other party or parties, elect to submit the Dispute to arbitration pursuant to Section 8.6.2. If a party's Executive Officer intends to be accompanied at a meeting by an attorney, the Executive Officers of the other party shall be given at least seventy-two (72) hours' notice of such intention and may also be accompanied by an attorney. All negotiations conducted pursuant to this Section 8.6.1, and all documents and information exchanged by the parties in furtherance of such negotiations, (i) are the Confidential Information (as defined in Section 8.6.4) of the parties, and (ii) shall be inadmissible in any arbitration conducted pursuant to this Section 8.6 or other proceeding with respect to a Dispute.

8.6.2 Arbitration .

(a) All Disputes arising out of, relating to or in connection with this Agreement, which have not been resolved pursuant to Section 8.6.1, shall be submitted to mandatory, final and binding arbitration before an arbitral tribunal pursuant to the Rules of Arbitration of the International Court of Arbitration of the International Chamber of Commerce (the “ ICC Rules ”), in effect at the time of filing of the request for arbitration, as modified hereby.

The International Court of Arbitration of the International Chamber of Commerce (the “ ICC Court ”) shall administer the arbitration.

(b) There shall be three (3) arbitrators. If there are two parties to the arbitration, then one arbitrator shall be nominated by the initiating claimant party in the request for arbitration, the second nominated by the respondent party within thirty (30) days of receipt of the request for arbitration, and the third (who shall act as chairperson of the arbitral tribunal) nominated by the two (2) party-appointed arbitrators within thirty (30) days of the selection of the second arbitrator. In the event that either party fails to nominate an arbitrator, or if the two party-appointed arbitrators are unable or fail to agree upon the third arbitrator, within the time periods specified herein, the ICC Court shall appoint the remaining arbitrator(s) required to comprise the arbitral tribunal. If there are more than two parties to the arbitration, the claimant(s) shall jointly nominate one arbitrator and the respondent(s) shall jointly nominate one arbitrator, within thirty (30) days of receipt by respondent(s) of a copy of the request for arbitration. For avoidance of doubt, where there are two or more claimant(s), none of the claimants has to nominate an arbitrator in their request for arbitration. The third arbitrator (who shall act as chairperson of the arbitral tribunal) shall be nominated by the two (2) party-appointed arbitrators within thirty (30) days of the nomination of the second arbitrator. If either the claimant(s) or the respondent(s) fail to timely nominate an arbitrator, or if the two party-appointed arbitrators are unable or fail to agree upon the third arbitrator, within the time periods specified herein, then on the request of any party, the ICC Court shall appoint the remaining arbitrator(s) required to comprise the arbitral tribunal. The claimant in the arbitration shall provide a copy of the request for arbitration to the respondent at the time such request is submitted to the Secretariat of the International Chamber of Commerce.

(c) Each arbitrator chosen under this Section shall speak, read, and write English fluently and shall be either (i) a practicing lawyer who has specialized in business litigation with at least ten (10) years of experience in a law firm, (ii) an arbitrator experienced with commercial disputes, or (iii) a retired judge.

(d) The place of arbitration shall be Paris, France. The language of the arbitral proceedings and of all submissions and written evidence and any award issued by the arbitral tribunal shall be English. Any party may, at its own expense, provide for translation of any documents submitted in the arbitration or translation or interpretation of any testimony taken at any hearing before the arbitral tribunal. For the avoidance of doubt, no party is under any obligation to provide for translation of any documents submitted in the arbitration or translation or interpretation of any testimony taken at any hearing before the arbitral tribunal.

(e) The award shall be in writing, state the reasons for the award and be final and binding. The arbitral tribunal shall, subject to its discretion, endeavor to issue its award within four (4) months of the end of the hearing, or as soon as possible thereafter. It is expressly understood and agreed by the parties that the rulings and award of the arbitral tribunal shall be binding on the parties, their successors and permitted assigns. Judgment on the award rendered by the arbitral tribunal may be entered in any court having competent jurisdiction.

(f) Each party shall bear its own costs and expenses and attorneys' fees, and the party that does not prevail in the arbitration proceeding, as determined by the arbitral tribunal, shall pay the arbitrator's fees and any administrative fees of arbitration. All proceedings

and decisions of the tribunal shall be deemed Confidential Information of each of the Parties, and shall be subject to Section 8.6.4.

8.6.3 Interim Relief .

(a) The arbitral tribunal shall have the power to grant any remedy or relief that it deems appropriate, whether provisional or final, including conservatory relief and injunctive relief, and any such measures ordered by the arbitral tribunal may, to the extent permitted by applicable law, be deemed to be a final award on the subject matter of the measures and shall be enforceable as such.

(b) In addition to the remedies and relief available under Section 8.6.3(a) above and the ICC Rules, and subject to Section 8.6.2 above, each party expressly retains the right at any time to apply to any court of competent jurisdiction for interim, injunctive, provisional or conservatory relief, including pre-arbitral attachments or injunctions, and any such request shall not be deemed incompatible with the agreement to arbitrate or a waiver of the right to arbitrate.

(c) For purposes of Section 8.6.3(b), each party hereby irrevocably and unconditionally consents and agrees that any action for interim, provisional and/or conservatory relief brought against it with respect to its obligations or liabilities under or arising out of or in connection with this Agreement may be brought in the courts located in Paris, France or the state or federal courts located in the Borough of Manhattan, New York City, New York, and each party hereby irrevocably accepts and unconditionally submits to the non-exclusive jurisdiction of the aforesaid courts in personam , with respect to any such action for interim, provisional or conservatory relief. In any such action, each of the parties irrevocably waives, to the fullest extent they may effectively do so, any objection, including any objection to the laying of venue or based on the grounds of forum non conveniens or any right of objection to jurisdiction on account of its place of incorporation or domicile, which it may now or hereafter have to the bringing of any such action or proceeding in the courts located in Paris, France or the state or federal courts located in the Borough of Manhattan, New York City, New York.

(d) Each party hereby irrevocably consents and agrees that the service of any and all legal process, summons, notices and documents which may be served in any action arising under this Agreement may be made by sending a copy thereof by express courier to the party to be served at the address set forth in the notice provision of this Agreement, with such service to be effective upon receipt. Nothing in this Agreement will affect the right of any party to this Agreement to serve process in any other manner permitted by law.

(e) Each party hereto hereby irrevocably waives any and all right to trial by jury in any legal proceeding brought pursuant to this Section 8.6.

8.6.4 Confidentiality . The Company and each of the Purchasers agree to use, and to use its reasonable best efforts to ensure that its authorized representatives use the same degree of care as such party uses to protect its own confidential information (but in no event less than reasonable care) to keep confidential the information provided to it pursuant to this Agreement, and any other information furnished to it which the disclosing party identifies as being confidential or proprietary (so long as such information is not in the public domain) or, under the circumstances surrounding disclosure, such party knows or has reason to know should

be treated as confidential (“ Confidential Information ”), unless otherwise required by law (provided that a party shall, to the extent permitted by law, promptly notify the other party of any required disclosure and take reasonable steps to minimize the extent of any such required disclosure); provided, however, that Confidential Information shall not include information, that (i) was in the public domain prior to the time it was furnished to such recipient, (ii) is at the time of the alleged breach (through no willful or improper action or inaction by such recipient) generally available to the public, (iii) was rightfully disclosed to such recipient by a third party without restriction or (iv) as of the time of the alleged breach, had been independently developed (as evidenced by written records) without any use of Confidential Information.

8.7. Severability . In the event that any provision of this Agreement or the application of any provision hereof is declared to be illegal, invalid, or otherwise unenforceable by a court of competent jurisdiction, the remainder of this Agreement shall not be affected except to the extent necessary to delete such illegal, invalid, or unenforceable provision unless that provision held invalid shall substantially impair the benefits of the remaining portions of this Agreement.

8.8. Headings . The headings in this Agreement are for convenience of reference only and shall not constitute a part of this Agreement, nor shall they affect its meaning, construction, or effect.

8.9. Entire Agreement . This Agreement embodies the entire understanding and agreement between the parties hereto with respect to the subject matter hereof and supersedes all prior agreements and understandings relating to the subject matter hereof.

8.10. Finder's Fee . The Company agrees that it shall be responsible for the payment of any placement agent's fees, financial advisory fees, or brokers' commissions (other than for Persons engaged by Purchaser) relating to or arising out of the transactions contemplated hereby. The Company shall pay, and hold each Purchaser harmless against, any liability, loss or expense (including, without limitation, attorney's fees and out-of-pocket expenses) arising in connection with any claim for any such fees or commissions.

8.11. Expenses . Each party will bear its own costs and expenses in connection with this Agreement.

8.12. Further Assurances . The parties agree to execute and deliver all such further documents, agreements and instruments and take such other and further action as may be necessary or appropriate to carry out the purposes and intent of this Agreement.

8.13. Counterparts . This Agreement may be executed in two or more counterparts, each of which shall constitute an original, but all of which, when taken together, shall constitute but one instrument, and shall become effective when one or more counterparts have been signed by each party hereto and delivered to the other party. Facsimile signatures shall be deemed originals for all purposes hereunder.

8.14. Independent Nature of Purchasers' Obligations and Rights . The obligations of each Purchaser under this Agreement are several and not joint with obligations of each other Purchaser, and no Purchaser shall be responsible in any way for the performance of the obligations of any other Purchaser under this Agreement or any other Transaction Agreements. The decision of each Purchaser to purchase Shares pursuant to this Agreement has been made by

such Purchaser independently of any other Purchaser and independently of any information, materials, statements or opinions as to the business, affairs, operations, assets, properties, liabilities, results of operations, condition (financial or otherwise) or prospects of the Company or any of its subsidiaries which may have been made or given by any other Purchaser or by any agent or employee of any other Purchaser, and no Purchaser or any of its agents or employees shall have any liability to any other Purchaser (or any other Person) relating to or arising from any such information, materials, statements or opinions. Nothing contained herein or in any ancillary document, and no action taken by any Purchaser pursuant thereto, shall be deemed to constitute the Purchasers as a partnership, an association, a joint venture or any other kind of entity, or create a presumption that the Purchasers are in any way acting in concert or as a group with respect to such obligations or the transactions contemplated by the Agreement. Each Purchaser acknowledges that no other Purchaser has or will be acting as agent of such Purchaser in enforcing its rights under this Agreement or any other Transaction Agreements. Each Purchaser shall be entitled to independently protect and enforce its rights, including without limitation the rights arising out of this Purchaser, and it shall not be necessary for any other Purchaser to be joined as an additional party in any proceeding for such purpose.

8.15. Waiver of Conflicts; Representation by Counsel . Each Purchaser and the Company is aware that Fenwick & West LLP (“ F&W ”) may have previously performed and may continue to perform certain legal services for certain of the Purchasers in matters unrelated to F&W's representation of the Company. In connection with its Purchaser representation, F&W may have obtained confidential information of such Purchasers that could be material to F&W's representation of the Company in connection with negotiation, execution and performance of this Agreement. By signing this Agreement, each Purchaser and the Company hereby acknowledges that the terms of this Agreement were negotiated among the Purchasers and the Company and are fair and reasonable and waives any potential conflict of interest arising out of such representation (including any future representation of such parties) or such possession of confidential information. Each Purchaser and the Company further represents that it has had the opportunity to be, or has been, represented by separate independent counsel in connection with the transactions contemplated by this Agreement, including, without limitation, the waivers contained in this Section 8.15.

[Signature pages follows]

This Securities Purchase Agreement is hereby confirmed and accepted by the Company as of December 24, 2012.

AMYRIS, INC.

By: /s/ John Melo

Name: John Melo

Title: President and CEO

PURCHASERS:

U.S. $42,249,990.02

Total Purchase Price

(U.S. $2.98 per Share)

Number of Shares: 14,177,849

By:

(signature)

Name:

(printed name)

Title: Managing Member

Address:

Facsimile No:

E-mail Address:

This Securities Purchase Agreement is hereby confirmed and accepted by the Purchasers as of December 24, 2012.

PURCHASERS:

U.S. $ 4,999,998.96

Total Purchase Price

(U.S. $2.98 per Share)

Number of Shares: 1,677,852

NAXYRIS S.A.

By: /s/ Christoph Piel /s/ Jacques Reckinger

(signature)

Name:

(printed name)

Title: Director

Address: 40, Boulevard Joseph II

L-1840 Luxembourg

Attention: Sam Reckinger and

Christoph Piel

Facsimile No: [* ]

E-mail Address: [*]

This Securities Purchase Agreement is hereby confirmed and accepted by the Purchasers as of

December 24, 2012.

PURCHASERS:

U.S. $ 4,999,998.96

Total Purchase Price

(U.S. $2.98 per Share)

Number of Shares: 1,677,852

FORIS VENTURES, LLC

By: /s/ Barbara Hager

(signature)

Name: Barbara S. Hager

(printed name)

Title: Manager

Address: c/o JEMA Management

555 Bryant Street, #722

Palo Alto, CA 94301

Attention: Barbara S. Hager

Facsimile No: [*]

E-mail Address: [*]

This Securities Purchase Agreement is hereby confirmed and accepted by the Purchasers as of

December 24, 2012.

PURCHASERS:

U.S. $ 1,999,997.20

Total Purchase Price

(U.S. $2.98 per Share)

Number of Shares: 671,140

TPG BIOTECHNOLOGY PARTNERS II, L.P.

By: TPG Biotechnology GenPar II, L.P., its

general partner

By: TPG Biotechnology GenPar II Advisors,

LLC, its general partner

By: /s/ Ronald Cami

(signature)

Name: Ronald Cami

(printed name)

Title: Vice President

Address: 301 Commerce Street, Suite 3300

Fort Worth, TX 76102

Facsimile No: [*]

Telephone No: [*]

E-mail Address: [*]

This Securities Purchase Agreement is hereby confirmed and accepted by the Purchasers as of

December 24, 2012.

PURCHASERS:

U.S. $ 249,998.16

Total Purchase Price

(U.S. $2.98 per Share)

Number of Shares: 83,892

SUALK CAPITAL LTD

By: /s/ Fernando Reinach

(signature)

Name: Fernando Reinach

(printed name)

Title: Director

Address: Marcy Building 2nd Floor

Purcell Estate

PO Box 2416

Road Town

Tortola, British Virgin Island

Facsimile No:

E-mail Address:

This Securities Purchase Agreement is hereby confirmed and accepted by the Company as of

December 24, 2012.

PURCHASERS:

U.S. $ 9,999,997.92

Total Purchase Price

(U.S. $2.98 per Share)

Number of Shares: 3,355,704

By: /s/ Sheikh Abdullah bin Khalifa Al Thani

(signature)

Name: Biolding Investment

(printed name)

Title: President

Address: 11 A BD Prince Henri

1724 Luxembourg

Facsimile No:

E-mail Address: illegible

This Securities Purchase Agreement is hereby confirmed and accepted by the Company as of

December 24, 2012.

PURCHASERS:

U.S. $ 9,999,998.96

Total Purchase Price

(U.S. $2.98 per Share)

Number of Shares: 1,677,852

TOTAL GAS & POWER USA, SAS

By: /s/ Arnaud Chaperon

(signature)

Name: Arnaud Chaperon

(printed name)

Title: President

Address: 2, Place Jean Millier

La Defense

92400 Courbevoie, France

Facsimile No: [*]

E-mail Address: [*]

This Securities Purchase Agreement is hereby confirmed and accepted by the Purchasers as of

December 24, 2012.

PURCHASERS:

U.S. $ 14,999,999.86

Total Purchase Price

(U.S. $2.98 per Share)

Number of Shares: 5,033,557

MAXWELL (MAURITIUS) PTE LTD

By: /s/ Fidah Alsagoff

(signature)

Name: Fidah Alsagoff

(printed name)

Title: Authorised Signatory

Address: 60B Orchard Road #06-18

Tower 2, The Atrium @ Orchard

Singapore 238891

Facsimile No: [* ]

E-mail Address:

Schedule I

Schedule of Purchasers



Purchaser	Shares Purchased	Cancellation of Indebtedness		Cash paid at Closing		Total Purchase Price
Maxwell (Mauritius) Pte Ltd	5,033,557			$	14,999,999.86	$	14,999,999.86
Biolding Investment SA	3,355,704			$	9,999,997.92	$	9,999,997.92
Naxyris SA	1,677,852			$	4,999,998.96	$	4,999,998.96
Foris Ventures, LLC	1,677,852			$	4,999,998.96	$	4,999,998.96
TPG Biotechnology Partners II, L.P.	671,140			$	1,999,997.20	$	1,999,997.20
Sualk Capital Ltd	83,892			$	249,998.16	$	249,998.16
Total Gas & Power USA, SAS	1,677,852	$	4,999,998.96			$	4,999,998.96
TOTAL	14,177,849	$	4,999,998.96	$	37,249,991.06	$	42,249,990.02

Schedule 2.2

Form of Payment Commitment Letter

December 24, 2012

Maxwell (Mauritius) Pte Ltd

Les Cascades, Edith Cavell Street

Port Louis, Mauritius

Dear Investor:

Effective today, Amyris, Inc. (the “Company”) is selling shares of the Company's Common Stock pursuant to that certain Securities Purchase Agreement dated as of December 24, 2012 (the “ SPA ”) among the Company, Maxwell (Mauritius) Pte Ltd ( “Investor”) and the other Purchasers named therein. In connection therewith, the Company and Investor are entering into this letter agreement (this “ Letter Agreemen t”). Capitalized terms used herein and not otherwise defined shall have the meaning given to such terms in the SPA.

The Company and Investor agree to the following:

1. Payment Commitment Obligation . Investor hereby acknowledges and irrevocably agrees that by no later than January 14, 2013 Investor will pay to the Company Investor's applicable Total Purchase Price as set forth on Schedule I of the SPA by wire transfer of immediately available funds.

2. Stock Certificate . The Company hereby acknowledges and agrees that (a) if Investor delivers to Company an Irrevocable Payment Instruction by Investor, then promptly upon receipt of such Irrevocable Payment Instruction, the Company (i) shall instruct its transfer agent to issue to the Investor a single stock certificate representing the number of Shares purchased by Investor pursuant to the SPA (“Investor's Stock Certificate”), (ii) shall instruct its transfer agent to deliver to Investor the Investor's Stock Certificate immediately upon the Company's confirmation to the transfer agent that it has received in its bank account the applicable Total Purchase Price from Investor, (iii) will not revoke the instructions referenced in clause (ii) of this paragraph, and (iv) will immediately notify its transfer agent once the Company has been notified by its bank that it has received by wire transfer Investor's applicable Total Purchase Price, or (b) if Investor does not deliver to Company an Irrevocable Payment Instruction, then immediately upon receipt by the Company in its bank account of the applicable Total Purchase Price from Investor the Company shall instruct its transfer agent to issue to, and deliver to, Investor Investor's Stock Certificate and the Company will not revoke such instructions.

3. Amendment and Waiver . No amendment, modification, termination or cancellation of this Letter Agreement shall be effective unless it is in writing signed by the Company and Investor. No waiver of any of the provisions of this Letter Agreement shall be deemed or shall constitute a waiver of any other provisions hereof (whether or not similar) nor shall such waiver constitute a continuing waiver.

4. Entire Agreement . This Letter Agreement, the SPA and the other documents referenced therein, set forth the entire understanding between the parties hereto relating to the subject matter hereof and supersede and merge all previous written and oral negotiations, commitments, understandings and agreements relating to the subject matter hereof between the Company and Investor.

5. Notices . All notices and other communications hereunder shall be in writing and shall be deemed given when delivered personally or by commercial messenger or courier service to the parties at the following addresses (or at such other address for a party as shall be specified by like notice) or when sent by facsimile transmission or email to the facsimile number or email address specified below (or such other facsimile number or email as shall be specified by like notice), upon machine or electronic

confirmation of receipt:


(a)	if to the Company, to:

Amyris, Inc.

5885 Hollis Street, Suite 100

Emeryville, CA 94608

Attention: General Counsel

Facsimile:

Email:


(b)	if to Investor, to:

Maxwell (Mauritius) Pte Ltd

Les Cascades, Edith Cavell Street

Port Louis, Mauritius

Attention:

Facsimile:

With a copy to:

60B Orchard Road

#06-18 Tower 2

The Atrium@Orchard

Singapore 238891

6. Governing Law . This Letter Agreement, and the provisions, rights, obligations and conditions set forth herein, and the legal relations between the parties hereto, including all disputes and claims, whether arising in contract, tort, or under statute, shall be governed by and construed in accordance with the laws of the State of Delaware without giving effect to its conflict of law provisions.

7. Counterparts . This Letter Agreement may be executed in one or more counterparts, which shall together constitute one agreement.

Please indicate your agreement to the terms of this Letter Agreement by executing the acknowledgment and agreement below and returning a copy to the attention of our General Counsel.

[Remainder of Page Intentionally Left Blank]

Very truly yours,

AMYRIS, INC.

Name: John G. Melo

Title : President and Chief Executive Officer

Acknowledged and Agreed as

of the date first written above:

INVESTOR

MAXWELL (MAURITIUS) PTE LTD

By :

Name:

Title:

[Signature Page to Letter Agreement]

Schedule 3.40

Form of Biolding Letter

(see Exhibit 4.17 Annual Report on Form 10-K for fiscal 2012 as filed on March 2013)

Schedule 6(h)

Form of Side Letter

December 24, 2012

[Insert Investor Name]

[Insert Investor Address]

Dear Investor:

Effective today, Amyris, Inc. (the “ Company ”) is selling shares of the Company's Common Stock pursuant to that certain Securities Purchase Agreement dated as of December 24, 2012 (the “ SPA ”) among the Company, [Insert Investor Name] ( “ Investor ”) and the other Purchasers named therein. In connection therewith, the Company and Investor are entering into this letter agreement (this “ Letter Agreement ”). Capitalized terms used herein and not otherwise defined shall have the meaning given to such terms in the SPA.

The Company and Investor agree to the following:

1. Irrevocable Payment Instruction . Investor hereby acknowledges and agrees that the Investor has given its payment instructions to its paying bank to make payment to the Company of the Investor's applicable Total Purchase Price pursuant to the SPA and will not revoke such payment instructions.

2. Stock Certificate . The Company hereby acknowledges and agrees that (i) the Company has instructed its transfer agent to issue to the Investor a single stock certificate representing the number of Shares purchased by Investor pursuant to the SPA (“ Investor's Stock Certificate ”) on December 24, 2012, of which a PDF copy will be delivered to the Company on December 26, 2012; (ii) the Company has instructed its transfer agent to deliver to Investor the Investor's Stock Certificate immediately upon the Company's confirmation to the transfer agent that it has received in its bank account the applicable Total Purchase Price from Investor, (iii) the Company will not revoke the instructions referenced in clause (ii) of this paragraph, and (iv) the Company will immediately notify its transfer agent once the Company has been notified by its bank that it has received by wire transfer Investor's applicable Total Purchase Price.

2. Amendment and Waiver . No amendment, modification, termination or cancellation of this Letter Agreement shall be effective unless it is in writing signed by the Company and Investor. No waiver of any of the provisions of this Letter Agreement shall be deemed or shall constitute a waiver of any other provisions hereof (whether or not similar) nor shall such waiver constitute a continuing waiver.

3. Entire Agreement . This Letter Agreement, the SPA and the other documents referenced therein, set forth the entire understanding between the parties hereto relating to the subject matter hereof and supersede and merge all previous written and oral negotiations, commitments, understandings and agreements relating to the subject matter hereof between the Company and Investor.

4. Notices . All notices and other communications hereunder shall be in writing and shall be deemed given when delivered personally or by commercial messenger or courier service to the parties at the following addresses (or at such other address for a party as shall be specified by like notice) or when sent by facsimile transmission or email to the facsimile number or email

address specified below (or such other facsimile number or email as shall be specified by like notice), upon machine or electronic confirmation of receipt:


(a)	if to the Company, to:

Amyris, Inc.

5885 Hollis Street, Suite 100

Emeryville, CA 94608

Attention:

Facsimile:

Email:


(b)	if to Investor, to:

[Insert Investor Address]

Attention:

Facsimile:

Email:

5. Governing Law . This Letter Agreement, and the provisions, rights, obligations and conditions set forth herein, and the legal relations between the parties hereto, including all disputes and claims, whether arising in contract, tort, or under statute, shall be governed by and construed in accordance with the laws of the State of Delaware without giving effect to its conflict of law provisions.

6. Counterparts . This Letter Agreement may be executed in one or more counterparts, which shall together constitute one agreement.

Please indicate your agreement to the terms of this Letter Agreement by executing the acknowledgement and agreement below and returning a copy to the attention of our General Counsel.

[Remainder of Page Intentionally Left Blank]

Very truly yours,

AMYRIS, INC.

Name: John G. Melo

Title : President and Chief Executive Officer

Acknowledged and Agreed as

of the date first written above:

INVESTOR

MAXWELL (MAURITIUS) PTE LTD

By :

Name:

Title:

[Signature Page to Letter Agreement]

Exhibit A

RIGHTS AGREEMENT AMENDMENT

(see Exhibit 4.04 Annual Report on Form 10-K for fiscal 2012 as filed on March 2013)

Exhibit B

PURCHASER SUITABILITY QUESTIONNAIRE

FOR

AMYRIS, INC.

This Questionnaire is to be completed by each INDIVIDUAL purchasing securities of Amyris, Inc., a Delaware corporation (the " Company "). The purpose of this Questionnaire is to assure the Company that each proposed investor will meet certain suitability standards in connection with investment in the Company and the purchase of shares of the Company's Common Stock, $0.0001 par value per share (the " Shares "), including those imposed by applicable state and federal securities laws and the regulations under those laws.

Individuals investing in the name of a trust should not complete this Questionnaire but should instead complete an "Investor Questionnaire for Entities." If the answer to any question is "None" or "Not Applicable," please so state. If more space is needed for any answer, additional sheets may be attached.

Your answers will be kept confidential at all times. However, by signing this Questionnaire, you agree that the Company may present this Questionnaire to such par-ties as it deems appropriate to establish the availability of exemptions from registration or qualification requirements under federal and state securities laws.

1. IDENTIFICATION

1.1 Name(s) in which the Shares are to be registered:


1.2	If the Shares are to be registered in the name of two or more individuals or are to be community property, check one of the following:

___________ Joint Tenants with Right of Survivorship*

___________ Tenants in Common*

___________ Community Property*

*Each joint tenant and tenant-in-common other than your spouse must complete a separate Questionnaire. Your spouse, if any, must execute this Questionnaire.

1.3 Social Security Number:


1.4	Principal Residence Address:


1.5	Telephone Number:

1.6 Principal Occupation (if retired, previous occupation):

Position or Title:

1.7. Education:

2. ACCREDITATION


2.1	Amount of the proposed investment: $________________________________________

Is your cash flow from all sources sufficient to satisfy your current needs, including possible contingencies, such that you have no need for liquidity in this proposed investment?

Yes_____ No_____

Do you have the ability to bear the economic risk of the investment, i.e., can you afford to lose your entire investment?

Yes_____ No_____

Do you, by reason of your business and financial experience or the business and financial experience of a professional advisor, have the capacity to evaluate the merits and risks of your proposed investment and to protect your own interests in connection with the investment?

Yes_____ No_____

IF YES , please describe your business and financial experience, indicating the factual basis for your conclusion that you have such capacity:

Are you relying on the business or financial experience of an accountant, attorney or other professional advisor in evaluating the merits and risks of this investment in order to protect your own interest?

Yes_____ No_____

IF YES , please (a) have your advisor complete the Company's form of Advisor's Questionnaire and submit it with this Questionnaire, and (b) identify the advisor.

Name of professional advisor:

Is the proposed investment less than 10% of your net worth, or joint net worth with your spouse?

Yes_____ No_____

Have you previously invested in private placements of securities of recently formed, non-public companies or of companies without a history of significant earnings or profits?

Never _____ Rarely_____ On Several Occasions_____


2.2	Please initial which, if any, of the following statements are applicable to you:

_____

My individual net worth, or my joint net worth with my spouse, exceeds $1,000,000. (NOTE: In computing the amount of net worth, please exclude both the value of your primary residence and the amount of indebtedness that is secured by your primary residence from the computation. However, if the amount of such indebtedness exceeds the value of your primary residence, include the excess (and only the excess) indebtedness amount in the computation of net worth, but still do not include the value of your primary residence in the computation. In addition, include in the computation any amount of such indebtedness, but not the value of your primary residence, that was incurred within 60 days preceding the proposed investment other than in connection with the acquisition of your primary residence.)


_____	My proposed total investment in the Company is at least $150,000 and does not exceed 10% of my net worth or joint net worth with my spouse.


_____	I personally have had an individual income in excess of $200,000 in each of the two (2) most recent years and I reasonably expect an income in excess of $200,000 in the current year.


_____	My joint income with my spouse is in excess of $300,000 in each of the two (2) most recent years and I reasonably expect a joint income in excess of $300,000 in the current year.


2.3	If you have not initialed one of the responses in Question 2.2 above, please answer the following questions:

My net worth or joint net worth with my spouse exceeds: $________________________.

(NOTE: In computing the amount of net worth, please exclude both the value of your primary residence and the amount of indebtedness that is secured by your primary residence from the computation. However, if the amount of such indebtedness exceeds the value of your primary residence, include the excess (and only the excess) indebtedness amount in the computation of net worth, but still do not include the value of your primary residence in the computation. In addition, include in the computation any amount of such indebtedness, but not the value of your primary residence, that was incurred within 60 days preceding the proposed investment other than in connection with the acquisition of your primary residence.)

My estimated gross income together with my spouse for this calendar year is: (check one)

_____ under $75,000 _____ $75,000 - $99,999

_____ $100,000 - $199,999 _____ $200,000 and over


2.4	Are you related in any way to any other person who also intends to purchase Shares in this offering? If so, please state the name and nature of the relationship of each such person:


2.5	If you have used the services of a securities broker or dealer or a finder in submitting subscription documentation for the Shares, please identify the broker, dealer or finder:

3. EXECUTION

The information provided in this Questionnaire is true and complete as of the date provided below in all material respects and the undersigned recognizes that the Company is relying on the truth and accuracy of such information. The undersigned agrees to notify the Company promptly of any changes in the foregoing information that may occur prior to the closing of the sale of Shares of the Company.

_________________________________ ___________________________________

(Signature of Purchaser) (Signature of Spouse, if any)

Name:____________________________ Name:______________________________

(Please Print or Type) (Please Print or Type)

Date:_____________________________ Date:______________________________

Exhibit C

PURCHASER SUITABILITY QUESTIONNAIRE

FOR

AMYRIS, INC.

This Questionnaire is to be completed by each ENTITY (trust, corporation, partnership or other organization) purchasing securities of Amyris, Inc., a Delaware corporation (the " Company "). The purpose of this Questionnaire is to assure the Company that each proposed investor will meet certain suitability standards in connection with investment in the Company and the purchase of shares of the Company's Common Stock, $0.0001 par value per share (the " Shares "), including those imposed by applicable state and federal securities laws and the regulations under those laws.

If the answer to any question is "None" or "Not Applicable," please so state. If more space is needed for any answer, additional sheets may be attached.

Your answers will be kept confidential at all times. However, by signing this Questionnaire, you agree that the Company may present this Questionnaire to such parties as it deems appropriate to establish the availability of exemptions from registration or qualification requirements under federal and state securities laws.

1. IDENTIFICATION

1.1 Name(s) in which the Shares are to be registered:

1.2 Tax Identification Number:

1.3 Address of principal place of business:

1.4 Telephone number:___________________________________________

1.5 Jurisdiction of formation or of incorporation (Name the State or Country):

1.6 Form of entity (e.g., corporation, general partnership, limited partnership, trust, etc.):

1.7 Nature of business (e.g., investment, banking, manufacturing, venture capital investment

fund, etc.):

2. ACCREDITATION

2.1 Amount of the proposed investment: $


2.2	Is the entity's cash flow from all sources sufficient to satisfy its current needs, including possible contingencies, such that the entity has no need for liquidity in this proposed investment?

Yes_____ No_____


2.3	Was the entity specifically formed for the purpose of investing in the Company?

Yes_____ No_____


2.4	Does the entity have the ability to bear the economic risk of the investment, i.e., can the entity afford to lose its entire investment?

Yes_____ No_____


2.5	Is the entity an employee benefit plan governed by the Employee Retirement Income Security Act of 1974 (a 401(k) Plan, Keogh Plan, pension plan, etc., maintained by an employer for its employees)?

Yes_____ No_____

IF YES , please indicate which, if any, of the following categories accurately describes the entity:

_____ the employee benefit plan has total assets in excess of $5,000,000.


_____	the plan is a self-directed plan with investment decisions made solely by persons listed in Section 2.6 below or who are individuals, and each such individual has a net worth in excess $1,000,000 or had an individual income in excess of $200,000 in each of the two most recent years and has a reasonable expectation of reaching the same income level in the current year.


_____	investment decisions are made by a plan fiduciary which is either a bank, savings and loan association, insurance company or registered investment advisor.

2.6 Please indicate which, if any, of the following categories accurately describes the entity:

_____ A bank.

_____ A savings and loan association.


_____	A broker-dealer registered under Section 15 of the Securities Exchange Act of 1934.

_____ An insurance company.


_____	An investment company registered under the Investment Company Act of 1940 or a business development company as defined in Section 2(a)(48) of that Act.


_____	A Small Business Investment Company licensed by the U.S. Small Business Administration under Section 301(c) or (d) of the Small Business Investment Act of 1958.


_____	A private business development company defined in Section 202(a)(22) of the Investment Advisors Act of 1940.


_____	An organization described in Section 501(c)(3) of the Internal Revenue Code with total assets in excess of $5,000,000 not formed for the purpose of investing in the Company.


_____	A corporation with total assets in excess of $5,000,000, not formed for the purpose of investing in the Company.


_____	A partnership with total assets in excess of $5,000,000, not formed for the purpose of investing in the Company.


_____	A Massachusetts or similar business trust with total assets in excess of $5,000,000, not formed for the purpose of investing in the Company.


_____	Any other trust with total assets in excess of $5,000,000, not formed for the purpose of investing in the Company.

2.7 Please indicate if one of the following describes the equity owners of the entity:


_____	Each equity owner of the entity (i.e., all shareholders, all general and/or limited partners or all beneficiaries, as applicable) is an individual whose net worth or joint net worth with his or her spouse exceeds $1,000,000.


_____	Each equity owner of the entity is an individual who had a personal income in excess of $200,000 in each of the two (2) most recent years or joint income with that person's spouse in excess of $300,000 in each of those years and reasonably expects to reach the same income level in the current year.


_____	Each equity owner of the entity is an entity described in at least one category of Question 2.6 above.


_____	Although not all equity owners are described in the same category above in this Question 2.7, each equity owner is described in at least one such category.

2.8 Please indicate which of the following also describes the equity owners of the entity:


_____	Each equity owner of the entity has, by reason of his, her or its business and financial experience, the capacity to evaluate the merits and risks of the entity's proposed investment and to protect his, her or its own interests in connection with the investment.


_____	Each of the equity owners of the entity is able to bear the economic risk of the entity's investment, i.e., can afford loss of the entity's entire investment.


_____	The beneficial interest of each equity owner in the entity's proposed investment is less than 10% of such equity owner's net worth, or joint net worth with his or her spouse.


_____	Although not all equity owners are described in the same category above in this Question 2.8, each equity owner is described in at least one such category.

3. ADDITIONAL INFORMATION


3.1	Has your entity previously invested in private placements of securities of newly-formed, non-public companies or companies without a history of significant profits or earnings?

Never _______ Rarely _______ On Several Occasions _______


3.2	Does your entity, by reason of its business and financial knowledge and experience, have the capacity to evaluate the merits and risks of the entity's proposed investment and to protect the entity's own interests in connection with its investment in the Company?

Yes _____ No _____

IF YES , please describe the business and financial knowledge and experience, indicating factual basis for your conclusion that the entity has such capacity.


3.3	Do the persons responsible for making the investment decision for the entity, by reason of their business and financial knowledge and experience, have the capacity to evaluate the merits and risks of the entity's proposed investment?

Yes _____ No _____

IF YES , please describe the business and financial knowledge and experience, indicating factual basis for your conclusion that those persons have such capacity.


3.4	If you have used the services of a securities broker or dealer or a finder in submitting subscription documentation for the Shares, please identify the broker, dealer or finder:


3.5	Are you relying on the business or financial experience of an accountant, attorney or other professional advisor in evaluating the merits and risks of this investment in order to protect your own interest?

Yes_____ No_____

IF YES , please (a) have your advisor complete the Company's form of Advisor's Questionnaire and submit it with this Questionnaire, and (b) identify the advisor.

Name of professional advisor:

4. EXECUTION

Name of Entity:

___________________________________________________________

(Please Print or Type)

By:________________________________________________________

(Signature)

Name:______________________________________________________

(Please Print or Type)

Title:_______________________________________________________

(Please Print or Type)

Date:_______________________________________________________

Exhibit D

OPINION OF COMPANY COUNSEL

December 24, 2012

To the Purchasers of Common Stock of

Amyris, Inc. Who are Listed as Investing

on the Date Hereof on the Signature Pages to the Purchase Agreement

Ladies and Gentlemen:

We have acted as counsel for Amyris, Inc., a Delaware corporation (the " Company "), in connection with the sale on the date hereof by the Company to you of 14,177,849 shares of the Company's Common Stock (the " Shares ") pursuant to the Stock Purchase Agreement, dated as of December 24, 2012 (the " Purchase Agreement "), among the Company and the parties whose names appear on the signature pages thereto (the " Purchasers "), and the execution and delivery by the Company of the Amendment No. 2 to Amended and Restated Investors' Rights Agreement (the " Rights Agreement "), dated as of December 24, 2012. This opinion is given to you pursuant to Article 6(d) of the Purchase Agreement in connection with the Closing of the sale of the Shares. The Purchase Agreement and the Rights Agreement are referred to herein together as the " Transaction Documents. " Unless defined herein, capitalized terms used herein have the meaning given to them in the Purchase Agreement.

We have examined such matters of law as we reasonably considered necessary for the purpose of rendering this opinion. As to matters of fact material to the opinions expressed herein, we have relied upon the representations and warranties as to factual matters contained in, and made by the Company pursuant to, the Purchase Agreement and upon certificates and statements of government officials and of officers of the Company, including but not limited to a certificate of the Company to us (the " Opinion Certificate "). In addition, we have examined originals or copies of documents, corporate records and other writings that are listed in Exhibit A attached hereto (the “ Reviewed Agreements” ) and have not conducted any other factual examination except as listed on Exhibit A . In such examination, we have assumed that the signatures on documents and instruments examined by us are authentic, that each is what it purports to be, and that all documents and instruments submitted to us as copies or facsimiles conform with the originals, which facts we have not independently verified.

In making our examination of documents (including the Transaction Documents) and rendering our opinions, we have further assumed that, except for the Company with respect to the Transaction Documents, (a) each party to such documents had the entity power and entity authority to enter into and perform all of such party's obligations thereunder, (b) each party to such documents has duly authorized, executed and delivered such documents and (c) each of such documents is enforceable against and binding upon the parties thereto. We have also assumed that (i) the representations and warranties of the Purchasers set forth in the Transaction Documents are accurate and complete, (ii) there is no fact or circumstance relating to you or your business that might prevent you from enforcing any of your rights provided for in the Transaction Documents and (iii) there are no extrinsic agreements or understandings among the parties to the Transaction Documents or among the parties to the Reviewed Agreements expressly identified on Exhibit A hereto, that would modify or interpret the terms of the

To the Purchasers of Common

Stock of Amyris, Inc. on the Date Hereof

December 24, 2012

Page 2

Transaction Documents or Reviewed Agreements or the respective rights or obligations of the parties thereto.

Notwithstanding the examination described above, the expressions " to our knowledge , " " known to us ," " our actual knowledge " or words of similar import when used in this opinion letter, refer to the current actual knowledge of attorneys within the firm who have rendered legal services to the Company in connection with the Transaction Documents and means that, while such attorneys have not been informed by the Company that a matter stated is factually incorrect, we have made no independent factual investigation with respect to such matter. No inference as to our knowledge of any matters bearing on the accuracy of any such statement should be drawn from the fact of our representation of the Company or the rendering of the opinions set forth below.

Where statements in this opinion concerning the Company, or an effect on the Company, are qualified by the term "material" or "materially , " those statements involve judgments and opinions as to the materiality or lack of materiality of any matter to the Company's business, assets, results of operations or financial condition that are entirely those of the Company and its officers.

We express no opinion as to matters governed by any laws other than the laws of the State of California, the Delaware General Corporation Law (the " DGCL ") and the federal law of the United States of America, including the rules and regulations promulgated by governmental authorities thereunder, as such laws, rules and regulations exist on the date hereof (collectively, " Applicable Laws "). We express no opinion as to whether the laws of any particular jurisdiction apply, or to the extent that the laws of any jurisdiction other than those identified above are applicable to the Transaction Documents or the transactions contemplated thereby.

In rendering the opinion set forth in paragraph (1) (Qualification to Do Business) below as to the

valid existence and good standing of the Company under the laws of the State of Delaware and as to its qualification to do business as a foreign corporation in good standing under the laws of the State of California, we have relied exclusively on certificates of public officials and the Opinion Certificate.

In rendering the opinion set forth in paragraph (2) (Authority and Power to Do Business) below concerning the Company's corporate power and corporate authority to conduct its business as it is presently conducted and as to the types of businesses the Company presently conducts, we have relied exclusively upon representations made to us in the Opinion Certificate. We note that the parties to the Purchase Agreement have designated the laws of the State of Delaware as the laws governing the Purchase Agreement. Notwithstanding the designation therein of the laws of the State of Delaware, our opinion in paragraph (4) (Enforceability) below as to the validity, binding effect and enforceability of the Purchase Agreement is premised upon the results that would be obtained if a California court were to apply the internal laws of the State of California to contracts made between California residents present in California when the Purchase Agreement is entered into and, where applicable, the currently effective DGCL, without regard to laws regarding choice of law or conflict of laws.

To the Purchasers of Common

Stock of Amyris, Inc. on the Date Hereof

December 24, 2012

Page 3

In rendering the opinion in paragraph (6) (No Violations) below relating to violations of Applicable Laws, and paragraph (7) (No Consents) below relating to consents, approvals, authorizations and filings under, or pursuant to, Applicable Laws, such opinions are limited to Applicable Laws that in our experience are typically applicable to transactions of the nature provided for in the Transaction Documents. Moreover, we render no opinion in such paragraphs, or in paragraph (4) (Enforceability), regarding the Company's compliance with applicable securities laws, including but not limited to laws regarding the registration or qualification of the offer and sale of securities, or the registration by the Company under any such securities laws, and no such opinion should be inferred from the language of those paragraphs. Any opinion rendered in connection with applicable securities laws is rendered solely and expressly in paragraphs (8) (Securities Law Compliance) and (9) (Not an Investment Company) below.

In rendering the opinion in paragraph (6) (No Violations) below regarding breach of, or default under, any Reviewed Agreements set forth in Exhibit A , we have not reviewed, and express no opinion on, (a) financial covenants or similar provisions requiring financial calculations or determinations to ascertain whether there is any breach or default nor (b) provisions relating to the occurrence of a "material adverse event" or words of similar import. We also do not express any opinion on parol evidence bearing on interpretation or construction of such Reviewed Agreements, or on any oral modifications to such Reviewed Agreements made by the parties thereto. Moreover, to the extent that any of the Reviewed Agreements are governed by the laws of any jurisdiction other than the State of California our opinion relating to those agreements is based solely upon the plain meaning of their language as though California law applied, without regard to interpretation or construction that might be indicated by the laws stated as governing those agreements.

In rendering the opinion expressed in paragraph (8) (Securities Law Compliance) below, we have assumed the accuracy of, and have relied upon, the Company's representations to us that the Company has made no offer to sell the Shares by means of any general solicitation or publication of any advertisement therefor, and we have assumed that the offer and sale of the Shares is not integrated with any future securities offering of the Company.

This opinion is qualified by, and we render no opinion with respect to, or as to the effect of, the following:

(a) bankruptcy, insolvency, reorganization, moratorium and other similar laws relating to or affecting the relief of debtors or the rights and remedies of creditors generally, including without limitation the effect of statutory or other law regarding fraudulent transfers, preferential transfers and equitable subordination;

(b) general principles of equity, including but not limited to judicial decisions holding that certain provisions are unenforceable when their enforcement would violate the implied covenant of good faith and fair dealing, would be commercially unreasonable or involve undue delay, whether or not such principles or decisions have been codified by statute, or that result from the exercise of the court's discretion;

To the Purchasers of Common

Stock of Amyris, Inc. on the Date Hereof

December 24, 2012

Page 4

(c) Section 1670.5 of the California Civil Code or any other California or United States federal law or provision of the DGCL or equitable principle which provides that a court may refuse to enforce, or may limit the application of, a contract or any clause thereof that the court finds to have been unconscionable at the time it was made, unconscionable in performance or contrary to public policy;

(d) any provision purporting to (i) exclude conflict of law principles under any law or (ii) select certain courts as the venue, or establish a particular jurisdiction as the forum, for the adjudication of any controversy;

(e) judicial decisions, that may permit the introduction of extrinsic evidence to modify the terms or the interpretation of any agreement;

(f) the tax or accounting consequences of any transaction contemplated in connection with the sale of the Shares under applicable tax laws and regulations and under applicable accounting rules, regulations, releases, statements, interpretations or technical bulletins;

(g) applicable antifraud statutes, rules or regulations of United States federal or applicable state laws concerning the issuance or sale of securities, including, without limitation, (i) the accuracy and completeness of the information provided by the Company to the Purchasers in connection with the offer and sale of the Shares, and (ii) the accuracy or fairness of the past, present or future fair market value of any securities;

(h) the effect any breach of the fiduciary duties of the members of the Company's Board of Directors, officers or principal stockholders would have on the enforceability authorization and performance of any agreement;

(i) whether or not any Transaction Document, and the transactions provided for therein, were fair and reasonable to the Company at the time of their authorization by the Company's Board of Directors and stockholders within the meaning of Section 144 of the DGCL;

(j) any provisions stating that (i) rights or remedies are not exclusive, (ii) rights or remedies may be exercised without notice, (iii) every right or remedy is cumulative and may be exercised in addition to or with any other right or remedy or (iv) the failure to exercise, or any delay in exercising, rights or remedies available under an agreement will not operate as a waiver of any such right or remedy;

(k) provisions stating that rights set forth in the agreement in which such provision appears may only be waived in writing if an implied agreement by trade practice or course of conduct has given rise to a waiver or that limit the effect of waivers by trade practice or course of conduct;

(l) any United States federal or other antitrust laws, statutes, rules or regulations, including without limitation the Hart-Scott-Rodino Antitrust Improvements

To the Purchasers of Common

Stock of Amyris, Inc. on the Date Hereof

December 24, 2012

Page 5

Act of 1976, or other laws relating to collusive or unfair trade practices or designed to promote competition in any jurisdiction;

(m) any provision purporting to (i) waive rights to trial by jury, service of process or objections to the laying of venue or forum in connection with any litigation arising out of or pertaining to the agreement in which such provision appears, (ii) change or waive the rules of evidence, make determinations conclusive or fix the method or quantum of proof or (iii) waive the statute of limitations;

(n) any choice of law clause, to the extent the provision to be governed by that law could be determined by the court (i) to be contrary to a public or fundamental policy of a state or country whose law would apply in the absence of a choice of law clause, and (ii) to involve an issue in which such state or country, or California State, has a materially greater interest in the determination of the particular issue than does the state whose law is chosen;

(o) any United States federal laws, statutes, rules or regulations, including without limitation the International Investment and Trade in Services Survey Act (Title 22 of the United States Code, Chapter 46, §§3101-3108), or other state or foreign investment laws, statutes, rules and regulations governing investments in the United States or in U.S. entities by persons that are not citizens of the United States; and

(p) indemnification and contribution provisions to the extent enforcement of such provisions is contrary to public policy, indemnify a party to a contract against such party's actions taken in bad faith or that constitute a breach of fiduciary duties, or indemnify a party against liability for future conduct or the party's own fraud or wrongful, reckless or negligent acts or omissions.

In accordance with Section 95 of the American Law Institute's Restatement (Third) of the Law Governing Lawyers (2000), this opinion letter is to be interpreted in accordance with customary practices of lawyers rendering opinions to third parties in transactions of the type provided for in the Transaction Documents.

Based upon and subject to the foregoing, and except as set forth in the Purchase Agreement, as of immediately prior to the Closing we are of the following opinion.

(1) The Company is a corporation duly incorporated, validly existing and in good standing under the laws of the State of Delaware. The Company is qualified to do business as a foreign corporation in good standing under the laws of the State of California.

(2) The Company has all corporate power and corporate authority required to execute, deliver and perform its obligations under the Transaction Documents.

(3) All corporate action has been taken on the part of the Company's Board of Directors and

stockholders that (a) is necessary for the execution and delivery of the Transaction Documents by the Company, (b) must be taken by the Company to authorize the sale and

To the Purchasers of Common

Stock of Amyris, Inc. on the Date Hereof

December 24, 2012

Page 6

issuance of the Shares on the date hereof and (c) must be taken by the Company as of the date hereof to authorize performance by the Company of its obligations under the Transaction Documents.

(4) Each of the Transaction Documents has been duly executed by the Company and has been delivered by the Company to the Purchasers. Each of the Transaction Documents constitutes a valid and binding obligation of the Company, enforceable by you against the Company in accordance with its terms.

(5) The Shares to be issued to you under the Purchase Agreement are duly authorized, and when issued in compliance with the provisions of the Purchase Agreement, will be validly issued, fully paid and non-assessable, and the issuance of such Shares will not be subject to any preemptive rights, rights of first refusal or rights of first offer set forth in the Restated Certificate or Bylaws or any Reviewed Agreement set forth on Exhibit A (other than the Side Letter for which appropriate waivers have been obtained).

(6) The execution, delivery and performance of the Transaction Documents by the Company do not, as of the Closing, result in (a) a violation by the Company of the Restated Certificate or Bylaws, (b) a material violation by the Company of any judgment or order of any court or governmental authority, (c) a material violation by the Company of Applicable Law or (d) a breach of, or a default under, any Reviewed Agreements set forth on Exhibit A.

(7) Other than those that previously may have been obtained or made, no consent, approval or authorization of, or filing with, any governmental authority pursuant to any Applicable Law is required to be made or obtained by the Company or any subsidiary of the Company in connection with the Company's (a) valid execution and delivery of the Transaction Documents, (b) performance of its obligations under the Purchase Agreement on the date hereof and (c) performance of its obligations under the other Transaction Documents as of the date hereof.

(8) Based in part upon the representations made by you in the Purchase Agreement, and subject to the filings of such securities law notices as may be required to be filed subsequent to the Closing, the offer, sale and issuance of the Shares to be issued to you in conformity with the terms of the Purchase Agreement constitute transactions exempt from the registration requirements of Section 5 of the Securities Act of 1933, as amended, and exempt from the qualification requirements of Section 25110 of the California Corporate Securities Law of 1968, as amended.

(9) The Company is not and, after giving effect to the offering and sale of the Shares, will not be, required to register as an “investment company” as such term is defined in the Investment Company Act

of 1940, as amended.

In addition to the foregoing opinions, based upon the foregoing and other than as set forth in the Purchase Agreement, we supplementally confirm the following to you as of immediately prior to the Closing.

To the Purchasers of Common

Stock of Amyris, Inc. on the Date Hereof

December 24, 2012

Page 7

Litigation Confirmation . To our knowledge, there is no action, suit, proceeding or investigation by or before any United States federal, California State or Delaware State court or governmental authority that is pending or threatened in writing against the Company and that questions the validity of the Transaction Documents or the right of the Company to enter into and perform its obligations under the Transaction Documents. Please note that we have not conducted a docket search in any jurisdiction with respect to any action, suit, proceeding or investigation that may be pending against the Company and we have not undertaken any search regarding any of its affiliates, officers or directors, nor, other than to request the Opinion Certificate from the Company, have we undertaken any further inquiry whatsoever in connection with the existence any such action, suit, proceeding or investigation.

[Remainder of Page Left Intentionally Blank]

This opinion is rendered as of the date first written above solely for your benefit in connection with the sale and issuance of the Shares pursuant to the Purchase Agreement and may not be relied on by, nor may any copy be delivered to, any other person or entity without our prior written consent. Our opinion is expressly limited to the matters set forth above and we render no opinion, whether by implication or otherwise, as to any other matters. We assume no obligation to inform you of any fact, circumstance, event or change in the law or the facts that may hereafter be brought to our attention that may alter, affect or modify the opinions expressed herein.

Very truly yours,

FENWICK & WEST LLP

By:

Daniel Winnike, a Partner

To the Purchasers of Common

Stock of Amyris, Inc. on the Date Hereof

December 24, 2012

Page 9

Exhibit A

Review of Documents

1) The Purchase Agreement and the Rights Agreement and the Letter Agreement dated February 23, 2012 (the “ Side Letter ”) by and among the Company and Naxyris S.A., Sualk Capital Ltd, Maxwell (Mauritius) Pte Ltd and Biolding Investment SA.

2) A copy of the Company's Restated Certificate of Incorporation, certified by the Delaware Secretary of State on September 30, 2010 (the " Restated Certificate ").

3) A copy of the Company's Bylaws certified by the Company's Secretary on September 30, 2010 (the " Bylaws ").

4) The Certificate of Incorporation of the Company filed with the Secretary of State of the State of California upon the Company's incorporation, the Certificate of Merger and Restated Certificate of Incorporation of the Company filed with the Secretary of State of the State of Delaware upon the Company's re-incorporation in Delaware, the California and Delaware bylaws of the Company initially adopted by the Company and minutes of meetings and actions by written consent of the Company's incorporator(s), shareholders and Board of Directors that are contained in the Company's minute books.

5) An Opinion Certificate addressed to us and dated of even date herewith executed by the Company (the " Opinion Certificate ").

6) A Certificate of Status regarding the Company issued by the Secretary of State of the Delaware, dated December __, 2012, indicating that the Company is qualified to do business, as a domestic corporation in that state (together with the letter referred to in item (7) below and the certificate referred to in item (8) below, the " Certificate of Good Standing ").

7) A letter from the California Franchise Tax Board dated December __, 2012 to the effect that the Company is in good standing with respect to its California franchise tax filings and has no known unpaid franchise tax liability.

8) A Certificate of Good Standing from the Secretary of State of the State of California, indicating that the Company is in good standing and is qualified to do business as a foreign corporation therein.

9) A copy of the Series D Preferred Stock Purchase Agreement dated June 21, 2010.

10) A copy of the Amended and Restated Investors' Rights Agreement dated June 21, 2010, as amended by Amendment No. 1 thereto dated February 23, 2012.

11) A copy of the Stock Purchase Agreement dated February 22, 2012 by and between the Company and the Purchasers listed on the signature pages thereto.

