Document:

Common Stock Purchase Warrant

 Exhibit 4.1 
 THIS WARRANT HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR ANY APPLICABLE STATE SECURITIES LAWS, AND MAY NOT BE SOLD OR TRANSFERRED UNLESS SUCH SALE OR TRANSFER IS IN ACCORDANCE WITH THE
REGISTRATION REQUIREMENTS OF SUCH ACT AND APPLICABLE LAWS OR SOME OTHER EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF SUCH ACT AND APPLICABLE LAWS IS AVAILABLE WITH RESPECT THERETO. 
 COMMON STOCK PURCHASE WARRANT 
  

					
	 Warrant No.                    

	 		 	Number of Shares: 150,000

 REPLIGEN CORPORATION 
 Void after April 6, 2014 
 1. Issuance. This Warrant is issued to Joel
Gottesfeld on this 6th day of April, 2007 (the “Original Issue Date”) by RepliGen Corporation, a Delaware corporation (hereinafter with its successors called the “Company”). 
 2. Purchase Price; Number of Shares. Subject to the terms and conditions hereinafter set forth, the registered holder of this Warrant (the
“Holder”) is entitled upon surrender of this Warrant with the subscription form annexed hereto duly executed, at the office of the Company, 41 Seyon Street, Building 1, Suite 100, Waltham, MA 02453, or such other office as the Company
shall notify the Holder of in writing, to purchase from the Company at a price per share of $0.01 (the “Purchase Price”), 150,000 fully paid and nonassessable shares of Common Stock, $.01 par value per share, of the Company (the
“Common Stock”). Until such time as this Warrant is exercised in full or expires, the Purchase Price and the securities issuable upon exercise of this Warrant are subject to adjustment as hereinafter provided. 
 3. Payment of Purchase Price. The Purchase Price may be paid in cash or by check. 
 4. Exercise. 
  

	 	(a)	This warrant may be exercised for the number of shares set forth below, only upon the occurrence of the related events. There is no penalty to the warrant holder if the events do
not occur, except for the failure of the warrant shares to become exercisable. 

			
	 Shares
	  	 Exercisable Upon

	 50,000
	  	First Patient Dosing
	 50,000
	  	Initiate Pivotal Study
	 50,000
	  	Submission of NDA

  

	 	(b)	For purposes of this Section 4, the following terms shall have the meanings ascribed to them: 

  

	 	i.	“First Patient Dosing” shall mean the first patient dosed in a US clinical study sponsored by the Company with a pharmaceutical for the treatment of Friedreichs
Ataxia or related neurodegenerative or neuromuscular diseases. 

  

	 	ii.	“Initiate Pivotal Study” shall mean the first patient dosed in a US Phase III clinical study sponsored by the Company for a pharmaceutical for the treatment of
Friedreichs Ataxia or related neurodegenerative or neuromuscular diseases. 

	 	

	 	iii.	“Submission of NDA” shall mean the submission by the Company and acceptance by the U.S. Food and Drug Administration of a new drug application (“NDA”)
with relating to a pharmaceutical for the treatment of Friedreichs Ataxia or related neurodegenerative or neuromuscular diseases. 

 5. Partial Exercise. This Warrant may be exercised in part, and the Holder shall be entitled to receive a new warrant, which shall be dated as of the date of this Warrant, covering the number of shares in respect of which this
Warrant shall not have been exercised. 
 6. Issuance Date. The person or persons in whose name or names any certificate representing
shares of Common Stock is issued hereunder shall be deemed to have become the holder of record of the shares represented thereby as at the close of business on the date this Warrant is exercised with respect to such shares, whether or not the
transfer books of the Company shall be closed. 
 7. Expiration Date. This Warrant shall expire at the close of business on
March 31, 2014, and shall be void thereafter. 
 8. Reserved Shares; Valid Issuance. The Company covenants that it will at all
times from and after the date hereof reserve and keep available such number of its authorized shares of Common Stock, free from all preemptive or similar rights therein, as will be sufficient to permit the exercise of this Warrant in full. The
Company further covenants that such shares as may be issued pursuant to the exercise of this Warrant will, upon issuance, be duly and validly issued, fully paid and nonassessable and free from all taxes, liens and charges with respect to the
issuance thereof other than those caused or suffered by the Holder hereof. 

