Exhibit 10.1


 


HELICOS
BIOSCIENCES CORPORATION


 


Change in
Control Agreement


 


AGREEMENT made as of this 28th day of January, 2009 by and between
Helicos BioSciences Corporation (the “Company”), and Ronald A. Lowy (the “Executive”).


 


1.                                       Purpose.  The Company considers it essential to the
best interests of its stockholders to promote and preserve the continuous
employment of key management personnel. 
The Board of Directors of the Company (the “Board”) recognizes that, as
is the case with many corporations, the possibility of a Change in Control (as
defined in Section 2 hereof) exists and that such possibility, and the
uncertainty and questions that it may raise among management, may result in the
departure or distraction of key management personnel to the detriment of the
Company and its stockholders.  Therefore,
the Board has determined that appropriate steps should be taken to reinforce
and encourage the continued attention and dedication of members of the Company’s
key management, including the Executive, to their assigned duties without
distraction in the face of potentially disturbing circumstances arising from
the possibility of a Change in Control. 
Nothing in this Agreement shall be construed as creating an express or
implied contract of employment and, except as otherwise agreed in writing
between the Executive and the Company, the Executive shall not have any right
to be retained in the employ of the Company.


 


2.                                       Change
in Control.  A “Change in Control”
shall be deemed to have occurred upon the occurrence of any one of the
following events:


 


(a)           any “Person,” as
such term is used in Sections 13(d) and 14(d) of the Securities
Exchange Act of 1934, as amended (the “Act”) (other than the Company, any of
its subsidiaries, or any trustee, fiduciary or other person or entity holding
securities under any employee benefit plan or trust of the Company or any of
its subsidiaries), together with all “affiliates” and “associates” (as such
terms are defined in Rule 12b-2 under the Act) of such person, shall
become the “beneficial owner” (as such term is defined in Rule 13d-3 under
the Act), directly or indirectly, of securities of the Company representing 50 percent or more of the combined
voting power of the Company’s then outstanding securities having the right to
vote in an election of the Company’s Board of Directors (“Voting Securities”)
(in such case other than as a result of an acquisition of securities directly
from the Company); or


 


(b)           persons who, as of
the date hereof, constitute the Company’s Board of Directors (the “Incumbent
Directors”) cease for any reason, including, without limitation, as a result of
a tender offer, proxy contest, merger or similar transaction, to constitute at
least a majority of the Board, provided that any person becoming a director of
the Company subsequent to the date hereof shall be considered an Incumbent
Director if such person’s election was approved by or such person was nominated
for election by either (A) a vote of at least a majority of the Incumbent
Directors or (B) a vote of at least a majority of the Incumbent Directors
who are members of a nominating committee comprised, in the majority, of
Incumbent Directors; but provided further, that any such person whose initial
assumption of office is in connection with an actual or threatened election
contest relating to the election of members of the Board of Directors 


 

















 


or other actual or
threatened solicitation of proxies or consents by or on behalf of a Person
other than the Board, including by reason of agreement intended to avoid or
settle any such actual or threatened contest or solicitation, shall not be
considered an Incumbent Director; or


 


(c)           the consummation of (A) any
consolidation or merger of the Company where the stockholders of the Company,
immediately prior to the consolidation or merger, would not, immediately after
the consolidation or merger, beneficially own (as such term is defined in Rule 13d-3
under the Act), directly or indirectly, shares representing in the aggregate
more than 50 percent of the voting shares of the Company issuing cash or
securities in the consolidation or merger (or of its ultimate parent
corporation, if any), or (B) any sale, lease, exchange or other transfer
(in one transaction or a series of transactions contemplated or arranged by any
party as a single plan) of all or substantially all of the assets of the
Company; or


 


(d)           the approval by the
Company’s stockholders of any plan or proposal for the liquidation or
dissolution of the Company.


 


3.                                       Terminating
Event.  A “Terminating Event” shall
mean any of the events provided in this Section 3:


 


(a)                                  Termination
by the Company.  Termination by the
Company of the employment of the Executive with the Company for any reason
other than for Cause, death or Disability. 
For purposes of this Agreement, “Cause” shall mean:


 


(i)            the substantial and continuing
failure or refusal of the Employee, after written notice thereof, to reasonably
attempt to perform his or her job duties and responsibilities (other than
failure or refusal resulting from incapacity due to physical disability or
mental illness) which failure or refusal is committed in bad faith and is not
in the best interest of the Company;


 


(ii)           gross negligence, willful misconduct
or material breach of fiduciary duty to the Company;


 


(iii)          the willful commission of an act of
embezzlement, misappropriation or fraud;


 


(iv)          deliberate and willful disregard of
the written rules or policies of the Company which results in a material
and substantial loss, damage or injury to the Company;


 


(v)           the unauthorized, deliberate and
willful disclosure of any material confidential, proprietary and/or trade
secret information of the Company or its customers which disclosure is
committed in bad faith and is not in the best interest of the Company;


 


(vi)          the willful and deliberate commission
of an act which induces any customer, supplier, employee or consultant to
adversely and substantially amend 


 


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or terminate their
relationship with the Company which act is committed in bad faith and is not in
the best interest of the Company; or


 


(vii)         the conviction of, or plea of nolo
contendere by the Employee, to a crime involving a felony of moral turpitude.