12) A copy of the Securities Purchase Agreement dated February 24, 2012 by and between the Company and the Purchasers listed on the signature pages thereto, the Senior

To the Purchasers of Common

Stock of Amyris, Inc. on the Date Hereof

December 24, 2012

Page 10

Unsecured Convertible Notes issued thereunder and the Registration Rights Agreement by and between the Company and Purchasers listed on the signature pages thereto, dated February 27, 2012.

13) Copies of those Common Stock Purchase Agreements dated May 18, 2012 by and between the Company and certain Company stockholders.

14) Securities Purchase Agreement dated July 30, 2012 by and between the Company and Total Gas & Power USA, SAS, the Senior Unsecured Convertible Notes issued thereunder and the Registration Rights Agreement by and between the Company and Total Gas & Power USA, SAS, dated July 30, 2012.

FOLLOW-ON INVESTMENT AGREEMENT

This Follow-On Investment Agreement (this “ Agreement ”) is entered into between Amyris, Inc., a Delaware corporation (the “ Company ”) and Biolding Investment SA (“ Biolding ”) on December 24, 2012.

RECITALS

A. The Company entered into that certain Letter Agreement, dated February 23, 2012 (the “ Letter Agreement ”), by and among the Company and the investors named therein, including Biolding. Capitalized terms used herein and not otherwise defined shall have the meaning ascribed to them in the Letter Agreement.

B. Pursuant to Section 3 of the Letter Agreement, upon completion of the Milestone, Biolding is obligated to purchase $15,000,000 worth of additional shares of the Company's Common Stock in the Follow-On Investment (such obligation, the “ Investment Obligation ”).

C. The Company intends to sell, in a private offering exempt from the registration requirements of the Securities Act of 1933, an aggregate of not to exceed 14,177,849 shares of its Common Stock, $0.0001 par value per share (the “ Shares ”), at a purchase price per share equal to the higher of the book value per Share or the last occurring consolidated closing bid price per Share (as defined by The NASDAQ Stock Market) as of the time of signing of the binding agreement to sell and issue the Shares, to certain existing investors of the Company (the “ Financing ”) and, Biolding will be purchasing $10,000,000 worth of the Shares (the “ Biolding Investment ”) in the Financing.

AGREEMENT

Now, therefore, in consideration of the foregoing recitals and the mutual promises hereinafter set forth, the parties hereto hereby agree as follows:

1. Payment Commitment Obligation . Biolding hereby acknowledges and irrevocably agrees that by no later than March 31, 2013, Biolding will purchase from the Company at least $5,000,000 of the Company's Common Stock (the “ Additional Shares ”) at a purchase price per share equal to the higher of the book value per share of the Company's Common Stock or the last occurring consolidated closing bid price per share of the Company's Common Stock (as defined by The NASDAQ Stock Market) as of the time of signing by the Company of the binding agreement to sell and issue the Additional Shares (such purchase, the “ Additional Biolding Investment ”); provided that Biolding's obligation hereunder to complete the Additional Biolding Investment shall be contingent upon (i) completion of the Milestone by the Company subject to Biolding's verification to its reasonable satisfaction that the Milestone has been achieved, and (ii) the Company's Leadership Development and Compensation Committee (the “ LDCC ”) approving minutes from the LDCC meeting held on December 19, 2012, which minutes shall include a resolution that provides that one of the most significant bases in determining the Company's Chief Executive Officer's 2013 bonus will be achieving [*].

2. Acknowledgment . The Company hereby acknowledges that upon the closing of the Biolding Investment, Biolding shall have satisfied $10,000,000 of the Investment Obligation under Section 3 of the Letter Agreement and upon completion of the Additional Biolding Investment, Biolding shall have satisfied all of its obligations under Section 3 of the Letter Agreement, and Biolding shall be under no obligation to invest additional funds in the Company pursuant to the Letter Agreement.

3. Rights under Side Letter . Other than as set forth above, this Acknowledgment shall not affect the rights and obligations of the Company and Biolding as set forth in the Letter Agreement.

4. Amendment and Waiver . No amendment, modification, termination or cancellation of this Agreement shall be effective unless it is in writing signed by the Company and Biolding. No waiver of any of the provisions of this Agreement shall be deemed or shall constitute a waiver of any other provisions hereof (whether or not similar) nor shall such waiver constitute a continuing waiver.

5. Governing Law . This Agreement, and the provisions, rights, obligations and conditions set forth herein, and the legal relations between the parties hereto, including all disputes and claims, whether arising in contract, tort, or under statute, shall be governed by and construed in accordance with the laws of the State of Delaware without giving effect to its conflict of law provisions.

6. Notices . All notices and other communications hereunder shall be in writing and shall be deemed given when delivered personally or by commercial messenger or courier service to the parties at the following addresses (or at such other address for a party as shall be specified by like notice) or when sent by facsimile transmission or email to the facsimile number or email address specified below (or such other facsimile number or email as shall be specified by like notice), upon machine or electronic confirmation of receipt:



	(a)	if to the Company, to:
		Amyris, Inc.
		5885 Hollis Street, Suite 100
		Emeryville, CA 94608
		Attention: Gary Loeb, General Counsel
		Facsimile: [*]
		Email: [*]



	(b)	if to Biolding, to
		Biolding Investment SA
		11A boulevard Prince Henri
		L 1724 Luxembourg.
		Attention: HH Sheikh Abdullah bin Khalifa Al Thani and M. Jean Paul Soulié
		Facsimile: [*]
		Email: [*]

7. Counterparts . This Agreement may be executed in one or more counterparts, which shall together constitute one agreement.

[Remainder of Page Intentionally Left Blank]

IN WITNESS WHEREOF, the undersigned has duly executed this Agreement as of the date first above written.

COMPANY :

AMYRIS, INC.

By: /s/ John G. Melo

Name: John G. Melo

Title: President and Chief Executive Officer

Acknowledged and Accepted by:

BIOLDING INVESTMENT SA

By:

Name:

Title:

[Signature Page to Follow-On Investment Agreement]

IN WITNESS WHEREOF, the undersigned has duly executed this Agreement as of the date first above written.

COMPANY :

AMYRIS, INC.

By:

Name:

Title:

Acknowledged and Accepted by:

BIOLDING INVESTMENT SA

By: /s/ Sheikh Abdullah bin Khalifa Al Thani

Name: Sheikh Abdullah bin Khalifa Al Thani

Title: Director

[Signature Page to Follow-On Investment Agreement]



CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

AMYRIS, INC.

AMENDMENT NO. 2 TO SECURITIES PURCHASE AGREEMENT AND

TRANCHE I NOTE AMENDMENT AGREEMENT

This Amendment No. 2 to Securities Purchase Agreement and Tranche I Note Amendment Agreement (this “ Amendment ”) is made and entered into as of December 24, 2013, by and among Amyris, Inc., a Delaware corporation (the “ Company ”), and each of Total Energies Nouvelles Activités USA (f.k.a. Total Gas & Power USA, SAS) (“ Total ”), Maxwell (Mauritius) Pte Ltd (“ Temasek ”) and the other Purchasers signatory hereto.

RECITALS

WHEREAS, the Company and the Purchasers are parties to that certain Securities Purchase Agreement dated August 8, 2013, as amended by that Amendment No. 1 to Securities Purchase Agreement dated October 16, 2013 (as amended, the “ Agreement ”). Capitalized terms used in this Amendment and not otherwise defined herein have the meanings ascribed to them in the Agreement.

WHEREAS, the Company issued Tranche I Notes on October 16, 2013 to each of Total, Temasek and the other Purchasers in an aggregate principal amount of $51,822,184.41 (collectively, the “ Tranche I Notes ”).

WHEREAS, the Company and each of Total, Temasek and the other Purchasers desire to amend the Agreement and the Tranche I Notes.

WHEREAS, pursuant to Section 9.15 of the Agreement, the Agreement may be amended with the written consent of each of the parties thereto (the “ Agreement Requisite Parties ”).

WHEREAS, pursuant to Section 8 of the Tranche I Notes, each Note may be amended with the written consent of the holders of at least a majority of the aggregate principal amount then outstanding of the Tranche I Notes (the “ Notes Requisite Parties ” and together with the Agreement Requisite Parties, the “ Requisite Parties ”).

WHEREAS, the undersigned parties constitute the Requisite Parties.

NOW, THEREFORE, the parties hereby agree as follows:

1. AMENDMENT OF PRELIMINARY STATEMENT OF THE AGREEMENT . The Preliminary Statement of the Agreement is hereby amended and restated in its entirety to read as follows:

convertible notes in the form attached hereto as Exhibit B . The Securities will be convertible into shares (the “ Underlying Securities ”) of the Company’s common stock, $0.0001 par value per share (the “ Common Stock ”), in accordance with the terms of the Securities.”

2. AMENDMENT OF SECTION 1.2 OF THE AGREEMENT . Section 1.2 of the Agreement is hereby amended and restated in its entirety to read as follows:

“1.2 Tranche II Closings . Subject to the terms and conditions hereof, from time to time at a Tranche II Closing (as defined in Section 2.2 ), the Company may elect to sell to each applicable Purchaser, and upon such election each such applicable Purchaser will purchase from the Company, (a) with respect to the first Tranche II Closing, a Tranche II Note in a principal amount equal to the amount set forth next to such Purchaser’s name on Schedule I hereto under the column “First Tranche II Closing Amount”, or (b) with respect to any other Tranche II Closing, a Tranche II Note in a principal amount equal to the product of (i) the aggregate principal amount of Tranche II Notes the Company elects to sell at such Tranche II Closing, and (ii) the percentage set forth next to such Purchaser’s name on Schedule I hereto under the column “Tranche II Closing Percentage” (each such amount described in clauses (a) and (b) of this Section 1.2 , a “ Tranche II Closing Total Purchase Price ”, with any Purchaser’s Tranche I Closing Total Purchase Price or any other Tranche II Closing Total Purchase Price being referred to herein as a “ Total Purchase Price ”); provided, however, that in no event shall the aggregate Tranche II Closing Total Purchase Price paid by any Purchaser exceed that amount set forth on Schedule I hereto under the column “Maximum Tranche II Closing Amount.” The total purchase price payable by each Purchaser for the Tranche II Notes that such Purchaser hereby agrees to purchase at any Tranche II Closing shall be the Tranche II Closing Total Purchase Price applicable to such Purchaser in connection with such Tranche II Closing. The sale and purchase of the Tranche II Notes to each Purchaser shall constitute a separate sale and purchase hereunder.”

3. AMENDMENT OF SECTION 2.2 OF THE AGREEMENT . Section 2.2 of the Agreement is hereby amended and restated in its entirety to read as follows:

“2.2 Tranche II Closings . At any time and from time to time after the satisfaction of the Tranche II Closing Conditions (as defined in Section 6.2 ), the Company may in its sole discretion elect to sell to each applicable Purchaser, on the terms and conditions set forth in this Agreement, without obtaining the signature, consent or permission of any of the Purchasers, in additional closings (each, a “ Tranche II Closing ”, with each of the Tranche I Closing and any other Tranche II Closing being referred to herein as a “ Closing ”), Tranche II Notes in a principal amount equal to the applicable Tranche II Closing Total Purchase Price for such Purchaser, provided that each such subsequent sale is consummated no later than two (2) years after the date of this Agreement, and (b) the aggregate principal amount of Tranche II Notes sold at all the Tranche II Closings shall not exceed $34,057,662.17. Schedule I to this Agreement shall be updated to reflect the principal amount of Tranche II Notes purchased by any Purchaser at each such Tranche II Closing and, if applicable, the cancellation or

conversion of convertible indebtedness of the Company to such applicable Purchaser in connection with such Tranche II Closing.”

4. AMENDMENT OF SECTION 6.2(b) OF THE AGREEMENT . Section 6.2(b) of the Agreement is hereby amended and restated in its entirety to read as follows:

“(b) Key Man . John Melo shall continue to serve as the Company’s Chief Executive Officer unless Mr. Melo shall have ceased to serve as the Company’s Chief Executive Officer due to death or Disability (as defined in Section 22(e)(3) of the Code) or, to the extent Mr. Melo is not the Company’s Chief Executive Officer, any such new Chief Executive Officer shall have been approved by (i) the Purchasers holding at least 50% in principal amount of all then outstanding Tranche I Notes and Tranche II Notes, and (ii) Temasek.”

5. AMENDMENT OF SECTION 7.8 OF THE AGREEMENT . Section 7.8 of the Agreement is hereby amended and restated in its entirety to read as follows:

“7.8 Change of Control . For so long as any Tranche I Notes or Tranche II Notes are outstanding, the Company shall not consummate a Change of Control (as defined in the Tranche I Notes) without the prior written consent of (i) the Purchasers holding at least 50% in principal amount of all then outstanding Tranche I Notes and Tranche II Notes, and (ii) Temasek.”

6. AMENDMENT OF SCHEDULE I OF THE AGREEMENT . Schedule I of the Agreement is hereby amended and restated in its entirety to read as set forth on Schedule I hereto.

7. AMENDMENT OF EXHIBIT B OF THE AGREEMENT . Exhibit B of the Agreement is hereby amended and restated in its entirety to read as set forth on Exhibit A hereto.

8. AMENDMENT OF SECTION 7(C) OF THE TRANCHE I NOTES . Section 7(c) of each of the Tranche I Notes is hereby amended and restated in its entirety to read as follows:

“(c) Purchase of Substantial Assets . The Company will not, and will not permit its subsidiaries to, without the prior written consent of (i) the holders of a majority of the then outstanding Notes and Tranche I Notes and (ii) Maxwell (Mauritius) Pte Ltd, purchase assets in one transaction or a series of related transactions in an amount greater than $20,000,000.”

9. ADDITION OF PARTIES TO AGREEMENT . Effective upon the execution of this Amendment, each of the parties set forth on Schedule II hereto shall become a party to the Agreement as a “Purchaser”, and in connection therewith they shall execute a counterpart signature page to the Agreement in substantially the form attached hereto as Exhibit B .

10. COMPANY CALL ELECTION . Pursuant to Section 2.2 of the Agreement, as amended by this Amendment (as amended, the “ Purchase Agreement ”), the Company hereby irrevocably elects to sell to each of Temasek, Total and Wolverine Flagship Fund Trading

Limited (“ Wolverine ”), Tranche II Notes with the principal amount set forth next to each such Purchaser’s name on Schedule I hereto under the column “First Tranche II Closing Amount” in accordance with the terms of the Purchase Agreement (the “ Called Notes ”). The Company and each of Temasek, Total and Wolverine hereby acknowledge that the purchase and sale of the Called Notes shall occur on January 14, 2014 (the “ Closing Date ”) and that each such Purchaser shall, subject to the satisfaction by the Company of the Tranche II Closing Conditions, be obligated on the Closing Date to wire funds, or, in the case of Total, submit to the Company for cancellation pre-existing indebtedness of the Company owed to Total, in each case, in an amount equal to the amount set forth next to each such Purchaser’s name under the column “First Tranche II Closing Amount” on Schedule I hereto. Notwithstanding the foregoing, the first Tranche II Closing scheduled to occur on the Closing Date shall be contingent upon the receipt by the Company of an aggregate of $25,000,000 in funds from Temasek and $3,000,000 in funds from Wolverine.

11. FULL FORCE AND EFFECT . Except as expressly modified by this Amendment, the terms of the Agreement and the Tranche I Notes shall remain in full force and effect.

12. GOVERNING LAW . This Amendment, and the provisions, rights, obligations, and conditions set forth herein, and the legal relations between the parties hereto, including all disputes and claims, whether arising in contract, tort, or under statute, shall be governed by and construed in accordance with the laws of the State of Delaware without giving effect to its conflict of law provisions.

13. INTEGRATION . This Amendment and the Agreement and the documents referred to herein and therein and the exhibits and schedules thereto, constitute the entire agreement and understanding of the parties with respect to the subject matter hereof, and supersede all prior understandings and agreements, whether oral or written, between or among the parties hereto with respect to the specific subject matter hereof.

14. COUNTERPARTS; FACSIMILE . This Amendment may be executed in two (2) or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. This Amendment may be executed and delivered by facsimile, or by email in portable document format (.pdf) and delivery of the signature page by such method will be deemed to have the same effect as if the original signature had been delivered to the other parties.

[Remainder of Page Intentionally Left Blank]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

COMPANY:

AMYRIS, INC.

By: /s/ John G. Melo

John G. Melo, President and Chief Executive Officer

[Signature Page to Amendment No. 2 to Securities Purchase Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:



			Maxwell (Mauritius) Pte Ltd
	By:		/s/ Rohit Sipamimalani
			(signature)





	Name:		Rohit Sipamimalani
			(printed name)

	Title:		Managing Member





Address:	60B Orchard Road #06-18 Tower 2, The Atrium @ Orchard Singapore 238891


Facsimile No:		[*]




	E-mail Address:		[*]

[Signature Page to Amendment No. 2 to Securities Purchase Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:



			Total Energies Nouvelles Activitйs USA (f.k.a. Total Gas & Power USA, SAS)
	By:		/s/ Bernard Clement
			(signature)





	Name:		Bernard Clйment
			(printed name)

	Title:		President





	Address:		24 Cours Michelet 92800 Puteaux, France







	Facsimile No:		[*]




	E-mail Address:		[*]

[Signature Page to Amendment No. 2 to Securities Purchase Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:

Pyramis Lifecycle Large Cap Stock Commingled Pool

By: Global Advisors Trust Company, as Trustee

By: /s/ Lynn M. Farrand

Name: Lynn M. Farrand

Title: Director

[Signature Page to Amendment No. 2 to Securities Purchase Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:

Variable Insurance Products Fund III: Growth & Income Portfolio

By: /s/ Stacie M. Smith

Name: Stacie M. Smith

Title: Deputy Treasurer

[Signature Page to Amendment No. 2 to Securities Purchase Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:

Fidelity Securities Fund: Fidelity Growth & Income Portfolio

By: /s/ Stacie M. Smith

Name: Stacie M. Smith

Title: Deputy Treasurer

[Signature Page to Amendment No. 2 to Securities Purchase Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:

Fidelity Commonwealth Trust: Fidelity Large Cap Stock Fund

By: /s/ Stacie M. Smith

Name: Stacie M. Smith

Title: Deputy Treasurer

[Signature Page to Amendment No. 2 to Securities Purchase Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:

Fidelity Hastings Street Trust: Fidelity Advisor Series Growth & Income Fund

By: /s/ Stacie M. Smith

Name: Stacie M. Smith

Title: Deputy Treasurer

[Signature Page to Amendment No. 2 to Securities Purchase Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:

Fidelity Hastings Street Trust: Fidelity Series Growth & Income Fund

By: /s/ Stacie M. Smith

Name: Stacie M. Smith

Title: Deputy Treasurer

[Signature Page to Amendment No. 2 to Securities Purchase Agreement]

EXHIBIT A

Form of Tranche II Note

EXHIBIT B

Counterpart Signature Page

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:

Wolverine Flagship Fund Trading Limited

By: Wolverine Asset Management,

its Investment Manager

By: /s/ Ken Nadel

Name: Ken Nadel

Title: Chief Operating Officer

Address: c/o Wolverine Asset Management, LLC

175 West Jackson Blvd, Ste 340

Chicago, IL 60604

[Signature Page to Amendment No. 2 to Securities Purchase Agreement]

Schedule I

SCHEDULE OF PURCHASERS



Purchaser	Tranche I Closing Amount		Tranche I Cancellation of Indebtedness			First Tranche II Closing Amount		Tranche II Closing Percentage			Maximum Tranche II Closing Amount		Maximum Tranche II Cancellation of Indebtedness			Tranche I Total Purchase Price		Tranche II Total Purchase Price
Maxwell (Mauritius) Pte Ltd (“Temasek”)	$	35,000,000.00	$	35,000,000.00	*	$	25,000,000.00		0.00	%	$	25,000,000.00				$	35,000,000.00	$	25,000,000.00
Total Energies Nouvelles Activitйs USA (“Total”)	$	9,252,184.41	$	9,252,184.41	**	$	6,042,064.77		0.00	%	$	6,057,662.17	$	6,042,064.77	***	$	9,252,184.41	$	6,042,064.77
Pyramis Lifecycle Large Cap Stock Commingled Pool	$	300,000.00							0.00	%	$	0.00				$	300,000.00
Variable Insurance Products Fund III: Growth & Income Portfolio	$	470,000.00							0.00	%	$	0.00				$	470,000.00
Fidelity Securities Fund: Fidelity Growth & Income Portfolio	$	2,800,000.00							0.00	%	$	0.00				$	2,800,000.00
Fidelity Commonwealth Trust: Fidelity Large Cap Stock Fund	$	900,000.00							0.00	%	$	0.00				$	900,000.00
Fidelity Hastings Street Trust: Fidelity Series Growth & Income Fund	$	2,350,000.00							0.00	%	$	0.00				$	2,350,000.00
Fidelity Hastings Street Trust: Fidelity Advisor Series Growth & Income Fund	$	750,000.00							0.00	%	$	0.00				$	750,000.00
Wolverine Flagship Fund Trading Limited	$	0.00				$	3,000,000.00		0.00	%	$	3,000,000.00				$	0.00	$	3,000,000.00
TOTAL	$	51,822,184.41	$	44,252,184.41					100.00	%	$	34,057,662.17	$	6,042,064.77		$	51,822,184.41	$	34,042,064.77

*Temasek hereby acknowledges that all obligations of the Company owed to Temasek pursuant to that certain Senior Promissory Note issued by the Company to Temasek on October 2, 2013 are cancelled in their entirety upon delivery by the Company to Temasek of a Tranche I Note with a principal amount of $35,000,000.00 and pre-existing accrued interest as of the date hereof of $192,500.00.

** Total hereby acknowledges that all obligations of the Company owed to Total pursuant to that certain 1.5% Senior Unsecured Convertible Note issued by the Company to Total on December 24, 2012 are cancelled in their entirety upon delivery by the Company to Total of (i) a Tranche I Note with a principal amount of $9,252,184.41 and no pre-existing accrued interest and (ii) a 1.5% Senior Unsecured Convertible Note with a principal amount of $24,047,816.63 and pre-existing accrued interest as of the date hereof of $645,287.52.

*** Total hereby acknowledges that all obligations of the Company owed to Total pursuant to that certain 1.5% Senior Unsecured Convertible Note in aggregate principal amount of $24,047,816.63 issued by the Company to Total on December 2,2013 are cancelled in their entirety upon delivery by the Company to Total of (i) a Tranche II Note with a principal amount of $6,042,064.77 and no pre-existing accrued interest and (ii) a 1.5% Senior Unsecured Convertible Note with a principal amount of $18,005,751.86 and pre-existing accrued interest as of the date hereof of $741,249.45.

Schedule II



Purchaser	Notice Address
Wolverine Flagship Fund Trading Limited	Wolverine Flagship Fund Trading Limited c/o Wolverine Asset Management, LLC 175 West Jackson Blvd., Ste 340 Chicago, IL 60604



CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

AMYRIS, INC.

AMENDMENT NO. 1 TO SECURITIES PURCHASE AGREEMENT

This Amendment No. 1 to Securities Purchase Agreement (this “ Amendment ”) is made and entered into as of October 16, 2013, by and among Amyris, Inc., a Delaware corporation (the “ Company ”), and each of Total Energies Nouvelles Activités USA (f.k.a. Total Gas & Power USA, SAS) (“ Total ”) and Maxwell (Mauritius) Pte Ltd (“ Temasek ”).

RECITALS

WHEREAS, the Company and the Purchasers are parties to that certain Securities Purchase Agreement dated August 8, 2013 (the “ Agreement ”). Capitalized terms used in this Amendment and not otherwise defined herein have the meanings ascribed to them in the Agreement.

WHEREAS, the Company and each of Total and Temasek desire to amend the Agreement.

WHEREAS, pursuant to Section 9.15 of the Agreement, the Agreement may be amended with the written consent of each of the parties thereto (the “ Requisite Parties ”).

WHEREAS, the undersigned parties constitute the Requisite Parties.

NOW, THEREFORE, the parties hereby agree as follows:

1. AMENDMENT OF PRELIMINARY STATEMENT OF THE AGREEMENT . The Preliminary Statement of the Agreement is hereby amended and restated in its entirety to read as follows:

“Subject to the terms and conditions hereof, the Purchasers desire to purchase, and the Company desires to offer and sell to the Purchasers, (a) $51,822,184.41 in principal amount of the Company’s Tranche I Senior Convertible Notes (the “ Tranche I Notes ”) and (b) $30,433,512.10 in principal amount of the Company’s Tranche II Senior Convertible Notes (the “ Tranche II Notes ,” and, together with the Tranche I Notes, the “ Securities ” and each, a “ Security ”). The Tranche I Notes will be evidenced by convertible notes in the form attached hereto as Exhibit A and the Tranche II Notes will be evidenced by convertible notes in the form attached hereto as Exhibit B . The Securities will be convertible into shares (the “ Underlying Securities ”) of the Company’s common stock, $0.0001 par value per share (the “ Common Stock ”), in accordance with the terms of the Securities.”

2. AMENDMENT OF SCHEDULE I OF THE AGREEMENT . Schedule I of the Agreement is hereby amended and restated in its entirety to read as set forth on Schedule I hereto.

3. AMENDMENT OF SECTION 6.1(K) OF THE AGREEMENT . Section 6.1(k) of the Agreement is hereby amended and restated in its entirety to read as follows:

“(k) Security Interest . Unless Total shall have previously released all security interests it holds with respect to the Company’s and its subsidiaries’ Intellectual Property, including, but not limited to, any such security interest created in favor of Total pursuant to the Intellectual Property Security Agreement dated as of April 26, 2013, by the Company in favor of Total, and any related security documents, Total, each of the other Purchasers (the “ New Secured Parties ”), and the Company shall have executed an agreement in accordance with the terms of the MOU whereby the New Secured Parties shall be given a security interest in collateral that shall be acceptable to the New Secured Parties but that will not include any intellectual property that has been or will be licensed exclusively to Total pursuant to the terms of the Master Framework Agreement, made and entered into as of July 30, 2012, between the Company and Total (the “ Master Framework Agreement ”) and any agreements or amendments entered into pursuant thereto or in connection therewith (the “ New Secured Party Collateral ”), and the Company shall have used commercially reasonable efforts to perfect such security interest in the New Secured Party Collateral in accordance with applicable law.”

4. ADDITION OF PARTIES TO AGREEMENT . Effective upon the execution of this Amendment, each of the parties set forth on Schedule II hereto shall become a party to the Agreement as a “Purchaser”, and in connection therewith they shall execute a counterpart signature page to the Agreement in substantially the form attached hereto as Exhibit A .

5. FULL FORCE AND EFFECT . Except as expressly modified by this Amendment, the terms of the Agreement shall remain in full force and effect.

6. GOVERNING LAW . This Amendment, and the provisions, rights, obligations, and conditions set forth herein, and the legal relations between the parties hereto, including all disputes and claims, whether arising in contract, tort, or under statute, shall be governed by and construed in accordance with the laws of the State of Delaware without giving effect to its conflict of law provisions.

7. INTEGRATION . This Amendment and the Agreement and the documents referred to herein and therein and the exhibits and schedules thereto, constitute the entire agreement and understanding of the parties with respect to the subject matter hereof, and supersede all prior understandings and agreements, whether oral or written, between or among the parties hereto with respect to the specific subject matter hereof.

8. COUNTERPARTS; FACSIMILE . This Amendment may be executed in two (2) or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. This Amendment may be executed and delivered by facsimile, or by email in portable document format (.pdf) and delivery of the signature page by such method will be deemed to have the same effect as if the original signature had been delivered to the other parties.

[Remainder of Page Intentionally Left Blank]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

COMPANY:

AMYRIS, INC.

By: /s/ John Melo

John Melo, Chief Executive Officer

[Signature Page to Amendment No. 1 to Securities Purchase Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:



			Maxwell (Mauritius) Pte Ltd
	By:		/s/ Rohit Sipamimalani
			(signature)





	Name:		Rohit Sipamimalani
			(printed name)

	Title:		Authorized Signatory





Address:	60B Orchard Road #06-18 Tower 2, The Atrium @ Orchard Singapore 238891


Facsimile No:		[*]




	E-mail Address:		[*]

[Signature Page to Amendment No. 1 to Securities Purchase Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:



			Total Energies Nouvelles Activitйs USA (f.k.a. Total Gas & Power USA, SAS)
	By:		/s/ Bernard Clement
			(signature)





	Name:		Bernard Clement
			(printed name)

	Title:		President





	Address:		24 Cours Michelet 92800 Puteaux, France








	Facsimile No:		+[*]




	E-mail Address:		[*]

[Signature Page to Amendment No. 1 to Securities Purchase Agreement]

EXHIBIT A

Counterpart Signature Page

[Signature Page to Amendment No. 1 to Securities Purchase Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:

Pyramis Lifecycle Large Cap Stock Commingled Pool

By: Pyramis Global Advisors Trust Company, as Trustee

By: /s/ Richard Synrod

Name: Richard Synrod

Title: Director

[Signature Page to Amendment No. 1 to Securities Purchase Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:

Variable Insurance Products Fund

III: Growth & Income Portfolio

By: /s/ Adrien Deberghes

Name: Adrien Deberghes

Title: Deputy Treasurer

[Signature Page to Amendment No. 1 to Securities Purchase Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:

Fidelity Securities Fund: Fidelity Growth & Income Portfolio

By: /s/ Adrien Deberghes

Name: Adrien Deberghes

Title: Deputy Treasurer

[Signature Page to Amendment No. 1 to Securities Purchase Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:

Fidelity Commonwealth Trust: Fidelity Large Cap Stock Fund

By: /s/ Adrien Deberghes

Name: Adrien Deberghes

Title: Deputy Treasurer

[Signature Page to Amendment No. 1 to Securities Purchase Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:

Fidelity Hastings Street Trust: Fidelity Series Growth & Income Fund

By: /s/ Adrien Deberghes

Name: Adrien Deberghes

Title: Deputy Treasurer

[Signature Page to Amendment No. 1 to Securities Purchase Agreement]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

PURCHASERS:

Fidelity Hastings Street Trust: Fidelity Advisor Series Growth & Income Fund

By: /s/ Adrien Deberghes

Name: Adrien Deberghes

Title: Deputy Treasurer

[Signature Page to Amendment No. 1 to Securities Purchase Agreement]

Schedule I

SCHEDULE OF PURCHASERS



Purchaser	Tranche I Closing Amount		Tranche I Cancellation of Indebtedness			Tranche II Closing Percentage			Maximum Tranche II Closing Amount		Maximum Tranche II Cancellation of Indebtedness		Tranche I Total Purchase Price		Tranche II Total Purchase Price
Maxwell (Mauritius) Pte Ltd (“Temasek”)	$	35,000,000.00	$	35,000,000.00	*		82.15	%	$	25,000,000.00			$	35,000,000.00
Total Energies Nouvelles Activitйs USA (“Total”)	$	9,252,184.41	$	9,252,184.41	**		17.85	%	$	5,433,512.10	$	5,433,512.10	$	9,252,184.41
Pyramis Lifecycle Large Cap Stock Commingled Pool	$	300,000.00					0.00	%					$	300,000.00
Variable Insurance Products Fund III: Growth & Income Portfolio	$	470,000.00					0.00	%					$	470,000.00
Fidelity Securities Fund: Fidelity Growth & Income Portfolio	$	2,800,000.00					0.00	%					$	2,800,000.00
Fidelity Commonwealth Trust: Fidelity Large Cap Stock Fund	$	900,000.00					0.00	%					$	900,000.00
Fidelity Hastings Street Trust: Fidelity Series Growth & Income Fund	$	2,350,000.00					0.00	%					$	2,350,000.00
Fidelity Hastings Street Trust: Fidelity Advisor Series Growth & Income Fund	$	750,000.00					0.00	%					$	750,000.00
TOTAL	$	51,822,184.41	$	44,252,184.41			100.00	%	$	30,433,512.10			$	51,822,184.41

Schedule II



Purchaser	Notice Address
Pyramis Lifecycle Large Cap Stock Commingled Pool	State Street Bank & Trust PO Box 5756 Boston, Massachusetts 02206 Attn: [*]
Variable Insurance Products Fund III: Growth & Income Portfolio	M.Gardiner & Co C/O JPMorgan Chase Bank, N.A P.O. Box 35308 Newark, NJ 07101-8006
Fidelity Securities Fund: Fidelity Growth & Income Portfolio	The Northern Trust Company Attn: Trade Securities Processing, C-1N 801 South Canal Street Chicago, IL 60607 Fidelity Securities Fund: Fidelity Growth & Income Portfolio. Reference Account# [*]
Fidelity Commonwealth Trust: Fidelity Large Cap Stock Fund	Brown Brothers Harriman & Co. 525 Washington Blvd Jersey City NJ 07310 Attn: [*] 15th Floor Corporate Actions
Fidelity Hastings Street Trust: Fidelity Series Growth & Income Fund	The Northern Trust Company Attn: Trade Securities Processing, C-1N 801 South Canal Street Chicago, IL 60607 Fidelity Securities Fund: Fidelity Growth & Income Portfolio. Reference Account# [*]
Fidelity Hastings Street Trust: Fidelity Advisor Series Growth & Income Fund	The Northern Trust Company Attn: Trade Securities Processing, C-1N 801 South Canal Street Chicago, IL 60607 Fidelity Securities Fund: Fidelity Growth & Income Portfolio. Reference Account# [*]



CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

MODIFICATION

TECHNOLOGY INVESTMENT AGREEMENT

BETWEEN

AMYRIS, INC.,

5885 HOLLIS STREET

SUITE 100

EMERYVILLE, CALIFORNIA 94608

AND

THE DEFENSE ADVANCED RESEARCH PROJECTS AGENCY

675 NORTH RANDOLPH STREET

ARLINGTON, VA 22203-2114

CONCERNING

IMPROVING DNA ASSEMBLY AND INTEGRATION ACROSS PLATFORMS WITH

BETTER SYSTEMS AND TOOLS

(LIVING FOUNDRIES)

Agreement No.: HR0011-12-3-0006

Modification No.: P00008

Purchase Request No.: HR001146140

Total Amount of the Agreement: $8,504,788

Phase 1: $3,358,334

Phase 2 (Option): $5,146,453

Total Estimated Government Funding: $7,654,309

Phase 1: $3,022,501

Phase 2 (Option): $4,631,808

Contactor Share Contribution: $850,479

Phase 1: $335,834

Phase 2 (Option): $514,645

Funds Obligated By This Modification: $552,931

Total Funds Obligated To Date: $5,654,929

Authority: Article III(C)(1)

HR0011-12-3-0006

P00008

Page 2 of 4

The purpose of this modification is to revise the Phase 2 Statement of Work and Payable

Milestones (Descriptions, Exit Criteria, and/or Payment Amounts), to make funding changes to

Phase 2 Payable Milestone No’s 6 through 9, and to add incremental funding in the amount of

$552,931 to Phase 2 Payable Milestone No’s 9 and 10. It is noted that the changes made to the

Phase 2 Payable Milestone amounts result from both changes in scope (an increase of $1,941,374

to the Total Amount of Phase II) and repricing due to a realized/anticipated cost underrun (a

decrease of $1,248,213 to the Total Amount of Phase II) – the net result which is an overall

increase of $693,161 to the Total Amount of Phase 2 and the Total Amount of the Agreement

(there are no changes being made to Phase 1 as part of this modification).

Accordingly, the following changes apply:


1.	The “Total Amount of the Agreement” has increased from $7,811,627 by $693,161 to $8,504,788.


2.	The “Total Estimated Government Funding of the Agreement” is hereby increased from $7,030,465 by $623,844 to $7,654,309.


3.	The “Contractor Share Contribution” is hereby increased from $781,163 by $69,316 to $850,479.


4.	Article I, “Scope of the Agreement,” Section C(3), is revised to reflect changes to the “Government Share,” “Performer Share,” and “Total Amount of the Agreement” as indicated below (changes in bold):

From:



	Phase 1	Phase 2/ Option 1 (Exercised)	Total Costs if All Options Exercised
Government Share (90%)	$3,022,501	$4,007,964	$7,030,465
Performer Share (10%)	$335,834	$445,329	$781,163
Total Amount of the Agreement	$3,358,334	$4,453,293	$7,811,627

To:



	Phase 1	Phase 2/ Option 1 (Exercised)	Total Costs if All Options Exercised
Government Share (90%)	$3,022,501	$4,631,808	$7,654,309
Performer Share (10%)	$335,834	$514,645	$850,479
Total Amount of the Agreement	$3,358,334	$5,146,453	$8,504,788

HR0011-12-3-0006

P00008

Page 3 of 4


5.	Article V, “Obligation and Payment,” Paragraph C, “Accounting and Appropriation Data,” is revised to reflect the obligation of $552,931 as indicated below:

AB 012199 097 0400 000 N 20132014 D 1320 HLIF6 2013.MBT-

02.CORE.A DARPA 255

From: $2,079,497

By: $ 552,931

To: $2,632,428


6.	The “Total Funds Obligated To Date” is hereby decreased from $5,101,998 by $552,931 to $5,654,929.


7.	The Attachment No. 1 “Statement of Work,” dated 3 May 2012, is deleted in its entirety and replaced with the revised Statement of Work, dated 25 October 2013.

The Attachment No. 3 “Schedule of Payments and Payable Milestones” is modified to reflect revisions to the Phase 2 Payable Milestone Descriptions, Exit Criteria, and/or Payment Amounts; to make funding changes to Phase 2 Payable Payable Milestone No’s 6 through 9; and to add incremental funding in the amount of $552,931 to Phase 2 Payable Milestone No’s 9 and 10. See Enclosure 1 (Conformed Agreement)

The revised funding per Phase 2 Milestone is as depicted in the below table.



MS	TASK	FUNDING CHANGES
	Phase 1	Performer Share			DARPA Share			Total
6	Task CIIa: Ligase mediated DNA assembly	$(39,649)			$(356,838)			$	(396,487	)
7	Task DIIa: High Throughput Sequencing QC of DNA Assemblies	$	(20,563	)	$	(185,070	)	$	(205,633	)
8	Task EIIa: Multiple Integrations	$	39,482		$	355,339		$	394,821
9	Task EIIb: Multiple Integrations	$	39,482		$	355,339		$	394,821
10	Task CIIb: Ligase mediated DNA assembly	$	42,685		$	384,161		$	426,846
11	Task CIIc: Ligase mediated DNA assembly	$-			$-			$-
12	Task EIIc: Multiple Integrations	$-			$-			$-
13	Task DIIb: High Throughput Sequencing QC of DNA Assemblies	$-			$-			$-
14	Task F: Integration of Microbe Engineering Cycle	$-			$-			$-
15	Final Report & Scientific Paper	$-			$-			$-
Total		$61,437			$552,931			$614,368

HR0011-12-3-0006

P00008

Page 4 of 4

Due to the decrease to the Government Share amounts for Milestone No’s 6 and 7, funding from these milestones has been moved to Milestone No’s 8 and 9 and indicated below:



From			To:
Milestone	Amount	ACRN	Milestone	Amount	ACRN
MS 6	$355,339	AB	MS 8	$355,339	AB
MS 6	$1,499	AB	MS 9	$1,499	AB
MS 7	185,070	AB	MS 9	185,070	AB
New	See Paragraph 4 above		MS 9	$168,770	AB
New	See Paragraph 4 above		MS 10	$384,161	AB


9.	The Attachment No. 4, “Funding Schedule” is modified to reflect the revised funding profile, See Enclosure 1 (Conformed Agreement).


10.	A fully conformed version of Agreement No. HR0011-12-3-0006 though P00008, reflecting the changes made herein, is provided as Enclosure 1 to this modification. All changes to Modification P00008 conformed Agreement are highlighted in yellow.


11.	Except as modified above, the terms and conditions of Agreement HR0011-12-3-0006 shall remail unchanged and in full force and effect.



FOR AMYRIS INC		FOR THE DEFENSE ADVANCED RESEARCH PRODUCTS AGENCY
/s/		/s/
(Signature & Date)		(Signature & Date)
Nicholas Khadder		Michael D. Blackstone
Senior Vice President & General Counsel		Agreements Officer

TECHNOLOGY INVESTMENT AGREEMENT

BETWEEN

AMYRIS, INC.,

5885 HOLLIS STREET

SUITE 100

EMERYVILLE, CALIFORNIA 94608

AND

THE DEFENSE ADVANCED RESEARCH PROJECTS AGENCY

675 NORTH RANDOLPH STREET

ARLINGTON, VA 22203-2114

CONCERNING

IMPROVING DNA ASSEMBLY AND INTEGRATION ACROSS PLATFORMS WITH BETTER

SYSTEMS AND TOOLS

(LIVING FOUNDRIES)

Agreement No.: HR0011-12-3-0006

ARPA Order No.: S351/00, S351/01, S351/02, HR001133399, HR001146140

Total Amount of the Agreement: $8,504,788

Phase 1: $3,358,334

Phase 2 (Option): $5,146,453

Total Estimated Government Funding: $7,654,309

Phase 1: $3,022,501

Phase 2 (Option): $4,631,808

Contactor Share Contribution: $850,479

Phase 1: $335,834

Phase 2 (Option): $514,645

Total Funds Obligated: $5,654,929

Authority: 10 U.S.C. § 2371

Line of Appropriation – See Article V.

This Agreement is entered into between the United States of America, hereinafter called the Government, represented by The Defense Advanced Research Projects Agency (DARPA), and AMYRIS, INC., a corporation organized and existing under the laws of the State of Delaware with its principal place of business at 5885 Hollis Street, Suite 100, Emeryville, California 94608 pursuant to and under U.S. Federal law.



Enclosure 1	Conformed Copy	P00008



FOR AMYRIS INC		FOR THE DEFENSE ADVANCED RESEARCH PRODUCTS AGENCY
// See Modification No. P00008//
(Signature & Date)		(Signature & Date)

		Michael D. Blackstone
		Agreements Officer
(Name, Title)		(Name, Title)



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Enclosure 1	Conformed Copy	P00008

TABLE OF CONTENTS



ARTICLES		PAGE
ARTICLE I	Scope of the Agreement	4
ARTICLE II	Term	7
ARTICLE III	Management of the Project	8
ARTICLE IV	Agreement Administration	9
ARTICLE V	Obligation and Payment	10
ARTICLE VI	Disputes	13
ARTICLE VII	Patent Rights	14
ARTICLE VIII	Data Rights	17
ARTICLE IX	Foreign Access to Technology	18
ARTICLE X	Title to and Disposition of Property	20
ARTICLE XI	Civil Rights Act	20
ARTICLE XII	Security	20
ARTICLE XIII	Subcontractors	21
ARTICLE XIV	Key Personnel	21
ARTICLE XV	Export Control	21
ARTICLE XVI	Order of Precedence	22
ARTICLE XVII	Execution	22
ARTICLE XVIII	Applicable Law	22
ARTICLE XIX	Severability	22
ARTICLE XX	Force Majeure	23





ATTACHMENTS

ATTACHMENT 1	Statement of Work
ATTACHMENT 2	Report Requirements
ATTACHMENT 3	Schedule of Payments and Payable Milestones
ATTACHMENT 4	Funding Schedule
ATTACHMENT 5	List of Intellectual Property Assertions



	Page 3 of 23
Enclosure 1	Conformed Copy	P00008

ARTICLE I: SCOPE OF THE AGREEMENT

A. Background

Amyris has been a leader in the synthetic biology technologies, using living organisms as “factories” or “manufacturing systems” to produce compounds. Although the synthetic biology movement has been intermittently successful in certain directed endeavors, there has been insufficient effort toward standardizing and optimizing synthetic biology tools, procedures and platforms. By focusing on the same principles that made the United States the leaders in traditional manufacturing, namely consistent engineering and efficiency, Amyris seeks, through funding in this Agreement , to research and develop a state of the art development cycle for an enhanced engineering cycle to realize living foundries. Amyris aims to achieve these innovations by developing tools increasing the speed of engineered DNA and microbes while simultaneously expanding the scope of the living systems that are readily engineered. Engineering living systems is slow, expensive, and unreliable. Even for seemingly straightforward applications such as developing a fermentable microbe capable of turning sugar into higher value chemicals can take many hundreds of person-years of effort. For example, genetic engineering has enabled the microbial production of non-native natural products such as 1,3-propanediol made in engineered E. coli (~575 years of effort) or artemisinic acid made in engineered S. cerevisiae (~130 years of effort).

For microbes to become a routine manufacture paradigm, offering an alternative to traditional chemicals

and petroleum feedstocks, and for living systems eventually to enable novel commercial and military

applications (self-healing or corrosion-resistant materials) the effort and expense associated with

developing new applications must be reduced by an order of magnitude. This entire enterprise is in its

infancy and the work required to reduce the time and effort needed to develop a new microbe is risky and

at odds with the work also needed to bring a product to market in a one-off manner, the chief goal of any

company seeking to capitalize on the technology. This Agreement supports research with a long-term

perspective to support that entire industry by funding efforts that will enable everyone to do more with

less.

B. Definitions

Agreement : The body of this Agreement and Attachments 1 – 4, which are expressly incorporated in

and made a part of the Agreement.

Collaborators : A third party in a contractual arrangement with the Performer whereby Amyris has agreed to jointly research, develop and/or commercialize and has an active role in such arrangement. For the avoidance of doubt, an “active role” by Amyris is a contractual relationship (1) that involves more than the mere transfer of intellectual property, and (2) where Amyris has a significant participation in decisionmaking and/or funding of the activities. Collaborators include all parties in collaborations with Amyris as of the effective date, even if the collaboration is modified or amended after the effective date.

Data : Recorded information, regardless of form or method of recording, which includes but is not limited to, technical data, software, and trade secrets. The term does not include financial, administrative, cost, pricing or management information and does not include Subject Inventions, included in Article VII.

Foreign Firm or Institution : A firm or institution organized or existing under the laws of a country other than the United States, its territories, or possessions. The term includes, for purposes of this



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Enclosure 1	Conformed Copy	P00008

Agreement, any agency or instrumentality of a foreign government; and firms, institutions or business organizations which are owned or substantially controlled by foreign governments, firms, institutions, or individuals.

Government : The United States of America, as represented by DARPA.

Government Purpose Rights : The rights to use, duplicate, or disclose Data, in whole or in part and in any manner, for Government purposes only, and to have or permit others to do so for Government purposes only.

Government Purpose : Any activity in which the United States Government is a party, including cooperative agreements with international or multi-national defense organizations or sales or transfers by the United States Government to foreign governments or international organizations. Government purposes include competitive procurement, but do not include the rights to use, modify, reproduce, release, perform, display, or disclose Data for commercial purposes or authorize others to do so.

Invention : Any invention or discovery which is or may be patentable or otherwise protectable under Title 35 of the United States Code.

Know-How : All information including, but not limited to discoveries, formulas, materials, Inventions, processes, ideas, approaches, concepts, techniques, methods, software, programs, documentation, procedures, firmware, hardware, technical data, specifications, devices, apparatus and machines.

Limited Rights : The rights to use, modifiy, reproduce, release, perform, display, or disclose Data, in whole or in part, within the Government. The Government may not, without the written permission of the party asserting limited rights, release or disclose the Data outside the Government.

Made : Relates to any Invention means the conception or first actual reduction to practice of such Invention.

Performer : AMYRIS, INC. a corporation organized and existing under the laws of the State of Delaware with its principal place of business at 5885 Hollis Street, Suite 100, Emeryville, California 94608

Practical Application : To manufacture, in the case of a composition of product; to practice, in the case of a process or method, or to operate, in the case of a machine or system; and, in each case, under such conditions as to establish that the Invention is capable of being utilized and that its benefits are, to the extent permitted by law or Government regulations, available to the public on reasonable terms. For the avoidance of doubt, the Parties acknowledge that “practical application” under this Agreement may not include actual commercialization of Subject Inventions hereunder because such Subject Inventions are likely to be research tools and platforms (e.g., it is envisioned that the tools and platforms resulting from the research carried out under this agreement will later – outside of this agreement - be used by the performer to develop commercial products).

Program : Research and development being conducted by the Performer, as set forth in Article I., paragraph C.

Property : Any tangible personal property other than property actually consumed during the execution of work under this agreement.



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Enclosure 1	Conformed Copy	P00008

Subject Invention : Any Invention conceived or first actually reduced to practice in the performance of work under this Agreement that is capable of use as a tool for making or altering a genetically modified organism, provided however, any Inventions, regardless when conceived or reduced to practice, covering the genetically modified organism, a strain, or any compound or product made by or from an organism or strain shall not be considered “Subject Inventions” hereunder. For the avoidance of doubt, no work performed prior to the effective date of this Agreement shall be considered performed “under this Agreement.”

Technology : Discoveries, innovations, Know-How and Inventions, whether patentable or not, including computer software, recognized under U.S. law as intellectual creations to which rights of ownership accrue, including, but not limited to, patents, trade secrets, and copyrights developed under this Agreement.

Unlimited Rights : Rights to use, duplicate, release, or disclose, Data in whole or in part, in any manner and for any purposes whatsoever, and to have or permit others to do so.

C. Scope

1. Amyris, Inc. (hereafter “the Performer”) shall perform a research and development program (Program) designed to develop improved DNA assembly and integration across platforms. The research shall be carried out in accordance with the Statement of Work incorporated in this Agreement as Attachment 1. The Performer shall submit or otherwise provide all documentation required by Attachment 2, Report Requirements.

2. The Performer shall be paid for each Payable Milestone accomplished in accordance with the Schedule of Payments and Payable Milestones set forth in Attachment 3 and the procedures of Article V. Both the Schedule of Payments and the Funding Schedule set forth in Attachments 3 and 4 respectively may be revised or updated in accordance with Article III, subject to mutual agreement of the Parties.

3. The Government and the Performer estimate that the Statement of Work of this Agreement can only be accomplished with a Performer aggregate resource contribution of



	Phase 1	Phase 2/ Option 1 (Exercised)	Total Costs if All Options Exercised
Government Share (90%)	$3,022,501	$4,631,808	$7,654,309
Performer Share (10%)	$335,834	$514,645	$850,479
Total Amount of the Agreement	$3,358,334	$5,146,453	$8,504,788

from the effective date of this Agreement, subject to the availability of funds. The Performer intends and, by entering into this Agreement, undertakes to cause these funds to be provided. The Performer’s contributions will be provided as detailed in the Funding Schedule set forth in Attachment 4. If either DARPA or the Performer is unable to provide its respective total contribution, the other Party may reduce its project funding by a proportional amount.



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Enclosure 1	Conformed Copy	P00008

D. Goals / Objectives

1. The goal of this Agreement is for the Government to fund a performance-based effort by the Performer to investigate and create platforms for increasing the speed of engineering DNA and microbes while simultaneously expanding the scope of the living systems that are readily engineered.

2. The Government will have continuous involvement with the Performer. The Government will also obtain access to research results and certain rights in data and patents pursuant to Articles VII and VIII. DARPA and the Performer are bound to each other by a duty of good faith and best research effort in achieving the goals of the Program.

3. This Agreement is an "other transaction" pursuant to 10 U.S.C. § 2371. The Parties agree that the principal purpose of this Agreement is for the Government to support and stimulate the Performer to provide their best effort in advanced research and technology development and not for the acquisition of property or services for the direct benefit or use of the Government. This Agreement can best be described as an accumulation of expenses approach with payments tied to Fixed Payable Milestones. The Performer will be paid for each Payable Milestone accomplished in accordance with the Schedule of Payments and Payable Milestones set forth in Attachment 3 and the procedures of Article V. The Schedule of Payments and Payable Milestones may be revised or updated in accordance with Article III. This Agreement is not intended to be, nor shall it be construed as, by implication or otherwise, a partnership, a corporation, or other business organization.

ARTICLE II: TERM

A. Term of this Agreement

The Program commences upon the date of the last signature hereon and continues for:

Phase 1 – Twelve (12) months.

Phase 2 (Exercised via P00005) – Twelve (12) months from date of option exercise.

If all funds are expended prior to the duration of any Phase of the Agreement, the Parties have no obligation to continue performance and may elect to cease development at that point.

Provisions of this Agreement, which, by their express terms or by necessary implication, apply for periods of time other than specified herein, shall be given effect, notwithstanding this Article.

B. Termination Provisions

Subject to a reasonable determination that the program will not produce beneficial results commensurate with the expenditure of resources, either Party may terminate this Agreement by written notice to the other Party, provided that such written notice is preceded by consultation between the Parties. In the event of a termination of the Agreement, it is agreed that disposition of Data developed under this Agreement, shall be in accordance with the provisions set forth in Article VIII, Data Rights. The Government and the Performer will negotiate in good faith a reasonable and timely adjustment of all outstanding issues between the Parties as a result of termination. Failure of the Parties to agree to a reasonable adjustment will be resolved pursuant to Article VI, Disputes. The Government has no obligation to pay the Performer beyond the last completed and paid milestone if the Performer decides to terminate. For the avoidance of doubt, any such termination does not require repayment of milestone amounts already received by Performer.



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C. Extending the Term (Phase 2)

The Parties may extend by mutual written agreement the term of this Agreement if funding availability and research opportunities reasonably warrant. Any extension shall be formalized through modification of the Agreement by the Agreements Officer and the Performer’s Administrator.

(i) The Government may extend the term of this agreement by written notice to the Performer within 12 months; provided that the Government gives the Performer a preliminary written notice of its intent to extend at least 14 days before the agreement expires. The preliminary notice does not commit the Government to an extension.

(ii) If the Government exercises this option, the extended agreement shall be considered to include this article.

(iii) The total duration of this agreement, including the exercise of any options under this article, shall not exceed 24 months.

(End of clause)

ARTICLE III: MANAGEMENT OF THE PROJECT

A. Management and Program Structure

The Performer shall be responsible for the overall technical and program management of the Program, and technical planning and execution shall remain with the Performer. The DARPA Agreements Officer’s Representative shall provide recommendations to Program developments and technical collaboration and be responsible for the review and verification of the Payable Milestones.

B. Program Management Planning Process

Program planning will consist of an Annual Program Plan with inputs and review from the Performer and DARPA management, containing the detailed schedule of research activities and payable milestones. The Annual Program Plan will consolidate quarterly adjustments in the research schedule, including revisions/modification to payable milestones.

1. Initial Program Plan: The Performer will follow the initial program plan that is contained in the Statement of Work (Attachment 1), and the Schedule of Payments and Payable Milestones (Attachment 3).

2. Overall Program Plan Annual Review

(a) The Performer, with DARPA Agreements Officer’s Representative review, will prepare an overall Annual Program Plan in the first quarter of each Agreement year. (For this purpose, each consecutive twelve (12) month period from (and including) the month of execution of this Agreement during which this Agreement shall remain in effect shall be considered an “Agreement Year”.) The Annual Program Plan will be presented and reviewed at an annual site review which will be attended by the performer’s Key Personnel, the DARPA Agreements Officer’s Representative, Senior DARPA management as appropriate, and other DARPA program managers and personnel as appropriate. The Performer, with DARPA participation and review, will prepare a final Annual Program Plan.



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(b) The Annual Program Plan provides a detailed schedule of research activities, commits the Performer to use its best efforts to meet specific performance objectives, includes forecasted expenditures and describes the Payable Milestones. The Annual Program Plan will consolidate all prior adjustments in the research schedule, including revisions/modifications to payable milestones. Recommendations for changes, revisions or modifications to the Agreement which result from the Annual Review shall be made in accordance with the provisions of Article III, Section C.