 9. Dividends. If after the Original Issue Date the Company shall subdivide the Common Stock, by
split-up or otherwise, or combine the Common Stock, or issue additional shares of Common Stock in payment of a stock dividend on the Common Stock, the number of shares issuable on the exercise of this Warrant shall forthwith be proportionately
increased in the case of a subdivision or stock dividend, or proportionately decreased in the case of a combination, and the Purchase Price shall forthwith be proportionately decreased in the case of a subdivision or stock dividend, or
proportionately increased in the case of a combination. 
 10. Mergers and Reclassifications. If after the Original Issue Date there
shall be any reclassification, capital reorganization or change of the Common Stock (other than as a result of a subdivision, combination or stock dividend provided for in Section 9 hereof), or any consolidation of the Company with, or merger
of the Company into, another corporation or other business organization (other than a consolidation or merger in which the Company is the continuing corporation and which does not result in any reclassification or change of the outstanding Common
Stock), or any sale or conveyance to another corporation or other business organization of all or substantially all of the assets of the Company, then, as a condition of such reclassification, reorganization, change, consolidation, merger, sale or
conveyance, lawful provisions shall be made, and duly executed documents evidencing the same from the Company or its successor shall be delivered to the Holder, so that the Holder shall thereafter have the right to purchase, at a total price not to
exceed that payable upon the exercise of this Warrant in full, the kind and amount of shares of stock and other securities and property receivable upon such reclassification, reorganization, change, consolidation, merger, sale or conveyance by a
holder of the number of shares of Common Stock which might have been purchased by the Holder immediately prior to such reclassification, reorganization, change, consolidation, merger, sale or conveyance, and in any such case appropriate provisions
shall be made with respect to the rights and interest of the Holder to the end that the provisions hereof (including without limitation, provisions for the adjustment of the Purchase Price and the number of shares issuable hereunder) shall
thereafter be applicable in relation to any shares of stock or other securities and property thereafter deliverable upon exercise hereof. In no event shall the Purchase Price per share be reduced to below the then existing par value for one share.

 11. Fractional Shares. In no event shall any fractional share of Common Stock be issued upon any exercise of this Warrant. If, upon
exercise of this Warrant as an entirety, the Holder would, except as provided in this Section 11, be entitled to receive a fractional share of Common Stock, then the Company shall issue the number of full shares of Common Stock which may be
issued upon exercise of this Warrant without issuing any fractional shares. 
 12. Certificate of Adjustment. Whenever the Purchase
Price is adjusted, as herein provided, the Company shall promptly deliver to the Holder a certificate of a firm of independent public accountants setting forth the Purchase Price after such adjustment and setting forth a brief statement of the facts
requiring such adjustment. 
 13. Notices of Record Date, Etc. In the event of: 
 (a) any taking by the Company of a record of the holders of any class of securities for the purpose of determining the holders thereof who are entitled to
receive any dividend or other distribution, or any right to subscribe for, purchase or otherwise acquire any shares of stock of any class or any other securities or property, or to receive any other right, 

 (b) any reclassification of the capital stock of the Company, capital reorganization of the Company,
consolidation or merger involving the Company, or sale or conveyance of all or substantially all of its assets, or 
 (c) any voluntary or
involuntary dissolution, liquidation or winding-up of the Company, 
 then and in each such event the Company will mail or cause to be mailed to the Holder a
notice specifying (i) the date on which any such record is to be taken for the purpose of such dividend, distribution or right, and stating the amount and character of such dividend, distribution or right, or (ii) the date on which any
such reclassification, reorganization, consolidation, merger, sale or conveyance, dissolution, liquidation or winding-up is to take place, and the time, if any is to be fixed, as of which the holders of record in respect of such event are to be
determined. The Company shall use commercially reasonable efforts to cause such notice to be mailed at least twenty (20) days prior to the date specified in such notice on which any such action is to be taken. 
 14. Amendment. The terms of this Warrant may be amended, modified or waived only with the written consent of the Company and the Holder hereof.