 


A Terminating Event shall not be deemed to have occurred pursuant to
this Section 3(a) solely as a result of the Executive being an
employee of any direct or indirect successor to the business or assets of the
Company, rather than continuing as an employee of the Company following a
Change in Control.  For purposes hereof,
the Executive will be considered “Disabled” if, as a result of the Executive’s
incapacity due to physical or mental illness, the Executive shall have been
absent from his duties to the Company on a full-time basis for 180 calendar
days in the aggregate in any 12-month period.


 


(b)           Termination
by the Executive for Good Reason. 
Termination by the Executive of the Executive’s employment with the
Company for Good Reason.  For purposes of
this Agreement, “Good Reason” shall mean the occurrence of any of the following
events:


 


(i)            a reduction in the Employee’s then-current annual base
salary or bonus opportunity or benefits; or


 


(ii)           the failure to pay the Employee any portion of his or her
current base salary, bonus or benefits within twenty (20) days of the date such
compensation is due, based upon the payment terms currently in effect; or


 


(iii)          the failure of the Company to obtain a reasonably
satisfactory agreement from any successor to assume and agree to perform this
Agreement.


 


4.                                       Change
in Control Payment.  Upon the earlier
of (1) the occurrence of a Terminating Event after a Change in Control or (2) 90
days after a Change in Control, the following shall occur:


 


(a)           the Company shall
pay to the Executive an amount equal to $120,000, payable in one lump-sum
payment no later than three days following the Date of Termination;


 


(b)           subject to the
Executive’s copayment of premium amounts at the active employees’ rate, the
Executive shall continue to participate in the Company’s group health and
dental program for six months; provided, however, that the continuation of
health benefits under this Section shall reduce and count against the
Executive’s rights under the Consolidated Omnibus Budget Reconciliation Act of
1985, as amended (“COBRA”); and


 


(c)           Notwithstanding
anything to the contrary in any applicable option agreement or stock-based
award agreement, upon the earlier of (1) the occurrence of a Terminating
Event after a Change in Control or (2) 90 days after a Change in Control,
all stock options and other stock-based awards granted to the Executive by the
Company shall 


 


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immediately
accelerate and become exercisable or non-forfeitable as of the effective date
of such date referred to in clause (1) or (2), as applicable, of this
paragraph (c).


 


(d)           Anything in this
Agreement to the contrary notwithstanding, if at the time of the Executive’s separation from service within the meaning of
Section 409A of the Code, the Company determines that the Executive is
a “specified employee” within the meaning of Section 409A(a)(2)(B)(i) of
the Internal Revenue Code of 1986, as amended (the “Code”), then to the extent any payment or benefit
that the Executive becomes entitled to under this Agreement on account of the Executive’s separation from
service would be considered deferred compensation subject to the 20 percent
additional tax imposed pursuant to Section 409A(a) of the Code as a
result of the application of Section 409A(a)(2)(B)(i) of the Code, such payment shall not be payable and such
benefit shall not be provided until the date that is the earlier of (A) six
months and one day after the
Executive’s separation from service,
or (B) the Executive’s death.  If
any such delayed cash payment is otherwise payable on an installment basis, the
first payment shall include a catch-up payment covering amounts that would
otherwise have been paid during the six-month period but for the application of
this provision, and the balance of the installments shall be payable in accordance
with their original schedule.


 


5.                                       Additional Limitation.


 


(i)            Anything in this Agreement to the contrary
notwithstanding, in the event that any compensation, payment or distribution by
the Company to or for the benefit of the Executive, whether paid or payable or
distributed or distributable pursuant to the terms of this Agreement or
otherwise (the “Severance Payments”), would be subject to the excise tax
imposed by Section 4999 of the Code, the following provisions shall apply:


 


(A)          If the Severance Payments,
reduced by the sum of (1) the Excise Tax and (2) the total of the
Federal, state, and local income and employment taxes payable by the Executive
on the amount of the Severance Payments which are in excess of the Threshold
Amount, are greater than or equal to the Threshold Amount, the Executive shall
be entitled to the full benefits payable under this Agreement.