C. Modifications

1. As a result of quarterly meetings (in person or videoconference), annual reviews, or at any time during the term of the Agreement, research progress or results may indicate that a change in the Statement of Work and/or the Payable Milestones, would be beneficial to program objectives. Recommendations for modifications, including justifications to support any changes to the Statement of Work and/or the Payable Milestones, will be documented in a letter and submitted by the Performer to the DARPA Agreements Officer’s Representative with a copy to the DARPA Agreements Officer. This documentation letter will detail the technical, chronological, and financial impact of the proposed modification to the research program. The Performer shall approve any Agreement modification. The Government is not obligated to pay for additional or revised Payable Milestones until the Payable Milestones Schedule (Attachment 3) is formally revised by the DARPA Agreements Officer and made part of this Agreement.

2. The DARPA Agreements Officer’s Representative shall be responsible for the review and verification of any recommendations to revise or otherwise modify the Agreement Statement of Work, Schedule of Payments or Payable Milestones, or other proposed changes to the terms and conditions of this Agreement.

3. For minor or administrative Agreement modifications (e.g. changes in the paying office or appropriation data, changes to Government or the Performer’s personnel identified in the Agreement, etc.) no signature is required by the Performer.

ARTICLE IV: AGREEMENT ADMINISTRATION

Unless otherwise provided in this Agreement, approvals permitted or required to be made by DARPA

may be made only by the DARPA Agreements Officer. Administrative and contractual matters under

this Agreement shall be referred to the following representatives of the parties:

A. Government Points of Contact:

Agreements Officer:

[*]

DARPA Program Manager:

[*]

Program Manager

[*]



	Page 9 of 23
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[*]

Agreements Officer’s Representative (AOR):

[*]

Administrative Agreements Officer (AAO):

[*]

B. Performer Points of Contact

Performer’s Administrative/Contracting:

[*]

General Counsel

[*]

Performer’s Program Manager:

[*]

Chief Science Officer

[*]

ARTICLE V: OBLIGATION AND PAYMENT

A. Obligation

1. The Government’s liability to make payments to the Performer is limited to only those funds obligated under the Agreement or by modification to the Agreement. DARPA may obligate funds to the Agreement incrementally.

2. If modification becomes necessary in performance of this Agreement, pursuant to Article III, paragraph B, the DARPA Agreements Officer and the Performer’s Administrator shall execute a revised Schedule of Payable Milestones consistent with the then current Program Plan.

B. Payments

1. The Performer has an established and agrees to maintain an established accounting system which complies with Generally Accepted Accounting Principles and the requirements of this Agreement, and shall ensure that appropriate arrangements have been made for receiving, distributing and accounting for all funding. An acceptable accounting system is one in which all cash receipts and disbursements are controlled and documented properly.

2. The Performer shall document the accomplishments of each Payable Milestone by submitting or otherwise providing the Payable Milestones Report required by Attachment 2, Part D.



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After written verification of the accomplishment of the Payable Milestone by the DARPA Agreements Officer’s Representative, and approval by the Agreements Officer, the associated invoice will be submitted to the payment office via Wide Area Workflow (WAWF), as detailed in paragraph B.6 of this Article. If deemed necessary by the Agreements Officer, payment approval for the final Payable Milestone will be made after reconciliation of DARPA funding with actual Performer contributions. Subject to change only through written Agreement modification, payment shall be made to the address of the Performer’s Administrator set forth below.

3. Address of Payee: AMYRIS, INC., 5885 Hollis Street, Suite 100, Emeryville, California 94608

4. Government funds shall be maintained in an interest-bearing account prior to disbursement. This account shall not be in U. S. Treasury Notes. Any interest earned shall be remitted annually to the DARPA Agreements Officer, or designee. Interest payments shall be made payable to the U. S. Treasury. Interest amounts less than $250 per year may be retained by the Performer for administrative expenses.

5. Payments will be made by the cognizant Defense Agencies Financial Services office, as indicated below, within thirty (30) calendar days of an accepted invoice in Wide Area Workflow (WAWF). Wide Area Workflow (WAWF) is a secure web-based system for electronic invoicing, receipt and acceptance. The WAWF application enables electronic form submission of invoices, government inspection, and acceptance documents in order to support DoD’s goal of moving to a paperless acquisition process. Authorized DoD users are notified of pending actions by e-mail and are presented with a collection of documents required to process the contracting or financial action. It uses Public Key Infrastructure (PKI) to electronically bind the digital signature to provide non-reputable proof that the user (electronically) signed the document with the contents. Benefits include online access and full spectrum view of document status, minimized re-keying and improving data accuracy, eliminating unmatched disbursements and making all documentation required for payment easily accessible.

The Performer is required to utilize the Wide Area Workflow system when processing invoices and receiving reports under this Agreement. The Performer shall (i) ensure an Electronic Business Point of Contact is designated in Central Contractor Registration at http://www.ccr.gov and (ii) register to use WAWF–RA at the https://wawf.eb.mil site, within ten (10) calendar days after award of this Agreement. Step by Step procedures to register are available at the https://wawf.eb.mil site. The Performer is directed to use the “2-in-1” format when processing invoices.


a.	For the Issue By DoDAAC enter HR0011


b.	For the Admin DoDAAC and Ship To fields, enter S0507A.


c.	For the Service Acceptor field, enter HR0011, Extension 01.


d.	Leave the Inspect by DoDAAC, Ship From Code DoDAAC and LPO DoDAAC fields blank unless otherwise directed by the Agreements Officer or Administrative Agreements Officer.


e.	The following guidance is provided for invoicing processed under this Agreement through WAWF:


•	The AOR identified at Article IV "Agreement Administration" shall continue to formally inspect and accept the deliverables/payable milestones. To the maximum extent practicable, the AOR shall review the deliverable(s)/payable milestone report(s) and either: 1) provide a written notice of rejection to the Performer which includes feedback



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regarding deficiencies requiring correction or 2) written notice of acceptance to the Administrative Agreements Officer (AAO), DARPA PM and Agreements Officer.


•	Acceptance within the WAWF system shall be performed by the Agreements Officer upon receipt of a confirmation email, or other form of transmittal, from the AOR.


•	The Performer shall send an email notice to the AOR and Agreements Officer upon submission of an invoice in WAWF (this can be done from within WAWF).


•	Payments shall be made by DFAS-CO/WEST (HQ0339)

•

The Performer agrees, when entering invoices entered in WAWF to utilize the CLINs associated with each payable milestone as delineated at Attachment 3. The description of the CLIN shall include reference to the associated milestone number along with other necessary descriptive information. The Performer agrees that the Government may reject invoices not submitted in accordance with this provision.

Note for DFAS: The Agreement shall be entered into the DFAS system by CLIN – Milestone association as delineated at Attachment 3. The Agreement is to be paid out by CLIN – Milestone association. Payments shall be made using the CLIN (MS)/ACRN association as delineated at Attachment 3.

6. Payee Information: As identified at Central Contractor Registration.


•	Cage Code: 47QN9


•	DUNS: 185930182


•	TIN: 55-0856151

7. Limitation of Funds: In no case shall the Government’s financial liability exceed the

amount obligated under this Agreement.

8. Payments shall be made in the amounts set forth in Attachment No. 3, provided the DARPA Agreements Officer’s Representative has verified the accomplishment of the Payable Milestones. It is recognized that the quarterly accounting of current expenditures reported in the “Quarterly Business Status Report” submitted in accordance with Attachment No. 2 is not necessarily intended or required to match the Payable Milestones until submission of the Final Report; however, payable milestones may be revised during the course of the program to reflect current and revised projected expenditures, subject to the requirements set forth in Article III.

account for all funding under this Agreement and shall maintain adequate records to account for the Performer’s funding provided under this Agreement. Upon completion or termination of this Agreement, whichever occurs earlier, the Performer’s Administrator shall furnish to the Agreements Officer a copy of the Final Report required by Attachment 2, Part E. The Performer’s relevant financial records are subject to examination or audit on behalf of DARPA by the Government for a period not to exceed three (3) years after expiration of the term of this Agreement. The Agreements Officer or designee shall have direct access to sufficient records and information of the Performer, to ensure full accountability for all funding under this Agreement. Such audit, examination, or access shall be performed during business hours on business days upon prior written notice and shall be subject to the security requirements of the audited party.

C. Accounting and Appropriation Data



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AA 9720400 1320 S351 P2D10 2525 DPAC 2 5205 S12136 61101E $3,022,501

AB 012199 097 0400 000 N 20132014 D 1320 HLIF6 2013.MBT-02.CORE.A DARPA 255

$2,632,428

ARTICLE VI: DISPUTES

A. General

The Parties shall communicate with one another in good faith and in a timely and cooperative manner

when raising issues under this Article.

B. Dispute Resolution Procedures

1. Any disagreement, claim or dispute between DARPA and the Performer concerning questions of fact or law arising from or in connection with this Agreement, and, whether or not involving an alleged breach of this Agreement, may be raised only under this Article.

2. Whenever disputes, disagreements, or misunderstandings arise, the Parties shall attempt to resolve the issue(s) involved by discussion and mutual agreement as soon as practicable. In no event shall a dispute, disagreement or misunderstanding which arose more than three (3) months prior to the notification made under subparagraph B.3 of this article constitute the basis for relief under this article unless the Director of DARPA in the interests of justice waives this requirement.

3. Failing resolution by mutual agreement, the aggrieved Party shall document the dispute, disagreement, or misunderstanding by notifying the other Party (through the DARPA Agreements Officer or the Performer’s Administrator, as the case may be) in writing of the relevant facts, identify unresolved issues, and specify the clarification or remedy sought. Within five (5) working days after providing notice to the other Party, the aggrieved Party may, in writing, request a joint decision by the DARPA Senior Procurement Executive, and senior executive (no lower than Vice President, Legal) appointed by the Performer. The other Party shall submit a written position on the matter(s) in dispute within thirty (30) calendar days after being notified that a decision has been requested. The DARPA Senior Procurement Executive, and the senior executive shall conduct a review of the matter(s) in dispute and render a decision in writing within thirty (30) calendar days of receipt of such written position. Any such joint decision is final and binding.

4. In the absence of a joint decision, upon written request to the Director of DARPA, made within thirty (30) calendar days of the expiration of the time for a decision under subparagraph B.3 above, the dispute shall be further reviewed. The Director of DARPA may elect to conduct this review personally or through a designee or jointly with a senior executive (no lower than (Vice President, Legal) level) appointed by the Performer. Following the review, the Director of DARPA or designee will resolve the issue(s)and notify the Parties in writing. Such resolution is not subject to further administrative review and, to the extent permitted by law, shall be final and binding.

C. Limitation of Damages



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Claims for damages of any nature whatsoever pursued under this Agreement shall be limited to direct damages only up to the aggregate amount of DARPA funding disbursed as of the time the dispute arises. In no event shall DARPA be liable for claims for consequential, punitive, special and incidental damages, claims for lost profits, or other indirect damages.

ARTICLE VII: PATENT RIGHTS

A. Allocation of Principal Rights

Unless the Performer shall have notified DARPA (in accordance with subparagraph B.2 below) that the Performer does not intend to retain title, the Performer shall retain the entire right, title, and interest throughout the world to each Subject Invention consistent with the provisions of this Article and 35 U.S.C. § 202. With respect to any Subject Invention in which the Performer retains title, DARPA shall have a nonexclusive, nontransferable, irrevocable, paid-up license to practice or have practiced on behalf of the United States the Subject Invention throughout the world.

B. Invention Disclosure, Election of Title, and Filing of Patent Application

1. The Performer shall disclose each Subject Invention to DARPA within four (4) months after the inventor discloses it in writing to his company personnel responsible for patent matters or, in the case of no internal writing from the inventor, within two (2) months after filing a provisional application, provided however that in the event the Performer does not file a provisional application, it shall disclose the Subject Invention to DARPA within two (2) months of determining that a particular set of experiments and or data qualify as a Subject Invention. The disclosure to DARPA shall be in the form of a written report and shall identify the Agreement under which the Subject Invention was made and the identity of the inventor(s). It shall be sufficiently complete in technical detail to convey a clear understanding to the extent known at the time of the disclosure, of the nature, purpose, operation, and the physical, chemical, biological, or electrical characteristics of the invention. The disclosure shall also identify any publication, sale, or public use of the invention and whether a manuscript describing the invention has been submitted for publication and, if so, whether it has been accepted for publication at the time of disclosure. The Performer shall also submit to DARPA an annual listing of Subject Inventions.

2. If the Performer determines that it does not intend to retain title to any such Subject Invention, the Performer shall notify DARPA, in writing, within eight (8) months of disclosure to DARPA. However, in any case where publication, sale, or public use has initiated the one (1)-year statutory period wherein valid patent protection can still be obtained in the United States, the period for such notice may be shortened by DARPA to a date that is no more than sixty (60) calendar days prior to the end of the statutory period.

3. The Performer shall file its initial patent application on a Subject Invention to which it elects to retain title within one (1) year after election of title or, if earlier, prior to the end of the statutory period wherein valid patent protection can be obtained in the United States after a publication, or sale, or public use. The Performer may elect to file patent applications in additional countries (including the European Patent Office and the Patent Cooperation Treaty) within either ten (10) months of the corresponding initial patent application or six (6) months from the date permission is granted by the Commissioner of Patents and Trademarks to file foreign patent applications, where such filing has been prohibited by a Secrecy Order.

4. Requests for extension of the time for disclosure election, and filing under Article VII,



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paragraph C, may, at the discretion of DARPA, and after considering the position of the Performer, be granted.

C. Conditions When the Government May Obtain Title

Upon DARPA’s written request, the Performer shall convey title to any Subject Invention to DARPA under any of the following conditions:

1. If the Performer fails to disclose or elects not to retain title to the Subject Invention within the times specified in paragraph C of this Article; provided, that DARPA may only request title within sixty (60) calendar days after learning of the failure of the Performer to disclose or elect within the specified times.

2. In those countries in which the Performer fails to file patent applications within the times specified in paragraph B of this Article; provided, that if the Performer has filed a patent application in a country after the times specified in paragraph B of this Article, but prior to its receipt of the written request by DARPA, the Performer shall continue to retain title in that country; or

3. In any country in which the Performer decides not to continue the prosecution of any application for, to pay the maintenance fees on, or defend in reexamination or opposition proceedings on, a patent on a Subject Invention.

D. Minimum Rights to the Performer and Protection of the Performer’s Right to File

1. The Performer shall retain a nonexclusive, royalty-free license throughout the world in each Subject Invention to which the Government obtains title, except if the Performer fails to disclose the invention within the times specified in paragraph B of this Article. The Performer’s license extends to subsidiaries and affiliates and Collaborators, if any, within the corporate structure of which the Performer is a party and includes the right to grant licenses of the same scope to the extent that the Performer was legally obligated to do so at the time the Agreement was awarded. The license is transferable only with the approval of DARPA, except when transferred to the successor of that part of the business to which the invention pertains. DARPA approval for license transfer shall not be unreasonably withheld.

2. The Performer’s license may be revoked or modified by DARPA to the extent necessary to achieve expeditious practical application of the Subject Invention pursuant to an application for an exclusive license submitted consistent with appropriate provisions at 37 CFR Part 404. This license shall not be revoked at any time when the Performer continues to practice the general technology developed hereunder in pursuit of commercial goals, including the goal of making the products derived from such platforms reasonably accessible to the public.

3 Before revocation or modification of the license, DARPA shall furnish the Performer a written notice of its intention to revoke or modify the license, and the Performer shall be allowed thirty (30) calendar days (or such other time as may be authorized for good cause shown) after the notice to show cause why the license should not be revoked or modified.

E. Action to Protect the Government’s Interest

1. The Performer agrees to execute or to have executed and promptly deliver to DARPA all instruments necessary to (i) establish or confirm the rights the Government has throughout the world in those Subject Inventions to which the Performer elects to retain title, and (ii) convey title to DARPA



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when requested under paragraph D of this Article and to enable the Government to obtain patent protection throughout the world in that Subject Invention.

2. The Performer agrees to require, by written agreement, its employees, other than clerical and non-technical employees, to disclose promptly in writing to personnel identified as responsible for the administration of patent matters and in a format suggested by the Performer each Subject Invention made under this Agreement in order that the Performer can comply with the disclosure provisions of paragraph C of this Article. The Performer shall instruct employees, through employee agreements or other suitable educational programs, on the importance of reporting inventions in sufficient time to permit the filing of patent applications prior to U. S. or foreign statutory bars.

3. The Performer shall notify DARPA of any decisions not to continue the prosecution of a patent application, pay maintenance fees, or defend in a reexamination or opposition proceedings on a patent, in any country, not less than thirty (30) calendar days before the expiration of the response period required by the relevant patent office.

4. The Performer shall include, within the specification of any United States patent application and any patent issuing thereon covering a Subject Invention, the following statement: “This invention was made with Government support under Agreement HR0011-12-3-0006, awarded by DARPA. The Government has certain rights in the invention.”

F. Lower Tier Agreements

The Performer shall include this Article, suitably modified, to identify the Parties, in all subcontracts or lower tier agreements, regardless of tier, for experimental, developmental, or research work.

G. Reporting on Utilization of Subject Inventions

The Performer agrees to submit, during the term of the Agreement, an annual report on the general subject matter research at Performer or its Collaborators, licensees or assignees in connection with utilization of a Subject Invention or on efforts at obtaining such utilization that is being made by the Performer or its Collaborators, licensees or assignees. Such reports shall include information regarding the general fields of potential products where such Subject Inventions may ultimately assist in commercial sales. The Performer also agrees to provide additional reports as may be requested by DARPA in connection with any march-in proceedings undertaken by DARPA in accordance with paragraph J of this Article. Consistent with 35 U.S.C. § 202(c)(5), DARPA agrees it shall not disclose such information to persons outside the Government without permission of the Performer.


2	All required reporting shall be accomplished, to the extent possible, using the i-Edison reporting website: https://s-edison.info.nih.gov/iEdison/. To the extent any such reporting cannot be carried out by use of i-Edison, reports and communications shall be submitted to the Agreements Officer and Administrative Agreements Officer.

H. Preference for American Industry

Notwithstanding any other provision of this clause, the Performer agrees that it shall not grant to any person the exclusive right to use or sell any Subject Invention in the United States or Canada unless such person agrees that any product embodying the Subject Invention or produced through the use of the Subject Invention shall be manufactured substantially in the United States or Canada except when such



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such rights are in connection with a Collaborator. However, in individual cases, the requirements for such an agreement beyond what is contemplated herein may be waived by DARPA upon a showing by the Performer (1) that reasonable but unsuccessful efforts have been made to grant licenses on similar terms to potential licensees that would be likely to manufacture substantially in the United States or (2) that, under the circumstances, domestic manufacture is not commercially feasible.

I. March-in Rights

The Performer agrees that, with respect to any Subject Invention in which it has retained title, DARPA has the right to require the Performer, an assignee, or exclusive licensee of a Subject Invention to grant a non-exclusive license to a responsible applicant or applicants, upon terms that are reasonable under the circumstances, and if the Performer, assignee, or exclusive licensee refuses such a request, DARPA has the right to grant such a license itself if DARPA determines that:

1. Such action is necessary because the Performer or assignee has not taken effective steps, consistent with the intent of this Agreement, to achieve practical application of the Subject Invention;

2. Such action is necessary to alleviate health or safety needs which are not reasonably satisfied by the Performer, assignee, or their licensees;

3. Such action is necessary to meet requirements for public use and such requirements are not reasonably satisfied by the Performer, assignee, or licensees; or

4. Such action is necessary because the agreement required by paragraph (I) of this Article has not been obtained or waived or because a licensee of the exclusive right to use or sell any Subject Invention in the United States is in breach of such Agreement.

ARTICLE VIII: DATA RIGHTS

A. Allocation of Principal Rights

1. This Agreement shall be performed with mixed Government and Performer funding. The Parties agree that in consideration for Government funding, the Performer intends to reduce to practical application items, components and processes developed under this Agreement.

2. The Performer agrees to retain and maintain in good condition until two (2) years after completion or termination of this Agreement, all Data necessary to achieve practical application. In the event of exercise of the Government’s March-in Rights as set forth under Article VII or subparagraph A.3 of this article, the Performer agrees, upon written request from the Government, to deliver at no additional cost to the Government, all Data necessary to achieve practical application within sixty (60) calendar days from the date of the written request. The Government shall retain Unlimited Rights, as defined in paragraph A above, to this delivered Data.

3. The Performer agrees that, with respect to Data necessary to achieve practical application, DARPA has the right to require the Performer to deliver all such Data to DARPA in accordance with its reasonable directions if DARPA determines that:



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(a) Such action is necessary because the Performer or assignee has not taken effective steps, consistent with the intent of this Agreement, to achieve practical application of the technology developed during the performance of this Agreement;

(b) Such action is necessary to alleviate health or safety needs which are not reasonably satisfied by the Performer, assignee, or their licensees; or

(c) Such action is necessary to meet requirements for public use and such requirements are not reasonably satisfied by the Performer, assignee, or licensees.

4. With respect to Data developed, generated or delivered under this Agreement, the Government shall receive Government Purpose Rights, except as noted in subparagraph (5) of this article.

5. With respect to all Data delivered, in the event of the Government’s exercise of its right under subparagraph B.2 of this article, the Government shall receive Unlimited Rights.

6. Any pre-existing Data to be utilized and delivered under this Agreement shall be delivered with restrictions as delineated in the Performer Identification and Assertion of Use, Release, or Disclosure Restrictions provided in Attachment 5.

B. Marking of Data

Pursuant to paragraph B above, any Data delivered under this Agreement shall be marked with the following legend:

Use, duplication, or disclosure is subject to the restrictions as stated in Agreement HR0011-12-3- 0006 between the Government and the Performer.

C. Lower Tier Agreements

The Performer shall include this Article, suitably modified to identify the Parties, in all subcontracts or lower tier agreements, regardless of tier, for experimental, developmental, or research work.

ARTICLE IX: FOREIGN ACCESS TO TECHNOLOGY

This Article shall remain in effect during the term of the Agreement and for two (2) years thereafter.

A. General

The Parties agree that research findings and technology developments arising under this Agreement may constitute a significant enhancement to the national defense, and to the economic vitality of the United States. Accordingly, access to important technology developments under this Agreement by Foreign Firms or Institutions must be carefully controlled. The controls contemplated in this Article are in addition to, and are not intended to change or supersede, the provisions of the International Traffic in Arms Regulation (22 CFR pt. 121 et seq.), the DoD Industrial Security Regulation (DoD 5220.22-R) and the Department of Commerce Export Regulation (15 CFR pt. 770 et seq.)

B. Restrictions on Sale or Transfer of Technology to Foreign Firms or Institutions



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1. In order to promote the national security interests of the United States and to effectuate the policies that underlie the regulations cited above, the procedures stated in subparagraphs C.2, C.3, and C.4 below shall apply to any transfer of Technology. For purposes of this paragraph, a transfer includes a sale of the company, and sales or licensing of Technology. Transfers do not include:

(a) sales of products or components, or

(b) licenses of software or documentation related to sales of products or components, or

(d) transfer which provides access to Technology to a Foreign Firm or Institution which is an approved source of supply or source for the conduct of research under this Agreement provided that such transfer shall be limited to that necessary to allow the firm or institution to perform its approved role under this Agreement.

2. The Performer shall provide timely notice to DARPA of any proposed transfers which occur after the effective date of this agreement from the Performer of Technology developed under this Agreement to Foreign Firms or Institutions. If DARPA determines that the transfer may have adverse consequences to the national security interests of the United States, the Performer, its vendors, and DARPA shall jointly endeavor to find alternatives to the proposed transfer which obviate or mitigate potential adverse consequences of the transfer but which provide substantially equivalent benefits to the Performer.

3. In any event, the Performer shall provide written notice to the DARPA Agreements Officer’s Representative and Agreements Officer of any proposed transfer to a foreign firm or institution at least sixty (60) calendar days prior to the proposed date of transfer. Such notice shall cite this Article and shall state specifically what is to be transferred and the general terms of the transfer. Within thirty (30) calendar days of receipt of the Performer’s written notification, the DARPA Agreements Officer shall advise the Performer whether it consents to the proposed transfer. In cases where DARPA does not concur or sixty (60) calendar days after receipt and DARPA provides no decision, the Performer may utilize the procedures under Article VI, Disputes. No transfer shall take place until a decision is rendered.

4. In the event a transfer of Technology to Foreign Firms or Institutions which is NOT approved by DARPA takes place, the Performer shall (a) refund to DARPA funds paid for the development of the Technology and (b) the Government shall have a non-exclusive, nontransferable, irrevocable, paid-up license to practice or have practiced on behalf of the United States the Technology throughout the world for Government and any and all other purposes, particularly to effectuate the intent of this Agreement. Upon request of the Government, the Performer shall provide written confirmation of such licenses.

C. Lower Tier Agreements



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ARTICLE X: TITLE TO AND DISPOSITION OF PROPERTY

A. Title to Property

The Performer will acquire property with an acquisition value greater than $5,000 under this Agreement as set forth in Attachment * to this Agreement which is necessary to further the research and development goals of this Program and is not for the direct benefit of the Government. Title to this property shall vest in the Performer upon acquisition. Title to any other items of property acquired under this Agreement with an acquisition value of $5,000 or less shall vest in the Performer upon acquisition with no further obligation of the Parties unless otherwise determined by the Agreements Officer. Should any other item of property with an acquisition value greater than $5,000 be required, the Performer shall obtain prior written approval of the Agreements Officer. Title to this property shall also vest in the Performer upon acquisition. The Performer shall be responsible for the maintenance, repair, protection, and preservation of all property at its own expense.

B. Disposition of Property

At the completion of the term of this Agreement, items of property set forth in Attachment * or any other items of property with an acquisition value greater than $5,000 shall be disposed of in the following manner:

1. Purchased by the Performer at an agreed-upon price, the price to represent fair market value, with the proceeds of the sale being returned to DARPA; or

2. Transferred to a Government research facility with title and ownership being transferred to the Government; or

3. Donated to a mutually agreed University or technical learning center for research purposes; or

4. Any other DARPA-approved disposition procedure.

ARTICLE XI: CIVIL RIGHTS ACT

This Agreement is subject to the compliance requirements of Title VI of the Civil Rights Act of 1964 as amended (42 U.S.C. 2000-d) relating to nondiscrimination in Federally assisted programs. The Performer has signed an Assurance of Compliance with the nondiscriminatory provisions of the Act.

ARTICLE XII: SECURITY

The Government does not anticipate the need for the Performer to develop and/or handle classified information in the performance of this Agreement. No DD254 is currently required for this Agreement.



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ARTICLE XIII: SUBCONTRACTORS

The Performer shall make every effort to satisfy the intent of competitive bidding of sub-agreements to the maximum extent practical. The Performer may use foreign entities or nationals as subcontractors, subject to compliance with the requirements of this Agreement and to the extent otherwise permitted by law.

ARTICLE XIV: KEY PERSONNEL


A.	The Performer shall notify the Agreements Officer in writing prior to making any change in key personnel. The following individuals are designated as key personnel for the purposes of this Agreement:



Name	Role/Title	% of time
Jack Newman	Chief Science Officer	60%
Sunil Chandran	Team Leader	100%


B.	When replacing any of the personnel identified above, the Performer must demonstrate that the qualifications of the prospective personnel are acceptable to the Government as reasonably determined by the Program Manager. Substitution of key personnel shall be documented by modification to the Agreement made in accordance with the procedures outlined in Article III, paragraph C.

ARTICLE XV: EXPORT CONTROL

(a) Definition . “Export-controlled items,” as used in this clause, means items subject to the Export Administration Regulations (EAR) (15 CFR Parts 730-774) or the International Traffic in Arms Regulations (ITAR) (22 CFR Parts 120-130). The term includes:

1) “Defense items,” defined in the Arms Export Control Act, 22 U.S.C. 2778(j)(4)(A), as defense articles, defense services, and related technical data, and further defined in the ITAR, 22 CFR Part 120.

2) “Items,” defined in the EAR as “commodities”, “software”, and “technology,” terms that are also defined in the EAR, 15 CFR 772.1.

(b) The Performer shall comply with all applicable laws and regulations regarding export-controlled items, including, but not limited to, the requirement for contractors to register with the Department of State in accordance with the ITAR. The Performer shall consult with the Department of State regarding any questions relating to compliance with the ITAR and shall consult with the Department of Commerce regarding any questions relating to compliance with the EAR.

(c) The Performer's responsibility to comply with all applicable laws and regulations regarding exportcontrolled items exists independent of, and is not established or limited by, the information provided by this clause.

(d) Nothing in the terms of this contract adds, changes, supersedes, or waives any of the requirements of applicable Federal laws, Executive orders, and regulations,



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including but not limited to—

(1) The Export Administration Act of 1979, as amended (50 U.S.C. App. 2401, et seq.);

(2) The Arms Export Control Act (22 U.S.C. 2751, et seq.);

(3) The International Emergency Economic Powers Act (50 U.S.C. 1701, et seq.);

(4) The Export Administration Regulations (15 CFR Parts 730-774);

(5) The International Traffic in Arms Regulations (22 CFR Parts 120-130);

and

(6) Executive Order 13222, as extended;

(e) The Performer shall include the substance of this clause, including this paragraph (e), in all subawards.

ARTICLE XVI: ORDER OF PRECEDENCE

In the event of any inconsistency between the terms of this Agreement and language set forth in the Attachments, the inconsistency shall be resolved by giving precedence in the following order: (1) The Agreement, and (2) all Attachments to the Agreement.

ARTICLE XVII: EXECUTION

This Agreement constitutes the entire agreement of the Parties and supersedes all prior and contemporaneous agreements, understandings, negotiations and discussions among the Parties, whether oral or written, with respect to the subject matter hereof. This Agreement may be revised only by written consent of the Performer and the DARPA Agreements Officer. This Agreement, or modifications thereto, may be executed in counterparts each of which shall be deemed as original, but all of which taken together shall constitute one and the same instrument.

ARTICLE XVIII: APPLICABLE LAW

United States federal law will apply to the construction, interpretation, and resolution of any disputes arising out of or in connection with this Agreement.

ARTICLE XIX: SEVERABILITY

In the event that any one or more of the provisions contained herein shall, for any reason, be held to be invalid, illegal or unenforceable in any respect, such invalidity, illegality or unenforceability shall not affect any other provisions of this Agreement, but this Agreement shall be construed as if such invalid, illegal or unenforceable provisions had never been contained herein, unless the deletion of such provision or provisions would result in such a material change so as to cause completion of the transactions contemplated herein to be unreasonable.



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ARTICLE XX: FORCE MAJEURE

Performer shall not be liable for delays or non-performance hereunder if such delay or non-performance is from causes beyond the control and without the fault or negligence of the Performer or its subcontractors, and is due, directly, to fire or other casualty; act of God; strike or labor dispute; war or other violence, or to acts of the Government in either its sovereign or contractual capacity.



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Agreement No. HR0011-12-3-0006 Attachment 1

Amyris, Inc.

Statement of Work

For

Living Foundries

Improving DNA Assembly and Integration Across Platforms with Better Systems and Tools

30 May 2012

(Amended through 25 October 2013)

Advanced Tools and Capabilities for Generalizable Platforms (ATCG) Program Background

Current approaches to engineering biology rely on an ad hoc, laborious, trial-and-error process, wherein one successful project often does not translate to enabling subsequent new designs. As a result, the state of the art development cycle for engineering a new biologically manufactured product often takes 7+ years and tens to hundreds of millions of dollars (e.g. microbial production of artemisinic acid for the treatment of malaria and the non-petroleum-based production 1, 3-propanediol). The impact of current approaches is two-fold. First, the number of new entrants and innovators into the biomanufacturing space is immediately limited – few have the expertise, capital and/or time necessary to develop and engineer a new product. Second, combined with the complexity of biological systems, an ad hoc approach results in one-off efforts limited to modifying only a small set of genes and constructing simple, isolated genetic circuits and metabolic pathways. Consequently, while progress has been made, industry is constrained to producing only a tiny fraction of the vast number of possible chemicals, materials, and functional systems that would be enabled by the ability to truly engineer biology. A new approach is needed.

This new approach is Living Foundries: develop and apply an engineering framework to biology that decouples biological design from fabrication, yields design rules and tools, and manages biological complexity through abstraction and standardization. One analogy is that Living Foundries aims to do for biological design what verylarge-scale integration (VLSI) did for integrated circuits. Applying an engineering framework to biology will remove barriers to researchers outside the biological sciences, bringing diverse expertise and new methods to biological design. The best innovations will introduce new architectures and tools that will form the foundational technology for engineering biology.

The vision of Living Foundries is one where new and multiple cellular functions are readily constructed, combined, and controlled by an integrated genetic circuitry. The ultimate effect of which will be to open up the full space of biologically produced materials and systems. To achieve this, new tools, technologies and methodologies that directly address our current limitations and expand our capabilities must be developed. The outcome should be an open technology platform that integrates these tools and capabilities, allowing new designs to rapidly move from conception to execution.

Advanced Tools and Capabilities for Generalizable Platforms, (ATCG) seeks translatable tools that can serve as parts of an “end-to-end platform” to support rapid, specific in its goals: DARPA seeks new technology to enable low-cost and rapid DNA synthesis and assembly, especially to shorten the design-test cycle surrounding the ambitious constructs that characterize the broadest visions in modern synthetic biology.

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Agreement No. HR0011-12-3-0006 Attachment 1

Research Tasks

Task A

[*]

Task A. [*] (Jed Dean, Amyris)

Task Objective :[*]

[*]

Milestone:[*]

Metrics/Completion Criteria :[*]

Deliverables : [*]

Subtask A.1 . [*]

[*]

Subtask A.2. [*]

[*]

Subtask A.3. [*]

[*]

This subtask completes the Milestone outlined above.

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Agreement No. HR0011-12-3-0006 Attachment 1

Task C

[*]

Task C.[*] (Sunil Chandran, Amyris)

Task Objective: [*]

[*]

Phase I

Milestone: [*]

Metrics/Completion Criteria : [*]

Deliverable : [*]

Subtask C.1 [*]

[*]

Subtask C.2 [*]

[*]

Subtask C.3 [*]

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Agreement No. HR0011-12-3-0006 Attachment 1

[*]

Subtask C.4 [*]

[*]

This subtask completes the Milestone outlined above.

Phase II

Milestone (CIIa) : [*]

Metrics/Completion Criteria : [*]

Subtask C.5 [*]

[*]

Subtask C.6 [*]

[*]

These subtasks complete the Milestone outlined above.

Milestone (CIIb):[*]

Metrics/Completion Criteria : [*]

Deliverable : [*]

Subtask C.7 [*]

[*]

Milestone (CIIc): [*]

Metrics/Completion Criteria : [*]

Deliverable : [*]

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Agreement No. HR0011-12-3-0006 Attachment 1

Subtask C.8 [*]

[*]

Task D

[*}

Task D. [*] (Sunil Chandran, Amyris)

Task Objective : [*]

Phase I

Milestone: [*]

Metrics/Completion Criteria : [*]

Deliverable : [*]

Subtask D.1 [*]

Subtask D.2 [*]

[*]

Subtask D.3 [*]

[*]

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Agreement No. HR0011-12-3-0006 Attachment 1

Subtask D.4 [*]

[*]

This subtask completes the Milestone outlined above.

Phase II

Milestone (DIIa):[*]

Metrics/Completion Criteria : [*]

Subtask D.5 [*]

[*]

Subtask D.6 [*]

[*]

This subtask completes the Milestone outlined above.

Milestone (DIIb) : [*]

Metrics/Completion Criteria : [*]

Deliverables : [*]

Subtask D.7 [*]

[*]

Subtask D.8 [*]

[*]

This subtask completes the Milestone outlined above.

Task E

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Agreement No. HR0011-12-3-0006 Attachment 1

[*]

Task E. [*] (Sunil Chandran, Amyris)

Task Objective : [*]

Phase IA

Milestone: []

Metrics/Completion Criteria : [*]

Deliverable : [*]

Subtask E.1. [*]

This subtask completes the Milestone outlined above.

Phase IB

Milestone: [*]

Metrics/Completion Criteria : [*]

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Agreement No. HR0011-12-3-0006 Attachment 1

Deliverable : [*]

Subtask E.3 [*]

[*]

This subtask completes the Milestone outlined above.

Phase II

Milestone (EIIa) : [*]

Metrics/Completion Criteria : [*]

Deliverable : [*]

Subtask E.5 [*]

[*]

This subtask completes the Milestone outlined above.

Milestone (EIIb) : [*]

Metrics/Completion Criteria : [*]

Deliverable : [*]

Subtask E.6 [*]

[*]

This subtask completes the Milestone outlined above.

Milestone (EIIc) : [*]

Metrics/Completion Criteria : [*]

Deliverable : [*]

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Agreement No. HR0011-12-3-0006 Attachment 1

Subtask E.7 [*]

[*]

Subtask E.8 [*]

[*]

This subtask completes the Milestone outlined above.

Task F

Task F. [*] (Sunil Chandran, Amyris)

Task objective : [*]

Phase II

Milestone: [*]

Metrics/Completion Criteria : [*]

[*]

Deliverable : [*]

Subtask F.1. [*]

[*]

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Agreement No. HR0011-12-3-0006 Attachment 1

[*]

Subtask F.2. [*]

[*]

This subtask completes the Milestone outlined above.

Task G (Bio-safety/Security)

Task Background : The research and engineering depicted in this Statement of Work seeks to make existing capabilities (e.g. genetic modification of microbes to produce commodity chemicals) more efficient with the intended purpose of speeding the development of Living Foundries. The goal of this research is to make better engineering tools, and not to produce microbes that may have Dual-Use potential. As noted in the performer’s technical proposal, a review of the research activities identified within this Statement of Work determined that this project will not enable technologies that are related to human, animal, or plant health. The performer’s choice of potential chassis or hosts will be made from amongst the list of microbes that, prior to genetic modification, are designated safely handled in a Biosafety Level 1 facility. Additionally, the resulting genetically modified organisms have no selective advantage in the environment.

Metrics/Completion Criteria: The performer shall demonstrate throughout the program that all methods and demonstrations of capability comply with national guidance for manipulation of genes and organisms and follow all guidance for biological safety and biosecurity. Demonstrations and testbeds must meet any applicable regulations designed to protect human health and the environment promulgated by the Environmental Protection Agency, National Institutes of Health, or other relevant agencies of the Federal Government. The performer shall use, store, and destroy biological material in accordance with all applicable regulations.

Deliverable: Include as part of the required monthly technical status reports an on-going status of efforts to develop and/or carry out their Advanced Tools and Capabilities for Generalizable Platforms (ATCG) Bio-Safety and Security plan.

Task H (Intellectual Property and Data Sharing)

Task Background : It is the goal of the Defense Advanced Research Projects Agency (DARPA) that its investment in the tools and capabilities developed under the ATCG program to be multiplied many-fold by adoption and improvement by researchers across the United States. In order to achieve this vision, the Living Foundries program aims to facilitate interoperability and open the field to new entrants.

Metrics/Completion Criteria : To facilitate interoperability, all applicable design tools and databases developed under the ATCG program should be compatible with Synthetic Biology Open Language (SBOL) core data model. The Performer shall make available the technologies developed under the ATCG effort to the broader synthetic biology community by presenting its ATCG research data at public meetings/conferences/workshops and publishing results in peer-reviewed journal articles. At a minimum, the types of information that will be made available to the broader synthetic biology community are as discussed below:

(i) Data and analysis necessary to evaluate the utility of the technologies, as well as standard operating procedures and design specifications enabling others to reconstitute the equipment, set up, and approaches developed.

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Agreement No. HR0011-12-3-0006 Attachment 1

(ii) The results of Design of Experiment work to arrive at the conditions for the best performance for untested or early stage technologies, describing the correlation between:


•	DNA ligase cycling parameters and the complexity, size, and success rate of the assembled full length DNA constructs.


•	Reaction parameters and the success and cost of performing sequencing QC on DNA assemblies.


•	Designer nuclease number, type, and targeting site and the integration efficiency in to the chassis genome.

(iii) Details required for both technical evaluation and transfer, including: full protocols, technical drawings of equipment built and specifications met, data on accuracy and precision of these systems, and results on procedures performed against large number of samples to investigate the robustness and readiness of the approaches for broader distribution – providing a trained reader with the information needed to recapitulate the methods and results described. In addition, the Principal Investigator shall be available to consult with third parties seeking to replicate the results.

If the work performed under this Statement of Work results in one or more patents, the Performer shall grant licenses on a royalty-free basis to academic and non-profit institutions. Additionally, the Performer shall make licenses available to commercial entities outside its key business areas.

Deliverable/s : The Performer shall include as part of required monthly technical status reports an on-going status of efforts to develop and/or carry out their proposed ATCG Intellectual Property and Data Sharing plan. Reporting shall include a summary of data sharing activities that have taken place during the reporting period and any data sharing activities planned to take place within three months of the reporting period. Reporting shall include a listing of the performers Subject Invention disclosures, Subject Invention patent applications and a brief discussion summarizing plans, if any, to license the resulting technology (e.g., intent and rationale regarding whether the performer intends to seek non-exclusive licensing, exclusive licensing for a particular field of use, or exclusive licensing across the board, etc.).

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Agreement No. HR0011-12-3-0006 Attachment 2

ATTACHMENT 2:

REPORT REQUIREMENTS

A. TECHNICAL STATUS REPORT

On or before sixty (60) calendar days after the effective date of the Agreement and monthly thereafter throughout the term of the Agreement, the Performer shall submit, via email, a monthly Technical Status Report to the DARPA Program Manager, DARPA Agreements Officer, Agreement Officer’s Representative (AOR), and DARPA/ADPM. The technical status report will detail technical progress to date and report on all problems, technical issues, major developments, and the status of external collaborations during the reporting period. Technical Status Reports shall be marked with Distribution Statement B:

“ DISTRIBUTION STATEMENT B . Distribution authorized to U.S. Government agencies only due to the inclusion of proprietary information. Other requests for this document shall be referred to DARPA Public Release Center (PRC) via email at PRC@darpa.mil.”

B. BUSINESS STATUS REPORT

On or before ninety (90) calendar days after the effective date of the Agreement and quarterly thereafter throughout the term of the Agreement, the Performer shall submit, via email, a quarterly Business Status Report to the DARPA Program Manager, DARPA Agreements Officer, Agreement Officer’s Representative (AOR), and DARPA/ADPM. The business status report shall provide summarized details of the resource status of this Agreement, including the status of the Performer’s contributions. This report will include a quarterly accounting of current expenditures as outlined in the Annual Program Plan. Any major deviations, over plus or minus 10%, shall be explained along with discussions of the adjustment actions proposed. The report will also include an accounting of any interest earned on Government funds. The Performer is reminded that interest in amounts greater than $250 per year is not expected to accrue under this Agreement. In the event that this interest does accrue on Government funds, the Performer is required to provide an explanation for the accrual in the business report. Depending on the circumstances, the Payable Milestones may require adjustment. Business Status Reports shall be marked with Distribution Statement B:

“ DISTRIBUTION STATEMENT B . Distribution authorized to U.S. Government agencies only due to the inclusion of proprietary information. Other requests for this



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Agreement No. HR0011-12-3-0006 Attachment 2

document shall be referred to DARPA Public Release Center (PRC) via email at PRC@darpa.mil.

C. ANNUAL PROGRAM PLAN DOCUMENT

The Performer shall submit via email or otherwise provide to the DARPA Agreements Officer’s Representative, DARPA Program Manager and DARPA Agreements Officer one (1) copy each of a report which describes the Annual Program Plan as described in Article III, Section B. This document shall be submitted not later than thirty (30) calendar days following the Annual Site Review as described in Article III, Section B. Annual Program Plans shall be marked with Distribution Statement B:

D. SPECIAL TECHNICAL REPORTS

The Performer shall submit via email or otherwise provide to the DARPA Agreements Officer’s Representative, the DARPA Program Manager and DARPA Agreements Officer one (1) copy each of special technical reports on significant events such as significant target accomplishments by the Performer, significant tests, experiments, or symposia, as discussed in the Attachment No. 1 Statement of Work. Special Technical Reports shall be marked with Distribution Statement B:

E. SCIENTIFIC PAPERS

The performer shall publish scientific papers in accordance with the Attachment No. Statement of Work. One (1) copy of each published scientific paper shall be submitted via email or otherwise provided to the DARPA Agreements Officer’s Representative, DARPA Program Manager, and DARPA Agreements Officer. Scientific Papers shall be marked with Distribution Statement A:



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Agreement No. HR0011-12-3-0006 Attachment 2

"Approved for public release; distribution is unlimited.”

E. PAYABLE MILESTONES REPORTS

The Performer shall submit via email or otherwise provide to the DARPA Agreements Officer’s Representative, the DARPA Program Manager and DARPA Agreements Officer documentation describing the extent of accomplishment of Payable Milestones. This information shall be as required by Article V, paragraph B and shall be sufficient for the DARPA Agreements Officer’s Representative to reasonably verify the accomplishment of the milestone in accordance with the Attachment No. 1 Statement of Work and Attachment No. 3 Payable Milestone Plan. Payable Milestone Reports shall be marked with Distribution Statement B:

F. FINAL REPORT (NOTE: The Final Report is included in the last Payable Milestone for the completed Agreement)

1. The Performer shall submit or otherwise provide a Final Report making full disclosure of all major developments by the Performer upon completion of the Agreement or within sixty (60) calendar days of termination of this Agreement. With the approval of the DARPA Agreements Officer’s Representative, reprints of published articles may be attached to the Final Report. The Final Report shall be submitted via email to the DARPA Program Manager, DARPA Agreements Officer, Agreement Officer’s Representative (AOR), DARPA/ADPM, and the Defense Technical Information Center.

2. The Final Report shall be marked with a distribution statement to denote the extent of its availability for distribution, release, and disclosure without additional approvals or authorizations. The Final Report shall be marked on the front page in a conspicuous place with the following marking:



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Agreement No. HR0011-12-3-0006 Attachment 2

G. FINAL REPORT MARKINGS

(1) The cover or title page of each of the above reports or publications prepared, will have the following citation:

Sponsored by

Defense Advanced Research Projects Agency

Microsystems Technology Office (MTO)

Program: Living Foundries

Issued by DARPA/CMO under Agreement No. HR0011-12-3-0006

(2) The title page shall include a disclaimer worded substantially as follows:

“The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressly or implied, of the Defense Advanced Research Projects Agency or the U.S. Government.”

(3) The Final Report shall include a Standard Form 298, August 1998.

(4) All reports shall be marked with the below Distribution Statement and Data Rights statements:

(a) Distribution Statement designations are listed above for each individual type of report.

(b) Government Purpose Rights.

“GOVERNMENT PURPOSE RIGHTS

Agreement Number: HR0011-12-3-0006

Contractor Name: Amyris, Inc.”

In accordance with Article VIII, as applicable, contained in the above identified Agreement, the Government has the right to use, duplicate, or disclose Data, in whole or in part and in any manner, for Government purposes only, and to have or permit others to do so for Government purposes only.”



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Agreement No. HR0011-12-3-0006 Attachment 2

“LIMITED RIGHTS

Agreement Number: HR0011-12-3-0006

Contractor Name: Amyris, Inc.”

In accordance with Article VIII, as applicable, contained in the above identified

Agreement, the Government has the right to use, modify, reproduce, release, perform,

display, or disclose Data, in whole or in part, within the Government. The Government

may not, without the written permission of the party asserting limited rights, release or

disclose the Data outside the Government.

H. EXECUTIVE SUMMARY

The Performer shall submit a one to two page executive-level summary of the major

accomplishments of the Agreement and the benefits of using the “other transactions”

authority pursuant to 10 U.S.C. § 2371 upon completion of the Agreement. This

summary shall include a discussion of the actual or planned benefits of the technologies

for both the military and commercial sectors. Two (2) copies shall be submitted to the

DARPA Agreements Officer.



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MILESTONE	Task	Month	Payable Milestones	Exit Criteria	Performer Payment	DARPA Payment	SUBLCIN/ ACRN
	Phase I
1	[*]	[*]	[*]	[*]	[*]	[*]	00101/AA
2	[*]	[*]	[*]	[*]	[*]	[*]	00201/AA
3	[*]	[*]	[*]	[*]	[*]	[*]	00301/AA
4	[*]	[*]	[*]	[*]	[*]	[*]	00401/AA
5	[*]	[*]	[*]	[*]	[*]	[*]	00501/AA
Total					$335,834	$3,022,501
	Phase 2
6	[*]	[*]	[*]	[*]	[*]	[*]	00601/AB
7	[*]	[*]	[*]	[*]	[*]	[*]	00701/AB
8	[*]	[*]	[*]	[*]	[*]	[*]	00801/AB
[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.



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9	[*]	[*]	[*]	[*]	[*]	[*]	00901/AB
10	[*]	[*]	[*]	[*]	[*]	[*]	01001/AB
11	[*]	[*]	[*]	[*]	[*]	[*]
12	[*]	[*]	[*]	[*]	[*]	[*]
13	[*]	[*]	[*]	[*]	[*]	[*]
14	[*]	[*]	[*]	[*]	[*]	[*]
15	[*]	[*]	[*]	[*]	[*]	[*]
Total					$514,645	$4,631,808
	Phase 1 & Phase 2
Total					$850,479	$7,654,309



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Agreement No. HR0011-12-3-0006 Attachment 4

ATTACHMENT 4:

FUNDING SCHEDULE

A. PROJECTED PROGRAM FUNDING COMMITMENTS



	DARPA Performer	Funding Contribution
Base (Phase I)

FY 12 (At time of award)	$3,595,518	$399,501
FY 13 (on or about November 2012)	$370,411	$41,158
Modification P00007 Reduction	($943,428)	($104,825)

Phase 1 Totals	$3,022,501	$335,834

Option (Phase 2)

FY 13 (At time of Exercise)	$2,079,497	$231,055
FY 13 ( Modification P00008)	$552,931	$61,437
FY 14 (On or about January 2014 )	$552,931	$61,437

Phase 2 Totals	$4,631,808	$514,645

AGREEMENT TOTALS	$7,654,309	$850,479

DARPA funding shall be applied toward the following expenses: Direct labor, to include indirect costs thereof, and direct materials/equipment purchases, to include indirect costs thereof, as included in Amyrsis’s Living Foundries proposal dated 3 May 2012 (as amended).

B. PERFORMER CONTRIBUTION



	Total Contribution	Cash*	In-kind**

Phase 1	$335,834	$335,834	$0
Phase 2	$514,645	$514,645	$0

Total	$850,479	$850,479	$0

* Cash contributions consist of: Direct labor, to include indirect costs thereof, and direct materials/equipment purchases, to include indirect costs thereof, as included in Amyrsis’s Living Foundries proposal dated 3 May 2012 (as amended). The aforementioned are considered cash contributions made by Amyris in support of the Living Foundries research program.

** In-kind contributions consist of: N/A



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Agreement No. HR0011-12-3-0006		Attachment 5

List of Intellectual Property Assertions



Technical Data Computer Software to be Furnished with Restrictions	Basis for Assertion	Asserted Rights Category	Name of Person Asserting Restrictions
Production of Isoprenoids, Application US 11/754,235, Patent No. US 7,659,097 (US 20080274523)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Production of Isoprenoids, ApplicationUS 12/638,771, Patent No. (US2011/0287476)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Production of Isoprenoids, Application PCT/US2007/069807, Patent No. (WO2007/140339)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Nucleic Acids, Compositions and Methods for the Excision of Target Nucleic Acids, Application US 12/978,061, Patent No. US 7,919,605	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Nucleic Acids, Compositions and Methods for the Excision of Target Nucleic Acids, Application US 13/220,553, Patent No. (US 2012/0052582)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Nucleic Acids, Compositions and Methods for the Excision of Target Nucleic Acids, Application PCT/US2011/049615, Patent No. (WO 2012/030747)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Compositions and Methods for the Rapid Assembly of Polynucleotides, Developed exclusively at private expense Application US 12/622,401, Patent No. (US 2010/0136633)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
Compositions and Methods for the Rapid Assembly of Polynucleotides, Application US 12/684,874, Patent No. US 8,110,360 (US 2010/0124768)	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.



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Agreement No. HR0011-12-3-0006		Attachment 5



Technical Data Computer Software to be Furnished with Restrictions	Basis for Assertion	Asserted Rights Category	Name of Person Asserting Restrictions
[*]
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Developed exclusively at private expense	Restricted Rights	Amyris, Inc.
[*]	Software suites were developed exclusively with private funding.	Limited Rights	Amyris, Inc.
[*]	Software suites were developed exclusively with private funding	Limited Rights	Amyris, Inc.
[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.



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Agreement No. HR0011-12-3-0006		Attachment 5



Technical Data Computer Software to be Furnished with Restrictions	Basis for Assertion	Asserted Rights Category	Name of Person Asserting Restrictions
[*]

[*]	Amyris has generated extensive information related to the isoprenoid pathways which will be used as a benchmark to assess performance of this proposal but the underlying comparative data was developed exclusively with private funding.	Restricted Rights	Amyris, Inc.



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ASSISTANCE AGREEMENT

1. Award No.

DE-EE0002869

2. Modification No.

003

3. Effective Date

12/28/2009

4. CFDA No.

81.087

5. Awarded To

AMYRIS BIOTECHNOLOGIES, INC.

Attn: KINKEAD REILING

5885 HOLLIS STREET

SUITE 100

EMERYVILLE CA 946082059

6. Sponsoring Office

Golden Field Office

U.S. Department of Energy

Golden Field Office

1617 Cole Blvd.

Golden CO 80401

7. Period of Performance

12/28/2009

through

06/30/2012

8. Type of Agreement

_ Grant

x Cooperative Agreement

_ Other

9. Authority

109-58 Energy Policy Act (2005)

111-5 Recovery Act (2009)

10. Purchase Request or Funding Document No.

10EE005822

11. Remittance Address

12. Total Amount

13. Funds Obligated

AMYRIS BIOTECHNOLOGIES, INC.

Attn: KINKEAD REILING

5885 HOLLIS STREET

SUITE 100

EMERYVILLE CA 946082059

Govt. Share: $ 24,341,409.00

Cost Share: $ 10,591,590.00

Total: $ 34,932,999.00

This action: $0.00

Total: $24,341,409.00

14. Principal Investigator

Neil Renninger

Phone: 510-740-7414

15. Program Manager

Fred W. Gerdeman

Phone: 303-275-4928

16. Administrator

Golden Field Office

U.S. Department of Energy

Golden Field Office

1617 Cole Blvd.

Golden CO 80401-3393

17. Submit Payment Requests To

OR for Golden

U.S. Department of Energy

Oak Ridge Financial Service Center

P.O. Box 4517

Oak Ridge TN 37831

18. Paying Office

OR for Golden

U.S. Department of Energy

Oak Ridge Financial Service Center

P.O. Box 4517

Oak Ridge TN 37831

19. Submit Reports To

20. Accounting and Appropriation Data

See Schedule

21. Research Title and/or Description of Project

RECOVERY ACT: SCALE-UP & MOBILIZATION OF RENEWABLE DIESEL & CHEMICAL PRODUCTION FROM COMMON INTERMEDIATE USING US-BASED FERMENTABLE SUGAR FEEDSTOCKS

For the Recipient

For the United States of America

22. Signature of Person Authorized to Sign

25. Signature of Grants/Agreements Officer

Signature on File

23. Name and Title

24. Date Signed

26. Name of Officer

Jon F. Olsen

27. Date Signed

07/02/2010



CONTINUATION SHEET		REFERENCE NO. OF DOCUMENT BEING CONTINUED DE-EE0002869/003			PAGE 2 OF 2

NAME OF OFFEROR OR CONTRACTOR AMYRIS BIOTECHNOLOGIES, INC.