 15. Warrant Register; Transfers, Etc. 
 A. The Company will maintain a register containing the names and addresses of the registered holders of the Warrant. The Holder may change its address as shown on the warrant register by written notice to the Company
requesting such change. Any notice or written communication required or permitted to be given to the Holder may be given by certified mail or delivered to the Holder at its address as shown on the warrant register. 
 B. Subject to compliance with applicable federal and state securities laws, this Warrant may be transferred by the Holder with respect to any or all of
the shares purchasable hereunder. Upon surrender of this Warrant to the Company, together with the assignment hereof properly endorsed, for transfer of this Warrant as an entirety by the Holder, the Company shall issue a new warrant of the same
denomination to the assignee. Upon surrender of this Warrant to the Company, together with the assignment hereof properly endorsed, by the Holder for transfer with respect to a portion of the shares of Common Stock purchasable hereunder, the Company
shall issue a new warrant to the assignee, in such denomination as shall be requested by the Holder hereof, and shall issue to such Holder a new warrant covering the number of shares in respect of which this Warrant shall not have been transferred.

 C. In case this Warrant shall be mutilated, lost, stolen or destroyed, the Company shall issue a new warrant of like tenor and
denomination and deliver the same (i) in exchange and substitution for and upon surrender and cancellation of any mutilated Warrant, or (ii) in lieu of any Warrant lost, stolen or destroyed, upon receipt of evidence reasonably satisfactory
to the 

 
Company of the loss, theft or destruction of such Warrant (including a reasonably detailed affidavit with respect to the circumstances of any loss, theft or
destruction) and of indemnity reasonably satisfactory to the Company. 
 16. No Impairment. The Company will not, by amendment of its
certificate of incorporation, as amended or through any reclassification, capital reorganization, consolidation, merger, sale or conveyance of assets, dissolution, liquidation, issue or sale of securities or any other voluntary action, avoid or seek
to avoid the observance or performance of any of the terms of this Warrant, but will at all times in good faith assist in the carrying out of all such terms and in the taking of all such action as may be necessary or appropriate in order to protect
the rights of the Holder. 
 17. Governing Law. The provisions and terms of this Warrant shall be governed by and construed in
accordance with the internal laws of the State of Delaware. 
 18. Successors and Assigns. This Warrant shall be binding upon the
Company’s successors and assigns and shall inure to the benefit of the Holder’s successors, legal representatives and permitted assigns. 
 19. Business Days. If the last or appointed day for the taking of any action required or the expiration of any right granted herein shall be a Saturday or Sunday or a legal holiday in the Commonwealth of Massachusetts, then such
action may be taken or right may be exercised on the next succeeding day which is not a Saturday or Sunday or such a legal holiday. 
 [signature page follows] 

							
	 Dated: April 6, 2007
	 		 	REPLIGEN CORPORATION
				
		 		 	By:	 	  

		 		 	Name:	 	Walter Herlihy
		 		 	Title:	 	President and CEO

 Exercise Notice 
 Subscription 
  

			
	 To:                                      
  
	 	Date:                    

 The undersigned hereby subscribes for
                     shares of Common Stock covered by this Warrant. The certificate(s) for such shares shall be issued in the name of the
undersigned or as otherwise indicated below: 
  

	
	  
 Signature

	
	  
 Name
for Registration

	
	  
 Mailing Address

 ASSIGNMENT 
 For value received
                                        
                     hereby sells, 
 assigns and
transfers unto
                                        
                                     
  

							
	                                      
                                        
                                        
                                        
                                   	 	

 Please print or typewrite name and address of Assignee 
  

							
	                                      
                                        
                                        
                                        
                                   	  	

 the within Warrant, and does hereby irrevocably constitute and appoint
                                        
its attorney to transfer the within Warrant on the books of the within named Company with full power of substitution on the premises. 
 Dated:                     
  