ITEM NO. (A)	SUPPLIES/SERVICES (B)	QUANTITY (C)	UNIT (D)	UNIT PRICE (E)	AMOUNT (F)
	DUNS Number: 185930182 The purpose of this modification is to: 1) Update the DOE Project Officer, as shown below and in Block 15. All other terms and conditions remain unchanged. In Block 7 of the Assistance Agreement, the Period of Performance reflects the beginning of the Project Period through the end of the current Budget Period, shown as 12/28/2009 through 6/30/2012. DOE Award Administrator: Brenda Dias E-mail: brenda.dias@go.doe.gov Phone: 303-275-6043 DOE Project Officer: Fred Gerdeman E-mail: fred.gerdeman@go.doe.gov Phone: 303-275-4928 Recipient Business Officer: Todd Pray E-mail: pray@amyris.com Phone: 510-740-7441 Recipient Principal Investigator: Neil Renninger E-mail: renninger@amyris.com Phone: 510-740-7414 “Electronic signature or signatures as used in this document means a method of signing an electronic message that-- (A) Identifies and authenticates a particular person as the source of the electronic message; (B) Indicates such person's approval of the information contained in the electronic message; and, (C) Submission via FedConnect constitutes electronically signed documents.” ASAP: NO Extent Competed: COMPETED Davis-Bacon Act: YES
JULY 2004

ASSISTANCE AGREEMENT

1. Award No.

DE-EE0002869

2. Modification No.

004

3. Effective Date

12/28/2009

4. CFDA No.

81.087

5. Awarded To

AMYRIS BIOTECHNOLOGIES, INC.

Attn: KINKEAD REILING

5885 HOLLIS STREET

SUITE 100

EMERYVILLE CA 946082059

6. Sponsoring Office

Golden Field Office

U.S. Department of Energy

Golden Field Office

1617 Cole Blvd.

Golden CO 80401

7. Period of Performance

12/28/2009

through

06/30/2012

8. Type of Agreement

_ Grant

x Cooperative Agreement

_ Other

9. Authority

109-58 Energy Policy Act (2005)

111-5 Recovery Act (2009)

10. Purchase Request or Funding Document No.

11. Remittance Address

12. Total Amount

13. Funds Obligated

AMYRIS BIOTECHNOLOGIES, INC.

Attn: KINKEAD REILING

5885 HOLLIS STREET

SUITE 100

EMERYVILLE CA 946082059

Govt. Share: $ 24,341,409.00

Cost Share: $ 10,591,590.00

Total: $ 34,932,999.00

This action: $0.00

Total: $24,341,409.00

14. Principal Investigator

Neil Renninger

Phone: 510-740-7414

15. Program Manager

Fred W. Gerdeman

Phone: 303-275-4928

16. Administrator

Golden Field Office

U.S. Department of Energy

Golden Field Office

1617 Cole Blvd.

Golden CO 80401-3393

17. Submit Payment Requests To

OR for Golden

U.S. Department of Energy

Oak Ridge Financial Service Center

P.O. Box 4517

Oak Ridge TN 37831

18. Paying Office

OR for Golden

U.S. Department of Energy

Oak Ridge Financial Service Center

P.O. Box 4517

Oak Ridge TN 37831

19. Submit Reports To

20. Accounting and Appropriation Data

See Schedule

21. Research Title and/or Description of Project

RECOVERY ACT: SCALE-UP & MOBILIZATION OF RENEWABLE DIESEL & CHEMICAL PRODUCTION FROM COMMON INTERMEDIATE USING US-BASED FERMENTABLE SUGAR FEEDSTOCKS

For the Recipient

For the United States of America

22. Signature of Person Authorized to Sign

25. Signature of Grants/Agreements Officer

Signature on File

23. Name and Title

24. Date Signed

26. Name of Officer

Lalida Crawford

27. Date Signed

12/27/2010



CONTINUATION SHEET		REFERENCE NO. OF DOCUMENT BEING CONTINUED DE-EE0002869/004			PAGE 2 OF 2

NAME OF OFFEROR OR CONTRACTOR AMYRIS BIOTECHNOLOGIES, INC.

ITEM NO. (A)	SUPPLIES/SERVICES (B)	QUANTITY (C)	UNIT (D)	UNIT PRICE (E)	AMOUNT (F)
	DUNS Number: 185930182 The purpose of this modification is to: 1) Assign a Technical Project Monitor/Engineer to the award. All other terms and conditions remain unchanged. In Block 7 of the Assistance Agreement, the Period of Performance reflects the beginning of the Project Period through the end of the current Budget Period, shown as 12/28/2009 through 6/30/2012. DOE Award Administrator: Brenda Dias E-mail: brenda.dias@go.doe.gov Phone: 303-275-6043 DOE Project Officer: Fred Gerdeman E-mail: fred.gerdeman@go.doe.gov Phone: 303-275-4928 Recipient Business Officer: Todd Pray E-mail: pray@amyris.com Phone: 510-740-7441 Recipient Principal Investigator: Neil Renninger E-mail: renninger@amyris.com Phone: 510-740-7414 “Electronic signature or signatures as used in this document means a method of signing an electronic message that-- (A) Identifies and authenticates a particular person as the source of the electronic message; (B) Indicates such person's approval of the information contained in the electronic message; and, (C) Submission via FedConnect constitutes electronically signed documents.” ASAP: NO Extent Competed: COMPETED Davis-Bacon Act: YES
JULY 2004

ASSISTANCE AGREEMENT

1. Award No.

DE-EE0002869

2. Modification No.

005

3. Effective Date

12/28/2009

4. CFDA No.

81.087

5. Awarded To

AMYRIS BIOTECHNOLOGIES, INC.

Attn: KINKEAD REILING

5885 HOLLIS STREET

SUITE 100

EMERYVILLE CA 946082059

6. Sponsoring Office

Golden Field Office

U.S. Department of Energy

Golden Field Office

1617 Cole Blvd.

Golden CO 80401

7. Period of Performance

12/28/2009

through

06/30/2012

8. Type of Agreement

_ Grant

x Cooperative Agreement

_ Other

9. Authority

109-58 Energy Policy Act (2005)

111-5 Recovery Act (2009)

10. Purchase Request or Funding Document No.

11EE002648

11. Remittance Address

12. Total Amount

13. Funds Obligated

AMYRIS BIOTECHNOLOGIES, INC.

Attn: KINKEAD REILING

5885 HOLLIS STREET

SUITE 100

EMERYVILLE CA 946082059

Govt. Share: $ 24,341,409.00

Cost Share: $ 10,591,590.00

Total: $ 34,932,999.00

This action: $0.00

Total: $24,341,409.00

14. Principal Investigator

Neil Renninger

Phone: 510-740-7414

15. Program Manager

Fred W. Gerdeman

Phone: 303-275-4928

16. Administrator

Golden Field Office

U.S. Department of Energy

Golden Field Office

1617 Cole Blvd.

Golden CO 80401-3393

17. Submit Payment Requests To

OR for Golden

U.S. Department of Energy

Oak Ridge Financial Service Center

P.O. Box 4517

Oak Ridge TN 37831

18. Paying Office

OR for Golden

U.S. Department of Energy

Oak Ridge Financial Service Center

P.O. Box 4517

Oak Ridge TN 37831

19. Submit Reports To

20. Accounting and Appropriation Data

See Schedule

21. Research Title and/or Description of Project

RECOVERY ACT: SCALE-UP & MOBILIZATION OF RENEWABLE DIESEL & CHEMICAL PRODUCTION FROM COMMON INTERMEDIATE USING US-BASED FERMENTABLE SUGAR FEEDSTOCKS

For the Recipient

For the United States of America

22. Signature of Person Authorized to Sign

25. Signature of Grants/Agreements Officer

Signature on File

23. Name and Title

24. Date Signed

26. Name of Officer

Lalida Crawford

27. Date Signed

03/22/2011



CONTINUATION SHEET		REFERENCE NO. OF DOCUMENT BEING CONTINUED DE-EE0002869/005			PAGE 2 OF 2

NAME OF OFFEROR OR CONTRACTOR AMYRIS BIOTECHNOLOGIES, INC.

ITEM NO. (A)	SUPPLIES/SERVICES (B)	QUANTITY (C)	UNIT (D)	UNIT PRICE (E)	AMOUNT (F)
	DUNS Number: 185930182 The purpose of this modification is to delete and replace the Special Terms and Conditions to incorporate Provision 31, "National Environmental Policy Act (NEPA) Requirements." All other terms and conditions remain unchanged. In Block 7 of the Assistance Agreement, the Period of Performance reflects the beginning of the Project Period through the end of the current Budget Period, shown as 12/28/2009 through 6/30/2012. For multiple Budget Periods, see Special Terms and Conditions, Provision 4, Award Project Period and Budget Periods. DOE Award Administrator: Brenda Dias E-mail: brenda.dias@go.doe.gov Phone: 303-275-6043 DOE Project Officer: Fred Gerdeman E-mail: fred.gerdeman@go.doe.gov Phone: 303-275-4928 Recipient Business Officer: Todd Pray E-mail: pray@amyris.com Phone: 510-740-7441 Recipient Principal Investigator: Neil Renninger E-mail: renninger@amyris.com Phone: 510-740-7414 “Electronic signature or signatures as used in this document means a method of signing an electronic message that-- (A) Identifies and authenticates a particular person as the source of the electronic message; (B) Indicates such person's approval of the information contained in the electronic message; and, (C) Submission via FedConnect constitutes electronically signed documents.” ASAP: NO Extent Competed: COMPETED Davis-Bacon Act: YES
JULY 2004

SPECIAL TERMS AND CONDITIONS

Table of Contents


Number	Subject Page


1.	RESOLUTION OF CONFLICTING CONDITIONS 2


2.	AWARD AGREEMENT TERMS AND CONDITIONS 2


3.	ELECTRONIC AUTHORIZATION OF AWARD DOCUMENTS 2


4.	AWARD PROJECT PERIOD AND BUDGET PERIODS 2


5.	PAYMENT PROCEDURES 3


6.	COST SHARING 4


7.	REBUDGETING AND RECOVERY OF INDIRECT COSTS 4


8.	FINAL INCURRED COST AUDIT 5


9.	STATEMENT OF FEDERAL STEWARDSHIP 5


10.	STATEMENT OF SUBSTANTIAL INVOLVEMENT 5


11.	SITE VISITS 6


12.	REPORTING REQUIREMENTS 6


13.	PUBLICATIONS 7


14.	FEDERAL, STATE, AND MUNICIPAL REQUIREMENTS 8


15.	INTELLECTUAL PROPERTY PROVISIONS AND CONTACT INFORMATION 8


16.	NATIONAL SECURITY: CLASSIFIABLE RESULTS ORIGINATING UNDER AN AWARD 8


17.	LOBBYING RESTRICTIONS 9


18.	NOTICE REGARDING THE PURCHASE OF AMERICAN-MADE EQUIPMENT

AND PRODUCTS -- SENSE OF CONGRESS 9


19.	PROPERTY 9


20.	DECONTAMINATION AND/OR DECOMMISSIONING (D&D) COSTS 10


21.	INSOLVENCY, BANKRUPTCY OR RECEIVERSHIP 10


22.	INDEMNITY 11


23.	SPECIAL PROVISIONS RELATING TO WORK FUNDED UNDER AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009 (May 2009) 11


24.	REPORTING AND REGISTRATION REQUIREMENTS UNDER SECTION 1512

OF THE RECOVERY ACT 15


25.	REQUIRED USE OF AMERICAN IRON, STEEL, AND MANUFACTURED

GOODS - SECTION 1605 OF THE AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009 16


26.	REQUIRED USE OF AMERICAN IRON, STEEL, AND MANUFACTURED

GOODS (COVERED UNDER INTERNATIONAL AGREEMENTS) - SECTION

1605 OF THE AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009 19


27.	RECOVERY ACT TRANSACTIONS LISTED IN SCHEDULE OF EXPENDITURES OF FEDERAL AWARDS AND RECIPIENT RESPONSIBILITIES FOR

INFORMING SUBRECIPIENTS 22


28.	WAGE RATE REQUIREMENTS UNDER SECTION 1606 OF THE RECOVERY ACT 23


29.	DAVIS BACON ACT AND CONTRACT WORK HOURS AND SAFETY

STANDARDS ACT 24


30.	CONTINGENCY 34


31.	NATIONAL ENVIRONMENTAL POLICY ACT (NEPA) REQUIREMENTS 35


1.	RESOLUTION OF CONFLICTING CONDITIONS

Any apparent inconsistency between Federal statutes and regulations and the terms and conditions contained in this award must be referred to the DOE Award Administrator for guidance.


2.	AWARD AGREEMENT TERMS AND CONDITIONS

This award/agreement consists of the Assistance Agreement, plus the following:


a.	Special Terms and Conditions.


b.	Attachments:

Attachment Number Title

1. Intellectual Property Provisions

2. Statement of Project Objectives

3. Federal Assistance Reporting Checklist and Instructions

4. Budget Pages (SF 424A)

5. Requirements for Contingency Funds for Integrated Biorefinery

Projects


c.	Applicable program regulations.


d.	DOE Assistance Regulations, 10 CFR Part 600 at http://ecfr.gpoaccess.gov .


e.	If the award is for research and the award is for a university or non-profit, the Research Terms & Conditions and the DOE Agency Specific Requirements at http://www.nsf.gov/bfa/dias/policy/rtc/index.jsp apply.


f.	Application/proposal as approved by DOE.


g.	National Policy Assurances to be incorporated as award terms in effect on date of award at http://management.energy.gov/business_doe/1374.htm .


3.	ELECTRONIC AUTHORIZATION OF AWARD DOCUMENTS

Acknowledgement of award documents by the Recipient's authorized representative through electronic systems used by the Department of Energy, specifically FedConnect, constitutes the Recipient's acceptance of the terms and conditions of the award. Acknowledgement via FedConnect by the Recipient's authorized representative constitutes the Recipient's electronic signature.


4.	AWARD PROJECT PERIOD AND BUDGET PERIODS

The Project Period for this award is 12/28/2009 through 6/30/2012, consisting of the following Budget Periods:



Budget Period	Start Date	End Date
1	12/28/2009	4/21/2010
2	4/22/2010	6/30/2012


5.	PAYMENT PROCEDURES


a.	Method of Payment . Payment will be made by reimbursement through ACH.


b.	Requesting Reimbursement . Requests for reimbursements must be made electronically through Department of Energy's Oak Ridge Financial Service Center (ORFSC) VIPERS. To access and use VIPERS, you must enroll at https://finweb.oro.doe.gov/vipers.htm . Detailed instructions on how to enroll are provided on the web site.

For non-construction awards, you must submit a Standard Form (SF) 270, “Request for Advance or Reimbursement,” at https://finweb.oro.doe.gov/vipers.htm and attach a file containing appropriate supporting documentation. The file attachment must show the total Federal share claimed on the SF 270, the non-Federal share claimed for the billing period if cost sharing is required, and cumulative expenditures to date (both Federal and non-Federal) for each of the following categories: salaries/wages and fringe benefits; equipment; travel; participant/training support costs, if any; other direct costs, including subawards/contracts; and indirect costs. For construction awards, you must submit a SF 271, “Outlay Report and Request for Reimbursement for Construction Programs,” through VIPERS.


c.	Timing of submittals. Submittal of the SF 270 or SF 271 should coincide with your normal billing pattern, but not more frequently than every two weeks. Requests for reimbursement must be limited to the amount of disbursements made during the billing period for the Federal share of direct project costs and the proportionate share of any allowable indirect costs incurred during that billing period.


d.	Adjusting payment requests for available cash. You must disburse any funds that are available from repayments to and interest earned on a revolving fund, program income, rebates, refunds, contract settlements, audit recoveries, credits, discounts, and interest earned on any of those funds before requesting additional cash payments from DOE.

Payments . The DOE approving official will approve the invoice as soon as practical, but not later than 30 days after your request is received, unless the billing is improper. Upon receipt of an invoice payment authorization from the DOE approving official, the ORFSC will disburse payment to you. You may check the status of payments at the VIPER web site. All payments are made by electronic funds transfer to the bank account identified on the ACH Vendor/Miscellaneous Payment Enrollment Form (SF 3881) that you filed.


6.	COST SHARING

a. Total Estimated Project Cost is the sum of the Federal Government share, including Federally Funded Research and Development Center (FFRDC) contractor costs, and Recipient share of the estimated project costs. The DOE FFRDC contractor cost is not included in the total approved budget for this award, because DOE will pay the DOE FFRDC contractor portion of the effort under an existing DOE contract. The Recipient is not responsible for reporting on that portion of the total estimated cost that is paid directly to the DOE FFRDC contractor.

The Recipient's cost share must come from non-Federal sources unless otherwise allowed by law. By accepting Federal funds under this award, you agree that you are liable for your percentage share of allowable project costs, on a budget period basis, even if the project is terminated early or is not funded to its completion. This cost is shared as follows:



Budget Period	DOE Cost Share, including FFRDC Costs		Recipient Cost Share $ / %	Total Estimated Costs
Budget Period	DOE $ / %	FFRDC $ / %	Recipient Cost Share $ / %	Total Estimated Costs
1	$4,207,301/70.2%	—	$1,782,480/29.8%	$5,989,781
2	$20,134,108/68.0%	$658,591/2.2%	$8,809,110/29.8%	$29,601,809
Total Project	$24,341,409	$658,591	$10,591,590	$35,591,590

b. If you discover that you may be unable to provide cost sharing of at least the amount identified in paragraph a of this Article, you should immediately provide written notification to the DOE Award Administrator, indicating whether you will continue the project or phase out the project. If you plan to continue the project, the notification must describe how replacement cost sharing will be secured.

c. You must maintain records of all project costs you claim as cost sharing, including in-kind costs, as well as records of costs to be paid by DOE. Such records are subject to audit.

d. Failure to provide the cost share required by this Article may result in the subsequent recovery by DOE of some or all the funds provided under the award.


7.	REBUDGETING AND RECOVERY OF INDIRECT COSTS


a.	If actual allowable indirect costs are less than those budgeted and funded under the award, you may use the difference to pay additional allowable direct costs during the project period. If at the completion of the award the Government's share of total allowable costs (i.e., direct and indirect), is less than the total costs reimbursed, you must refund the difference.


b.	Recipients are expected to manage their indirect costs. DOE will not amend an award solely to provide additional funds for changes in indirect cost rates. DOE recognizes that the inability to obtain full reimbursement for indirect costs means the Recipient must absorb the underrecovery. Such underrecovery may be allocated as part of the organization's required cost sharing .


8.	FINAL INCURRED COST AUDIT

In accordance with 10 CFR 600, DOE reserves the right to initiate a final incurred cost audit on this award. If the audit has not been performed or completed prior to the closeout of the award, DOE retains the right to recover an appropriate amount after fully considering the recommendations on disallowed costs resulting from the final audit.


9.	STATEMENT OF FEDERAL STEWARDSHIP

DOE will exercise normal Federal stewardship in overseeing the project activities performed under this award. Stewardship activities include, but are not limited to, conducting site visits; reviewing performance and financial reports; providing technical assistance and/or temporary intervention in unusual circumstances to correct deficiencies which develop during the project; assuring compliance with terms and conditions; and reviewing technical performance after project completion to ensure that the award objectives have been accomplished.


10.	STATEMENT OF SUBSTANTIAL INVOLVEMENT


a.	Government Insight

In order to adequately monitor project progress and provide technical direction and/or redirection to the Recipient, DOE must be provided an adequate level of insight into various Recipient activities. Government Insight activities by DOE include attendance at Recipient meetings, reviews and tests, as well as access for DOE's consultants to perform independent evaluations of Recipient's plans and processes. Recipient shall notify the DOE Project Officer of meetings, reviews, and tests in sufficient time to permit DOE participation, and provide all appropriate documentation for DOE review.

b. Specific activities to be conducted by DOE

1. Risk Evaluation -DOE will review the Recipient's initial Risk Mitigation Plan (RMP) for quality and completeness. DOE will also monitor updates to the RMP and actions taken by the Recipient during the performance of its award to mitigate risks and improve the probability of successful execution of the integrated Biorefinery project. At DOE's discretion, additional independent risk analyses of the project by DOE consultants may be requested.

2. Independent Engineering Assessments -DOE will engage a private, independent engineering (IE) firm to assist in assessing the progress of the project and provide timely and accurate reports to DOE. The Recipient will ensure that the IE has access to any and all relevant documentation sufficient to allow the IE to provide independent evaluations to DOE on the progress of the project. Such documentation includes but is not limited to the following:

• Drawings and specifications

• Construction and Execution plans

• Resource loaded schedules

• Design functions and requirements for the site final design review

• Risk management plans

• Value management and engineering studies and/or plans

• Acquisition strategies

• Project execution plans

• Project controls including earned value management systems

• Qualifications of the integrated project team.

• Financial strategy for funding the construction project

• Updated marketing and business plan

• Invoices submitted to DOE

DOE will evaluate the quality and completeness of information and documentation provided by the Recipient to DOE and its consultants in order to allow DOE to provide technical direction and/or redirection to the Recipient about how best to achieve the purposes of the award. Consultants to DOE may not provide technical direction and/or redirection to the Recipient.


11.	SITE VISITS

DOE's authorized representatives have the right to make site visits at reasonable times to review project accomplishments and management control systems and to provide technical assistance, if required. You must provide, and must require your subawardees to provide, reasonable access to facilities, office space, resources, and assistance for the safety and convenience of the government representatives in the performance of their duties. All site visits and evaluations must be performed in a manner that does not unduly interfere with or delay the work.


12.	REPORTING REQUIREMENTS

Requirements . The reporting requirements for this award are identified on the Federal Assistance Reporting Checklist, DOE F 4600.2, attached to this award. Failure to comply with these reporting requirements is considered a material noncompliance with the terms of the award. Noncompliance may result in withholding of future payments, suspension or termination of the current award, and withholding of future awards. A willful failure to perform, a history of failure to perform, or unsatisfactory performance of this and/or other financial assistance awards, may also result in a debarment action to preclude future awards by Federal agencies.

Dissemination of scientific/technical reports . Scientific/technical reports submitted under this award will be disseminated on the Internet via the DOE Information Bridge ( www.osti.gov/bridge ), unless the report contains patentable material, protected data or SBIR/STTR data. Citations for journal articles produced under the award will appear on the DOE Energy Citations Database ( www.osti.gov/energycitations ).


c.	Restrictions . Reports submitted to the DOE Information Bridge must not contain any Protected Personal Identifiable Information (PII), limited rights data (proprietary data), classified information, information subject to export control classification, or other information not subject to release.


13.	PUBLICATIONS


a.	You are encouraged to publish or otherwise make publicly available the results of the work conducted under the award.


b.	An acknowledgment of DOE support and a disclaimer must appear in the publication of any material, whether copyrighted or not, based on or developed under this project, as follows:

Acknowledgment : “This material is based upon work supported by the Department of Energy [National Nuclear Security Administration] [add name(s) of other agencies, if applicable] under Award Number(s) [enter the award number(s)].”

Disclaimer : “This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.”


14.	FEDERAL, STATE, AND MUNICIPAL REQUIREMENTS

You must obtain any required permits and comply with applicable federal, state, and municipal laws, codes, and regulations for work performed under this award.


15.	INTELLECTUAL PROPERTY PROVISIONS AND CONTACT INFORMATION


a.	The intellectual property provisions applicable to this award are provided as an attachment to this award or are referenced in the Assistance Agreement.


b.	Questions regarding intellectual property matters should be referred to the DOE Award Administrator identified and the Patent Counsel designated as the service provider for the DOE office that issued the award.

Patent Counsel for the Golden Field Office is Julia Moody, who may be reached at julia.moody@go.doe.gov or 303-275-4867.


16.	NATIONAL SECURITY: CLASSIFIABLE RESULTS ORIGINATING UNDER AN AWARD

This award is intended for unclassified, publicly releasable research. You will not be granted access to classified information. DOE does not expect that the results of the research project will involve classified information. Under certain circumstances, however, a classification review of information originated under the award may be required. The Department may review research work generated under this award at any time to determine if it requires classification.

Executive Order 12958 (60 Fed. Reg. 19,825 (1995)) states that basic scientific research information not clearly related to the national security shall not be classified. Nevertheless, some information concerning (among other things) scientific, technological, or economic matters relating to national security or cryptology may require classification. If you originate information during the course of this award that you believe requires classification, you must promptly:


1.	Notify the DOE Project Officer and the DOE Award Administrator;


2.	Submit the information by registered mail directly to the Director, Office of Classification and Information Control, SO-10.2; U.S. Department of Energy; P.O. Box A; Germantown, MD 20875-0963, for classification review.


3.	Restrict access to the information to the maximum extent possible until you are informed that the information is not classified, but no longer than 30 days after receipt by the Director, Office of Classification and Information Control


c.	If you originate information concerning the production or utilization of special nuclear material (i.e., plutonium, uranium enriched in the isotope 233 or 235, and any other material so determined under section 51 of the Atomic Energy Act) or nuclear energy, you must:


1.	Notify the DOE Project Officer and the DOE Award Administrator;


2.	Submit the information by registered mail directly to the Director, Office of Classification and Information Control, SO-10.2; U.S. Department of Energy; P. O. Box A; Germantown, MD 20875-0963 for classification review within 180 days of the date the Recipient first discovers or first has reason to believe that the information is useful in such production or utilization; and


3.	Restrict access to the information to the maximum extent possible until you are informed that the information is not classified, but no longer than 90 days after receipt by the Director, Office of Classification and Information Control.


d.	If DOE determines any of the information requires classification, you agree that the Government may terminate the award by mutual agreement in accordance with 10 CFR 600.25(d). All material deemed to be classified must be forwarded to DOE, in a manner specified by DOE.


e.	If DOE does not respond within the specified time periods, you are under no further obligation to restrict access to the information.


17.	LOBBYING RESTRICTIONS

By accepting funds under this award, you agree that none of the funds obligated on the award shall be expended, directly or indirectly, to influence congressional action on any legislation or appropriation matters pending before Congress, other than to communicate to Members of Congress as described in 18 U.S.C. 1913. This restriction is in addition to those prescribed elsewhere in statute and regulation.


18.	NOTICE REGARDING THE PURCHASE OF AMERICAN-MADE EQUIPMENT AND PRODUCTS -- SENSE OF CONGRESS

It is the sense of the Congress that, to the greatest extent practicable, all equipment and products purchased with funds made available under this award should be American-made.


19.	PROPERTY

Real property and equipment acquired by the Recipient shall be subject to the rules set forth in 10 CFR 600.130-137, 10 CFR 600.231-233, or 10 CFR 600.320-324, as applicable.

Consistent with the goals and objectives of this project, the Recipient may continue to use Recipient acquired property beyond the Period of Performance, without obligation, during the period of such use, to extinguish DOE's conditional title to such property as described in 10 CFR 600.132-135, 10 CFR 600.231-233, or 600.321-324, subject to the following: (a) the Recipient continues to utilize such property for the objectives of the project as set forth in the Statement of Project Objectives; (b) DOE retains the right to periodically ask for, and the Recipient agrees to provide, reasonable information concerning the use and condition of the property; and (c) the Recipient follows the property disposition rules set forth in the applicable sections of 10 CFR Part 600, if the property is no longer used by the Recipient for the objectives of the project, and the fair market value of property exceeds $5,000.

Once the per unit fair market value of the property is less than $5,000, pursuant to the applicable sections of 10 CFR Part 600, DOE's residual interest in the property shall be extinguished and the Recipient shall have no further obligation to the DOE with respect to the property.

The regulations as set forth in 10 CFR Part 600 and the requirements of this article shall also apply to property in the possession of any team member, sub-recipient or other entity where such property was acquired in whole or in part with funds provided by DOE under this award or where such property was counted as cost-sharing under the award.


20.	DECONTAMINATION AND/OR DECOMMISSIONING (D&D) COSTS

Notwithstanding any other provisions of this Agreement, the Government shall not be responsible for or have any obligation to the Recipient for (i) Decontamination and/or Decommissioning (D&D) of any of the Recipient's facilities, or (ii) any costs which may be incurred by the Recipient in connection with the D&D of any of its facilities due to the performance of the work under this Agreement, whether said work was performed prior to or subsequent to the effective date of the Agreement.


21.	INSOLVENCY, BANKRUPTCY OR RECEIVERSHIP

a. You shall immediately notify the DOE of the occurrence of any of the following events: (i) you or your parent's filing of a voluntary case seeking liquidation or reorganization under the Bankruptcy Act; (ii) your consent to the institution of an involuntary case under the Bankruptcy Act against you or your parent; (iii) the filing of any similar proceeding for or against you or your parent, or your consent to the dissolution, winding-up or readjustment of your debts, appointment of a receiver, conservator, trustee, or other officer with similar powers over you, under any other applicable state or federal law; or (iv) your insolvency due to its inability to pay debts generally as they become due.

b. Such notification shall be in writing and shall: (i) specifically set out the details of the occurrence of an event referenced in paragraph (a); (ii) provide the facts surrounding that event; and (iii) provide the impact such event will have on the project being funded by this award.

c. Upon the occurrence of any of the four events described in paragraph a. of this provision, DOE reserves the right to conduct a review of your award to determine your compliance with the required elements of the award (including such items as cost share, progress towards technical project objectives, and submission of required reports). If the DOE review determines that there are significant deficiencies or concerns with your performance under the award, DOE reserves the right to impose additional requirements, as needed, including (i) change of payment method; or (ii) institute payment controls.

d. Failure of the Recipient to comply with this provision may be considered a material noncompliance of this financial assistance award by the Contracting Officer.


22.	INDEMNITY

The Recipient shall indemnify the Government and its officers, agents, or employees for any and all liability, including litigation expenses and attorneys' fees, arising from suits, actions, or claims of any character for death, bodily injury, or loss of or damage to property or to the environment, resulting from the project, except to the extent that such liability results from the direct fault or negligence of Government officers, agents or employees, or to the extent such liability may be covered by applicable allowable costs provisions.


23.	SPECIAL PROVISIONS RELATING TO WORK FUNDED UNDER AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009 (May 2009)

Preamble

The American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, (Recovery Act) was enacted to preserve and create jobs and promote economic recovery, assist those most impacted by the recession, provide investments needed to increase economic efficiency by spurring technological advances in science and health, invest in transportation, environmental protection, and other infrastructure that will provide long-term economic benefits, stabilize State and local government budgets, in order to minimize and avoid reductions in essential services and counterproductive State and local tax increases. Recipients shall use grant funds in a manner that maximizes job creation and economic benefit.

The Recipient shall comply with all terms and conditions in the Recovery Act relating generally to governance, accountability, transparency, data collection and resources as specified in Act itself and as discussed below.

Recipients should begin planning activities for their first tier subrecipients, including obtaining a DUNS number (or updating the existing DUNS record), and registering with the Central Contractor Registration (CCR).

Be advised that Recovery Act funds can be used in conjunction with other funding as necessary to complete projects, but tracking and reporting must be separate to meet the reporting requirements of the Recovery Act and related guidance. For projects funded by sources other than the Recovery Act, Contractors must keep separate records for Recovery Act funds and to ensure those records comply with the requirements of the Act.

The Government has not fully developed the implementing instructions of the Recovery Act, particularly concerning specific procedural requirements for the new reporting requirements. The Recipient will be provided these details as they become available. The Recipient must comply with all requirements of the Act. If the recipient believes there is any inconsistency between ARRA requirements and current award terms and conditions, the issues will be referred to the Contracting Officer for reconciliation.

Definitions

For purposes of this clause, Covered Funds means funds expended or obligated from appropriations under the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5. Covered Funds will have special accounting codes and will be identified as Recovery Act funds in the grant, cooperative agreement or TIA and/or modification using Recovery Act funds. Covered Funds must be reimbursed by September 30, 2015.

Non-Federal employer means any employer with respect to covered funds -- the contractor, subcontractor, grantee, or recipient, as the case may be, if the contractor, subcontractor, grantee, or recipient is an employer; and any professional membership organization, certification of other professional body, any agent or licensee of the Federal government, or any person acting directly or indirectly in the interest of an employer receiving covered funds; or with respect to covered funds received by a State or local government, the State or local government receiving the funds and any contractor or subcontractor receiving the funds and any contractor or subcontractor of the State or local government; and does not mean any department, agency, or other entity of the federal government.

Recipient means any entity that receives Recovery Act funds directly from the Federal government (including Recovery Act funds received through grant, loan, or contract) other than an individual and includes a State that receives Recovery Act Funds.

Special Provisions

A. Flow Down Requirement

Recipients must include these special terms and conditions in any subaward.

B. Segregation of Costs

Recipients must segregate the obligations and expenditures related to funding under the Recovery Act. Financial and accounting systems should be revised as necessary to segregate, track and maintain these funds apart and separate from other revenue streams. No part of the funds from the Recovery Act shall be commingled with any other funds or used for a purpose other than that of making payments for costs allowable for Recovery Act projects.

C. Prohibition on Use of Funds

None of the funds provided under this agreement derived from the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, may be used by any State or local government, or any private entity, for any casino or other gambling establishment, aquarium, zoo, golf course, or swimming pool.

D. Access to Records

With respect to each financial assistance agreement awarded utilizing at least some of the funds appropriated or otherwise made available by the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, any representative of an appropriate inspector general appointed under section 3 or 8G of the Inspector General Act of 1988 (5 U.S.C. App.) or of the Comptroller General is authorized --

(1) to examine any records of the contractor or grantee, any of its subcontractors or subgrantees, or any State or local agency administering such contract that pertain to, and involve transactions that relate to, the subcontract, subcontract, grant, or subgrant; and

(2) to interview any officer or employee of the contractor, grantee, subgrantee, or agency regarding such transactions.

E. Publication

An application may contain technical data and other data, including trade secrets and/or privileged or confidential information, which the applicant does not want disclosed to the public or used by the Government for any purpose other than the application. To protect such data, the applicant should specifically identify each page including each line or paragraph thereof containing the data to be protected and mark the cover sheet of the application with the following Notice as well as referring to the Notice on each page to which the Notice applies:

Notice of Restriction on Disclosure and Use of Data

The data contained in pages ---- of this application have been submitted in confidence and contain trade secrets or proprietary information, and such data shall be used or disclosed only for evaluation purposes, provided that if this applicant receives an award as a result of or in connection with the submission of this application, DOE shall have the right to use or disclose the data here to the extent provided in the award. This restriction does not limit the Government's right to use or disclose data obtained without restriction from any source, including the applicant.

Information about this agreement will be published on the Internet and linked to the website www.recovery.gov, maintained by the Accountability and Transparency Board. The Board may exclude posting contractual or other information on the website on a case-by-case basis when necessary to protect national security or to protect information that is not subject to disclosure under sections 552 and 552a of title 5, United States Code.

F. Protecting State and Local Government and Contractor Whistleblowers .

The requirements of Section 1553 of the Act are summarized below. They include, but are not limited to:

Prohibition on Reprisals: An employee of any non-Federal employer receiving covered funds under the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, may not be discharged, demoted, or otherwise discriminated against as a reprisal for disclosing, including a disclosure made in the ordinary course of an employee's duties, to the Accountability and Transparency Board, an inspector general, the Comptroller General, a member of Congress, a State or Federal regulatory or law enforcement agency, a person with supervisory authority over the employee (or other person working for the employer who has the authority to investigate, discover or terminate misconduct), a court or grant jury, the head of a Federal agency, or their representatives information that the employee believes is evidence of:

- gross management of an agency contract or grant relating to covered funds;

- a gross waste of covered funds;

- a substantial and specific danger to public health or safety related to the implementation or use of covered funds;

- an abuse of authority related to the implementation or use of covered funds; or

- as violation of law, rule, or regulation related to an agency contract (including the competition for or negotiation of a contract) or grant, awarded or issued relating to covered funds.

Agency Action: Not later than 30 days after receiving an inspector general report of an alleged reprisal, the head of the agency shall determine whether there is sufficient basis to conclude that the non-Federal employer has subjected the employee to a prohibited reprisal. The agency shall either issue an order denying relief in whole or in part or shall take one or more of the following actions:

- Order the employer to take affirmative action to abate the reprisal.

- Order the employer to reinstate the person to the position that the person held before the reprisal, together with compensation including back pay, compensatory damages, employment benefits, and other terms and conditions of employment that would apply to the person in that position if the reprisal had not been taken.

- Order the employer to pay the employee an amount equal to the aggregate amount of all costs and expenses (including attorneys' fees and expert witnesses' fees) that were reasonably incurred by the employee for or in connection with, bringing the complaint regarding the reprisal, as determined by the head of a court of competent jurisdiction.

Nonenforceablity of Certain Provisions Waiving Rights and remedies or Requiring Arbitration: Except as provided in a collective bargaining agreement, the rights and remedies provided to aggrieved employees by this section may not be waived by any agreement, policy, form, or condition of employment, including any predispute arbitration agreement. No predispute arbitration agreement shall be valid or enforceable if it requires arbitration of a dispute arising out of this section.

Requirement to Post Notice of Rights and Remedies: Any employer receiving covered funds under the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, shall post notice of the rights and remedies as required therein. (Refer to section 1553 of the American Recovery and Reinvestment Act of 2009, Pub. L. 111-5, www.Recovery.gov, for specific requirements of this section and prescribed language for the notices.).

G. RESERVED

H. False Claims Act

Recipient and sub-recipients shall promptly refer to the DOE or other appropriate Inspector General any credible evidence that a principal, employee, agent, contractor, sub-grantee, subcontractor or other person has submitted a false claim under the False Claims Act or has committed a criminal or civil violation of laws pertaining to fraud, conflict of interest, bribery, gratuity or similar misconduct involving those funds.

I. Information in Support of Recovery Act Reporting

Recipient may be required to submit backup documentation for expenditures of funds under the Recovery Act including such items as timecards and invoices. Recipient shall provide copies of backup documentation at the request of the Contracting Officer or designee.

J. Availability of Funds

Funds appropriated under the Recovery Act and obligated to this award are available for reimbursement of costs until September 30, 2015.


24.	REPORTING AND REGISTRATION REQUIREMENTS UNDER SECTION 1512 OF THE RECOVERY ACT

(a) This award requires the recipient to complete projects or activities which are funded under the American Recovery and Reinvestment Act of 2009 (Recovery Act) and to report on use of Recovery Act funds provided through this award. Information from these reports will be made available to the public.

(b) The reports are due no later than ten calendar days after each calendar quarter in which the Recipient receives the assistance award funded in whole or in part by the Recovery Act.

(c) Recipients and their first-tier subrecipients must maintain current registrations in the Central Contractor Registration ( http://www.ccr.gov ) at all times during which they have active federal awards funded with Recovery Act funds. A Dun and Bradstreet Data Universal Numbering System (DUNS) Number ( http://www.dnb.com ) is one of the requirements for registration in the Central Contractor Registration.

(d) The recipient shall report the information described in section 1512(c) of the Recovery Act using the reporting instructions and data elements that will be provided online at http://www.FederalReporting.gov and ensure that any information that is pre-filled is corrected or updated as needed.


25.	REQUIRED USE OF AMERICAN IRON, STEEL, AND MANUFACTURED GOODS - SECTION 1605 OF THE AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009

If the Recipient determines at any time that any construction, alteration, or repair activity on a public building or public works will be performed during the course of the project, the Recipient shall notify the Contracting Officer prior to commencing such work and the following provisions shall apply.

(a) Definitions. As used in this award term and condition-

(1) Manufactured good means a good brought to the construction site for incorporation into the building or work that has been-

(i) Processed into a specific form and shape; or

(ii) Combined with other raw material to create a material that has different properties than the properties of the individual raw materials.

(2) Public building and public work means a public building of, and a public work of, a governmental entity (the United States; the District of Columbia; commonwealths, territories, and minor outlying islands of the United States; State and local governments; and multi-State, regional, or interstate entities which have governmental functions). These buildings and works may include, without limitation, bridges, dams, plants, highways, parkways, streets, subways, tunnels, sewers, mains, power lines, pumping stations, heavy generators, railways, airports, terminals, docks, piers, wharves, ways, lighthouses, buoys, jetties, breakwaters, levees, and canals, and the construction, alteration, maintenance, or repair of such buildings and works.

(3) Steel means an alloy that includes at least 50 percent iron, between .02 and 2 percent carbon, and may include other elements.

(b) Domestic preference. (1) This award term and condition implements Section 1605 of the American Recovery and Reinvestment Act of 2009 (Recovery Act) (Pub. L. 111-5), by requiring that all iron, steel, and manufactured goods used in the project are produced in the United States except as provided in paragraph (b)(3) of this section and condition.

(2) This requirement does not apply to the material listed by the Federal Government as follows:

none

(3) The award official may add other iron, steel, and/or manufactured goods to the list in paragraph (b)(2) of this section and condition if the Federal Government determines that-

(i) The cost of the domestic iron, steel, and/or manufactured goods would be unreasonable. The cost of domestic iron, steel, or manufactured goods used in the project is unreasonable when the cumulative cost of such material will increase the cost of the overall project by more than 25 percent;

(ii) The iron, steel, and/or manufactured good is not produced, or manufactured in the United States in sufficient and reasonably available quantities and of a satisfactory quality; or

(iii) The application of the restriction of section 1605 of the Recovery Act would be inconsistent with the public interest.

(c) Request for determination of inapplicability of Section 1605 of the Recovery Act . (1)(i) Any recipient request to use foreign iron, steel, and/or manufactured goods in accordance with paragraph (b)(3) of this section shall include adequate information for Federal Government evaluation of the request, including-

(A) A description of the foreign and domestic iron, steel, and/or manufactured goods;

(B) Unit of measure;

(D) Cost;

(E) Time of delivery or availability;

(F) Location of the project;

(G) Name and address of the proposed supplier; and

(H) A detailed justification of the reason for use of foreign iron, steel, and/or manufactured goods cited in accordance with paragraph (b)(3) of this section.

(ii) A request based on unreasonable cost shall include a reasonable survey of the market and a completed cost comparison table in the format in paragraph (d) of this section.

(iii) The cost of iron, steel, and/or manufactured goods material shall include all delivery costs to the construction site and any applicable duty.

(iv) Any recipient request for a determination submitted after Recovery Act funds have been obligated for a project for construction, alteration, maintenance, or repair shall explain why the recipient could not reasonably foresee the need for such determination and could not have requested the determination before the funds were obligated. If the recipient does not submit a satisfactory explanation, the award official need not make a determination.

(2) If the Federal Government determines after funds have been obligated for a project for construction, alteration, maintenance, or repair that an exception to section 1605 of the Recovery Act applies, the award official will amend the award to allow use of the foreign iron, steel, and/or relevant manufactured goods. When the basis for the exception is nonavailability or public interest, the amended award shall reflect adjustment of the award amount, redistribution of budgeted funds, and/or other actions taken to cover costs associated with acquiring or using the foreign iron, steel, and/or relevant manufactured goods. When the basis for the exception is the unreasonable cost of the domestic iron, steel, or manufactured goods, the award official shall adjust the award amount or redistribute budgeted funds by at least the differential established in 2 CFR 176.110(a).

(3) Unless the Federal Government determines that an exception to section 1605 of the Recovery Act applies, use of foreign iron, steel, and/or manufactured goods is noncompliant with section 1605 of the American Recovery and Reinvestment Act.

(d) Data. To permit evaluation of requests under paragraph (b) of this section based on unreasonable cost, the Recipient shall include the following information and any applicable supporting data based on the survey of suppliers:

Foreign and Domestic Items Cost Comparison



Description	Unit of measure	Quantity	Cost (dollars)*
Item 1:
Foreign steel, iron, or manufactured good	_________	_________	_________
Domestic steel, iron, or manufactured good	_________	_________	_________
Item 2:
Foreign steel, iron, or manufactured good	_________	_________	_________
Domestic steel, iron, or manufactured good	_________	_________	_________

List name, address, telephone number, email address, and contact for suppliers surveyed. Attach copy of response; if oral, attach summary.

Include other applicable supporting information.

*Include all delivery costs to the construction site.


26.	REQUIRED USE OF AMERICAN IRON, STEEL, AND MANUFACTURED GOODS (COVERED UNDER INTERNATIONAL AGREEMENTS) - SECTION 1605 OF THE AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009

(a) Definitions. As used in this award term and condition-

Designated country - (1) A World Trade Organization Government Procurement Agreement country (Aruba, Austria, Belgium, Bulgaria, Canada, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hong Kong, Hungary, Iceland, Ireland, Israel, Italy, Japan, Korea (Republic of), Latvia, Liechtenstein, Lithuania, Luxembourg, Malta, Netherlands, Norway, Poland, Portugal, Romania, Singapore, Slovak Republic, Slovenia, Spain, Sweden, Switzerland, and United Kingdom;

(2) A Free Trade Agreement (FTA) country (Australia, Bahrain, Canada, Chile, Costa Rica, Dominican Republic, El Salvador, Guatemala, Honduras, Israel, Mexico, Morocco, Nicaragua, Oman, Peru, or Singapore); or

(3) A United States-European Communities Exchange of Letters (May 15, 1995) country: Austria, Belgium, Bulgaria, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Ireland, Italy, Latvia, Lithuania, Luxembourg, Malta, Netherlands, Poland, Portugal, Romania, Slovak Republic, Slovenia, Spain, Sweden, and United Kingdom.

Designated country iron, steel, and/or manufactured goods - (1) Is wholly the growth, product, or manufacture of a designated country; or

(2) In the case of a manufactured good that consist in whole or in part of materials from another country, has been substantially transformed in a designated country into a new and different manufactured good distinct from the materials from which it was transformed.

Domestic iron, steel, and/or manufactured good - (1) Is wholly the growth, product, or manufacture of the United States; or

(2) In the case of a manufactured good that consists in whole or in part of materials from another country, has been substantially transformed in the United States into a new and different manufactured good distinct from the materials from which it was transformed. There is no requirement with regard to the origin of components or subcomponents in manufactured goods or products, as long as the manufacture of the goods occurs in the United States.

Foreign iron, steel, and/or manufactured good means iron, steel and/or manufactured good that is not domestic or designated country iron, steel, and/or manufactured good.

Manufactured good means a good brought to the construction site for incorporation into the building or work that has been-

(1) Processed into a specific form and shape; or

(2) Combined with other raw material to create a material that has different properties than the properties of the individual raw materials.

Public building and public work means a public building of, and a public work of, a governmental entity (the United States; the District of Columbia; commonwealths, territories, and minor outlying islands of the United States; State and local governments; and multi-State, regional, or interstate entities which have governmental functions). These buildings and works may include, without limitation, bridges, dams, plants, highways, parkways, streets, subways, tunnels, sewers, mains, power lines, pumping stations, heavy generators, railways, airports, terminals, docks, piers, wharves, ways, lighthouses, buoys, jetties, breakwaters, levees, and canals, and the construction, alteration, maintenance, or repair of such buildings and works.

Steel means an alloy that includes at least 50 percent iron, between .02 and 2 percent carbon, and may include other elements.

(b) Iron, steel, and manufactured goods. (1) The award term and condition described in this section implements-

(i) Section 1605(a) of the American Recovery and Reinvestment Act of 2009 (Pub. L. 111-5) (Recovery Act), by requiring that all iron, steel, and manufactured goods used in the project are produced in the United States; and

(ii) Section 1605(d), which requires application of the Buy American requirement in a manner consistent with U.S. obligations under international agreements. The restrictions of section 1605 of the Recovery Act do not apply to designated country iron, steel, and/or manufactured goods. The Buy American requirement in section 1605 shall not be applied where the iron, steel or manufactured goods used in the project are from a Party to an international agreement that obligates the recipient to treat the goods and services of that Party the same as domestic goods and services. This obligation shall only apply to projects with an estimated value of $7,443,000 or more.

(2) The recipient shall use only domestic or designated country iron, steel, and manufactured goods in performing the work funded in whole or part with this award, except as provided in paragraphs (b)(3) and (b)(4) of this section.

(3) The requirement in paragraph (b)(2) of this section does not apply to the iron, steel, and manufactured goods listed by the Federal Government as follows:

none

(4) The award official may add other iron, steel, and manufactured goods to the list in paragraph (b)(3) of this section if the Federal Government determines that-

(i) The cost of domestic iron, steel, and/or manufactured goods would be unreasonable. The cost of domestic iron, steel, and/or manufactured goods used in the project is unreasonable when the cumulative cost of such material will increase the overall cost of the project by more than 25 percent;

(ii) The iron, steel, and/or manufactured good is not produced, or manufactured in the United States in sufficient and reasonably available commercial quantities of a satisfactory quality; or

(iii) The application of the restriction of section 1605 of the Recovery Act would be inconsistent with the public interest.

(c) Request for determination of inapplicability of section 1605 of the Recovery Act or the Buy American Act. (1)(i) Any recipient request to use foreign iron, steel, and/or manufactured goods in accordance with paragraph (b)(4) of this section shall include adequate information for Federal Government evaluation of the request, including-

(A) A description of the foreign and domestic iron, steel, and/or manufactured goods;

(B) Unit of measure;

(D) Cost;

(E) Time of delivery or availability;

(F) Location of the project;

(G) Name and address of the proposed supplier; and

(H) A detailed justification of the reason for use of foreign iron, steel, and/or manufactured goods cited in accordance with paragraph (b)(4) of this section.

(ii) A request based on unreasonable cost shall include a reasonable survey of the market and a completed cost comparison table in the format in paragraph (d) of this section.

(iii) The cost of iron, steel, or manufactured goods shall include all delivery costs to the construction site and any applicable duty.

(2) If the Federal Government determines after funds have been obligated for a project for construction, alteration, maintenance, or repair that an exception to section 1605 of the Recovery Act applies, the award official will amend the award to allow use of the foreign iron, steel, and/or relevant manufactured goods. When the basis for the exception is nonavailability or public interest, the amended award shall reflect adjustment of the award amount, redistribution of budgeted funds, and/or other appropriate actions taken to cover costs associated with acquiring or using the foreign iron, steel, and/or relevant manufactured goods. When the basis for the exception is the unreasonable cost of the domestic iron, steel, or manufactured goods, the award official shall adjust the award amount or redistribute budgeted funds, as appropriate, by at least the differential established in 2 CFR 176.110(a).

(3) Unless the Federal Government determines that an exception to section 1605 of the Recovery Act applies, use of foreign iron, steel, and/or manufactured goods other than designated country iron, steel, and/or manufactured goods is noncompliant with the applicable Act.

(d) Data. To permit evaluation of requests under paragraph (b) of this section based on unreasonable cost, the applicant shall include the following information and any applicable supporting data based on the survey of suppliers:

Foreign and Domestic Items Cost Comparison



Description	Unit of measure	Quantity	Cost (dollars)*
Item 1:
Foreign steel, iron, or manufactured good	_________	_________	_________
Domestic steel, iron, or manufactured good	_________	_________	_________
Item 2:
Foreign steel, iron, or manufactured good	_________	_________	_________
Domestic steel, iron, or manufactured good	_________	_________	_________

List name, address, telephone number, email address, and contact for suppliers surveyed. Attach copy of response; if oral, attach summary.

Include other applicable supporting information.

*Include all delivery costs to the construction site.


27.	RECOVERY ACT TRANSACTIONS LISTED IN SCHEDULE OF EXPENDITURES OF FEDERAL AWARDS AND RECIPIENT RESPONSIBILITIES FOR INFORMING SUBRECIPIENTS

(a) To maximize the transparency and accountability of funds authorized under the American Recovery and Reinvestment Act of 2009 (Pub. L. 111-5) (Recovery Act) as required by Congress and in accordance with 2 CFR 215.21 “Uniform Administrative Requirements for Grants and Agreements” and OMB Circular A-102 Common Rules provisions, recipients agree to maintain records that identify adequately the source and application of Recovery Act funds. OMB Circular A-102 is available at http://www.whitehouse.gov/omb/circulars/a102/a102.html.

(b) For recipients covered by the Single Audit Act Amendments of 1996 and OMB Circular A-133, “Audits of States, Local Governments, and Non-Profit Organizations,” recipients agree to separately identify the expenditures for Federal awards under the Recovery Act on the Schedule of Expenditures of Federal Awards (SEFA) and the Data Collection Form (SF-SAC) required by OMB Circular A-133. OMB Circular A-133 is available at http://www.whitehouse.gov/omb/circulars/a133/a133.html. This shall be accomplished by identifying expenditures for Federal awards made under the Recovery Act separately on the SEFA, and as separate rows under Item 9 of Part III on the SF-SAC by CFDA number, and inclusion of the prefix “ARRA-” in identifying the name of the Federal program on the SEFA and as the first characters in Item 9d of Part III on the SF-SAC.

(c) Recipients agree to separately identify to each subrecipient, and document at the time of subaward and at the time of disbursement of funds, the Federal award number, CFDA number, and amount of Recovery Act funds. When a recipient awards Recovery Act funds for an existing program, the information furnished to subrecipients shall distinguish the subawards of incremental Recovery Act funds from regular subawards under the existing program.

(d) Recipients agree to require their subrecipients to include on their SEFA information to specifically identify Recovery Act funding similar to the requirements for the recipient SEFA described above. This information is needed to allow the recipient to properly monitor subrecipient expenditure of ARRA funds as well as oversight by the Federal awarding agencies, Offices of Inspector General and the Government Accountability Office.


28.	WAGE RATE REQUIREMENTS UNDER SECTION 1606 OF THE RECOVERY ACT

(a) Section 1606 of the Recovery Act requires that all laborers and mechanics employed by contractors and subcontractors on projects funded directly by or assisted in whole or in part by and through the Federal Government pursuant to the Recovery Act shall be paid wages at rates not less than those prevailing on projects of a character similar in the locality as determined by the Secretary of Labor in accordance with subchapter IV of chapter 31 of title 40, United States Code.

Pursuant to Reorganization Plan No. 14 and the Copeland Act, 40 U.S.C. 3145, the Department of Labor has issued regulations at 29 CFR parts 1, 3, and 5 to implement the Davis-Bacon and related Acts. Regulations in 29 CFR 5.5 instruct agencies concerning application of the standard Davis-Bacon contract clauses set forth in that section. Federal agencies providing grants, cooperative agreements, and loans under the Recovery Act shall ensure that the standard Davis-Bacon contract clauses found in 29 CFR 5.5(a) are incorporated in any resultant covered contracts that are in excess of $2,000 for construction, alteration or repair (including painting and decorating).

(b) For additional guidance on the wage rate requirements of section 1606, contact your awarding agency. Recipients of grants, cooperative agreements and loans should direct their initial inquiries concerning the application of Davis-Bacon requirements to a particular federally assisted project to the Federal agency funding the project. The Secretary of Labor retains final coverage authority under Reorganization Plan Number 14.


29.	DAVIS BACON ACT AND CONTRACT WORK HOURS AND SAFETY STANDARDS ACT

If the Recipient determines at any time that any construction, alteration, or repair activity as defined by 29 CFR 5.2(j) ( http://cfr.vlex.com/vid/5-2-definitions-19681309 ) will be performed during the course of the project, the Recipient shall notify the Contracting Officer prior to commencing such work and the following provisions shall apply. A modification to the award which incorporates the appropriate Davis-Bacon wage rate determination(s) will constitute the Contracting Officer's approval to proceed.

Definitions: For purposes of this provision, “Davis Bacon Act and Contract Work Hours and Safety Standards Act,” the following definitions are applicable:

(1) “Award” means any grant, cooperative agreement or technology investment agreement made with Recovery Act funds by the Department of Energy (DOE) to a Recipient. Such Award must require compliance with the labor standards clauses and wage rate requirements of the Davis-Bacon Act (DBA) for work performed by all laborers and mechanics employed by Recipients (other than a unit of State or local government whose own employees perform the construction) Subrecipients, Contractors, and subcontractors.

(2) “Contractor” means an entity that enters into a Contract. For purposes of these clauses, Contractor shall include (as applicable) prime contractors, Recipients, Subrecipients, and Recipients' or Subrecipients' contractors, subcontractors, and lower-tier subcontractors. “Contractor” does not mean a unit of State or local government where construction is performed by its own employees.”

(3) “Contract” means a contract executed by a Recipient, Subrecipient, prime contractor, or any tier subcontractor for construction, alteration, or repair. It may also mean (as applicable) (i) financial assistance instruments such as grants, cooperative agreements, technology investment agreements, and loans; and, (ii) Sub awards, contracts and subcontracts issued under financial assistance agreements. “Contract” does not mean a financial assistance instrument with a unit of State or local government where construction is performed by its own employees.

(4) “Contracting Officer” means the DOE official authorized to execute an Award on behalf of DOE and who is responsible for the business management and non-program aspects of the financial assistance process.

(5) “Recipient” means any entity other than an individual that receives an Award of Federal funds in the form of a grant, cooperative agreement, or technology investment agreement directly from the Federal Government and is financially accountable for the use of any DOE funds or property, and is legally responsible for carrying out the terms and conditions of the program and Award.

(6) “Subaward” means an award of financial assistance in the form of money, or property in lieu of money, made under an award by a Recipient to an eligible Subrecipient or by a Subrecipient to a lower-tier subrecipient. The term includes financial assistance when provided by any legal agreement, even if the agreement is called a contract, but does not include the Recipient's procurement of goods and services to carry out the program nor does it include any form of assistance which is excluded from the definition of “Award” above.

(7) “Subrecipient” means a non-Federal entity that expends Federal funds received from a Recipient to carry out a Federal program, but does not include an individual that is a beneficiary of such a program.

(a) Davis Bacon Act

(1) Minimum wages.

(i) All laborers and mechanics employed or working upon the site of the work (or under the United States Housing Act of 1937 or under the Housing Act of 1949 in the construction or development of the project), will be paid unconditionally and not less often than once a week, and, without subsequent deduction or rebate on any account (except such payroll deductions as are permitted by regulations issued by the Secretary of Labor under the Copeland Act (29 CFR part 3)), the full amount of wages and bona fide fringe benefits (or cash equivalents thereof) due at time of payment computed at rates not less than those contained in the wage determination of the Secretary of Labor which is attached hereto and made a part hereof, regardless of any contractual relationship which may be alleged to exist between the Contractor and such laborers and mechanics.

determination for the classification of work actually performed, without regard to skill, except as provided in § 5.5(a)(4). Laborers or mechanics performing work in more than one classification may be compensated at the rate specified for each classification for the time actually worked therein, provided that the employer's payroll records accurately set forth the time spent in each classification in which work is performed. The wage determination (including any additional classification and wage rates conformed under paragraph (a)(1)(ii) of this section) and the Davis-Bacon poster (WH-1321) shall be posted at all times by the Contractor and its subcontractors at the site of the work in a prominent and accessible place where it can be easily seen by the workers.

(ii)(A) The Contracting Officer shall require that any class of laborers or mechanics, including helpers, which is not listed in the wage determination and which is to be employed under the Contract shall be classified in conformance with the wage determination. The Contracting Officer shall approve an additional classification and wage rate and fringe benefits therefore only when the following criteria have been met:

(1) The work to be performed by the classification requested is not performed by a classification in the wage determination;

(2) The classification is utilized in the area by the construction industry; and

(3) The proposed wage rate, including any bona fide fringe benefits, bears a reasonable relationship to the wage rates contained in the wage determination.

(B) If the Contractor and the laborers and mechanics to be employed in the classification (if known), or their representatives, and the Contracting Officer agree on the classification and wage rate (including the amount designated for fringe benefits where appropriate), a report of the action taken shall be sent by the Contracting Officer to the Administrator of the Wage and Hour Division, U.S. Department of Labor, Washington, DC 20210. The Administrator, or an authorized representative, will approve, modify, or disapprove every additional classification action within 30 days of receipt and so advise the Contracting Officer or will notify the Contracting Officer within the 30-day period that additional time is necessary.

(C) In the event the Contractor, the laborers or mechanics to be employed in the classification or their representatives, and the Contracting Officer do not agree on the proposed classification and wage rate (including the amount designated for fringe benefits, where appropriate), the Contracting Officer shall refer the questions, including the views of all interested parties and the recommendation of the Contracting Officer, to the Administrator for determination. The Administrator, or an authorized representative, will issue a determination within 30 days of receipt and so advise the Contracting Officer or will notify the Contracting Officer within the 30-day period that additional time is necessary.

(D) The wage rate (including fringe benefits where appropriate) determined pursuant to paragraphs (a)(1)(ii)(B) or (C) of this section, shall be paid to all workers performing work in the classification under this Contract from the first day on which work is performed in the classification.

(iii) Whenever the minimum wage rate prescribed in the Contract for a class of laborers or mechanics includes a fringe benefit which is not expressed as an hourly rate, the Contractor shall either pay the benefit as stated in the wage determination or shall pay another bona fide fringe benefit or an hourly cash equivalent thereof.

(iv) If the Contractor does not make payments to a trustee or other third person, the Contractor may consider as part of the wages of any laborer or mechanic the amount of any costs reasonably anticipated in providing bona fide fringe benefits under a plan or program, provided that the Secretary of Labor has found, upon the written request of the Contractor, that the applicable standards of the Davis-Bacon Act have been met. The Secretary of Labor may require the Contractor to set aside in a separate account assets for the meeting of obligations under the plan or program.

(2) Withholding. The Department of Energy or the Recipient or Subrecipient shall upon its own action or upon written request of an authorized representative of the Department of Labor withhold or cause to be withheld from the Contractor under this Contract or any other Federal contract with the same prime contractor, or any other federally-assisted contract subject to Davis-Bacon prevailing wage requirements, which is held by the same prime contractor, so much of the accrued payments or advances as may be considered necessary to pay laborers and mechanics, including apprentices, trainees, and helpers, employed by the Contractor or any subcontractor the full amount of wages required by the Contract. In the event of failure to pay any laborer or mechanic, including any apprentice, trainee, or helper, employed or working on the site of the work (or under the United States Housing Act of 1937 or under the Housing Act of 1949 in the construction or development of the project), all or part of the wages required by the Contract, the Department of Energy, Recipient, or Subrecipient, may, after written notice to the Contractor, sponsor, applicant, or owner, take such action as may be necessary to cause the suspension of any further payment, advance, or guarantee of funds until such violations have ceased.

(3) Payrolls and basic records.

the United States Housing Act of 1937, or under the Housing Act of 1949, in the construction or development of the project). Such records shall contain the name, address, and social security number of each such worker, his or her correct classification, hourly rates of wages paid (including rates of contributions or costs anticipated for bona fide fringe benefits or cash equivalents thereof of the types described in section 1(b)(2)(B) of the Davis-Bacon Act), daily and weekly number of hours worked, deductions made, and actual wages paid. Whenever the Secretary of Labor has found under 29 CFR 5.5(a)(1)(iv) that the wages of any laborer or mechanic include the amount of any costs reasonably anticipated in providing benefits under a plan or program described in section 1(b)(2)(B) of the Davis-Bacon Act, the Contractor shall maintain records which show that the commitment to provide such benefits is enforceable, that the plan or program is financially responsible, and that the plan or program has been communicated in writing to the laborers or mechanics affected, and records which show the costs anticipated or the actual cost incurred in providing such benefits. Contractors employing apprentices or trainees under approved programs shall maintain written evidence of the registration of apprenticeship programs and certification of trainee programs, the registration of the apprentices and trainees, and the ratios and wage rates prescribed in the applicable programs.

(ii) (A) The Contractor shall submit weekly for each week in which any Contract work is performed a copy of all payrolls to the Department of Energy if the agency is a party to the Contract, but if the agency is not such a party, the Contractor will submit the payrolls to the Recipient or Subrecipient (as applicable), applicant, sponsor, or owner, as the case may be, for transmission to the Department of Energy. The payrolls submitted shall set out accurately and completely all of the information required to be maintained under 29 CFR 5.5(a)(3)(i), except that full social security numbers and home addresses shall not be included on weekly transmittals. Instead, the payrolls shall only need to include an individually identifying number for each employee (e.g., the last four digits of the employee's social security number). The required weekly payroll information may be submitted in any form desired. Optional Form WH-347 is available for this purpose from the Wage and Hour Division Web site at http://www.dol.gov/esa/whd/forms/wh347instr.htm or its successor site. The prime Contractor is responsible for the submission of copies of payrolls by all subcontractors. Contractors and subcontractors shall maintain the full social security number and current address of each covered worker, and shall provide them upon request to the Department of Energy if the agency is a party to the Contract, but if the agency is not such a party, the Contractor will submit them to the Recipient or Subrecipient (as applicable), applicant, sponsor, or owner, as the case may be, for transmission to the Department of Energy, the Contractor, or the Wage and Hour Division of the Department of Labor for purposes of an investigation or audit of compliance with prevailing wage requirements. It is not a violation of this section for a prime contractor to require a subcontractor to provide addresses and social security numbers to the prime contractor for its own records, without weekly submission to the sponsoring government agency (or the Recipient or Subrecipient (as applicable), applicant, sponsor, or owner).

(B) Each payroll submitted shall be accompanied by a “Statement of Compliance,” signed by the Contractor or subcontractor or his or her agent who pays or supervises the payment of the persons employed under the Contract and shall certify the following:

(1) That the payroll for the payroll period contains the information required to be provided under § 5.5 (a)(3)(ii) of Regulations, 29 CFR part 5, the appropriate information is being maintained under § 5.5 (a)(3)(i) of Regulations, 29 CFR part 5, and that such information is correct and complete;

(2) That each laborer or mechanic (including each helper, apprentice, and trainee) employed on the Contract during the payroll period has been paid the full weekly wages earned, without rebate, either directly or indirectly, and that no deductions have been made either directly or indirectly from the full wages earned, other than permissible deductions as set forth in Regulations, 29 CFR part 3;

(3) That each laborer or mechanic has been paid not less than the applicable wage rates and fringe benefits or cash equivalents for the classification of work performed, as specified in the applicable wage determination incorporated into the Contract.

(C) The weekly submission of a properly executed certification set forth on the reverse side of Optional Form WH-347 shall satisfy the requirement for submission of the “Statement of Compliance” required by paragraph (a)(3)(ii)(B) of this section.

(D) The falsification of any of the above certifications may subject the Contractor or subcontractor to civil or criminal prosecution under section 1001 of title 18 and section 3729 of title 31 of the United States Code.

(iii) The Contractor or subcontractor shall make the records required under paragraph (a)(3)(i) of this section available for inspection, copying, or transcription by authorized representatives of the Department of Energy or the Department of Labor, and shall permit such representatives to interview employees during working hours on the job. If the Contractor or subcontractor fails to submit the required records or to make them available, the Federal agency may, after written notice to the Contractor, sponsor, applicant, or owner, take such action as may be necessary to cause the suspension of any further payment, advance, or guarantee of funds. Furthermore, failure to submit the required records upon request or to make such records available may be grounds for debarment action pursuant to 29 CFR 5.12.

(4) Apprentices and trainees-

(i) Apprentices. Apprentices will be permitted to work at less than the predetermined rate for the work they performed when they are employed pursuant to and individually registered in a bona fide apprenticeship program registered with the U.S. Department of Labor, Employment and Training Administration, Office of Apprenticeship Training, Employer and Labor Services, or with a State Apprenticeship Agency recognized by the Office, or if a person is employed in his or her first 90 days of probationary employment as an apprentice in such an apprenticeship program, who is not individually registered in the program, but who has been certified by the Office of Apprenticeship Training, Employer and Labor Services or a State Apprenticeship Agency (where appropriate) to be eligible for probationary employment as an apprentice. The allowable ratio of apprentices to journeymen on the job site in any craft classification shall not be greater than the ratio permitted to the Contractor as to the entire work force under the registered program. Any worker listed on a payroll at an apprentice wage rate, who is not registered or otherwise employed as stated above, shall be paid not less than the applicable wage rate on the wage determination for the classification of work actually performed. In addition, any apprentice performing work on the job site in excess of the ratio permitted under the registered program shall be paid not less than the applicable wage rate on the wage determination for the work actually performed. Where a Contractor is performing construction on a project in a locality other than that in which its program is registered, the ratios and wage rates (expressed in percentages of the journeyman's hourly rate) specified in the Contractor's or subcontractor's registered program shall be observed. Every apprentice must be paid at not less than the rate specified in the registered program for the apprentice's level of progress, expressed as a percentage of the journeymen hourly rate specified in the applicable wage determination. Apprentices shall be paid fringe benefits in accordance with the provisions of the apprenticeship program. If the apprenticeship program does not specify fringe benefits, apprentices must be paid the full amount of fringe benefits listed on the wage determination for the applicable classification. If the Administrator determines that a different practice prevails for the applicable apprentice classification, fringes shall be paid in accordance with that determination. In the event the Office of Apprenticeship Training, Employer and Labor Services, or a State Apprenticeship Agency recognized by the Office, withdraws approval of an apprenticeship program, the Contractor will no longer be permitted to utilize apprentices at less than the applicable predetermined rate for the work performed until an acceptable program is approved.

journeymen on the job site shall not be greater than permitted under the plan approved by the Employment and Training Administration. Every trainee must be paid at not less than the rate specified in the approved program for the trainee's level of progress, expressed as a percentage of the journeyman hourly rate specified in the applicable wage determination. Trainees shall be paid fringe benefits in accordance with the provisions of the trainee program. If the trainee program does not mention fringe benefits, trainees shall be paid the full amount of fringe benefits listed on the wage determination unless the Administrator of the Wage and Hour Division determines that there is an apprenticeship program associated with the corresponding journeyman wage rate on the wage determination which provides for less than full fringe benefits for apprentices. Any employee listed on the payroll at a trainee rate who is not registered and participating in a training plan approved by the Employment and Training Administration shall be paid not less than the applicable wage rate on the wage determination for the classification of work actually performed. In addition, any trainee performing work on the job site in excess of the ratio permitted under the registered program shall be paid not less than the applicable wage rate on the wage determination for the work actually performed. In the event the Employment and Training Administration withdraws approval of a training program, the Contractor will no longer be permitted to utilize trainees at less than the applicable predetermined rate for the work performed until an acceptable program is approved.

(iii) Equal employment opportunity. The utilization of apprentices, trainees, and journeymen under this part shall be in conformity with the equal employment opportunity requirements of Executive Order 11246, as amended and 29 CFR part 30.

(5) Compliance with Copeland Act requirements. The Contractor shall comply with the requirements of 29 CFR part 3, which are incorporated by reference in this Contract.

(6) Contracts and Subcontracts. The Recipient, Subrecipient, the Recipient's, and Subrecipient's contractors and subcontractor shall insert in any Contracts the clauses contained herein in(a)(1) through (10) and such other clauses as the Department of Energy may by appropriate instructions require, and also a clause requiring the subcontractors to include these clauses in any lower tier subcontracts. The Recipient shall be responsible for the compliance by any subcontractor or lower tier subcontractor with all of the paragraphs in this clause.

(7) Contract termination: debarment. A breach of the Contract clauses in 29 CFR 5.5 may be grounds for termination of the Contract, and for debarment as a contractor and a subcontractor as provided in 29 CFR 5.12.

(8) Compliance with Davis-Bacon and Related Act requirements. All rulings and interpretations of the Davis-Bacon and Related Acts contained in 29 CFR parts 1, 3, and 5 are herein incorporated by reference in this Contract.

(9) Disputes concerning labor standards. Disputes arising out of the labor standards provisions of this Contract shall not be subject to the general disputes clause of this Contract. Such disputes shall be resolved in accordance with the procedures of the Department of Labor set forth in 29 CFR parts 5, 6, and 7. Disputes within the meaning of this clause include disputes between the Recipient, Subrecipient, the Contractor (or any of its subcontractors), and the contracting agency, the U.S. Department of Labor, or the employees or their representatives.

(10) Certification of eligibility.

(i) By entering into this Contract, the Contractor certifies that neither it (nor he or she) nor any person or firm who has an interest in the Contractor's firm is a person or firm ineligible to be awarded Government contracts by virtue of section 3(a) of the Davis-Bacon Act or 29 CFR 5.12(a)(1).

(ii) No part of this Contract shall be subcontracted to any person or firm ineligible for award of a Government contract by virtue of section 3(a) of the Davis-Bacon Act or 29 CFR 5.12(a)(1).

(iii) The penalty for making false statements is prescribed in the U.S. Criminal Code, 18 U.S.C. 1001.

(b) Contract Work Hours and Safety Standards Act. As used in this paragraph, the terms laborers and mechanics include watchmen and guards.

(1) Overtime requirements. No Contractor or subcontractor contracting for any part of the Contract work which may require or involve the employment of laborers or mechanics shall require or permit any such laborer or mechanic in any workweek in which he or she is employed on such work to work in excess of forty hours in such workweek unless such laborer or mechanic receives compensation at a rate not less than one and one-half times the basic rate of pay for all hours worked in excess of forty hours in such workweek.

(2) Violation; liability for unpaid wages; liquidated damages. In the event of any violation of the clause set forth in paragraph (b)(1) of this section, the Contractor and any subcontractor responsible therefor shall be liable for the unpaid wages. In addition, such Contractor and subcontractor shall be liable to the United States (in the case of work done under contract for the District of Columbia or a territory, to such District or to such territory), for liquidated damages. Such liquidated damages shall be computed with respect to each individual laborer or mechanic, including watchmen and guards, employed in violation of the clause set forth in paragraph (b)(1) of this section, in the sum of $10 for each calendar day on which such individual was required or permitted to work in excess of the standard workweek of forty hours without payment of the overtime wages required by the clause set forth in paragraph (b)(1) of this section.

(3) Withholding for unpaid wages and liquidated damages. The Department of Energy or the Recipient or Subrecipient shall upon its own action or upon written request of an authorized representative of the Department of Labor withhold or cause to be withheld, from any moneys payable on account of work performed by the Contractor or subcontractor under any such contract or any other Federal contract with the same prime Contractor, or any other federally-assisted contract subject to the Contract Work Hours and Safety Standards Act, which is held by the same prime contractor, such sums as may be determined to be necessary to satisfy any liabilities of such Contractor or subcontractor for unpaid wages and liquidated damages as provided in the clause set forth in paragraph (b)(2) of this section.

(4) Contracts and Subcontracts. The Recipient, Subrecipient, and Recipient's and Subrecipient's contractor or subcontractor shall insert in any Contracts, the clauses set forth in paragraph (b)(1) through (4) of this section and also a clause requiring the subcontractors to include these clauses in any lower tier subcontracts. The Recipient shall be responsible for compliance by any subcontractor or lower tier subcontractor with the clauses set forth in paragraphs (b)(1) through (4) of this section.

(5) The Contractor or subcontractor shall maintain payrolls and basic payroll records during the course of the work and shall preserve them for a period of three years from the completion of the Contract for all laborers and mechanics, including guards and watchmen, working on the Contract. Such records shall contain the name and address of each such employee, social security number, correct classifications, hourly rates of wages paid, daily and weekly number of hours worked, deductions made, and actual wages paid. The records to be maintained under this paragraph shall be made available by the Contractor or subcontractor for inspection, copying, or transcription by authorized representatives of the Department of Energy and the Department of Labor, and the Contractor or subcontractor will permit such representatives to interview employees during working hours on the job.

(1) On behalf of the Department of Energy (DOE), Recipient shall perform the following functions:

(i) Obtain, maintain, and monitor all Davis Bacon Act (DBA) certified payroll records submitted by the Subrecipients and Contractors at any tier under this Award;

(ii) Review all DBA certified payroll records for compliance with DBA requirements, including applicable DOL wage determinations;

(iii) Notify DOE of any non-compliance with DBA requirements by Subrecipients or Contractors at any tier, including any non-compliances identified as the result of reviews performed pursuant to paragraph (ii) above;

(iv) Address any Subrecipient and any Contractor DBA non-compliance issues; if DBA non-compliance issues cannot be resolved in a timely manner, forward complaints, summary of investigations and all relevant information to DOE;

(v) Provide DOE with detailed information regarding the resolution of any DBA non-compliance issues;

(vi) Perform services in support of DOE investigations of complaints filed regarding noncompliance by Subrecipients and Contractors with DBA requirements;

(vii) Perform audit services as necessary to ensure compliance by Subrecipients and Contractors with DBA requirements and as requested by the Contracting Officer; and

(viii) Provide copies of all records upon request by DOE or DOL in a timely manner.

(d) Rates of Wages

The minimum wages to be paid laborers and mechanics under this award involved in performance of work at the project site, as determined by the Secretary of Labor to be prevailing for the corresponding classes of laborers and mechanics employed on projects of a character similar to the contract work in the pertinent locality, are found at http://www.wdol.gov/ , by clicking on “Selecting DBA WDs”. The Wage Determination Number(s) and General Decision Number(s) specific to this award are found below. These wage rates are minimum rates and are not intended to represent the actual wage rates that the Contractor may have to pay.



CONSTRUCTION TYPE	WAGE DETERMINATION NUMBER	GENERAL DECISION NUMBER
Building	CA29, CO7, CA25, KS8	CA100029 03/19/2010 CA29 CO100007 03/12/2010 CO7 CA100025 03/12/2010 CA25 KS100008 03/19/2010 KS8
Highway	n/a	n/a
Residential	n/a	n/a


30.	CONTINGENCY

(a)

Contingency Requirement . A minimum amount of Contingency is required for awards selected under Funding Opportunity Announcement DE-FOA-0000096. “Contingency” is defined in the Appendix as: “a provision in the Project Management Plan to mitigate cost and/or schedule risk.” Contingency funds must be (a) liquid, (b) immediately available, and (c) unrestricted funds dedicated exclusively to the Project for the purpose of mitigating project performance baseline risk. Contingency funds may come from a variety of sources, as approved by the Contracting Officer on a case-by-case basis in accordance with the Appendix to these Special Terms and Conditions (Attachment 5).


(b)	Minimum Amount of Contingency . Initial Contingency funds shall be not less than 25 percent of the Total Project Cost that begins with Budget Period 2, as more specifically described in Section B(2) of the Appendix to these Special Terms and Conditions (Attachment 5).


(c)	Contingency Not Counted Toward Cost Share or DOE Reimbursement . Contingency is in addition to the Total Project Cost and cannot count toward cost share or result in reimbursement by DOE above the share approved in the award.


(d)	Appendix . All of the terms and conditions set forth in this provision shall be further subject to the requirements and clarifications of Attachment 5.


31.	NATIONAL ENVIRONMENTAL POLICY ACT (NEPA) REQUIREMENTS

For this award, DOE has made a final NEPA determination for all activities under this award that are listed in the Statement of Project Objectives (SOPO) formally approved by DOE through incorporation into and attached to the award. You (Recipient) may proceed with the activities as described in the SOPO. This NEPA determination is specific to the project as described in the SOPO formally approved by DOE through incorporation into and attached to the award.

If you later add to or modify the activities in the above-referenced SOPO, you must submit the revised SOPO to the DOE Project Officer. Those additions or modifications are subject to review by the NEPA Compliance Officer and approval by the DOE's Contracting Officer. Recipients are restricted from taking any action using Federal funds, which would have an adverse effect on the environment or limit the choice of reasonable alternatives prior to DOE providing a final NEPA determination. Any new activities or modification of activities is subject to additional NEPA review and is not authorized for federal funding until DOE provides a NEPA determination on those additions or modifications. DOE may require the Recipient to submit additional information to support a revised NEPA determination. Should you move forward with activities that are not authorized for Federal funding by the DOE Contracting Officer in advance of the final NEPA determination, you are doing so at risk of not receiving Federal funding and such costs may not be recognized as allowable cost share.

ASSISTANCE AGREEMENT

1. Award No.

DE-EE0002869

2. Modification No.

006

3. Effective Date

12/28/2009

4. CFDA No.

81.087

5. Awarded To

AMYRIS BIOTECHNOLOGIES, INC.

Attn: KINKEAD REILING

5885 HOLLIS STREET

SUITE 100

EMERYVILLE CA 946082059

6. Sponsoring Office

Golden Field Office

U.S. Department of Energy

Golden Field Office

1617 Cole Blvd.

Golden CO 80401

7. Period of Performance

12/28/2009

through

06/30/2012

8. Type of Agreement

_ Grant

x Cooperative Agreement

_ Other

9. Authority

109-58 Energy Policy Act (2005)

111-5 Recovery Act (2009)

10. Purchase Request or Funding Document No.

11EE005464

11. Remittance Address

12. Total Amount

13. Funds Obligated

AMYRIS BIOTECHNOLOGIES, INC.

Attn: KINKEAD REILING

5885 HOLLIS STREET

SUITE 100

EMERYVILLE CA 946082059

Govt. Share: $ 24,341,409.00

Cost Share: $ 10,591,590.00

Total: $ 34,932,999.00

This action: $0.00

Total: $24,341,409.00

14. Principal Investigator

Neil Renninger

Phone: 510-740-7414

15. Program Manager

Fred W. Gerdeman

Phone: 303-275-4928

16. Administrator

Golden Field Office

U.S. Department of Energy

Golden Field Office

1617 Cole Blvd.

Golden CO 80401-3393

17. Submit Payment Requests To

OR for Golden

U.S. Department of Energy

Oak Ridge Financial Service Center

P.O. Box 4517

Oak Ridge TN 37831

18. Paying Office

OR for Golden

U.S. Department of Energy

Oak Ridge Financial Service Center

P.O. Box 4517

Oak Ridge TN 37831

19. Submit Reports To

20. Accounting and Appropriation Data

See Schedule

21. Research Title and/or Description of Project

RECOVERY ACT: SCALE-UP & MOBILIZATION OF RENEWABLE DIESEL & CHEMICAL PRODUCTION FROM COMMON INTERMEDIATE USING US-BASED FERMENTABLE SUGAR FEEDSTOCKS

For the Recipient

For the United States of America

22. Signature of Person Authorized to Sign

25. Signature of Grants/Agreements Officer

Signature on File

23. Name and Title

24. Date Signed

26. Name of Officer

Laura Merrick

27. Date Signed

07/26/2011



CONTINUATION SHEET		REFERENCE NO. OF DOCUMENT BEING CONTINUED DE-EE0002869/006			PAGE 2 OF 2

NAME OF OFFEROR OR CONTRACTOR AMYRIS BIOTECHNOLOGIES, INC.

ITEM NO. (A)	SUPPLIES/SERVICES (B)	QUANTITY (C)	UNIT (D)	UNIT PRICE (E)	AMOUNT (F)
	DUNS Number: 185930182 The purpose of this modification is to delete and replace Attachment 3, Reporting Requirements Checklist and Instructions, DOE F 4600.2, revising the following sections: A. Management Reporting, D. Closeout Reporting, E. Other Reporting, and Instructions attached to the Reporting Checklist. All other terms and conditions remain unchanged. In Block 7 of the Assistance Agreement, the Period of Performance reflects the beginning of the Project Period through the end of the current Budget Period, shown as 12/28/2009 through 6/30/2012. For multiple Budget Periods, see Special Terms and Conditions, Provision 4, Award Project Period and Budget Periods. DOE Award Administrator: Brenda Dias E-mail: brenda.dias@go.doe.gov Phone: 303-275-6043 DOE Project Officer: Fred Gerdeman E-mail: fred.gerdeman@go.doe.gov Phone: 303-275-4928 Recipient Business Officer: Todd Pray E-mail: pray@amyris.com Phone: 510-740-7441 Recipient Principal Investigator: Neil Renninger E-mail: renninger@amyris.com Phone: 510-740-7414 “Electronic signature or signatures as used in this document means a method of signing an electronic message that-- (A) Identifies and authenticates a particular person as the source of the electronic message; (B) Indicates such person's approval of the information contained in the electronic message; and, (C) Submission via FedConnect constitutes electronically signed documents.” ASAP: NO : STD IMMEDIATE Extent Competed: COMPETED Davis-Bacon Act: YES
JULY 2004



1. Identification Number: DE-EE0002869.006	2. Program/Project Title: Recovery Act: Scale-up and Mobilization of Renewable Diesel and Chemical Production from Common Intermediate using US-based Fermentable Sugar Feedstocks
3. Recipient: Amyris Biotechnologies, Inc.
4. Reporting Requirements:	Frequency	Addresses
A. MANAGEMENT REPORTING X Research Performance Progress Report (RPPR) X Special Status Report B. SCIENTIFIC/TECHNICAL REPORTING (Reports/Products must be submitted with appropriate DOE F 241. The 241 forms are available at www.osti.gov/elink) Report/Product Form X Final Scientific Report DOE F 241.3 X Conference papers/proceedings* DOE F 241.3 __ Software/Manual DOE F 241.4 __ Other (see special instructions) DOE F 241.3 * Scientific and technical conferences only C. FINANCIAL REPORTING X SF-425, Federal Financial Report FQ D. CLOSEOUT REPORTING X Patent Certification X SF-428 & 428B Final Property Report __ Other E. OTHER REPORTING X Annual Indirect Cost Proposal X Audit of For-Profit Recipients __ SF-428 Tangible Personal Property Report Forms Family X Other	Q A F A FQ F F Y180 Y180 AY	https://www.eere-pmc.energy.gov/ https://www.eere-pmc.energy.gov/SubmitReports.aspx http://www.osti.gov/elink-2413 http://www.osti.gov/elink-2413 http://www.osti.gov/estsc/241-4pre.jsp http://www.osti.gov/elink-2413 https://www.eere-pmc.energy.gov/ https://www.eere-pmc.energy.gov/SubmitReports.aspx https://www.eere-pmc.energy.gov/SubmitReports.aspx https://www.eere-pmc.energy.gov/SubmitReports.aspx See block 5 below for instructions. See block 5 below for addresses. https://www.eere-pmc.energy.gov/SubmitReports.aspx https://www.eere-pmc.energy.gov/SubmitReports.aspx
FREQUENCY CODES AND DUE DATES: A - Within 5 calendar days after events or as specified. F - Final; 90 calendar days after expiration or termination of the award. Y - Yearly; 90 days after the end of the reporting period. S - Semiannually; within 30 days after end of the reporting period. Q - Quarterly; within 30 days after end of the reporting period. Y180 - Yearly; 180 days after end of the recipient's fiscal year. O - Other; See instructions for further details.
5. Special Instructions: Annual Indirect Cost Proposal - If DOE is the Cognizant Federal Agency, then the proposal should be sent to https://www.eere-pmc.energy.gov/SubmitReports.aspx . Otherwise, it should be sent to the Cognizant Federal Agency. Audit of For-Profit Recipients must be sent to 2 different addresses in accordance with the final audit guidance. A copy for the Contracting Officer shall be submitted via https://www.eere-pmc.energy.gov/SubmitReports.aspx ; a copy must also be e-mailed to the CFO at DOE-Audit-Submissions@hq.doe.gov OTHER REPORTING Special Instructions: 1) A Project Management Plan (PMP) is due to the Project Officer 30 days after award and should be revised on a yearly basis. An electronic template will be provided to the Recipient to complete or update as needed. 2) An Annual Technical and Financial Report must be developed and submitted to the DOE Project Officer after award and must be updated annually throughout the duration of the award. Subject to the availability of project funding, the Report will also be due annually for three (3) years after the facility is substantially completed. The schedule for submission will be established by the DOE Project Officer after award. The format for the report with instructions for completion, the electronic template for reporting data, and the schedule will be forwarded to the Recipient after award. 3) Comprehensive Annual Project Review - The Recipient will be required to present the Annual Technical and Financial Report at a Comprehensive Annual Project Review meeting. The schedule for the Comprehensive Annual Project Review will be established by the DOE Project Officer after the award. AMERICAN RECOVERY AND REINVESTMENT ACT REPORTING: See the Special Terms and Conditions for Recovery Act reporting requirements, along with the following website: http://www.federalreporting.gov. The required reports are due no later than ten calendar days after each calendar quarter in which the Recipient receives the assistance award funded in whole or in part by the Recovery Act. Recipients are to report according to ARRA reporting instructions.

Federal Assistance Reporting Instructions (3/11)

A. MANAGEMENT REPORTING

Research Performance Progress Report (RPPR)

See attached document entitled "Research Performance Progress Report".

Special Status Report

The recipient must report the following events by e-mail as soon as possible after they occur:

1. Developments that have a significant favorable impact on the project.

2. Problems, delays, or adverse conditions which materially impair the recipient's ability to meet the objectives of the award or which may require DOE to respond to questions relating to such events from the public. The recipient must report any of the following incidents and include the anticipated impact and remedial action to be taken to correct or resolve the problem/condition:

a. Any single fatality or injuries requiring hospitalization of five or more individuals.

b. Any significant environmental permit violation.

c. Any verbal or written Notice of Violation of any Environmental, Safety, and Health statutes.

d. Any incident which causes a significant process or hazard control system failure.

e. Any event which is anticipated to cause a significant schedule slippage or cost increase.

f. Any damage to Government-owned equipment in excess of $50,000.

g. Any other incident that has the potential for high visibility in the media.

B. SCIENTIFIC/TECHNICAL REPORTS

Final Scientific/Technical Report

Content . The final scientific/technical report must include the following information and any other information identified under Special Instructions on the Federal Assistance Reporting Checklist:

1. Identify the DOE award number; name of recipient; project title; name of project director/principal investigator; and consortium/teaming members.

2. Display prominently on the cover of the report any authorized distribution limitation notices, such as patentable material or protected data. Reports delivered without such notices may be deemed to have been furnished with unlimited rights, and the Government assumes no liability for the disclosure, use or reproduction of such reports.

3. Provide an executive summary, which includes a discussion of: (1) how the research adds to the understanding of the area investigated; (2) the technical effectiveness and economic feasibility of the methods or techniques investigated or demonstrated; or (3) how the project is otherwise of benefit to the public. The discussion should be a minimum of one paragraph and written in terms understandable by an educated layman.

4. Provide a comparison of the actual accomplishments with the goals and objectives of the project.

5. Summarize project activities for the entire period of funding, including original hypotheses, approaches used, problems encountered and departure from planned methodology, and an assessment of their impact on the project results. Include, if applicable, facts, figures, analyses, and assumptions used during the life of the project to support the conclusions.

6. Identify products developed under the award and technology transfer activities, such as:


a.	Publications (list journal name, volume, issue), conference papers, or other public releases of results. If not provided previously, attach or send copies of any public releases to the DOE Program Manager identified in Block 15 of the Assistance Agreement Cover page;


b.	Web site or other Internet sites that reflect the results of this project;


c.	Networks or collaborations fostered;


d.	Technologies/Techniques;


e.	Inventions/Patent Applications, licensing agreements; and


f.	Other products, such as data or databases, physical collections, audio or video, software or netware, models, educational aid or curricula, instruments or equipment.

7. For projects involving computer modeling, provide the following information with the final report:


a.	Model description, key assumptions, version, source and intended use;


b.	Performance criteria for the model related to the intended use;


c.	Test results to demonstrate the model performance criteria were met (e.g., code verification/validation, sensitivity analyses, history matching with lab or field data, as appropriate);


d.	Theory behind the model, expressed in non-mathematical terms;


e.	Mathematics to be used, including formulas and calculation methods;


f.	Whether or not the theory and mathematical algorithms were peer reviewed, and, if so, include a summary of theoretical strengths and weaknesses;


g.	Hardware requirements; and


h.	Documentation (e.g., users guide, model code).

Electronic Submission . The final scientific/technical report must be submitted electronically via the DOE Energy Link System (E-Link) accessed at http://www.osti.gov/elink-2413 .

Electronic Format . Reports must be submitted in the ADOBE PORTABLE DOCUMENT FORMAT (PDF) and be one integrated PDF file that contains all text, tables, diagrams, photographs, schematic, graphs, and charts. Materials, such as prints, videos, and books, that are essential to the report but cannot be submitted electronically, should be sent to the DOE Administrator at the address listed in Block 16 of the Assistance Agreement Cover Page.

Submittal Form . The report must be accompanied by a completed electronic version of DOE Form 241.3, “U.S. Department of Energy (DOE), Announcement of Scientific and Technical Information (STI).” You can complete, upload, and submit the DOE F 241.3 online via ELink. You are encouraged not to submit patentable material or protected data in these reports, but if there is such material or data in the report, you must: (1) clearly identify patentable or protected data on each page of the report; (2) identify such material on the cover of the report; and (3) mark the appropriate block in Section K of the DOE F 241 3. Reports must not contain any limited rights data (proprietary data), classified information, information subject to export control classification, or other information not subject to release. Protected data is specific technical data, first produced in the performance of the award that is protected from public release for a period of time by the terms of the award agreement.

Conference Papers/Proceedings

Content . The recipient must submit a copy of any conference papers/proceedings, with the following information: (1) Name of conference; (2) Location of conference; (3) Date of conference; and (4) Conference sponsor.

Electronic Submission . Scientific/technical conference paper/proceedings must be submitted electronically via the DOE Energy Link System (E-Link) at http://www.osti.gov/elink-2413 . Non-scientific/technical conference papers/proceedings must be sent to the URL listed on the Reporting Checklist.

Electronic Format . Conference papers/proceedings must be submitted in the ADOBE PORTABLE DOCUMENT FORMAT (PDF) and be one integrated PDF file that contains all text, tables, diagrams, photographs, schematic, graphs, and charts. If the proceedings cannot be submitted electronically, they should be sent to the DOE

Administrator at the address listed in Block 16 of the Assistance Agreement Cover Page.

Submittal Form . Scientific/technical conference papers/proceedings must be accompanied by a completed DOE Form 241.3. The form and instructions are available on E-Link at

http://www.osti.gov/elink-2413 . This form is not required for non-scientific or non-technical conference papers or proceedings.

Software/Manual

Content . Unless otherwise specified in the award, the following must be delivered: source code, the executable object code and the minimum support documentation needed by a competent user to understand and use the software and to be able to modify the software in subsequent development efforts.

Electronic Submission . Submissions may be submitted electronically via the DOE Energy Link System (E-Link) at http://www.osti.gov/estsc/241-4pre.jsp . They may also be submitted via regular mail to:

Energy Science and Technology Software Center

P.O. Box 1020

Oak Ridge, TN 37831

Submittal Form . Each software deliverable and its manual must be accompanied by a completed DOE Form 241.4, “Announcement of U.S. Department of Energy Computer Software.” The form and instructions are available on E-Link at http://www.osti.gov/estsc/241-4pre.jsp .

Protected Personally Identifiable Information (PII) . Management Reports or Scientific/Technical Reports must not contain any Protected PII. PII is any information about an individual which can be used to distinguish or trace an individual's identity. Some information that is considered to be PII is available in public sources such as telephone books, public websites, university listings, etc. This type of information is considered to be Public PII and includes, for example, first and last name, address, work telephone number, e-mail address, home telephone number, and general educational credentials. In contrast, Protected PII is defined as an individual's first name or first initial and last name in combination with any one or more of types of information, including, but not limited to, social security number, passport number, credit card numbers, clearances, bank numbers, biometrics, date and place of birth, mother's maiden name, criminal, medical and financial records, educational transcripts, etc.

C. FINANCIAL REPORTING

Recipients must complete the SF-425 as identified on the Reporting Checklist in accordance with the report instructions. A fillable version of the form is available at

http://www.whitehouse.gov/omb/grants/grants_forms.aspx .

D. CLOSEOUT REPORTS

Final Invention and Patent Report

The recipient must provide a DOE Form 2050.11 , “PATENT CERTIFICATION.” This form

is available at http://management.energy.gov/business_doe/business_forms.htm

Final Property Report

See instructions under SF-428 Tangible Personal Property Report Forms Family below.

E. OTHER REPORTING

Annual Indirect Cost Proposal and Reconciliation

Requirement. In accordance with the applicable cost principles, the recipient must submit an annual indirect cost proposal, reconciled to its financial statements, within six months after the close of the recipient's fiscal year, unless the award is based on a predetermined or fixed indirect rate(s), or a fixed amount for indirect or facilities and administration (F&A) costs. Cognizant Agency. The recipient must submit its annual indirect cost proposal directly to the cognizant agency for negotiating and approving indirect costs. If the DOE awarding office is the cognizant agency, submit the annual indirect cost proposal to https://www.eerepmc.energy.gov/SubmitReports.aspx .

Audit of For-Profit Recipients

As required by 10 CFR 600.316, as supplemented by For-Profit Audit Guidance Parts I through IV, audits must be performed of For-Profit Recipients of financial assistance awards (prime awards) and sub-awards. For-Profit Audit Guidance Parts I through IV to assist for-profit recipients in complying with the audit requirements of 10 CFR 600.316 are posted on the Financial Assistance Forms page of the MA home page under the 'Coverage of Independent Audits' subheading, http://management.energy.gov/business_doe/business_forms.htm . Submission: For recipients, financial statement and compliance audit submissions are due to DOE within six months of the recipients' fiscal year-end dates. For sub-awardees, financial statement and compliance audit submissions are due to the pass-through entity within six months of the sub-awardees' fiscal year-end dates. For recipients, the compliance audits must be submitted, along with audited financial statements, to the appropriate DOE Contracting Officer at https://www.eere-pmc.energy.gov/SubmitReports.aspx as well as to the DOE Office of the Chief Financial Officer at DOE-Audit-Submission@hq.doe.gov

SF-428 Tangible Personal Property Report Forms Family

Requirement. The SF-428 is a forms family consisting of 5 forms: the SF-428, SF-428-A, SF- 428-B, SF-428-C, and SF-428S. Fillable versions of the SF-428 forms are available at http://management.energy.gov/business_doe/business_forms.htm .

• The SF-428 is the cover page and the submitter attaches the appropriate form or forms as

listed on the SF-428.

• The SF-428-A is the Annual report, due Oct. 30th of each calendar year.

• The SF-428-B is the Final Award Closeout Report, due at award completion.

• The SF-428-C is the Disposition Report/Request.

• The SF-428S is the supplemental form for the SF-428-A, SF-428-B and SF-428-C.

If at any time during the award the recipient is provided Government-furnished property or acquires property with project funds and the award specifies that the property vests in the Federal Government (i.e. federally owned property), the recipient must submit an annual inventory of this property to the DOE Administrator using the SF-428 and SF-428-A forms at the address on page 1 of this checklist no later than October 30th of each calendar year, to cover an annual reporting period ending on the preceding September 30th. The SF-428 and SF-428-B reports are required during closeout.

Content of Inventory . As required on the SF-428-A form, the inventory must include a description of the property, tag number, acquisition date, and acquisition cost, if purchased with project funds. The location of property should be listed under the Comments section. The report must list all federally owned property, including property located at subcontractor's facilities or other locations.

Attachment 1

Reporting Requirements Checklist for RD&D awards

RESEARCH PERFORMANCE PROGRESS REPORT

Standard Cover Page Data Elements and Reporting Categories

The standard cover page data elements shown below, as well as mandatory and optional components comprise the complete research performance progress report format.

Each category in the RPPR is a separate reporting component. Each component is marked to indicate if it is optional or mandatory. Mandatory components must be addressed in each report, optional are at your discretion.

If you have nothing significant to report during the reporting period on a question or item, state

"Nothing To Report".

1. COVER PAGE DATA ELEMENTS : Mandatory


•	Federal Agency and Organization Element to Which Report is Submitted


•	Federal Grant or Other Identifying Number Assigned by Agency


•	Project Title


•	PD/PI Name, Title and Contact Information (e-mail address and phone number)


•	Name of Submitting Official, Title, and Contact Information (e-mail address and phone number), if other than PD/PI


•	Submission Date


•	DUNS Number


•	Recipient Organization (Name and Address)


•	Project/Grant Period (Start Date, End Date)


•	Reporting Period End Date


•	Report Term or Frequency (annual, semi-annual, quarterly, other)


•	Signature of Submitting Official (electronic signatures (i.e., Adobe Acrobat) are acceptable)

2. ACCOMPLISHMENTS : Mandatory

What was done? What was learned?

The information provided in this section allows the agency to assess whether satisfactory progress has been made during the reporting period.

INSTRUCTIONS - Accomplishments

The PI is reminded that the grantee is required to obtain prior written approval from the Contracting Officer whenever there are significant changes in the project or its

direction. Requests for prior written approval must be submitted to the Contracting Officer (submission via Fedconnect is acceptable).


•	What are the major goals and objectives of the project?


•	What was accomplished under these goals?


•	What opportunities for training and professional development has the project provided?


•	How have the results been disseminated to communities of interest?


•	What do you plan to do during the next reporting period to accomplish the goals and

objectives?

What are the major goals of the project?

List the major goals of the project as stated in the approved application or as approved by the agency. If the application lists milestones/target dates for important activities or phases of the project, identify these dates and show actual completion dates or the percentage of completion. Generally, the goals will not change from one reporting period to the next. However, if the awarding agency approved changes to the goals during the reporting period, list the revised goals and objectives. Also explain any significant changes in approach or methods from the agency approved application or plan.

What was accomplished under these goals?

For this reporting period describe: (1) major activities; (2) specific objectives; (3) significant results, including major findings, developments, or conclusions (both positive and negative); and (4) key outcomes or other achievements. Include a discussion of stated goals not met. As the project progresses, the emphasis in reporting in this section should shift from reporting activities to reporting accomplishments.

What opportunities for training and professional development has the project provided?

Describe opportunities for training and professional development provided to anyone who worked on the project or anyone who was involved in the activities supported by the project. “Training” activities are those in which individuals with advanced professional skills and experience assist others in attaining greater proficiency. Training activities may include, for example, courses or one-on-one work with a mentor. “Professional development” activities result in increased knowledge or skill in one's area of expertise and may include workshops, conferences, seminars, study groups, and individual study. Include participation in conferences, workshops, and seminars not listed under major activities.

How have the results been disseminated to communities of interest?

Describe how the results have been disseminated to communities of interest. Include any outreach activities that have been undertaken to reach members of communities who are not

usually aware of these research activities, for the purpose of enhancing public understanding and increasing interest in learning and careers in science, technology, and the humanities.

What do you plan to do during the next reporting period to accomplish the goals?

Describe briefly what you plan to do during the next reporting period to accomplish the goals and objectives.

3. PRODUCTS : [Optional/Mandatory]

What has the project produced?

Publications are the characteristic product of research. Agencies evaluate what the publications demonstrate about the excellence and significance of the research and the efficacy with which the results are being communicated to colleagues, potential users, and the public, not the number of publications. Many projects (though not all) develop significant products other than publications. Agencies assess and report both publications and other products to Congress, communities of interest, and the public.

INSTRUCTIONS - Products

List any products resulting from the project during the reporting period. Examples of products include:


•	Publications, conference papers, and presentations;


•	Website(s) or other Internet site(s);


•	Technologies or techniques;


•	Inventions, patent applications, and/or licenses;


•	Other products, such as data or databases, physical collections, audio or video products, software or NetWare, models, educational aids or curricula, instruments, or equipment; and Any other public release of information related to the project.

Publications, conference papers, and presentations

Report only the major publication(s) resulting from the work under this award. There is no restriction on the number. However, agencies are interested in only those publications that most reflect the work under this award in the following categories:

•

Journal publications. List peer-reviewed articles or papers appearing in scientific, technical, or professional journals. Include any peer-reviewed publication in the periodically published proceedings of a scientific society, a conference, or the like. A publication in the proceedings of a one-time conference, not part of a series, should be reported under "Books or other non-periodical, one-time publications." Identify for each publication: Author(s); title; journal; volume: year; page numbers; status of publication (published; accepted, awaiting publication; submitted, under review; other); acknowledgement of federal support (yes/no).


•	Books or other non-periodical, one-time publications. Report any book, monograph, dissertation, abstract, or the like published as or in a separate publication, rather than a periodical or series. Include any significant publication in the proceedings of a one-time conference or in the report of a one-time study, commission, or the like.

Identify for each one-time publication: author(s); title; editor; title of collection, if applicable; bibliographic information; year; type of publication (book, thesis or dissertation, other); status of publication (published; accepted, awaiting publication; submitted, under review; other); acknowledgement of federal support (yes/no).


•	Other publications, conference papers and presentations. Identify any other publications, conference papers and/or presentations not reported above. Specify the status of the publication as noted above.

Website(s) or other Internet site(s)

List the URL for any Internet site(s) that disseminates the results of the research activities. A short description of each site should be provided. It is not necessary to include the publications already specified above in this section.

Technologies or techniques

Identify technologies or techniques that have resulted from the research activities. Describe the technologies or techniques and how they are being shared.

Inventions, patent applications, and/or licenses

Identify inventions, patent applications with date, and/or licenses that have resulted from the research. Submission of this information as part of an interim research performance progress report is not a substitute for any other invention reporting required under the terms and conditions of an award.

Other products

Identify any other significant products that were developed under this project. Describe the product and how it is being shared. Examples of other products are:


•	Databases;


•	Physical collections;


•	Audio or video products;


•	Software or NetWare;


•	Models;


•	Educational aids or curricula;


•	Instruments or equipment;


•	Data & Research Material (e.g., cell lines, DNA probes, animal models); and


•	Other.

4. PARTICIPANTS & OTHER COLLABORATING ORGANIZATIONS:

[Optional/Mandatory]

Who has been involved?

Agencies need to know who has worked on the project to gauge and report performance in promoting partnerships and collaborations.

INSTRUCTIONS - Participants & Other Collaborating Organizations

Provide the following information on participants:


•	What individuals have worked on the project?


•	What other organizations have been involved as partners?


•	Have other collaborators or contacts been involved?

What individuals have worked on the project?

Provide the following information for: (1) principal investigator(s)/project director(s) (PIs/PDs); and (2) each person who has worked at least one person month per year on the project during the reporting period, regardless of the source of compensation (a person month equals approximately 160 hours of effort).

•

Provide the name and identify the role the person played in the project . Do NOT include any other identifying information on individuals. Indicate the nearest whole person month (Calendar, Academic, Summer) that the individual worked on the project. Show the most senior role in which the person has worked on the project for any significant length of time. For example, if an undergraduate student graduates, enters graduate school, and continues to work on the project, show that person as a graduate student, preferably explaining the change in involvement.


•	Describe how this person contributed to the project and with what funding support . If information is unchanged from a previous submission, provide the name only and indicate “no change”.


•	Identify whether this person is collaborating internationally . Specifically is the person collaborating with an individual located in a foreign country and whether the person had traveled to the foreign country as part of that collaboration and duration of stay. The foreign country(ies) should be identified.

Example:

Name: Mary Smith

Project Role: Graduate Student

Nearest person month worked: 5

Contribution to Project: Ms. Smith has performed work in the area of

combined error-control and constrained coding.

Funding Support: The Ford Foundation (Complete only if the

funding provided from other than this award.)

Collaborated with individual in

foreign country: Yes

Country(ies) of foreign collaborator: China

Traveled to foreign country: Yes

If traveled to foreign country(ies),

duration of stay: 5 months

What other organizations have been involved as partners?

Describe partner organizations - academic institutions, other nonprofits, industrial or commercial firms, state or local governments, schools or school systems, or other organizations (foreign or domestic) - that have been involved with the project. Partner organizations may provide financial or in-kind support, supply facilities or equipment, collaborate in the research, exchange personnel, or otherwise contribute.

Provide the following information for each partnership:

Organization Name :

Location of Organization : (if foreign location list country)

Partner's contribution to the project : (identify one or more)


•	Financial support;


•	In-kind support (e.g., partner makes software, computers, equipment, etc., available to project staff);


•	Facilities (e.g., project staff use the partner's facilities for project activities);


•	Collaborative research (e.g., partner's staff work with project staff on the project); and


•	Personnel exchanges (e.g., project staff and/or partner's staff use each other's facilities, work at each other's site).


•

More detail on partner and contribution (foreign or domestic).

Have other collaborators or contacts been involved?

Some significant collaborators or contacts within the recipient's organization may not be covered by "What people have worked on the project?" Likewise, some significant collaborators or contacts outside the recipient's organization may not be covered under "What other organizations have been involved as partners?" For example, describe any significant:


•	collaborations with others within the recipient's organization; especially interdepartmental or interdisciplinary collaborations;


•	collaborations or contact with others outside the organization; and


•	collaborations or contacts with others outside the United States or with an international organization.


•	country(ies) of collaborations or contacts.

It is likely that many recipients will have no other collaborators or contacts to report.

5. IMPACT : [Optional/Mandatory]

What is the impact of the project? How has it contributed?

Over the years, this base of knowledge, techniques, people, and infrastructure is drawn upon again and again for application to commercial technology and the economy, to health and safety, to cost-efficient environmental protection, to the solution of social problems, to numerous other aspects of the public welfare, and to other fields of endeavor.

The taxpaying public and its representatives deserve a periodic assessment to show them how the investments they make benefit the nation. Through this reporting format, and especially this section, recipients provide that assessment and make the case for Federal funding of research and education.

Agencies use this information to assess how their research programs:


•	increase the body of knowledge and techniques;


•	enlarge the pool of people trained to develop that knowledge and techniques or put it to use;

and


•	improve the physical, institutional, and information resources that enable those people to get

their training and perform their functions.

INSTRUCTIONS - Impact

This component will be used to describe ways in which the work, findings, and specific products of the project have had an impact during this reporting period. Describe distinctive contributions, major accomplishments, innovations, successes, or any change in practice or behavior that has come about as a result of the project relative to:


•	the development of the principal discipline(s) of the project;


•	other disciplines;


•	the development of human resources;


•	physical, institutional, and information resources that form infrastructure;


•	technology transfer (include transfer of results to entities in government or industry,

adoption of new practices, or instances where research has led to the initiation of a startup

company); or


•	society beyond science and technology.