	
	  

 In the Presence of:Offer Letter to Timothy Stultz

 Exhibit 10.1 
  

							
	

	 		  	Nanometrics Incorporated	  	Tel: 408.435.9600
	 		  	1550 Buckeye Drive	  	Fax: 408.232.5910
	 		  	Milpitas, CA 95035	  	www.nanometrics.com

 July 17, 2007 
  
 Dear Tim: 
 I am pleased to offer you the position of President and Chief
Executive Officer of Nanometrics Incorporated (the “Company”) on a full-time basis. In addition, should you accept this offer, you will be appointed as a member of the Company’s Board of Directors. 
 The elements of our offer are as follows: 
  

	 	•	 	 You will render such business and professional services in the performance of your duties, consistent with your position within the Company, as shall reasonably be
assigned to you by the Company’s Board of Directors (the “Board”). 

  

	 	•	 	 Your initial base salary in this position will be an annual salary of $377,000, earned and payable at the bi-weekly rate of $14,500 in accordance with our standard
payroll schedule and procedures and subject to all applicable tax withholdings. 

  

	 	•	 	 Your relocation expenses will be reimbursed in accordance with the Relocation Letter set forth as Addendum A to this offer letter. In addition, as part of the
relocation benefits being provided to you, we will provide you with a living allowance of $8,000 per month for up to 12 months, provided you remain employed by us through each relevant date such allowance is paid. The total living allowance and
temporary housing allowance provided in the Relocation Policy shall not exceed $8,000 per month. 

  

	 	•	 	 You will receive a one-time lump sum cash bonus payment of $100,000, less applicable withholdings, upon your completion of one month of service with us and provided
that you remain an employee in good standing with the Company at such time. 

  

	 	•	 	 The Company will either provide you with an automobile allowance of $1,200 per month or the use of a Company-leased car of equivalent value, in each case provided
you remain employed by us through each relevant date such allowance is paid. 

  

	 	•	 	 Subject to approval by the Board or the Compensation Committee of the Board (the “Committee”), you will be granted (i) a non-qualified stock option
to purchase an aggregate of 200,000 shares of Company common stock (the “Option”) and (ii) 50,000 restricted stock units (the “RSU”). Both equity awards will be granted under our 2005 Equity Incentive Plan, and pursuant to
standard agreements thereunder. The Option shall vest over a three-year period from the date of grant, with one-third 

	 	 
of the total number of shares underlying the Option vesting on the first anniversary of the date of grant, and 1/36th of the total number of shares underlying each equity award vesting ratably on a monthly basis thereafter, subject to your continued employment with the Company through each such
date. The Option shall have a seven-year maximum term and shall have an exercise price per share equal to one hundred percent (100%) of the fair market value of a share of Company common stock on the date of grant. The RSU shall vest over a
three-year period from the date of grant, with one-third of the total number of shares underlying the RSU vesting on each annual anniversary of the date of grant, subject to your continued employment with the Company through each such date. 

  

	 	•	 	 You will be eligible to receive severance payments and benefits under certain conditions, pursuant to the terms and conditions of the Executive Severance Agreement
set forth as Addendum B to this offer letter. 

  

	 	•	 	 You will be eligible to participate in the Company’s excellent benefit programs, as they may be in place from time to time, which currently include health,
dental, vision, life and long term disability insurance coverage. The Company also offers you a supplemental reimbursement policy, Execucare, to reimburse certain out of pocket insurance expenses. We will pay a portion of the cost of your insurance
coverage and a portion for your dependents, all in accordance with the terms and conditions of the applicable benefit programs as they may be in place from time to time. The Company reserves the right to cancel or change the benefit plans and
programs it offers to its employees at any time. 

  

	 	•	 	 You will be covered by the Indemnification Agreement provided to the Company’s executive officers. 