What is the impact on the development of the principal discipline(s) of the project?

Describe how findings, results, techniques that were developed or extended, or other products from the project made an impact or are likely to make an impact on the base of knowledge, theory, and research and/or pedagogical methods in the principal disciplinary field(s) of the project. Summarize using language that an intelligent lay audience can understand ( Scientific American style).

How the field or discipline is defined is not as important as covering the impact the work has had on knowledge and technique. Make the best distinction possible, for example, by using a "field" or "discipline", if appropriate, that corresponds with a single academic department (i.e., physics rather than nuclear physics).

What is the impact on other disciplines?

Describe how the findings, results, or techniques that were developed or improved, or other products from the project made an impact or are likely to make an impact on other disciplines.

What is the impact on the development of human resources?

Describe how the project made an impact or is likely to make an impact on human resource development in science, engineering, and technology. For example, how has the project:


•	provided opportunities for research and teaching in the relevant fields;


•	improved the performance, skills, or attitudes of members of underrepresented groups that will improve their access to or retention in research, teaching, or other related professions;


•	developed and disseminated new educational materials or provided scholarships; or


•	provided exposure to science and technology for practitioners, teachers, young people, or other members of the public?

What is the impact on physical, institutional, and information resources that form

infrastructure?

Describe ways, if any, in which the project made an impact, or is likely to make an impact, on

physical, institutional, and information resources that form infrastructure, including:


•	physical resources such as facilities, laboratories, or instruments;


•	institutional resources (such as establishment or sustenance of societies or organizations); or


•	information resources, electronic means for accessing such resources or for scientific communication, or the like.

What is the impact on technology transfer?

Describe ways in which the project made an impact, or is likely to make an impact, on commercial technology or public use, including:


•	transfer of results to entities in government or industry;


•	instances where the research has led to the initiation of a start-up company; or


•	adoption of new practices.

What is the impact on society beyond science and technology?

Describe how results from the project made an impact, or are likely to make an impact, beyond the bounds of science, engineering, and the academic world on areas such as:


•	improving public knowledge, attitudes, skills, and abilities;


•	changing behavior, practices, decision making, policies (including regulatory policies), or

social actions; or


•	improving social, economic, civic, or environmental conditions.

What dollar amount of the award's budget is being spent in foreign country(ies)?

Describe what percentage of the award's budget is being spent in foreign country(ies). If more than one foreign country, identify the distribution between the foreign countries.

6. CHANGES/PROBLEMS : [Optional/Mandatory]

The PI is reminded that the grantee is required to obtain prior written approval from the Contracting Officer whenever there are significant changes in the project or its direction. Requests for prior written approval must be submitted to the Contracting Officer (submission via Fedconnect is acceptable). If not previously reported in writing, provide the following additional information, if applicable:


•	Changes in approach and reasons for change.


•	Actual or anticipated problems or delays and actions or plans to resolve them.


•	Changes that have a significant impact on expenditures.


•	Significant changes in use or care of animals, human subjects, and/or biohazards.

INSTRUCTIONS - Changes/Problems

Changes in approach and reasons for change

Describe any changes in approach during the reporting period and reasons for these changes. Remember that significant changes in objectives and scope require prior approval of the agency.

Actual or anticipated problems or delays and actions or plans to resolve them

Describe problems or delays encountered during the reporting period and actions or plans to resolve them.

Changes that have a significant impact on expenditures

Describe changes during the reporting period that may have a significant impact on expenditures, for example, delays in hiring staff or favorable developments that enable meeting objectives at less cost than anticipated.

Significant changes in use or care of human subjects, vertebrate animals, and/or

Biohazards

Describe significant deviations, unexpected outcomes, or changes in approved protocols for the use or care of human subjects, vertebrate animals, and/or biohazards during the reporting period. If required, were these changes approved by the applicable institution committee and reported to the agency? Also specify the applicable Institutional Review Board/Institutional Animal Care and Use Committee approval dates.

Change of primary performance site location from that originally proposed

Identify any change to the primary performance site location identified in the proposal, as originally submitted.

7. SPECIAL REPORTING REQUIREMENTS : [Optional/Mandatory]

Respond to any special reporting requirements specified in the award terms and conditions, as well as any award specific reporting requirements.

8. BUDGETARY INFORMATION : [Optional/Mandatory]

This component will be used to collect budgetary data from the recipient organization. The information will be used in conducting periodic administrative/budgetary reviews. Budgetary data should be submitted in an Excel spreadsheet format.

ASSISTANCE AGREEMENT

1. Award No.

DE-EE0002869

2. Modification No.

007

3. Effective Date

12/28/2009

4. CFDA No.

81.087

5. Awarded To

AMYRIS, INC.

Attn: NEIL RENNINGER

5885 HOLLIS STREET

SUITE 100

EMERYVILLE CA 946082059

6. Sponsoring Office

Energy Effcy & Renewable Energy

7. Period of Performance

12/28/2009

through

06/30/2012

8. Type of Agreement

_ Grant

x Cooperative Agreement

_ Other

9. Authority

109-58 Energy Policy Act (2005)

111-5 Recovery Act (2009)

10. Purchase Request or Funding Document No.

12EE001279

11. Remittance Address

12. Total Amount

13. Funds Obligated

AMYRIS, INC.

Attn: NEIL RENNINGER

5885 HOLLIS STREET

SUITE 100

EMERYVILLE CA 946082059

Govt. Share: $ 24,341,409.00

Cost Share: $ 10,591,590.00

Total: $ 34,932,999.00

This action: $0.00

Total: $24,341,409.00

14. Principal Investigator

Neil Renninger

Phone: 510-740-7414

15. Program Manager

Bryna E. Berendzen

Phone: 720-356-1442

16. Administrator

Golden Field Office

U.S. Department of Energy

Golden Field Office

1617 Cole Blvd.

Golden CO 80401-3393

17. Submit Payment Requests To

OR for Golden

U.S. Department of Energy

Oak Ridge Financial Service Center

P.O. Box 4517

Oak Ridge TN 37831

18. Paying Office

OR for Golden

U.S. Department of Energy

Oak Ridge Financial Service Center

P.O. Box 4517

Oak Ridge TN 37831

19. Submit Reports To

20. Accounting and Appropriation Data

See Schedule

21. Research Title and/or Description of Project

RECOVERY ACT: SCALE-UP & MOBILIZATION OF RENEWABLE DIESEL & CHEMICAL PRODUCTION FROM COMMON INTERMEDIATE USING US-BASED FERMENTABLE SUGAR FEEDSTOCKS

For the Recipient

For the United States of America

22. Signature of Person Authorized to Sign

25. Signature of Grants/Agreements Officer

Signature on File

23. Name and Title

24. Date Signed

26. Name of Officer

Brenda L. Dias

27. Date Signed

01/20/2012



CONTINUATION SHEET		REFERENCE NO. OF DOCUMENT BEING CONTINUED DE-EE0002869/007			PAGE 2 OF 2

NAME OF OFFEROR OR CONTRACTOR AMYRIS, INC.

ITEM NO. (A)	SUPPLIES/SERVICES (B)	QUANTITY (C)	UNIT (D)	UNIT PRICE (E)	AMOUNT (F)
	DUNS Number: 185930182 The purpose of this modification are to: 1) Complete a novation/change of name, changing the recipient from Amyris Biotechnologies, Inc. to Amyris, Inc. See attachment for a copy of the signed and executed novation and change of name agreement which by this modification is incorporated by reference into this award; and, 2) Update the DOE Project Officer, as shown below. All others and conditions remain unchanged. In Block 7 of the Assistance Agreement, the Period of Performance reflects the beginning of the Project Period through the end of the current Budget Period, shown as 12/28/2009 through 6/30/2012. For multiple Budget Periods, see Special Terms and Conditions, Provision 4, Award Project Period and Budget Periods. DOE Award Administrator: Brenda Dias E-mail: brenda.dias@go.doe.gov Phone: 720-356-1519 DOE Project Officer: Bryna Berendzen E-mail: bryna.berendzen@go.doe.gov Phone: 720-356-1442 Recipient Business Officer: Todd Pray E-mail: pray@amyris.com Phone: 510-740-7441 Recipient Principal Investigator: Neil Renninger E-mail: renninger@amyris.com Phone: 510-740-7414 “Electronic signature or signatures as used in this document means a method of signing an electronic message that-- (A) Identifies and authenticates a particular person as the source of the electronic message; (B) Indicates such person's approval of the information contained in the electronic message; and, (C) Submission via FedConnect constitutes electronically signed documents.” ASAP: NO: STD IMMEDIATE Extent Competed: COMPETED Davis-Bacon Act: YES
JULY 2004

NOVATION AND CHANGE OF NAME AGREEMENT

Amyris, Inc. (Transferee), a corporation duly organized and existing under the laws of Delaware, with its principal office in Emeryville, CA; and the United States of America (Government), enter into this Novation and Change of Name Agreement (Agreement) in accordance with the terms set forth below.

WHEREAS, on or about December 30, 2009, the Government, represented by Contracting Officer(s) of the Department of Energy, awarded Cooperative Agreement Number DE-EE0002869, entitled "Recovery Act: Scale-up & Mobilization of Renewable Diesel & Chemical Production from Common Intermediate Using US-Based Fermentable Sugar Feedstocks" (hereinafter, including all modifications, referred to as "the Award") to Amyris Biotechnologies, Inc. a California corporation (Predecessor), who was Transferee's predecessor-in-interest; and

WHEREAS, the Transferee has requested that the Award be assigned to the Transferee as a result of a corporate merger by conversion of shares, change of name and reincorporation; and

WHEREAS, the Transferee represents and warrants the following facts to the Government in support of its request to assign the Award:

1. By virtue of a certain Agreement and Plan of Merger (attached hereto and incorporated herein by reference as Exhibit A ), as verified by that certain Certificate of Merger of Amyris Biotechnologies, Inc., a California corporation, With and Into Amyris Biotechnologies, Inc., a Delaware corporation ("Amyris Delaware") (attached hereto and incorporated herein by reference as Exhibit B ), both executed as of June 10, 2010, all of Predecessor's personnel, assets (including intellectual property), and liabilities were transferred to Amyris Delaware; and

2. By virtue of a certain Restated Certificate of Incorporation, executed as of June 21, 2010 (attached hereto and incorporated herein by reference as Exhibit C ), Amyris Delaware changed its name from Amyris Biotechnologies, Inc., to Amyris, Inc.; and

3. The Transferee owns, or has acquired, all the assets necessary to perform the Award by virtue of the foregoing transactions; and

4. The Transferee has assumed all obligations and liabilities of the Predecessor under the Award by virtue of the above transactions and this Novation; and

5. The Transferee unconditionally guarantees, inter alia, the Transferee's performance of all obligations required under the Award; and

6. The Transferee is in a position to fully perform all obligations that may exist under the Award (see also additional representations contained in the Recipient Change Request Questionnaire and the legal opinion letter dated November 8, 2011, both of which are attached hereto and incorporated herein by reference as Exhibits D and E respectively).

NOW, THEREFORE, in consideration of these facts, guarantees and representations and other good and valuable consideration, the parties agree that by this Novation and Change of Name Agreement:

1. It is consistent with the Government's interest to recognize the Transferee as the successor party to the Award.

2. The Transferee confirms that as the successor-in-interest to Predecessor, the assignment of the Award, and all of its rights and responsibilities under the Award, were in fact transferred to the Transferee, and that the Predecessor no longer exists as a legal entity and therefore any claims and rights that the Predecessor may have had against the Government or may have had in the future in connection with the Award, including all claims to any unexpended and uncommitted funds, are no longer of any legal force or effect as to the Predecessor.

3. The Transferee agrees to be bound by, and to perform in accordance with the conditions contained in the Award. The Transferee also assumes all obligations and liabilities of, and all claims against, the Predecessor under the Award as if the Transferee were the original party to the Award.

4. The Transferee ratifies all previous actions taken by the Predecessor with respect to the Award, with the same force and effect as if the action had been taken by the Transferee.

5. The Government recognizes the Transferee as the Predecessor's successor-in-interest in and to the Award. The Transferee by this Agreement becomes entitled to all rights, titles, and interests of the Predecessor in and to the Award as if the Transferee were the original party to the Award.

6. Except as expressly provided in this Agreement, nothing in it shall be construed as a waiver of any rights of the Government against the Predecessor or the Transferee.

7. All payments and reimbursements previously made by the Government to the Predecessor, and all other previous actions taken by the Government under the Award, shall be considered to have discharged those parts of the Government's obligations under the Award . All payments and reimbursements made by the Government after the date of this Agreement in the name of or to the Predecessor shall have the same force and effect as if made to the Transferee, and shall constitute a complete discharge of the Government's obligations under the Award, to the extent of the amounts paid or reimbursed.

8. The Transferee agrees that the Government is not obligated to pay or reimburse it for, or otherwise give effect to, any costs, taxes, or other expenses, or any related increases, directly or indirectly arising out of or resulting from the transfer of the Award or this Agreement, other than those that the Government in the absence of this transfer or Agreement would have been obligated to pay or reimburse under the terms of the Award.

9. The Government's execution of this Agreement does not constitute approval by the Government of the terms or conditions of the documents submitted by the Predecessor and Transferee in support of their request to assign the Award nor does it constitute a determination by the Government regarding the allow ability of costs incurred by the Transferee pursuant to those documents.

10. If Transferee is not going to perform an aspect of the award itself and chooses to utilize the services or resources of any of its related companies, the related company will be treated as a sub-recipient and will not be allowable as a vendor.

11. The Award shall remain in full force and effect, except as modified by this Agreement, and nothing contained herein shall limit the Government's ability to modify the terms and conditions of the Award as the Government finds necessary.

12. The Award will be modified by substituting the name "Amyris, Inc." for the name "Amyris Biotechnologies, Inc" wherever it appears in the Award.

13. This Agreement will take effect as of the date the Government formally incorporates this Agreement into the Award through an Award modification.

THE UNITED STATES OF AMERICA

By /s/ Jon Olsen Date: 11/18/2011

Title: Contracting Officer for the Department of Energy

AMYRIS, INC.

By /s/ Mario Portela Date: 11/16/2011

Title: President, Global Operations

CERTIFICATE

I, Tamara L. Tompkins, certify that I am the Secretary of Amyris, Inc., a Delaware corporation, and that Mario Portela, who signed this Agreement for this entity, was then the President, Global Operations of this entity; and that this Agreement was duly signed for and on behalf of this entity by authority of its governing body and within the scope of its corporate powers. Witness my hand and the seal of this corporation this day of November 16, 2011.

By /s/ Tamara L. Tompkins

[Corporate Seal]

EXHIBIT A

AGREEMENT AND PLAN OF MERGER

THIS AGREEMENT AND PLAN OF MERGER (this “ Merger Agreement ”) is entered into as of June 10, 2010, by and between Amyris Biotechnologies, Inc., a California corporation (“ Amyris California ”), and Amyris Biotechnologies, Inc., a Delaware corporation (“ Amyris Delaware ”). Amyris California and Amyris Delaware are hereinafter sometimes collectively referred to as the “ Constituent Corporations ”.

R E C I T A L S

A. Amyris California was incorporated on July 17, 2003. Its current authorized capital stock consists of: (i) 38,000,000 shares of Common Stock (“ Amyris California Common Stock ”), of which 5,121,545 shares are issued and outstanding; and (ii) 23,862,355 shares of Preferred Stock (“ Amyris California Preferred Stock ”), of which 21,385,969 shares are issued and outstanding.

B. Amyris Delaware was incorporated on April 15, 2010. Its authorized capital stock consists of: (i) 38,000,000 shares of Common Stock, with a par value of $0.0001 per share (“ Amyris Delaware Common Stock ”), of which one thousand (1,000) shares are issued and outstanding; and (ii) 23,862,355 shares of Preferred Stock, with a par value of $0.0001 per share (“ Amyris Delaware Preferred Stock ”), none of which shares are issued and outstanding.

C. The respective Boards of Directors of Amyris California and Amyris Delaware deem it advisable and to the advantage of each of the Constituent Corporations that Amyris California merge with and into Amyris Delaware upon the terms and subject to the conditions set forth in this Merger Agreement for the purpose of effecting a change of the state of incorporation of Amyris California from California to Delaware.

D. The Boards of Directors of each of the Constituent Corporations have approved this Merger Agreement.

NOW, THEREFORE, the parties do hereby adopt the plan of reorganization set forth in this Merger Agreement and do hereby agree that Amyris California shall merge with and into Amyris Delaware on the following terms, conditions and other provisions:

1. Merger and Effective Time . At the Effective Time (as defined below), Amyris California shall be merged with and into Amyris Delaware (the “ Merger ”), and Amyris Delaware shall be the surviving corporation of the Merger (the “ Surviving Corporation ”). The Merger shall become effective upon the close of business on the date when a duly executed copy of this Merger Agreement (or a Certificate of Merger in lieu thereof) is filed with the Secretary of State of the State of Delaware, provided that such Merger Agreement (or the Certificate of Merger in lieu thereof) is filed with the Secretary of State of the State of California within the time period required by law (the “ Effective Time ”).

2. Effect of Merger . At the Effective Time, the separate corporate existence of Amyris California shall cease; the corporate identity, existence, powers, rights and immunities of Amyris Delaware as the Surviving Corporation shall continue unimpaired by the Merger; and Amyris Delaware shall succeed to and shall possess all the assets, properties, rights, privileges, powers, franchises, immunities and purposes, and be subject to all the debts, liabilities, obligations, restrictions and duties of Amyris California, all without further act or deed.

3. Name Change; Governing Documents . At the Effective Time, (i) the name of Amyris Delaware shall be Amyris Biotechnologies, Inc. and (ii) the Certificate of Incorporation of Amyris Delaware in effect immediately prior to the Effective Time shall be amended and restated by virtue of the Merger to read as set forth in full in Exhibit “A” hereto (the “ Restated Certificate ”).

4. Directors and Officers . At the Effective Time, the directors of Amyris Delaware shall be and become the directors of the Surviving Corporation, and the officers of Amyris Delaware shall be and become the officers (holding the same offices) of the Surviving Corporation, and after the Effective Time shall serve in accordance with the Restated Certificate and Bylaws of the Surviving Corporation.

5. Conversion of Shares of Amyris California . At the Effective Time, by virtue of the Merger and without any further action on the part of the Constituent Corporations or their shareholders, (i) each share of Amyris California Common Stock issued and outstanding immediately prior thereto shall be converted into one (1) fully paid and nonassessable share of Amyris Delaware Common Stock, (ii) each share of Amyris California Series A Preferred Stock outstanding immediately prior thereto shall be automatically changed and converted into one (1) fully paid and nonassessable, issued and outstanding share of Amyris Delaware Series A Preferred Stock, (iii) each share of Amyris California Series B Preferred Stock outstanding immediately prior thereto shall be automatically changed and converted into one (1) fully paid and nonassessable, issued and outstanding share of Amyris Delaware Series B Preferred Stock, (iv) each share of Amyris California Series B-1 Preferred Stock outstanding immediately prior thereto shall be automatically changed and converted into one (1) fully paid and nonassessable, issued and outstanding share of Amyris Delaware Series B-1 Preferred Stock, (v) each share of Amyris California Series C Preferred Stock outstanding immediately prior thereto shall be automatically changed and converted into one (1) fully paid and nonassessable, issued and outstanding share of Amyris Delaware Series C Preferred Stock, and (vi) each share of Amyris California Series C-1 Preferred Stock outstanding immediately prior thereto shall be automatically changed and converted into one (1) fully paid and nonassessable, issued and outstanding share of Amyris Delaware Series C-1 Preferred Stock

6. Cancellation of Shares of Amyris Delaware . At the Effective Time, by virtue of the Merger and without any further action on the part of the Constituent Corporations or their shareholders, all of the previously issued and outstanding shares of Amyris Delaware Common Stock that were issued and outstanding immediately prior to the Effective Time shall be automatically canceled without consideration and returned to the status of authorized but unissued shares.

7. Stock Certificates . At and after the Effective Time, all of the outstanding certificates that, prior to that date, represented shares of Amyris California Common Stock shall be deemed for all purposes to evidence ownership of and to represent the number of shares of Amyris Delaware Common Stock into which such shares of Amyris California Common Stock are converted as provided herein. At and after the Effective Time, all of the outstanding certificates that, prior to that date, represented shares of a series of Amyris California Preferred Stock shall be deemed for all purposes to evidence ownership of and to represent the number of shares of the series of shares of Amyris Delaware Preferred Stock, into which such shares of Amyris California Preferred Stock are converted as provided herein. The registered owner on the books and records of Amyris California of any such outstanding stock certificate for Amyris

California Common Stock or Amyris California Preferred Stock shall, until such certificate is surrendered for transfer or otherwise accounted for to Amyris Delaware or its transfer agent, be entitled to exercise any voting and other rights with respect to, and to receive any dividend and other distributions upon, the shares of Amyris Delaware Common Stock or Amyris Delaware Preferred Stock evidenced by such outstanding certificate as provided above.

8. Assumption of Options . At the Effective Time, all outstanding and unexercised portions of all options to purchase Amyris California Common Stock under Amyris California's 2005 Stock Option/Stock Issuance Plan (the “ Existing Plan ”), and all other outstanding options to purchase Amyris California Common Stock, shall be assumed by Amyris Delaware and become options to purchase the same number of shares of Amyris Delaware Common Stock at the same exercise price per share at which such option was exercisable immediately prior to the Merger, and shall, to the extent permitted by law and otherwise reasonably practicable, have the same term, exercisability, vesting schedule, acceleration provision, if applicable, status as an “incentive stock option” under Section 422 of the Internal Revenue Code of 1986, as amended (the “ Code ”), if applicable, and all other material terms and conditions (including but not limited to the terms and conditions applicable to such options by virtue of the Existing Plan). Continuous employment with Amyris California will be credited to an optionee for purposes of determining the vesting of the number of shares of Amyris Delaware Common Stock subject to exercise under an assumed Amyris California option at the Effective Time. At the Effective Time, Amyris Delaware shall adopt and assume the Existing Plan, as amended.

10. Assumption of Warrants . At the Effective Time, all outstanding and unexercised portions of all warrants to purchase Amyris California Preferred Stock, shall be assumed by Amyris Delaware and become warrants to purchase the same number of shares of the corresponding series of Amyris Delaware Preferred Stock at the same exercise price per share at which such warrant was exercisable immediately prior to the Merger, and shall, to the extent permitted by law and otherwise reasonably practicable, have the same term, exercisability, vesting schedule, acceleration provision, if applicable, and all other material terms and conditions.

11. Employee Benefit Plans . At the Effective Time, the obligations of Amyris California under or with respect to every plan, trust, program and benefit then in effect or administered by Amyris California for the benefit of the directors, officers and employees of Amyris California or any of its subsidiaries shall become the lawful obligations of Amyris Delaware and shall be implemented and administered in the same manner and without interruption until the same are amended or otherwise lawfully altered or terminated. Effective at the Effective Time, Amyris Delaware hereby expressly adopts and assumes all obligations of Amyris California under such employee benefit plans.

12. Further Assurances . From time to time, as and when required by the Surviving Corporation or by its successors or assigns, there shall be executed and delivered on behalf of Amyris California such deeds, assignments and other instruments, and there shall be taken or caused to be taken by it all such further action, as shall be appropriate, advisable or necessary in order to vest, perfect or confirm, of record or otherwise, in the Surviving Corporation the title to and possession of all property, interests, assets, rights, privileges, immunities, powers, franchises and authority of Amyris California, and otherwise to carry out the purposes of this Merger Agreement. The officers and directors of the Surviving Corporation are fully authorized in the name of and on behalf of Amyris California, or otherwise, to take any and all such actions and to

execute and deliver any and all such deeds and other instruments as may be necessary or appropriate to accomplish the foregoing.

13. Condition . The consummation of the Merger is subject to the approval of this Merger Agreement and the Merger contemplated hereby by the shareholders of Amyris California and by the sole stockholder of Amyris Delaware, prior to or at the Effective Time.

14. Abandonment . At any time before the Effective Time, this Merger Agreement may be terminated and the Merger abandoned by the Board of Directors of Amyris California or Amyris Delaware, notwithstanding approval of this Merger Agreement by the shareholders of Amyris California and the sole stockholder of Amyris Delaware.

15. Amendment . At any time before the Effective Time, this Merger Agreement may be amended, modified or supplemented by the Boards of Directors of the Constituent Corporations, notwithstanding approval of this Merger Agreement by the shareholders of Amyris California and the sole stockholder of Amyris Delaware; provided, however, that any amendment made subsequent to the adoption of this Merger Agreement by the shareholders of Amyris California or the sole stockholder of Amyris Delaware shall not materially: (i) alter or change the amount or kind of shares, securities, cash, property and/or rights to be received in exchange for or upon conversion of any shares of any class or series of Amyris California; (ii) alter or change any of the terms of the Certificate of Incorporation of the Surviving Corporation to be effected by the Merger; or (iii) alter or change any of the terms or conditions of this Merger Agreement if such alteration or change would adversely affect the holders of any shares of any class or series of Amyris California or Amyris Delaware.

16. Tax-Free Reorganization . The Merger is intended to be a tax-free plan of reorganization within the meaning of Section 368(a)(1)(F) of the Code.

17. Governing Law . This Merger Agreement shall be governed by and construed under the internal laws of the State of California as applied to agreements among California residents entered into and to be performed entirely within California, without reference to the principles of conflicts of law or choice of laws, except to the extent that the laws of the State of Delaware would apply in matters relating to the internal affairs of Amyris Delaware and the Merger.

18. Counterparts . In order to facilitate the filing and recording of this Merger Agreement, it may be executed in any number of counterparts, each of which shall be deemed to be an original, but all of which together shall constitute one and the same instrument.

[REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]

IN WITNESS WHEREOF, the parties hereto have caused this Merger Agreement to be duly executed on the date and year first above written.

Amyris Biotechnologies, Inc., a Delaware

Corporation

By: /s/ John G. Melo

Name: John G. Melo

Title: Chief Executive Officer

Amyris Biotechnologies, Inc., a California

Corporation

By: /s/ John G. Melo

Name: John G. Melo

Title: Chief Executive Officer

[Signature Page to Agreement and Plan of Merger]

EXHIBIT “A”

RESTATED CERTIFICATE OF INCORPORATION

AMYRIS BIOTECHNOLOGIES, INC.

RESTATED CERTIFICATE OF INCORPORATION

(Pursuant to Sections 242 and 245 of the

General Corporation Law of the State of Delaware)

Amyris Biotechnologies, Inc., a corporation organized and existing under and by virtue of the provisions of the General Corporation Law of the State of Delaware (the “ General Corporation Law ”), does hereby certify as follows.

1. The name of this corporation is Amyris Biotechnologies, Inc. and that this corporation was originally incorporated pursuant to the General Corporation Law on April 15, 2010 under the name Amyris Biotechnologies, Inc.

2. The Board of Directors of this corporation duly adopted resolutions proposing to amend and restate the Certificate of Incorporation of this corporation, declaring said amendment and restatement to be advisable and in the best interests of this corporation and its stockholders, and authorizing the appropriate officers of this corporation to solicit the consent of the stockholders therefor, which resolution setting forth the proposed amendment and restatement is as follows.

RESOLVED, that the Certificate of Incorporation of this corporation be amended and restated in its entirety to read as set forth on Exhibit A attached hereto and incorporated herein by this reference.

3. Exhibit A referred to above is attached hereto as Exhibit A and is hereby incorporated herein by this reference. This Restated Certificate of Incorporation was approved by the holders of the requisite number of shares of this corporation in accordance with Section 228 of the General Corporation Law.

4. This Restated Certificate of Incorporation, which restates and integrates and further amends the provisions of this corporation's Certificate of Incorporation, has been duly adopted in accordance with Sections 242 and 245 of the General Corporation Law.

IN WITNESS WHEREOF , this Restated Certificate of Incorporation has been executed by a duly authorized officer of this corporation on this 10th day of June, 2010.

By: /s/ John Melo

John Melo, President

EXHIBIT A

AMYRIS BIOTECHNOLOGIES, INC.

RESTATED CERTIFICATE OF INCORPORATION

ARTICLE I : NAME

The name of the corporation is Amyris Biotechnologies, Inc. (the “ Company ”).

ARTICLE II : REGISTERED OFFICE

The address of the registered office of the Corporation in the State of Delaware is 3500 South Dupont Highway, in the City of Dover, County of Kent, Delaware 19901. The name of its registered agent at such address is Incorporation Services, Ltd.

ARTICLE III : PURPOSE

The nature of the business or purposes to be conducted or promoted is to engage in any lawful act or activity for which corporations may be organized under the General Corporation Law.

ARTICLE IV : AUTHORIZED SHARES

The total number of shares of all classes of stock which the Corporation shall have authority to issue is (a) 61,862,355 shares of Common Stock, $0.0001 par value per share (“ Common Stock ”), and (b) 23,862,355 shares of Preferred Stock, $0.0001 par value per share (“ Preferred Stock ”). The Preferred Stock may be issued from time to time in one or more series, each of such series to consist of such number of shares and to have such terms, rights, powers and preferences, and the qualifications and limitations with respect thereto, as stated or expressed herein. As of the effective date of this Restated Certificate of Incorporation (this “ Restated Certificate ”), 9,475,000 shares of the authorized Preferred Stock of the Corporation are hereby designated “ Series A Preferred Stock ”, 1,929,641 shares of the authorized Preferred Stock of the Corporation are hereby designated “ Series B Preferred Stock ”, 4,700,000 shares of the authorized Preferred Stock of the Corporation are hereby designated “ Series B-1 Preferred Stock ”, 4,976,000 shares of the authorized Preferred Stock of the Corporation are hereby designated “ Series C Preferred Stock ”, and 2,781,714 shares of the authorized Preferred Stock of the Corporation are hereby designated “ Series C-1 Preferred Stock ”. The following is a statement of the designations and the rights, powers and privileges, and the qualifications, limitations or restrictions thereof, in respect of each class of capital stock of the Corporation.

A. COMMON STOCK

1. General . The voting, dividend and liquidation rights of the holders of the Common Stock are subject to and qualified by the rights, powers and privileges of the holders of the Preferred Stock set forth herein.

2. Voting . The holders of the Common Stock are entitled to one vote for each share of Common Stock held at all meetings of stockholders (and written actions in lieu of meetings).

Unless required by law, there shall be no cumulative voting. The number of authorized shares of Common Stock may be increased or decreased (but not below the number of shares thereof then outstanding) by (in addition to any vote of the holders of one or more series of Preferred Stock that may be required by the terms of the Certificate of Incorporation) the affirmative vote of the holders of shares of capital stock of the Corporation representing a majority of the votes represented by all outstanding shares of capital stock of the Corporation entitled to vote, irrespective of the provisions of Section 242(b)(2) of the General Corporation Law.

B. PREFERRED STOCK

The following rights, powers and privileges, and restrictions, qualifications and limitations, shall apply to the Preferred Stock. Unless otherwise indicated, references to “Sections” in this Part B of this Article IV refer to sections of this Part B.

1. Dividends.

a. Preferred Stock Dividends. The holders of Series A Preferred Stock, Series B Preferred Stock, Series B-1 Preferred Stock, Series C Preferred Stock and Series C-1 Preferred Stock shall be entitled to receive non-cumulative dividends, on a pari passu basis, at the rate of 8% of the Series A Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series A Preferred Stock, at the rate of 8% of the Series B Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series B Preferred Stock, at the rate of 8% of the Series B-1 Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series B-1 Preferred Stock, at the rate of 8% of the Series C Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series C Preferred Stock, and at the rate of 8% of the Series C-1 Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series C-1 Preferred Stock, payable out of funds legally available therefor. Such dividends shall be payable only when, as, and if declared by the Board of Directors and shall be non-cumulative.

No dividends (other than those payable solely in the Common Stock of the Company) shall be paid or other distribution made on any Common Stock of the Company, or purchase, redemption or other acquisition of Common Stock for value during any fiscal year of the Company until dividends, in the amount of 8% of the Series A Issue Price (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series A Preferred Stock, 8% of the Series B Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series B Preferred Stock, 8% of the Series B-1 Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series B-1 Preferred Stock, 8% of the Series C Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series C Preferred Stock, and 8% of the Series C-1 Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series C-1 Preferred Stock shall have been paid or declared and set apart during that fiscal year, except for:

(i) acquisitions of Common Stock by the Company pursuant to agreements which permit the Company to repurchase such shares at cost (or the lesser of cost or fair market value) upon termination of services to the Company;

(ii) acquisitions of Common Stock in exercise of the Company's right of first refusal to repurchase such shares; or

(iii) distributions to holders of Common Stock in accordance with Section 2.

b. Common Stock Dividends. In the event the Company shall declare a distribution or dividend on any Common Stock (other than dividends payable solely in Common Stock of the Company), then, in each such case, the holders of the Preferred Stock shall be entitled to a proportionate share of any such distribution as though the holders of the Preferred Stock were the holders of the number of shares of Common Stock of the Company into which their respective shares of Preferred Stock are convertible as of the record date fixed for the determination of the holders of Common Stock of the Company entitled to receive such distribution.

2. Liquidation Preference.

a. Payments to Holders of Preferred Stock. In the event of any liquidation, dissolution or winding up of the Company (a “ Liquidation ”), whether voluntary or involuntary, the holders of the Series A Preferred Stock, Series B Preferred Stock, Series B-1 Preferred Stock, Series C Preferred Stock and Series C-1 Preferred Stock shall be entitled to receive, on a pari passu basis but prior and in preference to any distribution of any of the legally available assets or surplus funds of the Company to the holders of the Common Stock by reason of their ownership thereof, (i) in the case of Series A Preferred Stock, the amount of $2.174 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares, (the “ Series A Issue Price ”), plus all declared but unpaid dividends, on each such share then held by them, (ii) in the case of Series B Preferred Stock, the amount of $24.88 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “ Series B Issue Price ”), plus all declared but unpaid dividends, on each such share then held by them, (iii) in the case of Series B-1 Preferred Stock, the amount of $25.26 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “ Series B-1 Issue Price ”), plus all declared but unpaid dividends, on each such share then held by them, (iv) in the case of Series C Preferred Stock, the amount of $12.46 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “ Series C Issue Price ”), and (v) in the case of Series C-1 Preferred Stock, the amount of $17.56 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “ Series C-1 Issue Price ”). If upon the occurrence of such event, the assets and funds thus distributed among the holders of the Preferred Stock shall be insufficient to permit the payment to such holders of the full aforesaid preferential amount, then the entire assets and funds of the Company legally available for distribution shall be distributed ratably among the holders of the Preferred Stock in proportion to the preferential amount each such holder is otherwise entitled to receive.

b. Payments to Holders of Common Stock. After payment to the holders of the Preferred Stock of the amounts set forth in Section 2.a above, the entire remaining

assets and funds of the Company legally available for distribution, if any, shall be distributed ratably among the holders of the Common Stock pro rata based on the number of shares of Common Stock held by each.

c. Conversion for Payments. Notwithstanding paragraphs (a) and (b) above, solely for purposes of determining the amount each holder of shares of Preferred Stock is entitled to receive with respect to a Liquidation, each series of Preferred Stock shall be treated as if all holders of such series had converted such holder's shares of such series into shares of Common Stock immediately prior to the Liquidation if, as a result of an actual conversion of any series of Preferred Stock (including taking into account the operation of this paragraph (c) with respect to all series of Preferred Stock), holders of such series would receive (with respect to such series), in the aggregate, an amount greater than the amount that would be distributed to holders of such series if such holders had not converted such series of Preferred Stock into shares of Common Stock.

d. Deemed Liquidation. For purposes of this Section 2, (i) any acquisition of the Company by means of merger or other form of corporate reorganization in which outstanding shares of the Company are exchanged for securities or other consideration issued, or caused to be issued, by the acquiring company or its subsidiary (other than a transaction effected solely to reincorporate the Company in another jurisdiction) and pursuant to which the holders of the outstanding voting securities of the Company immediately prior to such consolidation, merger or other transaction fail to hold equity securities representing a majority of the voting power of the Company or surviving entity immediately following such consolidation, merger or other transaction (an “ Acquisition ”) or (ii) a sale of all or substantially all of the assets of the Company (an “ Asset Sale ”), shall be treated as a Liquidation of the Company and shall entitle the holders of Preferred Stock to receive at the closing of such transaction in cash, securities or other property (valued as provided in Section 2.e below) the amounts as specified in Section 2.a above; provided that an Acquisition shall not include any transaction or series of transactions principally for bona fide equity financing purposes in which cash is received by the Company or any successor or indebtedness of the Company is cancelled or converted or a combination thereof.

e. Amount Deemed Paid or Distributed. Whenever the distribution provided for in this Section 2 shall be payable in securities or property other than cash, the value of such distribution shall be the fair market value of such securities or other property. Any securities shall be valued as follows:

(i) If traded on a securities exchange, the value shall be deemed to be the average of the closing prices of the securities on such exchange or system over the thirty (30) day period ending three (3) days prior to the closing;

(ii) If actively traded over-the-counter, the value shall be deemed to be the average of the closing bid or sale prices (whichever is applicable) over the thirty (30) day period ending three (3) days prior to the closing; and

(iii) If there is no active market, the value shall be the fair market value thereof, as determined in good faith by the Board of Directors of the Company.

3. Voting Rights. Except as otherwise provided herein or as required by law, the Preferred Stock will be voted equally with the shares of the Common Stock and not as a separate class, at any annual or special meeting of stockholders of the Company, and may act by written consent in the same manner as the Common Stock, in either case upon the following basis: each holder of shares of the Preferred Stock shall be entitled to the number of votes equal to the respective number of shares of Common Stock into which such shares of Preferred Stock could be converted immediately after the close of business on the record date fixed for such meeting or the effective date of such written consent, and shall be entitled to notice of any stockholders' meeting in accordance with the Bylaws of the Company. Fractional votes shall not, however, be permitted and any fractional voting rights resulting from the above formula (after aggregating all shares into which shares of Preferred Stock held by each holder could be converted) shall be rounded to the nearest whole number (with one-half being rounded upward).

4. Conversion. The holders of the Preferred Stock shall have conversion rights as follows:

a. Right to Convert. Each share of Preferred Stock shall be convertible, at the option of the holder thereof, at any time after the date of issuance of such share, at the office of the Company or any transfer agent for such stock, into fully paid and nonassessable shares of Common Stock. The number of shares of Common Stock to which a holder of Preferred Stock shall be entitled upon conversion shall be determined by dividing the Series A Issue Price, Series B Issue Price, Series B-1 Issue Price, Series C Issue Price, or Series C-1 Issue Price, as applicable, by the conversion price for such share in effect at the time that such certificate is surrendered for conversion, and then multiplying by the number of shares of Preferred Stock being converted. The conversion price per share (the “ Conversion Price ”) as of the Original Issue Date (as defined below) shall be (i) for shares of Series A Preferred Stock $2.174 per share, (ii) for shares of Series B Preferred Stock shall be $21.86 per share, (iii) for shares of Series B-1 Preferred Stock shall be $22.14 per share, (iv) for shares of Series C Preferred Stock shall be $12.46 per share, and (v) for shares of Series C-1 Preferred Stock, $17.56 per share, in each case each subject to adjustment as hereinafter provided.

b. Automatic Conversion.

(i) Each share of Series A Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price upon the earlier to occur of (i) the date specified by written consent or agreement of stockholders holding at least a majority of the then outstanding shares of Series A Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of the sale of the Company's Common Stock in a firm commitment, underwritten public offering registered under the Securities Act of 1933, as amended (the “ Securities Act ”), which results in aggregate proceeds to the Company (before deduction for underwriters' discounts and expenses relating to the issuance, including without limitation fees of the Company's counsel) equal to at least $30,000,000 (a “ Qualified IPO ”). Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

holding at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class, and (B) stockholders holding at least a majority of the then outstanding shares of Series B Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of a Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

(iii) Each share of Series B-1 Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price upon the earlier to occur of (i) the date specified by written consent or agreement of (A) stockholders holding at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class, and (B) stockholders holding at least a majority of the then outstanding shares of Series B-1 Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of a Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

(iv) Each share of Series C Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price upon the earlier to occur of (i) the date specified by written consent or agreement of (A) stockholders holding at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class, and (B) stockholders holding at least a majority of the then outstanding shares of Series C Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of a Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

(v) Each share of Series C-1 Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price upon the earlier to occur of (i) the date specified by written consent or agreement of (A) stockholders holding at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class, and (B) stockholders holding at least a majority of the then outstanding shares of Series C-1 Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of a Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

c. Mechanics of Conversion .

the Board as of the date of conversion) the value of any fractional share of Common Stock otherwise issuable to any holder of Preferred Stock. Such conversion shall be deemed to have been made immediately prior to the close of business on the date of surrender of the shares of Preferred Stock to be converted, and the person or persons entitled to receive the shares of Common Stock issuable upon such conversion shall be treated for all purposes as the record holder or holders of such shares of Common Stock on such date.

(ii) If the conversion is in connection with an underwritten offering of securities pursuant to the Securities Act, the conversion may, at the option of any holder tendering shares of Preferred Stock for conversion, be conditioned upon the closing with the underwriters of the sale of securities pursuant to such offering, in which event the person(s) entitled to receive the Common Stock upon conversion of the Preferred Stock shall not be deemed to have converted such Preferred Stock until immediately prior to the closing of such sale of securities.

d. Adjustments to Conversion Price for Certain Diluting Issues.

(i) Special Definitions. For purposes of this Section 4, the following definitions apply:

(1) “ Options ” shall mean rights, options or warrants to subscribe for, purchase or otherwise acquire either Common Stock or Convertible Securities (as defined below).

(2) “ Original Issue Date ” shall mean the date of the filing with the Delaware Secretary of State of the Certificate of Merger (the “ Certificate of Merger ”) of the Company and Amyris Biotechnologies, Inc., a California corporation (“ Amyris California ”).

(3) “ Convertible Securities ” shall mean any evidences of indebtedness, shares (other than Common Stock, Series A Preferred Stock, Series B Preferred Stock, Series B-1 Preferred Stock, Series C Preferred Stock or Series C-1 Preferred Stock) or other securities convertible into or exchangeable for Common Stock, including securities described in Section 4.d.(i)(4).

(4) “ Additional Shares of Common Stock ” shall mean all shares of Common Stock issued (or, pursuant to Section 4.d(iii) deemed to be issued) by the Company after the Original Issue Date, other than shares of Common Stock issued or issuable after the Original Issue Date:

(A) upon conversion of shares of Preferred Stock;

(B) pursuant to or issuable upon exercise of options or warrants to purchase shares of Common stock, issued to employees, officers, directors or consultants of the Company or a subsidiary pursuant to stock option or stock purchase plans or other arrangements in each case on terms approved by at least 76% of the members of the Board of Directors of the Company;

(C) pursuant to transactions involving research or development funding, technology licensing, joint ventures, strategic alliances, partnering arrangements, bank financings or lease arrangements pursuant to agreements in each case approved by at least 76% of the members of the Board of Directors of the Company;

(D) pursuant to the acquisition of another corporation or entity by the corporation by way of merger, purchase of assets, stock for stock exchange or other reorganization or recapitalization in each case approved by at least 76% of the members of the Board of Directors of the Company;

(E) in a Qualified IPO;

(F) pursuant to a transaction described in Section 4.e or 4.f;

(G) for which adjustment of the applicable Conversion Price is made pursuant to this Section 4;

(H) pursuant to or issuable upon exercise of warrants, options or other rights to acquire securities of the Company outstanding as of the Original Issue Date and any securities issuable upon conversion thereof;

(I) pursuant to or issuable upon conversion, exchange or cancellation of shares of Amyris Brasil S.A., a majority-owned subsidiary of the Company;

(J) in connection with the merger effected by the Certificate of Merger (the “ Merger ”) or pursuant to or issuable upon conversion, exchange or cancellation of shares of Amyris California in connection with the Merger; or

(K) upon the affirmative vote of at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class on an as-if converted basis.

(ii) No Adjustment of Conversion Price. Any provision herein to the contrary notwithstanding, no adjustment in the applicable Conversion Price shall be made in respect of the issuance of Additional Shares of Common Stock unless the consideration per share (determined pursuant to Section 4.d(v) hereof) for an Additional Share of Common Stock issued or deemed to be issued by the Company is less than the applicable Conversion Price in effect immediately prior to such issue.

(iii) Deemed Issue of Additional Shares of Common Stock. In the event the Company at any time or from time to time after the Original Issue Date shall issue any Options or Convertible Securities (other than shares of Series C-1 Preferred Stock authorized herein) or shall fix a record date for the determination of holders of any class of securities then entitled to receive any such Options or Convertible Securities, then the maximum number of shares (as set forth in the instrument relating thereto without regard to any provisions contained therein designed to protect against dilution) of Common Stock issuable upon the exercise of such Options or, in the case of Convertible Securities and Options therefor, the conversion or

exchange of such Convertible Securities, shall be deemed to be Additional Shares of Common Stock issued as of the time of such issue or, in case such a record date shall have been fixed, as of the close of business on such record date, provided further that in any such case in which Additional Shares of Common Stock are deemed to be issued:

(1) no further adjustments in the applicable Conversion Price shall be made upon the subsequent issue of Convertible Securities or shares of Common Stock upon the exercise of such Options or conversion or exchange of such Convertible Securities;

(2) if such Options or Convertible Securities by their terms provide, with the passage of time or otherwise, for any increase in the consideration payable to the Company, or decrease in the number of shares of Common Stock issuable, upon the exercise, conversion or exchange thereof, the applicable Conversion Price computed upon the original issue thereof (or upon the occurrence of a record date with respect thereto), and any subsequent adjustments based thereon, shall, upon any such increase or decrease becoming effective, be recomputed to reflect such increase or decrease insofar as it affects such Options or the rights of conversion or exchange under such Convertible Securities (provided, however, that no such adjustment of the Conversion Price shall affect Common Stock previously issued upon conversion of the Preferred Stock);

(3) upon the expiration of any such options or rights, the termination of any such rights to convert or exchange or the expiration of any options or rights related to such convertible or exchangeable securities, the applicable Conversion Price to the extent in any way affected by or computed using such options, rights or securities or options or rights related to such securities, shall be recomputed to reflect the issuance of only the number of shares of Common Stock (and convertible or exchangeable securities which remain in effect) actually issued upon the exercise of such options or rights, upon the conversion or exchange of such securities or upon the exercise of the options or rights related to such securities;

(4) no readjustment pursuant to clause (2) or (3) above shall have the effect of increasing the applicable Conversion Price to an amount which exceeds the lower of (a) the Conversion Price on the original adjustment date or (b) the Conversion Price that would have resulted from any issuance of Additional Shares of Common Stock between the original adjustment date and such readjustment date.

denominator of which shall be the number of shares of Common Stock deemed outstanding (as defined below) immediately prior to such issuance plus the number of such Additional Shares of Common Stock so issued. For the purpose of the above calculation, the number of shares of Common Stock outstanding immediately prior to such issue shall be calculated on a fully diluted basis, as if all shares of Preferred Stock and all outstanding Convertible Securities had been fully converted into shares of Common Stock and any outstanding warrants, outstanding options or other rights outstanding for the purchase of shares of stock or convertible securities had been fully exercised (and the resulting securities fully converted into shares of Common Stock, if so convertible) as of such date. For the purposes of adjusting the applicable Conversion Price of a series of Preferred Stock, the grant, issue or sale of Additional Shares of Common consisting of the same class of security and warrants to purchase such security issued or issuable at the same price at two or more closings held within a six (6) month period shall be aggregated and shall be treated as one sale of Additional Shares of Common occurring on the earliest date on which such securities were granted, issued or sold.

(v) Determination of Consideration. For purposes of this Section 4.d, the consideration received by the Company for the issue of any Additional Shares of Common Stock shall be computed as follows:

(1) Cash and Property. Such consideration shall:

(A) insofar as it consists of cash, be computed at the aggregate amount of cash received by the Company, excluding amounts paid or payable for accrued interest or declared but unpaid dividends;

(B) insofar as it consists of property other than cash, be computed at the fair value thereof at the time of such issue, as determined in good faith by the Board of Directors; and

(C) in the event Additional Shares of Common Stock are issued together with other shares or securities or other assets of the Company for consideration which covers both, be the proportion of such consideration so received, computed as provided in clauses (A) and (B) above, as determined in good faith by the Board of Directors.

(2) Options and Convertible Securities. The consideration per share received by the Company for Additional Shares of Common Stock deemed to have been issued pursuant to Section 4.d(iii), relating to Options and Convertible Securities shall be determined by dividing

(A) the total amount, if any, received or receivable by the Company as consideration for the issue of such Options or Convertible Securities, plus the minimum aggregate amount of additional consideration (as set forth in the instruments relating thereto, without regard to any provision contained therein designed to protect against dilution) payable to the Company upon the exercise of such Options or the conversion or exchange of such Convertible Securities, or in the case of Options for Convertible Securities, the exercise of such Options for Convertible Securities and the conversion or exchange of such Convertible Securities by

(B) the maximum number of shares of Common Stock (as set forth in the instruments relating thereto, without regard to any provision contained therein designed to protect against the dilution) issuable upon the exercise of such Options or conversion or exchange of such Convertible Securities.

e. Adjustments for Stock Dividends and for Combinations or Subdivisions of Common Stock. In the event that this Company at any time or from time to time after the Original Issue Date shall declare or pay, without consideration, any dividend on the Common Stock payable in Common Stock or in any right to acquire Common Stock for no consideration, or shall effect a subdivision of the outstanding shares of Common Stock into a greater number of shares of Common Stock (by stock split, reclassification or otherwise than by payment of a dividend in Common Stock or in any right to acquire Common Stock), or in the event the outstanding shares of Common Stock shall be combined or consolidated, by reclassification or otherwise, into a lesser number of shares of Common Stock, then the conversion price for any series of Preferred Stock in effect immediately prior to such event shall, concurrently with the effectiveness of such event, be proportionately decreased or increased, as appropriate. In the event that the Company shall declare or pay, without consideration, any dividend on the Common Stock payable in any right to acquire Common Stock for no consideration then the Company shall be deemed to have made a dividend payable in Common Stock in an amount of shares equal to the maximum number of shares issuable upon exercise of such rights to acquire Common Stock.

f. Adjustments for Reclassification and Reorganization. If the Common Stock issuable upon conversion of any series of Preferred Stock shall be changed into the same or a different number of shares of any other class or classes of stock, whether by capital reorganization, reclassification or otherwise (other than a subdivision or combination of shares provided for in Section 4.e above or a merger or other reorganization referred to in Section 2.d above), the Conversion Price for any series of Preferred Stock then in effect shall, concurrently with the effectiveness of such reorganization or reclassification, be proportionately adjusted so that the Preferred Stock shall be convertible into, in lieu of the number of shares of Common Stock which the holders would otherwise have been entitled to receive, a number of shares of such other class or classes of stock equivalent to the number of shares of Common Stock that would have been subject to receipt by the holders upon conversion of the Preferred Stock immediately before that change, respectively.

g. Certificates as to Adjustments. Upon the occurrence of each adjustment or readjustment of any conversion price pursuant to this Section 4, the Company at its expense shall promptly compute such adjustment or readjustment in accordance with the terms hereof and prepare and furnish to each holder of Preferred Stock a certificate executed by the Company's President or a Vice President setting forth such adjustment or readjustment and showing in detail the facts upon which such adjustment or readjustment is based. The Company shall, upon the written request at any time of any holder of Preferred Stock, furnish or cause to be furnished to such holder a like certificate setting forth (i) such adjustments and readjustments, (ii) the conversion price for such series of Preferred Stock at the time in effect, and (iii) the number of shares of Common Stock and the amount, if any, of other property which at the time would be received upon the conversion of the Preferred Stock.

h. Notices of Record Date. In the event that the Company shall propose at any time (i) to declare any dividend or distribution upon its Common Stock, whether in cash, property, stock or other securities, whether or not a regular cash dividend and whether or not out of earnings or earned surplus, (ii) a Liquidation or any voluntary or involuntary dissolution or winding up of the Company, or (iii) to offer for subscription pro rata to the holders of any class or series of its stock any additional shares of stock of any class or series or other rights, then, in connection with each such event, unless otherwise waived by a majority of Preferred Stock, the Company shall send to the holders of Preferred Stock at least twenty (20) days' prior written notice of the date on which a record shall be taken for such dividend, distribution, Liquidation, dissolution, winding up or subscription rights.

i. Reservation of Stock Issuable Upon Conversion. The Company shall at all times reserve and keep available out of its authorized but unissued shares of Common Stock, solely for the purpose of effecting the conversion of the shares of the Preferred Stock, such number of its shares of Common Stock as shall from time to time be sufficient to effect the conversion of all outstanding shares of the Preferred Stock; and if at any time the number of authorized but unissued shares of Common Stock shall not be sufficient to effect the conversion of all then outstanding shares of the Preferred Stock, the Company will take such corporate action as may, in the opinion of its counsel, be necessary to increase its authorized but unissued shares of Common Stock to such number of shares as shall be sufficient for such purpose, including, without limitation, engaging in best efforts to obtain the requisite stockholder approval of any necessary amendment to this Restated Certificate.

j. Fractional Shares. No fractional share shall be issued upon the conversion of any share or shares of Preferred Stock. All shares of Common Stock (including fractions thereof) issuable upon conversion of more than one share of Preferred Stock by a holder thereof shall be aggregated for purposes of determining whether the conversion would result in the issuance of any fractional share. If, after the aforementioned aggregation, the conversion would result in the issuance of a fraction of a share of Common Stock, the Company shall, in lieu of issuing any fractional share, pay the holder otherwise entitled to such fraction a sum in cash equal to the fair market value of such fraction on the date of conversion (as determined in good faith by the Board of Directors).

k. Notices. Any notice required by the provisions of this Section 4 shall be in writing and shall be deemed effectively given: (i) upon personal delivery to the party to be notified, (ii) when sent by confirmed electronic mail or facsimile if sent during normal business hours of the recipient; if not, then on the next business day, (iii) five (5) days after deposit in the United States mail, by registered or certified mail, postage prepaid and properly addressed to the party to be notified, or (iv) one (1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt. All notices shall be addressed to each holder of record at the address of such holder appearing on the books of the Company.

5. Board Representation. In addition to the rights of the holders of Preferred Stock to vote on an as converted basis with holders of Common Stock pursuant to Section 3 above, with respect to election of directors:

a. For so long as any shares of Series A Preferred Stock remain outstanding, the holders of Series A Preferred Stock, voting as a separate class, shall be entitled to elect three (3) members of the Board of Directors (each a “ Series A Director ”) at each meeting or pursuant to each consent of the Company's stockholders for the election of directors, and to remove from office such directors and to fill any vacancy caused by the resignation, death or removal of such directors.

b. The holders of Common Stock, voting as a separate class, shall be entitled to elect two (2) members of the Board of Directors (each a “ Common Director ”) at each meeting or pursuant to each consent of the Company's stockholders for the election of directors, and to remove from office such directors and to fill any vacancy caused by the resignation, death or removal of such directors.

c. The holders of Preferred Stock and the holders of Common Stock, voting together as a single class on an as-if converted basis, shall be entitled to elect any additional members of the Board of Directors (each an “ Independent Director ”), and to remove from office such directors and to fill any vacancy caused by the resignation, death or removal of such directors.

6. Redemption. The Preferred Stock shall not be redeemable.

7. Restrictions and Limitations. So long as at least 20% of the shares of the Preferred Stock sold by the Company (as adjusted for stock splits, dividends, combinations, recapitalizations and the like) remain outstanding, consent of the holders of at least the majority of the Preferred Stock shall be required for any action that (whether by amendment, merger, reorganization or otherwise):

a. alters or changes the rights, preferences or privileges of the Common Stock or the Preferred Stock,

b. increases or decreases the authorized number of shares of Common or Preferred Stock,

c. creates (by reclassification or otherwise) any new class or series of shares having rights, preferences or privileges senior to or on a parity with the Preferred Stock,

d. results in the redemption of any shares of Preferred Stock or Common Stock (other than pursuant to equity incentive agreements with employees and other service providers giving the Company the right to repurchase shares upon the termination of employment or such other service relationship, at their original cost),

e. results in a Liquidation or other corporate reorganization, including any reorganization or other transaction involving any parent or subsidiary of the Company,

f. amends or waives any provision of the Company's certificate of incorporation or bylaws,

g. increases or decreases the authorized size of the Company's Board of Directors, or

h. results in the payment or declaration of any dividend on any shares of Common or Preferred Stock;

provided , however , that for any amendment or waiver of any provision of the Company's certificate of incorporation or bylaws that would have a material, adverse and disproportionate effect on a series of Preferred Stock relative to any other series of Preferred Stock, consent of the holders of at least the majority of such series of Preferred Stock voting as a separate class shall be required.

8. No Reissuance of Preferred Stock. No share or shares of Preferred Stock acquired by the Company by reason of redemption, purchase, conversion, or otherwise shall be reissued; and, in addition, the certificate of incorporation shall be appropriately amended to effect the corresponding reduction in the Company's authorized stock.

ARTICLE V : PREEMPTIVE RIGHTS .

No stockholder of the Corporation shall have a right to purchase shares of capital stock of the Corporation sold or issued by the Corporation except to the extent that such a right may from time to time be set forth in a written agreement between the Corporation and any stockholder.

ARTICLE VI : STOCK REPURCHASES .

In connection with repurchases by the Corporation of its Common Stock from Service Providers pursuant to agreements under which the Corporation has the option to repurchase such shares at cost upon the occurrence of certain events, such as the termination of employment, Sections 502 and 503 of the Corporations Code of the State of California shall not apply in all or in part with respect to such repurchases.

ARTICLE VII : BYLAW PROVISIONS .

A. AMENDMENT OF BYLAWS. Subject to any additional vote required by the Restated Certificate or Bylaws, in furtherance and not in limitation of the powers conferred by statute, the Board is expressly authorized to make, repeal, alter, amend and rescind any or all of the Bylaws of the Corporation.

B. NUMBER OF DIRECTORS. Subject to any additional vote required by the Restated Certificate, the number of directors of the Corporation shall be determined in the manner set forth in the Bylaws of the Corporation.

C. BALLOT. Elections of directors need not be by written ballot unless the Bylaws of the Corporation shall so provide.

D. MEETINGS AND BOOKS. Meetings of stockholders may be held within or without the State of Delaware, as the Bylaws of the Corporation may provide. The books of the Corporation may be kept outside the State of Delaware at such place or places as may be designated from time to time by the Board or in the Bylaws of the Corporation.

ARTICLE VIII : DIRECTOR LIABILITY .

A. LIMITATION. To the fullest extent permitted by law, a director of the Corporation shall not be personally liable to the Corporation or its stockholders for monetary damages for breach of fiduciary duty as a director. If the General Corporation Law or any other law of the State of Delaware is amended after approval by the stockholders of this Article VIII to authorize corporate action further eliminating or limiting the personal liability of directors, then the liability of a director of the Corporation shall be eliminated or limited to the fullest extent permitted by the General Corporation Law as so amended. Any repeal or modification of the foregoing provisions of this Article VIII by the stockholders of the Corporation shall not adversely affect any right or protection of a director of the Corporation existing at the time of, or increase the liability of any director of the Corporation with respect to any acts or omissions of such director occurring prior to, such repeal or modification.

B. INDEMNIFICATION . To the fullest extent permitted by applicable law, the Corporation is authorized to provide indemnification of (and advancement of expenses to) directors, officers and agents of the Corporation (and any other persons to which General Corporation Law permits the Corporation to provide indemnification) through Bylaw provisions, agreements with such agents or other persons, vote of stockholders or disinterested directors or otherwise, in excess of the indemnification and advancement otherwise permitted by Section 145 of the General Corporation Law.

C. MODIFICATION . Any amendment, repeal or modification of the foregoing provisions of this Article VIII shall not adversely affect any right or protection of any director, officer or other agent of the Corporation existing at the time of such amendment, repeal or modification.

ARTICLE IX : CREDITOR AND STOCKHOLDER COMPROMISES

Whenever a compromise or arrangement is proposed between the Corporation and its creditors or any class of them and/or between the Corporation and its stockholders or any class of them, any court of equitable jurisdiction within the State of Delaware may, on the application in a summary way of the Corporation or of any creditor or stockholder thereof or on the application of any receiver or receivers appointed for the Corporation under the provisions of §291 of Title 8 of the General Corporation Law or on the application of trustees in dissolution or of any receiver or receivers appointed for this Corporation under §279 of Title 8 of the General Corporation Law order a meeting of the creditors or class of creditors, and/or of the stockholders or class of stockholders of the Corporation, as the case may be, to be summoned in such manner as the said court directs. If a majority in number representing three-fourths in value of the creditors or class of creditors, and/or of the stockholders or class of stockholders of the Corporation, as the case may be, agree to any compromise or arrangement and to any reorganization of the Corporation as a consequence of such compromise or arrangement, the said compromise or arrangement and the said reorganization shall, if sanctioned by the court to which the said application has been made, be binding on all the creditors or class of creditors, and/or on all the stockholders or class of stockholders, of the Corporation, as the case may be, and also on the Corporation.

* * * * *

EXHIBIT B

CERTIFICATE OF MERGER OF AMEYRIS BIOTECHNOLOGIES, INC.

WITH AND INTO

AMYRIS BIOTECHNOLOGIES, INC.

D1025001

State of California

Secretary of State

I, DEBRA BOWEN, Secretary of State of the State of California, hereby certify:

That the attached transcript of 20 page(s) is a full, true and correct copy of the original record in the custody of this office.

IN WITNESS WHEREOF , I execute this certificate and affix the Great Seal of the State of California this day of

JUN 10 2010

/s/ Debra Bowen

DEBRA BOWEN

Secretary of State

D1025001

ENDORSED - FILED

in the office of the Secretary of State

of the State of California

JUN 10 2010

DELAWARE

The First State

I, JEFFREY W. BULLOCK, SECRETARY OF STATE OF THE STATE OF DELAWARE, DO HEREBY CERTIFY THE ATTACHED IS A TRUE AND CORRECT COPY OF THE CERTIFICATE OF MERGER, WHICH MERGES:

"AMYRIS BIOTECHNOLOGIES, INC.", A CALIFORNIA CORPORATION,

WITH AND INTO "AMYRIS BIOTECHNOLOGIES, INC." UNDER THE NAME OF "AMYRIS BIOTECHNOLOGIES, INC.', A CORPORATION ORGANIZED AND EXISTING UNDER THE LAWS OF THE STATE OF DELAWARE, AS RECEIVED AND FILED IN THIS OFFICE THE TENTH DAY OF JUNE, A.D. 2010, AT 2:10 O'CLOCK P.M.

A FILED COPY OF THIS CERTIFICATE HAS BEEN FORWARDED TO THE KENT COUNTY RECORDER OF DEEDS.

/s/ Jeffrey W. Bullock

Jeffrey W. Bullock, Secretary of State

AUTHENTICATION: 8046722

DATE: 06-10-10

4768633 8100M

100646250

You may verify this certificate online

at corp.delaware.gov/authver.shtml

State of Delaware

Secretary of State

Division of Corporations

Delivered 02:10 PM 06/10/2010

FILED 02:10 PM 06/10/2010

SRV 100646250 - 4768633 FILE

CERTIFICATE OF MERGER OF

AMYRIS BIOTECHNOLOGIES, INC., a California corporation

WITH AND INTO

AMYRIS BIOTECHNOLOGIES, INC., a Delaware corporation

Pursuant to Section 252(c) of the

General Corporation Law of the State of Delaware

Amyris Biotechnologies, Inc., a Delaware corporation (“ Amyris Delaware ”) , does hereby certify to the following facts relating to the merger (the “ Merger ”) of Amyris Biotechnologies, Inc., a California corporation (“ Amyris California ”), with and into Amyris Delaware, with Amyris Delaware remaining as the surviving corporation of the Merger (the “ Surviving Corporation ”):


FIRST:	Amyris Delaware is incorporated pursuant to the General Corporation Law of the State of Delaware (“ DGCL ”). Amyris California is incorporated pursuant to the General Corporation Law of the State of California. Amyris Delaware and Amyris California are the constituent corporations in the Merger.


SECOND:	An Agreement and Plan of Merger has been approved, adopted, certified, executed and acknowledged by Amyris Delaware and Amyris California in accordance with the provisions of subsection (c) of Section 252 of the DGCL.


THIRD:	The name of the Surviving Corporation shall be Amyris Biotechnologies, Inc.


FOURTH:	Upon the effectiveness of the Merger, the certificate of incorporation of the Surviving Corporation shall be amended and restated to read in its entirety as set forth in the Restated Certificate of Incorporation attached hereto as Attachment A .


FIFTH:	The executed Agreement and Plan of Merger is on file at the principal place of business of Amyris Delaware, the Surviving Corporation, 5885 Hollis Street, Suite 100, Emeryville, CA 94608, United States of America.


SIXTH:	A copy of the executed Agreement and Plan of Merger will be furnished by Amyris Delaware, the Surviving Corporation, on request and without cost, to any stockholder of any constituent corporation of the Merger


SEVENTH:	The authorized capital stock of Amyris California is 38,000,000 shares of Common Stock, no par value, and 23,862,355 shares of Preferred Stock, no par value.


EIGHTH:	The Surviving Corporation is a corporation formed and existing under the laws of Delaware.


NINTH:	This Certificate of Merger shall become effective upon filing.

IN WITNESS WHEREOF , Amyris Delaware has caused this Certificate of Merger to be executed by its duly authorized officers as of June 10 , 2010.

AMYRIS BIOTECHNOLOGIES, INC.

By: /s/ John Melo

John G. Melo, President

By: /s/ Tamara Tompkins

Tamara Tompkins, Secretary

Attachment A

Restated Certificate of Incorporation

(see Exhibit "A" to the Exhibit A Agreement and Plan of Merger)

EXHIBIT C

RESTATED CERTIFICATE OF INCORPORATION

DELAWARE

The First State

I, JEFFREY W. BULLOCK, SECRETARY OF STATE OF THE STATE OF DELAWARE, DO HEREBY CERTIFY THE ATTACHED IS A TRUE AND CORRECT COPY OF THE RESTATED CERTIFICATE OF "AMYRIS BIOTECHNOLOGIES, INC.", CHANGING ITS NAME FROM "AMYRIS BIOTECHNOLOGIES, INC." TO "AMYRIS, INC.", FILED IN THIS OFFICE ON THE TWENTY-FIRST DAY OF JUNE, A.D. 2010, AT 8:25 O'CLOCK A.M.

A FILED COPY OF THIS CERTIFICATE HAS BEEN FORWARDED TO THE KENT COUNTY RECORDER OF DEEDS.

/s/ Jeffrey W. Bullock

Jeffrey W. Bullock, Secretary of State

AUTHENTICATION: 8064893

DATE: 06-21-10

4768633 8100

100672905

You may verify this certificate online

at corp.delaware.gov/authver.shtml

State of Delaware

Secretary of State

Division of Corporations

Delivered 08:29 AM 06/21/2010

FILED 08:25 AM 06/21/2010

SRV 100672905 - 4768633 FILE

AMYRIS BIOTECHNOLOGIES, INC.

RESTATED CERTIFICATE OF INCORPORATION

(Pursuant to Sections 242 and 245 of the

General Corporation Law of the State of Delaware)

IN WITNESS WHEREOF , this Restated Certificate of Incorporation has been executed by a duly authorized officer of this corporation on this 18th day of June, 2010.

By: /s/ John Melo

John Melo, President

EXHIBIT A

AMYRIS BIOTECHNOLOGIES, INC.

RESTATED CERTIFICATE OF INCORPORATION

ARTICLE I : NAME

The name of the corporation is Amyris, Inc. (the “ Company ”).

ARTICLE II : REGISTERED OFFICE

ARTICLE III : PURPOSE

The nature of the business or purposes to be conducted or promoted is to engage in any lawful act or activity for which corporations may be organized under the General Corporation Law.

ARTICLE IV : AUTHORIZED SHARES

The total number of shares of all classes of stock which the Corporation shall have authority to issue is (a) 70,000,000 shares of Common Stock, $0.0001 par value per share (“ Common Stock ”), and (b) 30,963,903 shares of Preferred Stock, $0.0001 par value per share (“ Preferred Stock ”). The Preferred Stock may be issued from time to time in one or more series, each of such series to consist of such number of shares and to have such terms, powers, preferences or rights, and the qualifications and limitations with respect thereto, as stated or expressed herein. As of the effective date of this Restated Certificate of Incorporation (this “ Restated Certificate ”), 9,475,000 shares of the authorized Preferred Stock of the Corporation are hereby designated “ Series A Preferred Stock ”, 1,929,641 shares of the authorized Preferred Stock of the Corporation are hereby designated “ Series B Preferred Stock ”, 4,700,000 shares of the authorized Preferred Stock of the Corporation are hereby designated “ Series B-1 Preferred Stock ”, 4,976,000 shares of the authorized Preferred Stock of the Corporation are hereby designated “ Series C Preferred Stock ”, 2,781,714 shares of the authorized Preferred Stock of the Corporation are hereby designated “ Series C-1 Preferred Stock ”, and 7,101,548 shares of the authorized Preferred Stock of the Corporation are hereby designated “ Series D Preferred Stock ”. The following is a statement of the designations and the powers, preferences or rights, and the qualifications, limitations or restrictions thereof, in respect of each class of capital stock of the Corporation.

A. COMMON STOCK

2. Voting . The holders of the Common Stock are entitled to one vote for each share of Common Stock held at all meetings of stockholders (and written actions in lieu of meetings). Unless required by law, there shall be no cumulative voting. The number of authorized shares of Common Stock may be increased or decreased (but not below the number of shares thereof then outstanding) by (in addition to any vote of the holders of one or more series of Preferred Stock that may be required by the terms of the Certificate of Incorporation) the affirmative vote of the holders of shares of capital stock of the Corporation representing a majority of the votes represented by all outstanding shares of capital stock of the Corporation entitled to vote, irrespective of the provisions of Section 242(b)(2) of the General Corporation Law.

B. PREFERRED STOCK

1. Dividends.

a. Preferred Stock Dividends. The holders of Series A Preferred Stock, Series B Preferred Stock, Series B-1 Preferred Stock, Series C Preferred Stock, Series C-1 Preferred Stock and Series D Preferred Stock shall be entitled to receive non-cumulative dividends, on a pari passu basis, at the rate of 8% of the Series A Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series A Preferred Stock, at the rate of 8% of the Series B Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series B Preferred Stock, at the rate of 8% of the Series B-1 Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series B-1 Preferred Stock, at the rate of 8% of the Series C Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series C Preferred Stock, at the rate of 8% of the Series C-1 Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series C-1 Preferred Stock, and at the rate of 8% of the Series D Issue Price as defined in Section 2.a. (as adjusted for any stock dividends, combinations or splits with respect to such shares) per annum for the Series D Preferred Stock, payable out of funds legally available therefor. Such dividends shall be payable only when, as, and if declared by the Board of Directors and shall be non-cumulative.

Company until dividends, in the amount of 8% of the Series A Issue Price (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series A Preferred Stock, 8% of the Series B Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series B Preferred Stock, 8% of the Series B-1 Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series B-1 Preferred Stock, 8% of the Series C Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series C Preferred Stock, 8% of the Series C-1 Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series C-1 Preferred Stock, and 8% of the Series D Issue Price as defined in Section 2.a (as adjusted for any stock dividends, combinations or splits with respect to such shares) on the Series D Preferred Stock shall have been paid or declared and set apart during that fiscal year, except for:

(ii) acquisitions of Common Stock in exercise of the Company's right of first refusal to repurchase such shares; or

(iii) distributions to holders of Common Stock in accordance with Section 2.

2. Liquidation Preference.

each such share then held by them, (iii) in the case of Series B-1 Preferred Stock, the amount of $25.26 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “ Series B-1 Issue Price ”), plus all declared but unpaid dividends, on each such share then held by them, (iv) in the case of Series C Preferred Stock, the amount of $12.46 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “ Series C Issue Price ”), (v) in the case of Series C-1 Preferred Stock, the amount of $17.56 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “ Series C-1 Issue Price ”), and (vi) in the case of Series D Preferred Stock, the amount of $18.75 per share, as adjusted for any stock dividends, combinations or splits with respect to such shares (the “ Series D Issue Price ”). If upon the occurrence of such event, the assets and funds thus distributed among the holders of the Preferred Stock shall be insufficient to permit the payment to such holders of the full aforesaid preferential amount, then the entire assets and funds of the Company legally available for distribution shall be distributed ratably among the holders of the Preferred Stock in proportion to the preferential amount each such holder is otherwise entitled to receive.

b. Payments to Holders of Common Stock. After payment to the holders of the Preferred Stock of the amounts set forth in Section 2.a above, the entire remaining

Company or any successor or indebtedness of the Company is cancelled or converted or a combination thereof.

(iii) If there is no active market, the value shall be the fair market value thereof, as determined in good faith by the Board of Directors of the Company.

4. Conversion. The holders of the Preferred Stock shall have conversion rights as follows:

a. Right to Convert. Each share of Preferred Stock shall be convertible, at the option of the holder thereof, at any time after the date of issuance of such share, at the office of the Company or any transfer agent for such stock, into fully paid and nonassessable shares of Common Stock. The number of shares of Common Stock to which a holder of Preferred Stock shall be entitled upon conversion shall be determined by dividing the Series A Issue Price, Series B Issue Price, Series B-1 Issue Price, Series C Issue Price, Series C-1 Issue Price or Series D Issue Price, as applicable, by the conversion price for such share in effect at the time that such certificate is surrendered for conversion, and then multiplying by the number of shares of Preferred Stock being converted. The conversion price per share (the “ Conversion Price ”) as of the Original Issue Date (as defined below) shall be (i) for shares of Series A Preferred Stock $2.174 per share, (ii) for shares of Series B Preferred Stock shall be $22.24 per share, (iii) for shares of Series B-1 Preferred Stock shall be $22.52 per share, (iv) for

shares of Series C Preferred Stock shall be $12.46 per share, (v) for shares of Series C-1 Preferred Stock, $17.56 per share, and (vi) for shares of Series D Preferred Stock, $18.75 per share, in each case each subject to adjustment as hereinafter provided.

b. Automatic Conversion.

(ii) Each share of Series B Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price upon the earlier to occur of (i) the date specified by written consent or agreement of (A) stockholders holding at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class, and (B) stockholders holding at least a majority of the then outstanding shares of Series B Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of a Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

(v) Each share of Series C-1 Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price

upon the earlier to occur of (i) the date specified by written consent or agreement of (A) stockholders holding at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class, and (B) stockholders holding at least a majority of the then outstanding shares of Series C-1 Preferred Stock, voting together as a single class, or (ii) immediately upon the closing of a Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1.

(vi) Each share of Series D Preferred Stock shall automatically be converted into shares of Common Stock at the then applicable Conversion Price upon the earlier to occur of (A) the date specified by written consent or agreement of stockholders holding at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class (provided that all other shares of Preferred Stock are converted into shares of Common Stock at the same time that the shares of Series D Preferred Stock are converted into shares of Common Stock), or (B) immediately upon the closing of a Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section 1. Notwithstanding the foregoing subclause (A), the consent of the holders of a majority of the Series D Preferred Stock shall also be required if the conversion of the shares of Series D Preferred Stock into shares of Common Stock is effected in connection with an Acquisition or Asset Sale in which the value of the consideration to be received (as determined in good faith by the Company's Board of Directors) in respect of the share or shares of Common Stock issuable upon conversion of a share of Series D Preferred Stock is less than the product of one hundred fifty percent (150%) multiplied by the Series D Issue Price.

c. Mechanics of Conversion .

(i) Except in the case of an automatic conversion pursuant to Section 4.b., before any holder of Preferred Stock shall be entitled to convert the same into shares of Common Stock, such holder shall surrender the certificate or certificates therefor, duly endorsed, at the office of the Company or of any transfer agent for such stock, and shall give written notice to the Company at such office that such holder elects to convert the same and shall state therein the name or names in which such holder wishes the certificate or certificates for shares of Common Stock to be issued. The Company shall, as soon as practicable thereafter, issue and deliver at such office to such holder of Preferred Stock a certificate or certificates for the number of shares of Common Stock to which such holder shall be entitled as aforesaid and shall promptly pay (i) in cash or, to the extent sufficient funds are not then legally available therefor, in Common Stock (at the Common Stock's fair market value determined by the Board as of the date of such conversion), any declared and unpaid dividends on the shares of Preferred Stock being converted and (ii) in cash (at the Common Stock's fair market value determined by the Board as of the date of conversion) the value of any fractional share of Common Stock otherwise issuable to any holder of Preferred Stock. Such conversion shall be deemed to have been made immediately prior to the close of business on the date of surrender of the shares of Preferred Stock to be converted, and the person or persons entitled to receive the shares of Common Stock issuable upon such conversion shall be treated for all purposes as the record holder or holders of such shares of Common Stock on such date.

(ii) If the conversion is in connection with an underwritten offering of securities pursuant to the Securities Act, the conversion may, at the option of any

holder tendering shares of Preferred Stock for conversion, be conditioned upon the closing with the underwriters of the sale of securities pursuant to such offering, in which event the person(s) entitled to receive the Common Stock upon conversion of the Preferred Stock shall not be deemed to have converted such Preferred Stock until immediately prior to the closing of such sale of securities.

d. Adjustments to Conversion Price for Certain Diluting Issues.

(i) Special Definitions. For purposes of this Section 4, the following definitions apply:

(1) “ Options ” shall mean rights, options or warrants to subscribe for, purchase or otherwise acquire either Common Stock or Convertible Securities (as defined below).

(2) “ Original Issue Date ” shall mean the date on which the first share of Series D Preferred Stock is issued.

(3) “ Convertible Securities ” shall mean any evidences of indebtedness, shares (other than Common Stock, Series A Preferred Stock, Series B Preferred Stock, Series B-1 Preferred Stock, Series C Preferred Stock, Series C-1 Preferred Stock or Series D Preferred Stock) or other securities convertible into or exchangeable for Common Stock, including securities described in Section 4.d.(i)(4) .

(A) upon conversion of shares of Series A Preferred Stock, Series B Preferred Stock, Series B-1 Preferred Stock, Series C Preferred Stock, Series C-1 Preferred Stock or Series D Preferred Stock;

(E) in a Qualified IPO;

(F) pursuant to a transaction described in Section 4.e or 4.f;

(G) for which adjustment of the applicable Conversion Price is made pursuant to this Section 4;

(I) pursuant to or issuable upon conversion, exchange or cancellation of shares of Amyris Brasil S.A., a majority-owned subsidiary of the Company; or

(J) upon the affirmative vote of at least a majority of the then outstanding shares of Preferred Stock, voting together as a single class on an as-if converted basis.

(iii) Deemed Issue of Additional Shares of Common Stock. In the event the Company at any time or from time to time after the Original Issue Date shall issue any Options or Convertible Securities or shall fix a record date for the determination of holders of any class of securities then entitled to receive any such Options or Convertible Securities, then the maximum number of shares (as set forth in the instrument relating thereto without regard to any provisions contained therein designed to protect against dilution) of Common Stock issuable upon the exercise of such Options or, in the case of Convertible Securities and Options therefor, the conversion or exchange of such Convertible Securities, shall be deemed to be Additional Shares of Common Stock issued as of the time of such issue or, in case such a record date shall have been fixed, as of the close of business on such record date, provided further that in any such case in which Additional Shares of Common Stock are deemed to be issued:

original issue thereof (or upon the occurrence of a record date with respect thereto), and any subsequent adjustments based thereon, shall, upon any such increase or decrease becoming effective, be recomputed to reflect such increase or decrease insofar as it affects such Options or the rights of conversion or exchange under such Convertible Securities (provided, however, that no such adjustment of the Conversion Price shall affect Common Stock previously issued upon conversion of the Preferred Stock);

(iv) Adjustment of Conversion Price Upon Issuance of Additional Shares of Common Stock. In the event the Company, at any time after the Original Issue Date shall issue Additional Shares of Common Stock (including Additional Shares of Common Stock deemed to be issued pursuant to Section 4.d(iii)) without consideration or for a consideration per share less than the applicable Conversion Price in effect on the date of and immediately prior to such issue, then, and in such event, the applicable Conversion Price shall be reduced, concurrently with such issue, to a price (calculated to the nearest cent) determined by multiplying the Conversion Price by a fraction, the numerator of which shall be the number of shares of Common Stock deemed outstanding (as defined below) immediately prior to such issuance plus the number of shares of Common Stock which the aggregate consideration received by the Company for the total number of Additional Shares of Common Stock so issued would purchase at the Conversion Price in effect immediately prior to such issuance, and the denominator of which shall be the number of shares of Common Stock deemed outstanding (as defined below) immediately prior to such issuance plus the number of such Additional Shares of Common Stock so issued. For the purpose of the above calculation, the number of shares of Common Stock outstanding immediately prior to such issue shall be calculated on a fully diluted basis, as if all shares of Preferred Stock and all outstanding Convertible Securities had been fully converted into shares of Common Stock and any outstanding warrants, outstanding options or other rights outstanding for the purchase of shares of stock or convertible securities had been fully exercised (and the resulting securities fully converted into shares of Common Stock, if so convertible) as of such date. For the purposes of adjusting the applicable Conversion Price of a series of Preferred Stock, the grant, issue or sale of Additional Shares of Common consisting of the same class of security and warrants to purchase such security issued or issuable at the same price at two or more closings held within a six (6) month period shall be aggregated and shall be

treated as one sale of Additional Shares of Common occurring on the earliest date on which such securities were granted, issued or sold.

(v) Determination of Consideration. For purposes of this Section 4.d, the consideration received by the Company for the issue of any Additional Shares of Common Stock shall be computed as follows:

(1) Cash and Property. Such consideration shall:

(A) insofar as it consists of cash, be computed at the aggregate amount of cash received by the Company, excluding amounts paid or payable for accrued interest or declared but unpaid dividends;

(B) insofar as it consists of property other than cash, be computed at the fair value thereof at the time of such issue, as determined in good faith by the Board of Directors; and

e. Adjustment of Conversion Price of Series D Preferred Stock Upon Qualified IPO . In the event of a Qualified IPO that closes (i) on or before September 30, 2010, in which the initial public offering price for the Common Stock in such Qualified IPO (the “ IPO Price ”) is less than the product of (a) 1.16 multiplied by (b) the Series D Preferred Stock Conversion Price then in effect, the Series D Preferred Stock Conversion Price shall be reduced to the quotient obtained by dividing (w) the IPO Price by (x) 1.16; or (ii) after September 30, 2010, in which the IPO Price is less than the product of (c) 1.30 multiplied by (d) the Series D Preferred Stock Conversion Price then in effect, the Series D Preferred Stock Conversion Price shall be reduced to the quotient obtained by dividing (y) the IPO Price by (z) 1.30.

f. Adjustments for Stock Dividends and for Combinations or Subdivisions of Common Stock . In the event that this Company at any time or from time to time after the Original Issue Date shall declare or pay, without consideration, any dividend on the Common Stock payable in Common Stock or in any right to acquire Common Stock for no consideration, or shall effect a subdivision of the outstanding shares of Common Stock into a greater number of shares of Common Stock (by stock split, reclassification or otherwise than by payment of a dividend in Common Stock or in any right to acquire Common Stock), or in the event the outstanding shares of Common Stock shall be combined or consolidated, by reclassification or otherwise, into a lesser number of shares of Common Stock, then the conversion price for any series of Preferred Stock in effect immediately prior to such event shall, concurrently with the effectiveness of such event, be proportionately decreased or increased, as appropriate. In the event that the Company shall declare or pay, without consideration, any dividend on the Common Stock payable in any right to acquire Common Stock for no consideration then the Company shall be deemed to have made a dividend payable in Common Stock in an amount of shares equal to the maximum number of shares issuable upon exercise of such rights to acquire Common Stock.

g. Adjustments for Reclassification and Reorganization . If the Common Stock issuable upon conversion of any series of Preferred Stock shall be changed into the same or a different number of shares of any other class or classes of stock, whether by capital reorganization, reclassification or otherwise (other than a subdivision or combination of shares provided for in Section 4.e above or a merger or other reorganization referred to in Section 2.d above), the Conversion Price for any series of Preferred Stock then in effect shall, concurrently with the effectiveness of such reorganization or reclassification, be proportionately adjusted so that the Preferred Stock shall be convertible into, in lieu of the number of shares of Common Stock which the holders would otherwise have been entitled to receive, a number of shares of such other class or classes of stock equivalent to the number of shares of Common Stock that would have been subject to receipt by the holders upon conversion of the Preferred Stock immediately before that change, respectively.

h. Certificates as to Adjustments . Upon the occurrence of each adjustment or readjustment of any conversion price pursuant to this Section 4, the Company at its expense shall promptly compute such adjustment or readjustment in accordance with the terms hereof and prepare and furnish to each holder of Preferred Stock a certificate executed by the Company's President, Chief Financial Officer or a Vice President setting forth such adjustment or readjustment and showing in detail the facts upon which such adjustment or readjustment is based. The Company shall, upon the written request at any time of any holder of Preferred Stock, furnish or cause to be furnished to such holder a like certificate setting forth (i) such adjustments and readjustments, (ii) the conversion price for such series of Preferred Stock at the time in effect, and (iii) the number of shares of Common Stock and the amount, if any, of other property which at the time would be received upon the conversion of the Preferred Stock.

i. Notices of Record Date . In the event that the Company shall propose at any time (i) to declare any dividend or distribution upon its Common Stock, whether

in cash, property, stock or other securities, whether or not a regular cash dividend and whether or not out of earnings or earned surplus, (ii) a Liquidation or any voluntary or involuntary dissolution or winding up of the Company, or (iii) to offer for subscription pro rata to the holders of any class or series of its stock any additional shares of stock of any class or series or other rights, then, in connection with each such event, unless otherwise waived by a majority of Preferred Stock, the Company shall send to the holders of Preferred Stock at least twenty (20) days' prior written notice of the date on which a record shall be taken for such dividend, distribution, Liquidation, dissolution, winding up or subscription rights.

j. Reservation of Stock Issuable Upon Conversion . The Company shall at all times reserve and keep available out of its authorized but unissued shares of Common Stock, solely for the purpose of effecting the conversion of the shares of the Preferred Stock, such number of its shares of Common Stock as shall from time to time be sufficient to effect the conversion of all outstanding shares of the Preferred Stock; and if at any time the number of authorized but unissued shares of Common Stock shall not be sufficient to effect the conversion of all then outstanding shares of the Preferred Stock, the Company will take such corporate action as may, in the opinion of its counsel, be necessary to increase its authorized but unissued shares of Common Stock to such number of shares as shall be sufficient for such purpose, including, without limitation, engaging in best efforts to obtain the requisite stockholder approval of any necessary amendment to this Restated Certificate.

k. Fractional Shares . No fractional share shall be issued upon the conversion of any share or shares of Preferred Stock. All shares of Common Stock (including fractions thereof) issuable upon conversion of more than one share of Preferred Stock by a holder thereof shall be aggregated for purposes of determining whether the conversion would result in the issuance of any fractional share. If, after the aforementioned aggregation, the conversion would result in the issuance of a fraction of a share of Common Stock, the Company shall, in lieu of issuing any fractional share, pay the holder otherwise entitled to such fraction a sum in cash equal to the fair market value of such fraction on the date of conversion (as determined in good faith by the Board of Directors).

l. Notices . Any notice required by the provisions of this Section 4 shall be in writing and shall be deemed effectively given: (i) upon personal delivery to the party to be notified, (ii) when sent by confirmed electronic mail or facsimile if sent during normal business hours of the recipient; if not, then on the next business day, (iii) five (5) days after deposit in the United States mail, by registered or certified mail, postage prepaid and properly addressed to the party to be notified, or (iv) one (1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt. All notices shall be addressed to each holder of record at the address of such holder appearing on the books of the Company.

a. For so long as any shares of Series A Preferred Stock remain outstanding, the holders of Series A Preferred Stock, voting as a separate class, shall be entitled

to elect three (3) members of the Board of Directors (each a “ Series A Director ”) at each meeting or pursuant to each consent of the Company's stockholders for the election of directors, and to remove from office such directors and to fill any vacancy caused by the resignation, death or removal of such directors. Notwithstanding the foregoing, the right of the holders of Series A Preferred Stock to elect the Series A Directors shall terminate upon the earliest to occur of the following: (i) an Acquisition; or (ii) an Asset Sale.

b. The holders of Series D Preferred Stock, voting as a separate class, shall be entitled to elect one (1) member of the Board of Directors (the “ Series D Director ”) at each meeting or pursuant to each consent of the Company's stockholders for the election of directors, and to remove from office such directors and to fill any vacancy caused by the resignation, death or removal of such directors. Notwithstanding the foregoing, the right of the holders of Series D Preferred Stock to elect the Series D Director shall terminate upon the earliest to occur of the following: (i) such time as the Investor (as defined in that certain Series D Preferred Stock Purchase Agreement dated on or about the date of filing of this Restated Certificate by and between the Company and the Investor (the “ Purchase Agreement ”)), together with its Affiliates (as defined below), holds less than fifty percent (50%) of the shares of Series D Preferred Stock purchased by it pursuant to the Purchase Agreement; (ii) an Acquisition; or (iii) an Asset Sale. “ Affiliate ” means with respect to a Person (as defined below), any Person that, directly or indirectly, through one or more intermediaries, controls, is controlled by or is under common control with such first Person. For purposes of this definition, “control” and, with correlative meanings, the terms “controlled by” and “under common control with” mean (x) the possession, directly or indirectly, of the power to direct the management or policies of a Person, whether through the ownership of voting securities, by contract relating to voting rights or corporate governance, or otherwise, or (y) the ownership, directly or indirectly, of more than 50% of the voting securities or other ownership interest of a Person. “ Person ” means an individual, sole proprietorship, partnership, limited partnership, limited liability partnership, corporation, limited liability company, business trust, joint stock company, trust, unincorporated association, joint venture or other similar entity or organization, including a government or political subdivision, department or agency of a government.

c. The holders of Common Stock, voting as a separate class, shall be entitled to elect two (2) members of the Board of Directors (each a “ Common Director ”) at each meeting or pursuant to each consent of the Company's stockholders for the election of directors, and to remove from office such directors and to fill any vacancy caused by the resignation, death or removal of such directors.

d. The holders of Preferred Stock and the holders of Common Stock, voting together as a single class on an as-if converted basis, shall be entitled to elect any additional members of the Board of Directors (each an “ Independent Director ”), and to remove from office such directors and to fill any vacancy caused by the resignation, death or removal of such directors.

6. Redemption . The Preferred Stock shall not be redeemable.

7. Restrictions and Limitations . So long as at least 20% of the shares of the Preferred Stock sold by the Company (as adjusted for stock splits, dividends, combinations,

recapitalizations and the like) remain outstanding, consent of the holders of at least the majority of the then outstanding shares of Preferred Stock shall be required for any action that (whether by amendment, merger, reorganization or otherwise):

a. alters or changes the powers, preferences or rights of the Common Stock or the Preferred Stock,

b. increases or decreases the authorized number of shares of Common or Preferred Stock,

c. creates (whether by amendment, merger, reorganization or otherwise) any new class or series of shares having powers, preferences or rights senior to or on a parity with the Preferred Stock,

e. results in a Liquidation or other corporate reorganization, including any reorganization or other transaction involving any parent or subsidiary of the Company,

f. amends or waives any provision of the Company's certificate of incorporation or bylaws,

g. increases or decreases the authorized size of the Company's Board of Directors, or

h. results in the payment or declaration of any dividend on any shares of Common or Preferred Stock.

8. Further Restrictions and Limitations . So long as at least 50% of the shares of the Series D Preferred Stock sold by the Company (as adjusted for stock splits, dividends, combinations, recapitalizations and the like with respect to such shares) remain outstanding, consent of the holders of at least the majority of the then outstanding shares of the Series D Preferred Stock shall be required for any action that (whether by amendment, merger, reorganization or otherwise):

a. approves or permits the approval of a “drag-along” provision, or any provision that functions as a “drag-along” that would require the holders of Series D Preferred Stock to vote in favor of or otherwise support an Acquisition or Asset Sale,

b. amends, alters or changes the powers, preferences or rights of the Series D Preferred Stock (provided that the creation (whether by amendment, merger, reorganization or otherwise) of any new class or series of shares having powers, preferences or rights on parity with the Series D Preferred Stock shall not constitute an amendment, alteration or change of the powers, preferences or rights of the Series D Preferred Stock),

c. increases the number of authorized shares of Series D Preferred Stock,

d. creates (whether by amendment, merger, reorganization or otherwise) any new class or series of shares having powers, preferences or rights senior to the Series D Preferred Stock, or

e. results in the redemption of any shares of Preferred Stock or Common Stock (other than (i) pursuant to equity incentive agreements with employees and other service providers giving the Company the right to repurchase shares upon the termination of employment or such other service relationship, at their original cost, or (ii) repurchases or redemptions of shares from any founder or service provider upon terms approved by the Company's Board of Directors),

f. increases the authorized size of the Board of Directors to more than eleven (11) members,

9. No Reissuance of Preferred Stock . No share or shares of Preferred Stock acquired by the Company by reason of redemption, purchase, conversion, or otherwise shall be reissued; and, in addition, the certificate of incorporation shall be appropriately amended to effect the corresponding reduction in the Company's authorized stock.

ARTICLE V : PREEMPTIVE RIGHTS .

ARTICLE VI : STOCK REPURCHASES .

ARTICLE VII : BYLAW PROVISIONS .

A. AMENDMENT OF BYLAWS . Subject to any additional vote required by the Restated Certificate or Bylaws, in furtherance and not in limitation of the powers conferred by statute, the Board is expressly authorized to make, repeal, alter, amend and rescind any or all of the Bylaws of the Corporation.

B. NUMBER OF DIRECTORS . Subject to any additional vote required by the Restated Certificate, the number of directors of the Corporation shall be determined in the manner set forth in the Bylaws of the Corporation.

C. BALLOT . Elections of directors need not be by written ballot unless the Bylaws of the Corporation shall so provide.

D. MEETINGS AND BOOKS . Meetings of stockholders may be held within or without the State of Delaware, as the Bylaws of the Corporation may provide. The books of the Corporation may be kept outside the State of Delaware at such place or places as may be designated from time to time by the Board or in the Bylaws of the Corporation.

ARTICLE VIII : DIRECTOR LIABILITY .

A. LIMITATION . To the fullest extent permitted by law, a director of the Corporation shall not be personally liable to the Corporation or its stockholders for monetary damages for breach of fiduciary duty as a director. If the General Corporation Law or any other law of the State of Delaware is amended after approval by the stockholders of this Article VIII to authorize corporate action further eliminating or limiting the personal liability of directors, then the liability of a director of the Corporation shall be eliminated or limited to the fullest extent permitted by the General Corporation Law as so amended. Any repeal or modification of the foregoing provisions of this Article VIII by the stockholders of the Corporation shall not adversely affect any right or protection of a director of the Corporation existing at the time of, or increase the liability of any director of the Corporation with respect to any acts or omissions of such director occurring prior to, such repeal or modification.

ARTICLE IX : CREDITOR AND STOCKHOLDER COMPROMISES

of creditors, and/or of the stockholders or class of stockholders of the Corporation, as the case may be, agree to any compromise or arrangement and to any reorganization of the Corporation as a consequence of such compromise or arrangement, the said compromise or arrangement and the said reorganization shall, if sanctioned by the court to which the said application has been made, be binding on all the creditors or class of creditors, and/or on all the stockholders or class of stockholders, of the Corporation, as the case may be, and also on the Corporation.

* * * * *

EXHIBIT D

RECIPIENT CHANGE REQUEST QUESTIONNAIRE

Recipient Name: Amyris Biotechnologies, Inc.

Address: 5885 Hollis Street, Suite 100, Emeryville, CA 94608

Principal Investigator: Neil Renninger

DOE Award #: DE-EE0002869

Type of Award: XX Competitive (FOA #DE-FOA-0000096)

(Check one) __ Congressionally Directed Project (CDP#_________)

__ Unsolicited Proposal

Primary Nature of the Project: __ Education and Outreach

(Check one) __ Research and Development

XX Demonstration or Commercialization

Date of Selection for Negotiation of Award: December 4, 2009

Date of Award: December 28, 2009

Date of event precipitating the need for this change request: June 10, 2010

Page 1 of 6

Approximate percentage of project completed to date: 40% (based on projected duration)

Total amount of award (total project cost): $24,341,409.00 ($34,932,999.00)

Required Cost Share Percentage: 29.6%

List any other DOE Financial Assistance Awards or DOE Contracts currently held by Recipient:

Subcontract ZFT-0-40623-01 under prime contract number DE-AC36-08GO28308.

Proposed Transferee: Amyris, Inc.

Address: 5885 Hollis Street, Suite 100, Emeryville, CA 94608

Principal Investigator: Neil Renninger

"Recipient" = the existing awardee or entity selected for negotiation of award

"Proposed Transferee" = the entity agreeing to perform the award and accept the Recipient's rights and responsibilities under the DOE Award

Page 2 of 6


1.	Please describe, in detail, the reason for the requested transfer of the DOE Award from Recipient to Proposed Transferee (attach additional pages if necessary):

Amyris Biotechnologies, Inc., a California corporation, WAS reincorporated in Delaware as Amyris Biotechnologies, Inc., a Delaware corporation, in connection with the company's initial public offering. There was no change in ownership of the company. The reincorporation was accomplished effective June 10, 2010, and name change of the surviving Delaware entity (from Amyris Biotechnologies, Inc. to Amyris, Inc.) was completed effective June 21, 2010.


2.	Please describe any financial considerations (including, for example, threat of bankruptcy) that are contributing to the reason for the requested transfer:

Amyris reincorporated in Delaware in connection with its initial public offering, which closed in September 2010. There were no financial considerations that contributed to the subsequent change in the name of the company.


3.	What is the existing legal relationship between the Recipient and the Proposed Transferee

(Check all that apply):

___ Unrelated entities (e.g. no common owner(s), assets, or employees)

___ Parent: __________ Subsidiary: ___________ % Owned: ____

(Please specify which entity is parent and which entity is Subsidiary)

___ Joint venture partner. Please describe the nature of the joint venture: ___________________

___ Proposed Transferee does not yet exist. Please note details re: formation of proposed Transferee,

e.g. formation date, founder, and reason for the formation of the Proposed Transferee:

XX Recipient is legally changing name to Amyris, Inc., but no assets, stock, employees, or other

ownership interests are changing. Effective date of name change is: June 21, 2010

*Attach a certified copy of the document effecting the name change.

XX Recipient and Proposed Transferee are Associate or Affiliate Companies (e.g., common owner(s),

assets or employees)

___ Proposed Transferee is a sub-recipient under the award.

___ Proposed Transferee is a vendor tinder the award.

XX Other, please describe:

Page 3 of 6

Above answers reflect a reincorporation of the Recipient in Delaware (from California) and a subsequent

name change. Copies of the Certificate of Merger (Reincorporation) and Restated Certificate of

Incorporation (name change) are attached for reference.


4.	What type of agreement has been or will be executed between the Recipient and the Proposed

Transferee that is precipitating the request for n change to the DOE Award:


___	Acquisition - of Recipient by Proposed Transferee

(Purchase of all assets and liabilities; Requiring company continues to function and acquired

company ceases to exist)

___ Asset Sale - from Recipient to Proposed Transferee

(No liabilities transferred, e.g. liquidation pursuant to bankruptcy)

XX Merger - of Recipient and Proposed Transferee

(Exchange of stock between Recipient and another company resulting in a single company, the

Proposed Transferee, replacing both of the old companies)

___ Consolidation - of Recipient into Proposed Transferee

(All assets and liabilities of Recipient are absorbed by Proposed Transferee and Proposed

Transferee retains original identity)

___ Downstream Merger - of Recipient into Proposed Transferee

(Partially owned subsidiary takes over its parent company)

XX No agreement will be executed because Proposed Transferee is not a legally separate entity from

Recipient and Recipient is only changing !lame to that of Proposed Transferee.

___ Assignment and Assumption of Award Agreement from Recipient to Sub-Recipient

XX Other, please explain: Above answers reflect a reincorporation of the Recipient in Delaware (from

California) and a subsequent name change. Copies of the Certificate of Merger (Reincorporation)

and Restated Certificate of Incorporation (name change) are attached for reference

Page 4 of 6


5.	Are there any Assets, stock, or ownership interests being sold or transferred to any person or entity

other than the Proposed Transferee:

___ Yes XX No ___ N/A


6.	Will the indirect cost rates change as a result of the transfer of the award from the Recipient to the Proposed Transferee:

___ Yes XX No


7.	Please provide (he following information:



Actual Federal Share Spent, As of Oct 31, 2010	Cost Share Accrued As of Oct 31, 2010
$7,587,029	$3,482,977

DUNS # of Proposed Transferee: 185930182

Taxpayer ID (TIN) of Proposed Transferee: 55-0856151


8.	Attach any diagrams depicting the existing and/or restructured relationship between the Recipient and the Proposed Transferee.

Not applicable


9.	Attach a list of assets related to the Award (including any Intellectual Property, cash or cash equivalents, service agreements, sublease agreements, and transferred licenses) that have been or are being transferred between the Recipient find the Proposed Transferee.

Any and all assets of the Recipient, related to the award or otherwise, are now owned by the Transferee.

10. Attach a certified copy of the Proposed Transferee's formation documentation (e.g. Certificate of

Incorporation or Organization).

Copy of Restated Certificate of Incorporation of Amyris, Inc. attached.


11.	Attach a copy of the instrument(s) effecting the transfer of assets from the Recipient to the Proposed Transferee (e.g., bill of sale, certificate of merger, contract, deed, agreement, court decree, etc.)

Copies of the Agreement and Plan of Merger (Reincorporation), Certificate of Merger

(Reincorporation) and Restated Certificate of Incorporation (name change) are attached for reference.

Page 5 of 6

I am a duly authorized representative of the Recipient and I certify that the answers above are correct to

the best of my knowledge.

/s/ Tamara Tompkins December 17, 2010

(Signature of Authorized Official) Date

Recipient/Transferor

Printed Name of Official: Tamara Tompkins

Title: SVP, General Counsel and Secretary

I am a duly authorized Representative of the Proposed Transferee and I certify that i have reviewed and agree with the Recipients' answers contained in the questionnaire.

/s/ Tamara Tompkins December 17, 2010

(Signature of Authorized Official) Date

Proposed Transferee

Printed Name of Official: Tamara Tompkins

Title: SVP, General Counsel and Secretary

Page 6 of 6

EXHIBIT E

LEGAL OPINION LETTER DATED NOVEMBER 8, 2011

November 8, 2011

Jon Olsen

Contracting Officer

U.S. Department of Energy

Golden Field Office

1617 Cole Boulevard

Golden, CO 80401

RE: Opinion Letter - Amyris Reincorporation & Name Change

Dear Mr. Olsen,

Pursuant to your request in relation to the Department oF Energy formally recognizing Amyris, Inc. as the successor in interest to Amyris Biotechnologies, Inc., the recipient of that certain Department of Energy Award under Cooperative agreement Number DE-EE0002869 (the "Award"), on behalf of Amyris, Inc., the undersigned, EVP, General Counsel and Secretary of Amyris, Inc., hereby warrants and represents the following facts:

That upon a merger of amyris Biotechnologies, Inc., a California corporation ("Amyris California") with and into amyris, Inc., a Delaware corporation ("Amyris Delaware") in connection with a reincorporation of Amyris California in the State of Delaware (the "Reincorporation") as part of an initial public offering of Amyris Delaware assumed all rights and obligations of Amyris California by operation of law;


2.	Amyris Delaware has the same Employer Identification Number as Amyris California, is engaged in essentially the same business activities as Amyris California was, and is otherwise the same enterprise in all material respects (other than the jurisdiction of incorporation and changes in the charter and similar documents necessitated by the Reincorporation and IPO);


3.	The merger of Amyris California and into Amyris Delaware was effected in accordance with applicable law and was effective on the date set forth in Certificate of Merger, a copy of which was previously provided to you; and as, a result of that merger, Amyris California no longer exists as a legal entity;


4.	The merger of Amyris California into Amyris Delaware did not itself result in any significant change to finances, assets, key personnel or other aspects of the business conducted by Amyris California and assumed by Amyris Delaware; and Amyris Delaware was, and continues to be, in substantially the same or better position to perform the Award as was Amyris California; and


5.	There have been no material changes in ownership of Amyris Delaware, such that it is still an eligible entity under the original requirements of the Funding Opportunity Announcement under which the Award was made.

Sincerely,

/s/ Tamara L. Tompkins

Tamara L. Tompkins

EVP, General Counsel & Secretary

ASSISTANCE AGREEMENT

1. Award No.

DE-EE0002869

2. Modification No.

008

3. Effective Date

12/28/2009

4. CFDA No.

81.087

5. Awarded To

AMYRIS, INC.

Attn: NEIL RENNINGER

5885 HOLLIS STREET

SUITE 100

EMERYVILLE CA 946082059

6. Sponsoring Office

Energy Effcy & Renewable Energy

7. Period of Performance

12/28/2009

through

12/31/2012

8. Type of Agreement

_ Grant

x Cooperative Agreement

_ Other

9. Authority

109-58 Energy Policy Act (2005)

111-5 Recovery Act (2009)

10. Purchase Request or Funding Document No.

12EE003800

11. Remittance Address

12. Total Amount

13. Funds Obligated

AMYRIS, INC.

Attn: NEIL RENNINGER

5885 HOLLIS STREET

SUITE 100

EMERYVILLE CA 946082059

Govt. Share: $ 24,341,409.00

Cost Share: $ 10,591,590.00

Total: $ 34,932,999.00

This action: $0.00

Total: $24,341,409.00

14. Principal Investigator

Todd Pray

Phone: 510-740-7441

15. Program Manager

Bryna E. Berendzen

Phone: 720-356-1442

16. Administrator

Golden Field Office

U.S. Department of Energy

Golden Field Office

1617 Cole Blvd.

Golden CO 80401-3393

17. Submit Payment Requests To

OR for Golden

U.S. Department of Energy

Oak Ridge Financial Service Center

P.O. Box 4517

Oak Ridge TN 37831

18. Paying Office

OR for Golden

U.S. Department of Energy

Oak Ridge Financial Service Center

P.O. Box 4517

Oak Ridge TN 37831

19. Submit Reports To

20. Accounting and Appropriation Data

See Schedule

21. Research Title and/or Description of Project

RECOVERY ACT: SCALE-UP & MOBILIZATION OF RENEWABLE DIESEL & CHEMICAL PRODUCTION FROM COMMON INTERMEDIATE USING US-BASED FERMENTABLE SUGAR FEEDSTOCKS

For the Recipient

For the United States of America

22. Signature of Person Authorized to Sign

25. Signature of Grants/Agreements Officer

Signature on File

23. Name and Title

24. Date Signed

26. Name of Officer

Jon F. Olsen

27. Date Signed

07/10/2012



CONTINUATION SHEET		REFERENCE NO. OF DOCUMENT BEING CONTINUED DE-EE0002869/008			PAGE 2 OF 3

NAME OF OFFEROR OR CONTRACTOR AMYRIS, INC.

ITEM NO. (A)	SUPPLIES/SERVICES (B)	QUANTITY (C)	UNIT (D)	UNIT PRICE (E)	AMOUNT (F)
	DUNS Number: 185930182 The purpose of this modification is to revise the budgets for Phase 1 and Phase 2. Accordingly, the following changes are made: 1) Extend the Period of Performance end date, as noted in Block 7; 2) Delete and replace Attachment #2, Statement of Project Objectives; 3) Delete and replace Attachment #4, Budget Information;All others and conditions remain unchanged. 4) In the Special Terms and Conditions, change the following: a) Delete and replace Provision 2, "Award Agreement Terms and Conditions"; b) Delete and replace Provision 4, "Award Project Period and Budget Periods"; c) Delete and replace Provision 5, "Payment Procedures"; d) Delete and replace Provision 6, "Cost Sharing"; e) Delete and replace Provision 15, "Intellectual Property Provisions and Contact Information"; f) Add Provision 32, "Subcontractor Approvals", and 5) Update the Recipient Principal Investigator, as noted below and in Block 14 of the Assistance Agreement. All other terms and conditions remain unchanged. In Block 7 of the Assistance Agreement, the Period of Performance reflects the beginning of the Project Period through the end of the current Budget Period. The total amounts reflected in Blocks 12 and 13 of the Assistance Agreement do not include the Federally Funded Research and Development Center (FFRDC) funding amount of $658,591, which is funded directly during Phase 2. DOE Award Administrator: Brenda Dias E-mail: brenda.dias@go.doe.gov Phone: 720-356-1519 Continued...
JULY 2004



CONTINUATION SHEET		REFERENCE NO. OF DOCUMENT BEING CONTINUED DE-EE0002869/008			PAGE 3 OF 3

NAME OF OFFEROR OR CONTRACTOR AMYRIS, INC.

ITEM NO. (A)	SUPPLIES/SERVICES (B)	QUANTITY (C)	UNIT (D)	UNIT PRICE (E)	AMOUNT (F)
	DOE Project Officer: Bryna Berendzen E-mail: bryna.berendzen@go.doe.gov Phone: 720-356-1442 Recipient Business Officer: Todd Pray E-mail: pray@amyris.com Phone: 510-740-7441 Recipient Principal Investigator: Todd Pray E-mail: pray@amyris.com Phone: 510-740-7441 “Electronic signature or signatures as used in this document means a method of signing an electronic message that-- (A) Identifies and authenticates a particular person as the source of the electronic message; (B) Indicates such person's approval of the information contained in the electronic message; and, (C) Submission via FedConnect constitutes electronically signed documents.” ASAP: NO: STD IMMEDIATE Extent Competed: COMPETED Davis-Bacon Act: YES
JULY 2004

DE-EE0002869/008

Attachment #2

STATEMENT OF PROJECT OBJECTIVES

Amyris Biotechnologies, Inc.