  

	 	 •
	 	 You will also be eligible for a performance bonus payable for the achievement of performance goals mutually agreed upon
between you and the Committee or the Board. The performance bonus will be guaranteed to be at least $50,000 per quarter for the first four quarters of your employment and $25,000 per quarter for the
following two quarters of your employment. Your bonus for the first quarter of your employment, including the amount of the minimum guaranteed bonus, will be pro-rated to your start date with such pro-rated amount to be calculated by multiplying
$50,000 (or, if greater, the amount of the earned performance bonus) by a fraction with a numerator equal to the number of days between your start date and the last date of the first quarter and a denominator equal to 365. You must be an employee in
good standing on the last day of each relevant quarter in order to be eligible to receive your bonus. Earned bonus amounts will be paid out within thirty (30) days of the date the performance goals are deemed achieved.

  

	 	•	 	 All payments made pursuant to this offer letter will be subject to withholding of applicable taxes. 

 The Company envisions that your initial focus as President and CEO of the Company will be: 
  

	 	1.	Completion of the integration of the two companies acquired by Nanometrics in 2006. 

  

	 	2.	Understanding the costs and mission of the Korean manufacturing subsidiary and determining its value to the corporation with appropriate action plan to maximize value from this
operation. 

  

	 	3.	Improve cash flow. 

  

	 	4.	Work to develop consistent business practices across all entities and eliminate redundant and excess legal entities and offices. 

  

	 	5.	Recruit a permanent CFO. 

 This offer of employment is contingent upon:

  

	 	(1)	Completion of the Nanometrics Employment Application 

  

	 	(2)	Signing of the Nanometrics Employee Patent & Confidential Information Agreement 

  

	 	(3)	Satisfactory completion of a criminal and/or educational background check as well as a Directors and Officers Questionnaire. 

  

	 	(4)	Providing verification of your eligibility for employment in the United States. Your continued employment is conditioned upon your maintaining authorization to work in the United
States. 

 Nanometrics is an at-will employer and your employment with the Company is at-will, which means that either you or the Company has
the right to terminate employment at any time, with or without advance notice, and with or without cause, for any reason. You understand and agree that neither your job performance nor promotions, commendations, bonuses or the like from the Company
give rise to or in any way serve as the basis for modification, amendment, or extension, by implication or otherwise, of your employment with the Company. 
 We ask that, if you have not already done so, you disclose to the Company any and all agreements relating to your prior employment that may affect your eligibility to be employed by the Company or limit the manner in which you may be
employed. It is the Company’s understanding that any such agreements will not prevent you from performing the duties of your position and you represent that such is the case. Moreover, you agree that, during the term of your employment with the
Company, you will perform your duties faithfully and to the best of your ability and will devote your full business efforts and time to the Company. For the duration of the period of your employment, you agree not to engage in any other employment,
occupation, consulting or other business activity for any direct or indirect remuneration without the prior approval of the Board, nor will you engage in any other activities that conflict with your obligations to the Company; provided, however,
that you may remain on the Imago Board of Directors. Similarly, you agree not to bring any third party confidential information to the Company, including that of your former employer, and that in performing your duties for the Company you will not
in any way utilize any such information. 

 This offer letter, along with its attachments and addenda, the Executive Severance Agreement between you and the Company
dated on or about the date herewith and any agreements relating to proprietary rights between you and the Company, constitute the full and complete statement of the parties’ understanding, supersede any other communication, whether verbal or
written, regarding your employment and the letter can only be modified by a written statement signed by you and an officer of the Company (or authorized delegate). This offer letter shall be governed by and construed in accordance with the laws of
the State of California (with the exception of its conflict of laws provisions). In the event that any provision hereof becomes or is declared by a court of competent jurisdiction to be illegal, unenforceable or void, this Agreement will continue in
full force and effect without said provision. The offer is valid until July 19, 2007. 
 Please acknowledge your acceptance of this offer by signing
below. The entire Nanometrics staff looks forward to you joining us and becoming a key person with our growing team. 
  

			
	Sincerely,
	
	Bruce C. Rhine
	Chief Executive Officer
	
	Agreed to and accepted:
		
	Signature:	 	  

	Printed Name:	 	Timothy J. Stultz
	
	Date: July     , 2007

  

	
	  
 Available Start Date

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