Recovery Act: Scale-up and Mobilization of Renewable Diesel and Chemical Production from Common

Intermediate using US-based Fermentable Sugar Feedstocks

A. PROJECT OBJECTIVES

The Amyris pilot-scale Integrated Biorefinery (IBR) will leverage and upgrade Amyris's existing Emeryville, California pilot plant and support labs to develop US-based production capabilities for No Compromise® renewable diesel fuel and petrochemical substitutes such as lubricants and polymers. These products will be derived semi-synthetically from high-impact biomass feedstocks via microbial fermentation to the same 15- carbon isoprenoid intermediate and subsequent chemical finishing. In particular, Amyris will adapt its current sugarcane juice-based processes to instead utilize sweet sorghum juice and lignocellulosic sugars as a domestic feedstock alternative. To this end, the Amyris IBR team will prepare standard operating procedures (SOPs) for diesel and chemical manufacturing from sweet sorghum, and potentially other high-impact feedstocks, at pilot scale. This will enable robust ongoing techno-economic analysis (TEA), regulatory approvals, and a conceptual design for demonstration- and commercial-scale manufacturing facilities at project closure.

B. PROJECT SCOPE

The primary product of the Amyris IBR is Amyris Renewable Diesel. Secondary products will include lubricants, polymers and other petro-chemical substitutes -- in particular, plasticizers present a significant opportunity as a polymer component used at very high percentages in bulk plastics. Amyris and its project partners will execute on a rapid project to integrate and leverage their collective expertise to enable the conversion of high-impact biomass feedstocks to these advanced, infrastructure-compatible fuel and chemical products. Amyris will perform large scale contract manufacturing for process and product testing to support regulatory and end-user acceptance for domestic production and utilization. Amyris will double the fermentation capacity at its pilot plant and add significant functionality to enable more flexible sugar-stream handling and product finishing unit operations.

For Amyris's IBR project the key feedstock focus will be the utilization of sweet sorghum in collaboration with project partners. The team will plant and harvest sweet sorghum within existing agricultural footprints, concentrate juice to syrup and ship syrup to Amyris and bagasse to Amyris's pretreatment partner. Sweet sorghum bagasse pretreatment conditions will be developed first at lab scale and then at pilot scale, based on feedback from Amyris regarding fermentation performance using different bagasse-derived sugar streams. Other lignocellulosic sugar streams are options as well, either as risk mitigation for sweet sorghum or as feedstock alternatives once sweet sorghum has been validated. Continuing to use its defined media and cane juice-based fermentation processing as reference points, Amyris will optimize sweet sorghum juice- and lignocellulosic sugar-based C15 production in its pilot plant and support labs using its suite of C6 sugar-utilizing Saccharomyces cerevisiae yeast strains. For downstream integration with product finishing and to utilize unfermented C5 sugars from bagasse, fermentation effluent vinasse will be treated by anaerobic digestion for biogas production. Biogas cleanup procedures will be developed and modeled for production of highly pure methane for conversion to hydrogen - a key component for Amyris product finishing - via steam-methane reformation.

Development of alternative products, in addition to diesel, is a core focus of the Amyris IBR project, with both scale-up efforts relying on a robust TEA. Amyris will leverage a variety of vendors with expertise in large-scale production and fuel and chemical product testing to support product acceptance objectives. Supplementing existing product approvals from 20% Amyris Diesel to higher blend percentages and

additional products is a focus area. Finally, readying Amyris from a regulatory standpoint for domestic manufacturing will be a component of this IBR project.

C. TASKS TO BE PERFORMED

Task A.0 Amyris Pilot Plant Upgrades and Operations

Unit operation upgrades and capacity augmentation for both fermentation and chemical processing at Amyris's existing Emeryville pilot plant form a core component of this IBR project. During the two budget periods of the project Amyris will leverage its experience in pilot plant design, construction and operation to rapidly execute with minimal incremental permitting required. In particular, Amyris anticipates little or no downtime of ongoing pilot operations during upgrade design and installation.

Subtask A.1 Amyris pilot plant upgrade design and approvals (Phase 1)

Amyris has scoped initial facility design and will rapidly move to complete this effort. Equipment has already been selected and a general contractor has been engaged. Working with the Department of Energy (DOE) Amyris will adapt a risk management plan from the original construction and initial start-up of the pilot plant in 2008 and ensure that necessary permitting is completed. During the design phase Amyris' pilot plant will continue to operate with current capacity using defined media and real-world feedstocks, such as cane syrup, in order to prototype and develop standard operating procedures (SOPs) and performance metrics for adaptation to sorghum utilization.

Subtask A.2 Amyris pilot plant upgrade installation (Phase 2)

This subtask will include construction and installation activities. Fermentors have the longest lead time and will most likely require nine months for delivery. Other unit operations for downstream processing and upstream feedstock handling will be installed earlier and as delivered pending construction completion in relevant process areas. Amyris's pilot plant will begin handling sweet sorghum-derived feedstreams from a contractor to develop early benchmark data and validate performance targets. During the course of upgrading the pilot plant facility, Amyris will continue ongoing operations and prototyping with defined media and cane-derived feedstreams to simulate and facilitate conversion of sorghum sugars to finished products. This will be accomplished using Amyris's existing pilot plant capacity and by integrating with additional unit operations as they come online.

Subtask A.3 Post-upgrade Amyris pilot plant operations (Phase 2)

Following installation and commissioning of pilot plant upgrades, Amyris will operate the pilot plant to produce comprehensive technical, operating and financial data facilitating conceptual design of a demonstration or commercial scale facility acceptable to DOE.

In addition to developing sweet sorghum pilot scale data, this operations phase will include continuing work with simulated sorghum juice (defined media) and cane-derived feedstreams to maintain reference processes in which the Amyris team has demonstrated consistent performance both in terms of communication and reporting.

Current in-process controls and SOPs will be expanded upon to ensure continued robust data collection and safe operations, leading to enabling data for the design of a US commercial plant using sweet sorghum or other highimpact feedstocks.

Task B.0 Scale-up and economic analysis of Amyris diesel production from sweet sorghum

To complement the pilot plant upgrades and operations in Task 1, Amyris and partners will focus significant effort on process optimization and integration from feedstock to final diesel product finishing processes and waste treatment.

Subtask B.1 Sweet sorghum development, syrup and bagasse production (Phase 1-2)

Amyris's partner will provide both sweet sorghum bagasse and syrup to support integrated processing to Amyris Renewable Diesel. This feedstock partner will manage all aspects of feedstock development and handling including land management, planting within existing agricultural footprints, harvesting, bagasse drying and juice concentration to syrup. They will ship syrup samples to Amyris and will also ship chopped and dried bagasse for lignocellulosic biomass pre-treatment to Amyris's pre-treatment partner.

Subtask B.2 Lignocellulosic pre-treatment development and scale-up (Phase 2)

Following receipt of dried, chopped biomass from sweet sorghum or other feedstocks Amyris's pretreatment partner will undertake three key research and development and scale-up activities. First, they will perform wet chemical compositional analysis of each biomass lot. Second, the partner will undertake parametric pilot-scale pretreatment studies to determine the effect of varying pretreatment conditions on hemi-cellulose conversion yields, enzymatic cellulose digestibility and fermentation performance at Amyris. Third, they will perform pilotscale pretreatment and enzymatic hydrolysis campaigns to produce concentrated sugar solutions. These sugar streams will be shipped to Amyris for fermentation and downstream process performance testing and scale-up.

Subtask B.3 Fermentation scale-up (Phase 1-2) Utilization of sugar streams from such sources as lignocellulosic bagasse and sweet sorghum syrup, as well as other potential feedstocks will result in significant need for medium optimization. This includes optimization of pre-treatment steps to precipitate undesired species, removal of particulates, and sterilization of the medium, as well as supplementation of trace nutrients needed for cost-effective gains in fermentation yield. Additionally, converting current processes to use syrup and lignocellulosic fermentable sugars will likely require significant changes to pre-fermentation handling of sugar streams as well as to operating conditions for fermentation itself.

Initially Amyris will acquire baseline fermentation process data using sweet sorghum syrup and bagasse sugar streams, along with defined and cane-derived media, in its support labs. Later in the project Amyris will develop sweet sorghum SOPs for comparison to cane-based media performance in terms of product yield and sugar utilization rates. Throughout the project Amyris will test S. cerevisiae yeast strains to monitor relative and absolute performance comparing production from defined, cane-derived and sweet sorghum-based media.

Subtask B.4 Anaerobic digestion development and hydrogen production (Phase 2)

In collaboration with partners, Amyris will develop and optimize an integrated hydrogen production process to utilize residual unfermented C5 sugars from fermentation effluent. This effluent, vinasse, will be exposed to one or two anaerobic digestion conditions for biogas production. Amyris will then lead collaborative efforts to develop and model proper biogas cleanup procedures to ensure effective conversion of methane to hydrogen via steam methane reforming.

Subtask B.5 Recovery, purification and diesel finishing scale-up (Phase 1-2)

Recovery yield and purity indicators will drive scale-up and process optimization for isolation of the waterimmiscible C15 isoprenoid oil phase from fermentation broth aqueous phase and solids components. Various product recovery unit operations will be adapted from defined media and cane syrup-based fermentation recovery processes and tested with sorghum syrup and bagasse sugar-derived media. Amyris

will first focus on developing baseline recovery data from sorghum media relative to defined and cane based fermentations. Later, Amyris will optimize and scale robust recovery processes with sorghum or other feedstocks.

The current base-case chemical finishing process for Amyris Diesel is catalytic hydrogenation of the C15 fermentation intermediate. Product yields are high under current process conditions, and the Amyris team will validate that sweet sorghum utilization in fermentation does not result in degradation of hydrogenation specificity and yield via impurities carried over from recovery. In addition, process engineering expertise will be required to test and ensure that potential impurities identified during biogas clean-up and hydrogen production do not impact final Amyris Diesel quality or cost.

Subtask B.6 TEA and LCA for Amyris Diesel production (Phase 1-2)

Amyris will lead efforts to merge pre-treatment process models with sugar-to-diesel conversion for an

overall TEA of the integrated process for sweet sorghum conversion to Amyris Diesel using Aspen Plus and other software tools. In addition, life cycle analyses (LCA) will be further refined to reflect up-to-date process configuration and conceptual designs for commercial scale production.

Task C.0 Development and scale-up of value-added products from diesel fermentation intermediate

The third task in this project focuses on the use of the C15 isoprenoid fermentation product used for diesel production as a raw material for the synthesis of a number of large-market, high-value chemicals. The work required in this task will be divided into the following sections:

Subtask C.1 Laboratory-scale development and chemical product synthesis (Phase 1-2)

High-volume or high-value market needs that are amenable to solutions using the C15 isoprenoid fermentation product will be identified. Scientific literature searches will be continuously performed to determine prior art for candidate product molecules. If patented, Amyris will evaluate whether these patents and patent applications would pose freedom to operate issues to Amyris. Screening experiments on a small (e.g. grams or less) scale will be used to identify an effective (but not necessarily optimum) synthesis and a full characterization of the product. The initial synthesis may have to be scaled up to tens of grams depending on the sample amounts required for any performance testing. Design and initial synthesis of a target product will be followed by comprehensive product and byproduct characterization and application-related product property testing. In particular, plasticizers are contemplated as a key focus in Phase 2 as high-volume, value-add complements to Amyris Diesel production.

Subtask C.2 Mid-scale synthesis and characterization (Phase 2)

Initial scale-up/optimization will be accomplished by using statistical design of experiments to identify and optimize the important process variables with a minimum number of experiments. This will provide an optimized scaled process for each candidate chemical product that will allow for a preliminary cost assessment, a safety evaluation and a process design that can be the basis of preparing a SOP for technology transfer to the pilot plant. In addition, it will provide large scale samples for more thorough characterization of product properties and sampling to potential customers, for their preliminary application testing, if applicable.

Subtask C.3 Pilot-scale production and chemical process technoeconomics (Phase 2)

Pre-pilot chemical product scale-up support efforts will comprise determining how the process described performs at scale and the collection of engineering data for plant design and process economics. It will also enable the pilotscale in-house manufacture of quantities of product suitable for larger scale customer

sampling. For any unit operations beyond the capabilities of the pilot plant Amyris IBR will rely on specialized contract research organizations offering custom synthesis and scale-up services.

The final phase of new chemical product development would be initiated by a reevaluation of project justification, cost scenarios and market status. These would build upon modeling throughout the project life span that is refined as data becomes available. The final outcome would indicate whether a toll manufacturing option or in house manufacture would be preferable. Either scenario would require preparation of the appropriate engineering data packages, preliminary commercial scale process design and costing and Capital Expenditure/Operating Expenditure assessments to integrate with the Amyris Diesel TEA and LCA performed in Task B.6.

Task D.0 Regulatory and end-user process and product acceptance

The establishment of market readiness for Amyris Diesel and chemical products is an essential component of the IBR project.

Subtask D.1 Fuel product approval and acceptance (Phase 1-2)

Under the scope of this project, registration of higher diesel fuel blend ratios (above the current Environmental Protection Agency (EPA) registration at 20% Amyris Diesel) will be pursued. Amyris will perform contract manufacturing and third-party laboratory testing to validate product properties and determine potential toxicity of chemical substances under EPA test procedures, fuel properties and combustion effects. Additional toxicity data collection will include occupational exposure risk assessment, if necessary.

Subtask D.2 Chemical product approval and acceptance (Phase 1-2)

Chemical registration dossiers for selected products, either as new products or bio-derived product equivalents will be submitted to EPA for pre-manufacture notice and to fulfill the reporting requirements of EPA under the North American Free Trade Agreement Chemical Assessment and Management Program obligations. Amyris will use contract manufacturing for volume production required for product acceptance testing and validation by potential end-users, contract laboratories, and regulatory agencies.

Subtask D.3 Use approvals for genetically modified microbes (Phase 1-2)

During the course of the IBR project Amyris will develop the strategy and data required to submit a microbial commercial activity notice (MCAN) for use of genetically modified microorganisms (GMM) in commercial US production.

Subtask D.4 Commercial production process approvals and acceptance (Phase 1-2)

During the course of the IBR project Amyris will develop and refine the path for commercial process and installation approvals, including any National Environmental Policy Act (NEPA), state or local regulations governing chemical manufacturing. Amyris will focus on states such as Hawaii, Florida, California, Louisiana and Alabama as potential sites for early US production from sweet sorghum and other feedstocks.

Task E.0 Project Management and Reporting (Phase 1-2)

Management of the timelines and key decision points will be monitored by Amyris using the Earned Value system using percentage completion of each task as a monthly performance-to-plan metric. A detailed baseline plan will be developed with project partners, and progress will be monitored using task start and finish dates to identify variance, major performance issues, key risks to completion, and to enable more accurate forecasting in later quarters. Linkage between task completion and project expenditures will be accomplished using project based accounting.

Applicant Name: Amyris, Inc. Award Number: DE-EE0002869/008 Attachment #4

BUDGET INFORMATION - NON CONSTRUCTION PROGRAMS

OMB Approval No. 0348-044



Section A - Budget Summary
		Estimated Unobligated Funds				New or Revised Budget
Grant Program Function or Activity (a)	Catalog of Federal Domestic Assistance Number (b)	Federal (c)		Non-Federal (d)		Federal (e)		Non-Federal (f)		Total (g)
1. Phase 1						$	3,008,260	$	1,702,920	$	4,711,180
2. Phase 2						$	21,991,740	$	8,230,079	$	30,221,819
3.
4.
5. Totals		$	—	$	—	$	25,000,000	$	9,932,999	$	34,932,999
Section B - Budget Categories
6. Object Class Categories		Grant Program, Function or Activity
6. Object Class Categories		(1) Phase 1		(2) Phase 2						Total (5)
a. Personnel		$	1,342,119	$	7,245,746					$	8,587,865
b. Fringe Benefits		$	289,629	$	1,563,632					$	1,853,261
c. Travel		$	9,168	$	18,064					$	27,232
d. Equipment		$	592,541	$	1,925,314					$	2,517,855
e. Supplies		$	209,745	$	2,074,668					$	2,284,413
f. Contractual		$	84,772	$	5,446,373					$	5,531,145
g. Construction		$	—	$	—					$	—
h. Other		$	304,239	$	1,803,978					$	2,108,217
i. Total Direct Charges (sum of 6a-6h)		$	2,832,213	$	20,077,775					$	22,909,988
j. Indirect Charges		$	1,878,967	$	10,144,044					$	12,023,011
k. Totals (sum of 6i-6j)		$	4,711,180	$	30,221,819					$	34,932,999

7. Program Income		$	—	$	—					$	—

SF-424A (Rev. 4-92)

Prescribed by OMB Circular A-102

Previous Edition Usable Authorized for Local Reproduction

DE-EE0002869/008

SPECIAL TERMS AND CONDITIONS

Table of Contents


Number	Subject Page


1.	RESOLUTION OF CONFLICTING CONDITIONS 2


2.	AWARD AGREEMENT TERMS AND CONDITIONS 2


3.	ELECTRONIC AUTHORIZATION OF AWARD DOCUMENTS 2


4.	AWARD PROJECT PERIOD AND BUDGET PERIODS 2


5.	PAYMENT PROCEDURES 3


6.	COST SHARING 4


7.	REBUDGETING AND RECOVERY OF INDIRECT COSTS 5


8.	FINAL INCURRED COST AUDIT 5


9.	STATEMENT OF FEDERAL STEWARDSHIP 5


10.	STATEMENT OF SUBSTANTIAL INVOLVEMENT 5


11.	SITE VISITS 6


12.	REPORTING REQUIREMENTS 7


13.	PUBLICATIONS 7


14.	FEDERAL, STATE, AND MUNICIPAL REQUIREMENTS 8


15.	INTELLECTUAL PROPERTY PROVISIONS AND CONTACT

INFORMATION 8


16.	NATIONAL SECURITY: CLASSIFIABLE RESULTS ORIGINATING

UNDER AN AWARD 8


17.	LOBBYING RESTRICTIONS 9


18.	NOTICE REGARDING THE PURCHASE OF AMERICAN-MADE EQUIPMENT

AND PRODUCTS -- SENSE OF CONGRESS 9


19.	PROPERTY 10


20.	DECONTAMINATION AND/OR DECOMMISSIONING (D&D) COSTS 10


21.	INSOLVENCY, BANKRUPTCY OR RECEIVERSHIP 10


22.	INDEMNITY 11


23.	SPECIAL PROVISIONS RELATING TO WORK FUNDED UNDER

AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009 (May 2009) 11


24.	REPORTING AND REGISTRATION REQUIREMENTS UNDER SECTION 1512

OF THE RECOVERY ACT 16


25.	REQUIRED USE OF AMERICAN IRON, STEEL, AND MANUFACTURED GOODS - SECTION 1605 OF THE AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009 16


26.	REQUIRED USE OF AMERICAN IRON, STEEL, AND MANUFACTURED GOODS (COVERED UNDER INTERNATIONAL AGREEMENTS) -

SECTION 1605 OF THE AMERICAN RECOVERY AND REINVESTMENT

ACT OF 2009 19


27.	RECOVERY ACT TRANSACTIONS LISTED IN SCHEDULE OF EXPENDITURES

OF FEDERAL AWARDS AND RECIPIENT RESPONSIBILITIES FOR INFORMING SUBRECIPIENTS 23


28.	WAGE RATE REQUIREMENTS UNDER SECTION 1606 OF THE

RECOVERY ACT 24


29.	DAVIS BACON ACT AND CONTRACT WORK HOURS AND SAFETY STANDARDS ACT 25


30.	CONTINGENCY 35


31.	NATIONAL ENVIRONMENTAL POLICY ACT (NEPA) REQUIREMENTS 36


32.	SUBCONTRACT APPROVALS 36


1.	RESOLUTION OF CONFLICTING CONDITIONS

Any apparent inconsistency between Federal statutes and regulations and the terms and conditions contained in this award must be referred to the DOE Award Administrator for guidance.


2.	AWARD AGREEMENT TERMS AND CONDITIONS

This award/agreement consists of the Assistance Agreement, plus the following:


a.	Special Terms and Conditions.


b.	Attachments:

Attachment Number Title

1. Intellectual Property Provisions

2. Statement of Project Objectives

3. Federal Assistance Reporting Checklist and Instructions

4. Budget Pages (SF 424A)

5. Requirements for Contingency Funds for Integrated Biorefinery Projects


c.	Applicable program regulations.


d.	DOE Assistance Regulations, 10 CFR Part 600 at http://ecfr.gpoaccess.gov .


e.	If the award is for research and the award is for a university or non-profit, the Research Terms & Conditions and the DOE Agency Specific Requirements at http://www.nsf.gov/bfa/dias/policy/rtc/index.jsp apply.


f.	Application/proposal as approved by DOE.


g.	National Policy Assurances to be incorporated as award terms in effect on date of award at http://energy.gov/management/downloads/national-policy-assurances-be-incorporated-award-terms


3.	ELECTRONIC AUTHORIZATION OF AWARD DOCUMENTS


4.	AWARD PROJECT PERIOD AND BUDGET PERIODS

The Project Period for this award is 12/28/2009 through 12/31/2012, consisting of the following Budget Periods:



Budget Period	Phase	Start Date	End Date
1	1	12/28/2009	4/21/2010
	2	4/22/2010	12/31/2012


5.	PAYMENT PROCEDURES


a.	Method of Payment . Payment will be made by reimbursement through ACH.


b.	Requesting Reimbursement . Requests for reimbursements must be made electronically through Department of Energy's Oak Ridge Financial Service Center (ORFSC) VIPERS. To access and use VIPERS, you must enroll at https://vipers.oro.doe.gov . Detailed instructions on how to enroll are provided on the web site.

For non-construction awards, you must submit a Standard Form (SF) 270, “Request for Advance or Reimbursement,” at https://vipers.oro.doe.gov and attach a file containing appropriate supporting documentation. The file attachment must show the total Federal share claimed on the SF 270, the non-Federal share claimed for the billing period if cost sharing is required, and cumulative expenditures to date (both Federal and non-Federal) for each of the following categories: salaries/wages and fringe benefits; equipment; travel; participant/training support costs, if any; other direct costs, including subawards/contracts; and indirect costs. For construction awards, you must submit a SF 271, “Outlay Report and Request for Reimbursement for Construction Programs,” through VIPERS.


c.	Timing of submittals. Submittal of the SF 270 or SF 271 should coincide with your normal billing pattern, but not more frequently than every two weeks. Requests for reimbursement must be limited to the amount of disbursements made during the billing period for the Federal share of direct project costs and the proportionate share of any allowable indirect costs incurred during that billing period.


d.	Adjusting payment requests for available cash. You must disburse any funds that are available from repayments to and interest earned on a revolving fund, program income, rebates, refunds, contract settlements, audit recoveries, credits, discounts, and interest earned on any of those funds before requesting additional cash payments from DOE.


6.	COST SHARING



Budget Period 1	Phase	DOE Cost Share, including FFRDC Costs		Recipient Cost Share $ / %	Total Estimated Costs
	Phase	DOE $ / %	FFRDC $ / %	Recipient Cost Share $ / %	Total Estimated Costs
	1	$3,008,260/63.1%	—	$1,702,920/36.9%	$4,711,180
	2	$21,333,149/69.1%	$658,591/2.1%	$8,888,670/28.8%	$30,880,410
	Total Project	$24,341,409/68.4%	$658,591/2.0%	$10,591,590/29.8%	$35,591,590

c. You must maintain records of all project costs you claim as cost sharing, including in-kind costs, as well as records of costs to be paid by DOE. Such records are subject to audit.

d. Failure to provide the cost share required by this Article may result in the subsequent recovery by DOE of some or all the funds provided under the award.


7.	REBUDGETING AND RECOVERY OF INDIRECT COSTS


a.	If actual allowable indirect costs are less than those budgeted and funded under the award, you may use the difference to pay additional allowable direct costs during the project period. If at the completion of the award the Government's share of total allowable costs (i.e., direct and indirect), is less than the total costs reimbursed, you must refund the difference.


b.	Recipients are expected to manage their indirect costs. DOE will not amend an award solely to provide additional funds for changes in indirect cost rates. DOE recognizes that the inability to obtain full reimbursement for indirect costs means the Recipient must absorb the underrecovery. Such underrecovery may be allocated as part of the organization's required cost sharing .


8.	FINAL INCURRED COST AUDIT


9.	STATEMENT OF FEDERAL STEWARDSHIP


10.	STATEMENT OF SUBSTANTIAL INVOLVEMENT


a.	Government Insight


b.	Specific activities to be conducted by DOE

Risk Evaluation - DOE will review the Recipient's initial Risk Mitigation Plan (RMP) for quality and completeness. DOE will also monitor updates to the RMP and actions taken by the Recipient during the performance of its award to mitigate risks and improve the probability of successful execution of the integrated Biorefinery project. At DOE's discretion, additional independent risk analyses of the project by DOE consultants may be requested.

Independent Engineering Assessments -DOE will engage a private, independent engineering (IE) firm to assist in assessing the progress of the project and provide timely and accurate reports to DOE. The Recipient will ensure that the IE has access to any and all relevant documentation sufficient to allow the IE to provide independent evaluations to DOE on the progress of the project. Such documentation includes but is not limited to the following:

• Drawings and specifications

• Construction and Execution plans

• Resource loaded schedules

• Design functions and requirements for the site final design review

• Risk management plans

• Value management and engineering studies and/or plans

• Acquisition strategies

• Project execution plans

• Project controls including earned value management systems

• Qualifications of the integrated project team.

• Financial strategy for funding the construction project

• Updated marketing and business plan

• Invoices submitted to DOE


11.	SITE VISITS


12.	REPORTING REQUIREMENTS


c.	Restrictions . Reports submitted to the DOE Information Bridge must not contain any Protected Personal Identifiable Information (PII), limited rights data (proprietary data), classified information, information subject to export control classification, or other information not subject to release.


13.	PUBLICATIONS


a.	You are encouraged to publish or otherwise make publicly available the results of the work conducted under the award.


b.	An acknowledgment of DOE support and a disclaimer must appear in the publication of any material, whether copyrighted or not, based on or developed under this project, as follows:


14.	FEDERAL, STATE, AND MUNICIPAL REQUIREMENTS

You must obtain any required permits and comply with applicable federal, state, and municipal laws, codes, and regulations for work performed under this award.


15.	INTELLECTUAL PROPERTY PROVISIONS AND CONTACT INFORMATION


a.	The intellectual property provisions applicable to this award are provided as an attachment to this award or are referenced in the Assistance Agreement.


b.	Questions regarding intellectual property matters should be referred to the DOE Award Administrator identified and the Patent Counsel designated as the service provider for the DOE office that issued the award.

Patent Counsel for the Golden Field Office is Julia Moody, who may be reached at julia.moody@go.doe.gov or 720-356-1669.


16.	NATIONAL SECURITY: CLASSIFIABLE RESULTS ORIGINATING UNDER AN AWARD


1.	Notify the DOE Project Officer and the DOE Award Administrator;


2.	Submit the information by registered mail directly to the Director, Office of Classification and Information Control, SO-10.2; U.S. Department of Energy; P.O. Box A; Germantown, MD 20875-0963, for classification review.


3.	Restrict access to the information to the maximum extent possible until you are informed that the information is not classified, but no longer than 30 days after receipt by the Director, Office of Classification and Information Control


c.	If you originate information concerning the production or utilization of special nuclear material (i.e., plutonium, uranium enriched in the isotope 233 or 235, and any other material so determined under section 51 of the Atomic Energy Act) or nuclear energy, you must:


1.	Notify the DOE Project Officer and the DOE Award Administrator;


2.	Submit the information by registered mail directly to the Director, Office of Classification and Information Control, SO-10.2; U.S. Department of Energy; P. O. Box A; Germantown, MD 20875-0963 for classification review within 180 days of the date the Recipient first discovers or first has reason to believe that the information is useful in such production or utilization; and


3.	Restrict access to the information to the maximum extent possible until you are informed that the information is not classified, but no longer than 90 days after receipt by the Director, Office of Classification and Information Control.


d.	If DOE determines any of the information requires classification, you agree that the Government may terminate the award by mutual agreement in accordance with 10 CFR 600.25(d). All material deemed to be classified must be forwarded to DOE, in a manner specified by DOE.


e.	If DOE does not respond within the specified time periods, you are under no further obligation to restrict access to the information.


17.	LOBBYING RESTRICTIONS


18.	NOTICE REGARDING THE PURCHASE OF AMERICAN-MADE EQUIPMENT AND PRODUCTS -- SENSE OF CONGRESS

It is the sense of the Congress that, to the greatest extent practicable, all equipment and products purchased with funds made available under this award should be American-made.


19.	PROPERTY

Real property and equipment acquired by the Recipient shall be subject to the rules set forth in 10 CFR 600.130-137, 10 CFR 600.231-233, or 10 CFR 600.320-324, as applicable.


20.	DECONTAMINATION AND/OR DECOMMISSIONING (D&D) COSTS


21.	INSOLVENCY, BANKRUPTCY OR RECEIVERSHIP

You shall immediately notify the DOE of the occurrence of any of the following events: (i) you or your parent's filing of a voluntary case seeking liquidation or reorganization under the Bankruptcy Act; (ii) your consent to the institution of an involuntary case under the Bankruptcy Act against you or your parent; (iii) the filing of any similar proceeding for or against you or your parent, or your consent to the dissolution, winding-up or readjustment of your debts, appointment of a receiver, conservator, trustee, or other officer with similar powers over you, under any other applicable state or federal law; or (iv) your insolvency due to its inability to pay debts generally as they become due.


b.	Such notification shall be in writing and shall: (i) specifically set out the details of the occurrence of an event referenced in paragraph (a); (ii) provide the facts surrounding that event; and (iii) provide the impact such event will have on the project being funded by this award.

Upon the occurrence of any of the four events described in paragraph a. of this provision, DOE reserves the right to conduct a review of your award to determine your compliance with the required elements of the award (including such items as cost share, progress towards technical project objectives, and submission of required reports). If the DOE review determines that there are significant deficiencies or concerns with your performance under the award, DOE reserves the right to impose additional requirements, as needed, including (i) change of payment method; or (ii) institute payment controls.


d.	Failure of the Recipient to comply with this provision may be considered a material noncompliance of this financial assistance award by the Contracting Officer.


22.	INDEMNITY


23.	SPECIAL PROVISIONS RELATING TO WORK FUNDED UNDER AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009 (May 2009)

Preamble

Definitions

Special Provisions

A. Flow Down Requirement

Recipients must include these special terms and conditions in any subaward.

B. Segregation of Costs

C. Prohibition on Use of Funds

D. Access to Records

(2) to interview any officer or employee of the contractor, grantee, subgrantee, or agency regarding such transactions.

E. Publication

Notice of Restriction on Disclosure and Use of Data

The data contained in pages ---- of this application have been submitted in confidence and contain trade secrets or proprietary information, and such data shall be used or disclosed only for

evaluation purposes, provided that if this applicant receives an award as a result of or in connection with the submission of this application, DOE shall have the right to use or disclose the data here to the extent provided in the award. This restriction does not limit the Government's right to use or disclose data obtained without restriction from any source, including the applicant.

F. Protecting State and Local Government and Contractor Whistleblowers .

The requirements of Section 1553 of the Act are summarized below. They include, but are not limited to:

- gross management of an agency contract or grant relating to covered funds;

- a gross waste of covered funds;

- a substantial and specific danger to public health or safety related to the implementation or use of covered funds;

- an abuse of authority related to the implementation or use of covered funds; or

- as violation of law, rule, or regulation related to an agency contract (including the competition for or negotiation of a contract) or grant, awarded or issued relating to covered funds.

- Order the employer to take affirmative action to abate the reprisal.

- Order the employer to pay the employee an amount equal to the aggregate amount of all

costs and expenses (including attorneys' fees and expert witnesses' fees) that were reasonably incurred by the employee for or in connection with, bringing the complaint regarding the reprisal, as determined by the head of a court of competent jurisdiction.

G. RESERVED

H. False Claims Act

I. Information in Support of Recovery Act Reporting

J. Availability of Funds

Funds appropriated under the Recovery Act and obligated to this award are available for reimbursement of costs until September 30, 2015.


24.	REPORTING AND REGISTRATION REQUIREMENTS UNDER SECTION 1512 OF THE RECOVERY ACT


(a)	This award requires the recipient to complete projects or activities which are funded under the American Recovery and Reinvestment Act of 2009 (Recovery Act) and to report on use of Recovery Act funds provided through this award. Information from these reports will be made available to the public.


(b)	The reports are due no later than ten calendar days after each calendar quarter in which the Recipient receives the assistance award funded in whole or in part by the Recovery Act.

(c)

Recipients and their first-tier subrecipients must maintain current registrations in the Central Contractor Registration ( http://www.ccr.gov ) at all times during which they have active federal awards funded with Recovery Act funds. A Dun and Bradstreet Data Universal Numbering System (DUNS) Number ( http://www.dnb.com ) is one of the requirements for registration in the Central Contractor Registration.


(d)	The recipient shall report the information described in section 1512(c) of the Recovery Act using the reporting instructions and data elements that will be provided online at http://www.FederalReporting.gov and ensure that any information that is pre-filled is corrected or updated as needed.


25.	REQUIRED USE OF AMERICAN IRON, STEEL, AND MANUFACTURED GOODS - SECTION 1605 OF THE AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009


(a)	Definitions. As used in this award term and condition-


(1)	Manufactured good means a good brought to the construction site for incorporation into the building or work that has been-


(i)	Processed into a specific form and shape; or


(ii)	Combined with other raw material to create a material that has different properties than the properties of the individual raw materials.

(2)


(3)	Steel means an alloy that includes at least 50 percent iron, between .02 and 2 percent carbon, and may include other elements.


(b)	Domestic preference. (1) This award term and condition implements Section 1605 of the American Recovery and Reinvestment Act of 2009 (Recovery Act) (Pub. L. 111-5), by requiring that all iron, steel, and manufactured goods used in the project are produced in the United States except as provided in paragraph (b)(3) of this section and condition.


(2)	This requirement does not apply to the material listed by the Federal Government as follows:

none


(3)	The award official may add other iron, steel, and/or manufactured goods to the list in paragraph (b)(2) of this section and condition if the Federal Government determines that-


(i)	The cost of the domestic iron, steel, and/or manufactured goods would be unreasonable. The cost of domestic iron, steel, or manufactured goods used in the project is unreasonable when the cumulative cost of such material will increase the cost of the overall project by more than 25 percent;


(ii)	The iron, steel, and/or manufactured good is not produced, or manufactured in the United States in sufficient and reasonably available quantities and of a satisfactory quality; or


(iii)	The application of the restriction of section 1605 of the Recovery Act would be inconsistent with the public interest.


(c)	Request for determination of inapplicability of Section 1605 of the Recovery Act . (1)(i) Any recipient request to use foreign iron, steel, and/or manufactured goods in accordance with paragraph (b)(3) of this section shall include adequate information for Federal Government evaluation of the request, including-


(A)	A description of the foreign and domestic iron, steel, and/or manufactured goods;


(B)	Unit of measure;


(C)	Quantity;


(D)	Cost;


(E)	Time of delivery or availability;


(F)	Location of the project;


(G)	Name and address of the proposed supplier; and


(H)	A detailed justification of the reason for use of foreign iron, steel, and/or manufactured goods cited in accordance with paragraph (b)(3) of this section.


(ii)	A request based on unreasonable cost shall include a reasonable survey of the market and a completed cost comparison table in the format in paragraph (d) of this section.


(iii)	The cost of iron, steel, and/or manufactured goods material shall include all delivery costs to the construction site and any applicable duty.

(iv)

Any recipient request for a determination submitted after Recovery Act funds have been obligated for a project for construction, alteration, maintenance, or repair shall explain why the recipient could not reasonably foresee the need for such determination and could not have requested the determination before the funds were obligated. If the recipient does not submit a satisfactory explanation, the award official need not make a determination.

(2)

If the Federal Government determines after funds have been obligated for a project for construction, alteration, maintenance, or repair that an exception to section 1605 of the Recovery Act applies, the award official will amend the award to allow use of the foreign iron, steel, and/or relevant manufactured goods. When the basis for the exception is nonavailability or public interest, the amended award shall reflect adjustment of the award amount, redistribution of budgeted funds, and/or other actions taken to cover costs associated with acquiring or using the foreign iron, steel, and/or relevant manufactured goods. When the basis for the exception is the unreasonable cost of the domestic iron, steel, or manufactured goods, the award official shall adjust the award amount or redistribute budgeted funds by at least the differential established in 2 CFR 176.110(a).


(3)	Unless the Federal Government determines that an exception to section 1605 of the Recovery Act applies, use of foreign iron, steel, and/or manufactured goods is noncompliant with section 1605 of the American Recovery and Reinvestment Act.


(d)	Data. To permit evaluation of requests under paragraph (b) of this section based on unreasonable cost, the Recipient shall include the following information and any applicable supporting data based on the survey of suppliers:

Foreign and Domestic Items Cost Comparison



Description	Unit of measure	Quantity	Cost (dollars)*
Item 1:
Foreign steel, iron, or manufactured good	_________	_________	_________
Domestic steel, iron, or manufactured good	_________	_________	_________
Item 2:
Foreign steel, iron, or manufactured good	_________	_________	_________
Domestic steel, iron, or manufactured good	_________	_________	_________

List name, address, telephone number, email address, and contact for suppliers surveyed. Attach copy of response; if oral, attach summary.

Include other applicable supporting information.

*Include all delivery costs to the construction site.


26.	REQUIRED USE OF AMERICAN IRON, STEEL, AND MANUFACTURED GOODS (COVERED UNDER INTERNATIONAL AGREEMENTS) - SECTION 1605 OF THE AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009

(a) Definitions. As used in this award term and condition-


(2)	A Free Trade Agreement (FTA) country (Australia, Bahrain, Canada, Chile, Costa Rica, Dominican Republic, El Salvador, Guatemala, Honduras, Israel, Mexico, Morocco, Nicaragua, Oman, Peru, or Singapore); or


(3)	A United States-European Communities Exchange of Letters (May 15, 1995) country: Austria, Belgium, Bulgaria, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Ireland, Italy, Latvia, Lithuania, Luxembourg, Malta, Netherlands, Poland, Portugal, Romania, Slovak Republic, Slovenia, Spain, Sweden, and United Kingdom.

Designated country iron, steel, and/or manufactured goods - (1) Is wholly the growth, product, or manufacture of a designated country; or


(2)	In the case of a manufactured good that consist in whole or in part of materials from another country, has been substantially transformed in a designated country into a new and different manufactured good distinct from the materials from which it was transformed.

Domestic iron, steel, and/or manufactured good - (1) Is wholly the growth, product, or manufacture of the United States; or

(2)

In the case of a manufactured good that consists in whole or in part of materials from another country, has been substantially transformed in the United States into a new and different manufactured good distinct from the materials from which it was transformed. There is no requirement with regard to the origin of components or subcomponents in manufactured goods or products, as long as the manufacture of the goods occurs in the United States.

Foreign iron, steel, and/or manufactured good means iron, steel and/or manufactured good that is not domestic or designated country iron, steel, and/or manufactured good.

Manufactured good means a good brought to the construction site for incorporation into the building or work that has been-


(1)	Processed into a specific form and shape; or


(2)	Combined with other raw material to create a material that has different properties than the properties of the individual raw materials.

Steel means an alloy that includes at least 50 percent iron, between .02 and 2 percent carbon, and may include other elements.


(b)	Iron, steel, and manufactured goods. (1) The award term and condition described in this section implements-


(i)	Section 1605(a) of the American Recovery and Reinvestment Act of 2009 (Pub. L. 111-5) (Recovery Act), by requiring that all iron, steel, and manufactured goods used in the project are produced in the United States; and

(ii)

Section 1605(d), which requires application of the Buy American requirement in a manner consistent with U.S. obligations under international agreements. The restrictions of section 1605 of the Recovery Act do not apply to designated country iron, steel, and/or manufactured goods. The Buy American requirement in section 1605 shall not be applied where the iron, steel or manufactured goods used in the project are from a Party to an international agreement that obligates the recipient to treat the goods and services of that Party the same as domestic goods and services. This obligation shall only apply to projects with an estimated value of $7,443,000 or more.


(2)	The recipient shall use only domestic or designated country iron, steel, and manufactured goods in performing the work funded in whole or part with this award, except as provided in paragraphs (b)(3) and (b)(4) of this section.


(3)	The requirement in paragraph (b)(2) of this section does not apply to the iron, steel, and manufactured goods listed by the Federal Government as follows:

none


(4)	The award official may add other iron, steel, and manufactured goods to the list in paragraph (b)(3) of this section if the Federal Government determines that-


(i)	The cost of domestic iron, steel, and/or manufactured goods would be unreasonable. The cost of domestic iron, steel, and/or manufactured goods used in the project is unreasonable when the cumulative cost of such material will increase the overall cost of the project by more than 25 percent;


(ii)	The iron, steel, and/or manufactured good is not produced, or manufactured in the United States in sufficient and reasonably available commercial quantities of a satisfactory quality; or


(iii)	The application of the restriction of section 1605 of the Recovery Act would be inconsistent with the public interest.


(c)	Request for determination of inapplicability of section 1605 of the Recovery Act or the Buy American Act. (1)(i) Any recipient request to use foreign iron, steel, and/or manufactured goods in accordance with paragraph (b)(4) of this section shall include adequate information for Federal Government evaluation of the request, including-


(A)	A description of the foreign and domestic iron, steel, and/or manufactured goods;


(B)	Unit of measure;


(C)	Quantity;


(D)	Cost;


(E)	Time of delivery or availability;


(F)	Location of the project;


(G)	Name and address of the proposed supplier; and


(H)	A detailed justification of the reason for use of foreign iron, steel, and/or manufactured goods cited in accordance with paragraph (b)(4) of this section.


(ii)	A request based on unreasonable cost shall include a reasonable survey of the market and a completed cost comparison table in the format in paragraph (d) of this section.


(iii)	The cost of iron, steel, or manufactured goods shall include all delivery costs to the construction site and any applicable duty.

(iv)

(2)

If the Federal Government determines after funds have been obligated for a project for construction, alteration, maintenance, or repair that an exception to section 1605 of the Recovery Act applies, the award official will amend the award to allow use of the foreign iron, steel, and/or relevant manufactured goods. When the basis for the exception is nonavailability or public interest, the amended award shall reflect adjustment of the award amount, redistribution of budgeted funds, and/or other appropriate actions taken to cover costs associated with acquiring or using the foreign iron, steel, and/or relevant manufactured goods. When the basis for the exception is the unreasonable cost of the domestic iron, steel, or manufactured goods, the award official shall adjust the award amount or redistribute budgeted funds, as appropriate, by at least the differential established in 2 CFR 176.110(a).


(3)	Unless the Federal Government determines that an exception to section 1605 of the Recovery Act applies, use of foreign iron, steel, and/or manufactured goods other than designated country iron, steel, and/or manufactured goods is noncompliant with the applicable Act.


(d)	Data. To permit evaluation of requests under paragraph (b) of this section based on unreasonable cost, the applicant shall include the following information and any applicable supporting data based on the survey of suppliers:

Foreign and Domestic Items Cost Comparison



Description	Unit of measure	Quantity	Cost (dollars)*
Item 1:
Foreign steel, iron, or manufactured good	_________	_________	_________
Domestic steel, iron, or manufactured good	_________	_________	_________
Item 2:
Foreign steel, iron, or manufactured good	_________	_________	_________
Domestic steel, iron, or manufactured good	_________	_________	_________

List name, address, telephone number, email address, and contact for suppliers surveyed. Attach copy of response; if oral, attach summary.

Include other applicable supporting information.

*Include all delivery costs to the construction site.


27.	RECOVERY ACT TRANSACTIONS LISTED IN SCHEDULE OF EXPENDITURES OF FEDERAL AWARDS AND RECIPIENT RESPONSIBILITIES FOR INFORMING SUBRECIPIENTS

(a)

To maximize the transparency and accountability of funds authorized under the American Recovery and Reinvestment Act of 2009 (Pub. L. 111-5) (Recovery Act) as required by Congress and in accordance with 2 CFR 215.21 “Uniform Administrative Requirements for Grants and Agreements” and OMB Circular A-102 Common Rules provisions, recipients agree to maintain records that identify adequately the source and application of Recovery Act funds. OMB Circular A-102 is available at http://www.whitehouse.gov/omb/circulars/a102/a102.html.

(b)

For recipients covered by the Single Audit Act Amendments of 1996 and OMB Circular A-133, “Audits of States, Local Governments, and Non-Profit Organizations,” recipients agree to separately identify the expenditures for Federal awards under the Recovery Act on the Schedule of Expenditures of Federal Awards (SEFA) and the Data Collection Form (SF-SAC) required by OMB Circular A-133. OMB Circular A-133 is available at http://www.whitehouse.gov/omb/circulars/a133/a133.html. This shall be accomplished by identifying expenditures for Federal awards made under the Recovery Act separately on the SEFA, and as separate rows under Item 9 of Part III on the SF-SAC by CFDA number, and inclusion of the prefix “ARRA-” in identifying the name of the Federal program on the SEFA and as the first characters in Item 9d of Part III on the SF-SAC.

(c)

Recipients agree to separately identify to each subrecipient, and document at the time of subaward and at the time of disbursement of funds, the Federal award number, CFDA number, and amount of Recovery Act funds. When a recipient awards Recovery Act funds for an existing program, the information furnished to subrecipients shall distinguish the subawards of incremental Recovery Act funds from regular subawards under the existing program.

(d)

Recipients agree to require their subrecipients to include on their SEFA information to specifically identify Recovery Act funding similar to the requirements for the recipient SEFA described above. This information is needed to allow the recipient to properly monitor subrecipient expenditure of ARRA funds as well as oversight by the Federal awarding agencies, Offices of Inspector General and the Government Accountability Office.


28.	WAGE RATE REQUIREMENTS UNDER SECTION 1606 OF THE RECOVERY ACT

(a)

Section 1606 of the Recovery Act requires that all laborers and mechanics employed by contractors and subcontractors on projects funded directly by or assisted in whole or in part by and through the Federal Government pursuant to the Recovery Act shall be paid wages at rates not less than those prevailing on projects of a character similar in the locality as determined by the Secretary of Labor in accordance with subchapter IV of chapter 31 of title 40, United States Code.

(b)

For additional guidance on the wage rate requirements of section 1606, contact your awarding agency. Recipients of grants, cooperative agreements and loans should direct their initial inquiries concerning the application of Davis-Bacon requirements to a particular federally assisted project to the Federal agency funding the project. The Secretary of Labor retains final coverage authority under Reorganization Plan Number 14.


29.	DAVIS BACON ACT AND CONTRACT WORK HOURS AND SAFETY STANDARDS ACT

Definitions: For purposes of this provision, “Davis Bacon Act and Contract Work Hours and Safety Standards Act,” the following definitions are applicable:

(1)

“Award” means any grant, cooperative agreement or technology investment agreement made with Recovery Act funds by the Department of Energy (DOE) to a Recipient. Such Award must require compliance with the labor standards clauses and wage rate requirements of the Davis-Bacon Act (DBA) for work performed by all laborers and mechanics employed by Recipients (other than a unit of State or local government whose own employees perform the construction) Subrecipients, Contractors, and subcontractors.


(2)	“Contractor” means an entity that enters into a Contract. For purposes of these clauses, Contractor shall include (as applicable) prime contractors, Recipients, Subrecipients, and Recipients' or Subrecipients' contractors, subcontractors, and lower-tier subcontractors. “Contractor” does not mean a unit of State or local government where construction is performed by its own employees.”

(3)

“Contract” means a contract executed by a Recipient, Subrecipient, prime contractor, or any tier subcontractor for construction, alteration, or repair. It may also mean (as applicable) (i) financial assistance instruments such as grants, cooperative agreements, technology investment agreements, and loans; and, (ii) Sub awards, contracts and subcontracts issued under financial assistance agreements. “Contract” does not mean a financial assistance instrument with a unit of State or local government where construction is performed by its own employees.


(4)	“Contracting Officer” means the DOE official authorized to execute an Award on behalf of DOE and who is responsible for the business management and non-program aspects of the financial assistance process.


(5)	“Recipient” means any entity other than an individual that receives an Award of Federal funds in the form of a grant, cooperative agreement, or technology investment agreement directly from the Federal Government and is financially accountable for the use of any DOE funds or property, and is legally responsible for carrying out the terms and conditions of the program and Award.

(6)

“Subaward” means an award of financial assistance in the form of money, or property in lieu of money, made under an award by a Recipient to an eligible Subrecipient or by a Subrecipient to a lower-tier subrecipient. The term includes financial assistance when provided by any legal agreement, even if the agreement is called a contract, but does not include the Recipient's procurement of goods and services to carry out the program nor does it include any form of assistance which is excluded from the definition of “Award” above.


(7)	“Subrecipient” means a non-Federal entity that expends Federal funds received from a Recipient to carry out a Federal program, but does not include an individual that is a beneficiary of such a program.

(a) Davis Bacon Act

(1) Minimum wages.

Contributions made or costs reasonably anticipated for bona fide fringe benefits under section 1(b)(2) of the Davis-Bacon Act on behalf of laborers or mechanics are considered wages paid to such laborers or mechanics, subject to the provisions of paragraph (a)(1)(iv) of this section; also, regular contributions made or costs incurred for more than a weekly period (but not less often than quarterly) under plans, funds, or programs which cover the particular weekly period, are deemed to be constructively made or incurred during such weekly period. Such laborers and mechanics shall be paid the appropriate wage rate and fringe benefits on the wage determination for the classification of work actually performed, without regard to skill, except as provided in § 5.5(a)(4). Laborers or mechanics performing work in more than one classification may be compensated at the rate specified for each classification for the time actually worked therein, provided that the employer's payroll records accurately set forth the time spent in each classification in which work is performed. The wage determination (including any additional classification and wage rates conformed under paragraph (a)(1)(ii) of this section) and the Davis-Bacon poster (WH-1321) shall be posted at all times by the Contractor and its subcontractors at the site of the work in a prominent and accessible place where it can be easily seen by the workers.

(ii)

(A) The Contracting Officer shall require that any class of laborers or mechanics, including helpers, which is not listed in the wage determination and which is to be employed under the Contract shall be classified in conformance with the wage determination. The Contracting Officer shall approve an additional classification and wage rate and fringe benefits therefore only when the following criteria have been met:

(1) The work to be performed by the classification requested is not performed by a classification in the wage determination;

(2) The classification is utilized in the area by the construction industry; and

(3) The proposed wage rate, including any bona fide fringe benefits, bears a reasonable relationship to the wage rates contained in the wage determination.

(3) Payrolls and basic records.

(i) Payrolls and basic records relating thereto shall be maintained by the Contractor during the course of the work and preserved for a period of three years thereafter for all laborers and mechanics working at the site of the work (or under the United States Housing Act of 1937, or under the Housing Act of 1949, in the construction or development of the project). Such records shall contain the name, address, and social security number of each such worker, his or her correct classification, hourly rates of wages paid (including rates of contributions or costs anticipated for bona fide fringe benefits or cash equivalents thereof of the types described in section 1(b)(2)(B) of the Davis-Bacon Act), daily and weekly number of hours worked, deductions made, and actual wages paid. Whenever the Secretary of Labor has found under 29 CFR 5.5(a)(1)(iv) that the wages of any laborer or mechanic include the amount of any costs reasonably anticipated in

providing benefits under a plan or program described in section 1(b)(2)(B) of the Davis-Bacon Act, the Contractor shall maintain records which show that the commitment to provide such benefits is enforceable, that the plan or program is financially responsible, and that the plan or program has been communicated in writing to the laborers or mechanics affected, and records which show the costs anticipated or the actual cost incurred in providing such benefits. Contractors employing apprentices or trainees under approved programs shall maintain written evidence of the registration of apprenticeship programs and certification of trainee programs, the registration of the apprentices and trainees, and the ratios and wage rates prescribed in the applicable programs.

(4) Apprentices and trainees-

Apprenticeship Agency recognized by the Office, or if a person is employed in his or her first 90 days of probationary employment as an apprentice in such an apprenticeship program, who is not individually registered in the program, but who has been certified by the Office of Apprenticeship Training, Employer and Labor Services or a State Apprenticeship Agency (where appropriate) to be eligible for probationary employment as an apprentice. The allowable ratio of apprentices to journeymen on the job site in any craft classification shall not be greater than the ratio permitted to the Contractor as to the entire work force under the registered program. Any worker listed on a payroll at an apprentice wage rate, who is not registered or otherwise employed as stated above, shall be paid not less than the applicable wage rate on the wage determination for the classification of work actually performed. In addition, any apprentice performing work on the job site in excess of the ratio permitted under the registered program shall be paid not less than the applicable wage rate on the wage determination for the work actually performed. Where a Contractor is performing construction on a project in a locality other than that in which its program is registered, the ratios and wage rates (expressed in percentages of the journeyman's hourly rate) specified in the Contractor's or subcontractor's registered program shall be observed. Every apprentice must be paid at not less than the rate specified in the registered program for the apprentice's level of progress, expressed as a percentage of the journeymen hourly rate specified in the applicable wage determination. Apprentices shall be paid fringe benefits in accordance with the provisions of the apprenticeship program. If the apprenticeship program does not specify fringe benefits, apprentices must be paid the full amount of fringe benefits listed on the wage determination for the applicable classification. If the Administrator determines that a different practice prevails for the applicable apprentice classification, fringes shall be paid in accordance with that determination. In the event the Office of Apprenticeship Training, Employer and Labor Services, or a State Apprenticeship Agency recognized by the Office, withdraws approval of an apprenticeship program, the Contractor will no longer be permitted to utilize apprentices at less than the applicable predetermined rate for the work performed until an acceptable program is approved.

(ii) Trainees. Except as provided in 29 CFR 5.16, trainees will not be permitted to work at less than the predetermined rate for the work performed unless they are employed pursuant to and individually registered in a program which has received prior approval, evidenced by formal certification by the U.S. Department of Labor, Employment and Training Administration. The ratio of trainees to journeymen on the job site shall not be greater than permitted under the plan approved by the Employment and Training Administration. Every trainee must be paid at not less than the rate specified in the approved program for the trainee's level of progress, expressed as a percentage of the journeyman hourly rate specified in the applicable wage determination. Trainees shall be paid fringe benefits in accordance with the provisions of the trainee program. If the trainee program does not mention fringe benefits, trainees shall be paid the full amount of fringe benefits listed on the wage determination unless the Administrator of the

Wage and Hour Division determines that there is an apprenticeship program associated with the corresponding journeyman wage rate on the wage determination which provides for less than full fringe benefits for apprentices. Any employee listed on the payroll at a trainee rate who is not registered and participating in a training plan approved by the Employment and Training Administration shall be paid not less than the applicable wage rate on the wage determination for the classification of work actually performed. In addition, any trainee performing work on the job site in excess of the ratio permitted under the registered program shall be paid not less than the applicable wage rate on the wage determination for the work actually performed. In the event the Employment and Training Administration withdraws approval of a training program, the Contractor will no longer be permitted to utilize trainees at less than the applicable predetermined rate for the work performed until an acceptable program is approved.