 


(B)           If the Threshold Amount is less than (x) the
Severance Payments, but greater than (y) the Severance Payments reduced by
the sum of (1) the Excise Tax and (2) the total of the Federal,
state, and local income and employment taxes on the amount of the Severance
Payments which are in excess of the Threshold Amount, then the benefits payable
under this Agreement shall be reduced (but not below zero) to the extent
necessary so that the maximum Severance Payments shall not exceed the Threshold
Amount.  To the extent that there is more
than one method of reducing the payments to bring them within the Threshold
Amount, the Executive shall determine which method shall be followed; provided
that if the Executive fails to make such determination within 45 days after the
Company has sent the Executive written notice of the need for 


 


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such reduction, the Company may determine the amount
of such reduction in its sole discretion.


 


(ii)           For the purposes of this Section 5(a), “Threshold Amount” shall
mean three times the Executive’s “base amount” within the meaning of Section 280G(b)(3) of
the Code and the regulations promulgated thereunder less one dollar ($1.00);
and “Excise Tax” shall mean the excise tax imposed by Section 4999 of the
Code, and any interest or penalties incurred by the Executive with respect to
such excise tax.


 


(iii)          The determination as to which of the alternative provisions of Section 5(a)(i) shall
apply to the Executive shall be made by a nationally recognized accounting firm
selected by the Company (the “Accounting Firm”), which shall provide detailed
supporting calculations both to the Company and the Executive within 15
business days of the Date of Termination, if applicable, or at such earlier
time as is reasonably requested by the Company or the Executive.  For purposes of determining which of the
alternative provisions of Section 5(a)(i) shall apply, the Executive
shall be deemed to pay federal income taxes at the highest marginal rate of
federal income taxation applicable to individuals for the calendar year in
which the determination is to be made, and state and local income taxes at the
highest marginal rates of individual taxation in the state and locality of the
Executive’s residence on the Date of Termination, net of the maximum reduction
in federal income taxes which could be obtained from deduction of such state
and local taxes.  Any determination by
the Accounting Firm shall be binding upon the Company and the Executive.


 


6.                                       Term.  This Agreement shall take effect on the date
first set forth above and shall terminate upon the earlier of (a) the
termination by the Company of the employment of the Executive for Cause or the
failure by the Executive to perform his duties with the Company by reason of
his death or Disability, (b) the resignation or termination of the
Executive’s employment for any reason prior to a Change in Control, or (c) the date which is 12 months after a Change in Control if
the Executive is still employed by the Company, provided that the provisions of
Section 10 shall survive termination of this Agreement for a period of
three years.


 


7.                                       Withholding.  All payments made by the Company under this
Agreement shall be net of any tax or other amounts required to be withheld by
the Company under applicable law.


 


8.                                       Notice
and Date of Termination.


 


(a)           Notice of
Termination.  After a Change in
Control and during the term of this Agreement, any purported termination of the
Executive’s employment (other than by reason of death) shall be communicated by
written Notice of Termination from one party hereto to the other party hereto
in accordance with this Section 8. 
For purposes of this Agreement, a “Notice of Termination” shall mean a
notice which shall indicate the specific termination provision in this
Agreement relied upon and the Date of Termination.


 


(b)           Date of
Termination.  “Date of Termination,”
with respect to any purported termination of the Executive’s employment after a
Change in Control and during the


 


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term of this
Agreement, shall mean the date specified in the Notice of Termination.  In the case of a termination by the Company
other than a termination for Cause (which may be effective immediately), the
Date of Termination shall not be less than 30 days after the Notice of
Termination is given.  In the case of a
termination by the Executive, the Date of Termination shall not be less than 30
days from the date such Notice of Termination is given.  Notwithstanding the foregoing, in the event
that the Executive gives a Notice of Termination to the Company, the Company
may unilaterally accelerate the Date of Termination and such acceleration shall
not result in a termination by the Company for purposes of this Agreement.


 


9.             No
Mitigation.  The Company agrees that,
if the Executive’s employment by the Company is terminated during the term of
this Agreement, the Executive is not required to seek other employment or to
attempt in any way to reduce any amounts payable to the Executive by the
Company pursuant to Section 4 hereof. 
Further, the amount of any payment provided for in this Agreement shall
not be reduced by any compensation earned by the Executive as the result of
employment by another employer, by retirement benefits, by offset against any
amount claimed to be owed by the Executive to the Company or otherwise.


 


10.           Arbitration
of Disputes.  Any controversy or
claim arising out of or relating to this Agreement or the breach thereof or
otherwise arising out of the Executive’s employment or the termination of that
employment (including, without limitation, any claims of unlawful employment
discrimination whether based on age or otherwise) shall, to the fullest extent
permitted by law, be settled by arbitration in any forum and form agreed upon
by the parties or, in the absence of such an agreement, under the auspices of
the American Arbitration Association (“AAA”) in Boston, Massachusetts in accordance with the Employment Dispute
Resolution Rules of the AAA, including, but not limited to, the rules and
procedures applicable to the selection of arbitrators.  In the event that any person or entity other
than the Executive or the Company may be a party with regard to any such
controversy or claim, such controversy or claim shall be submitted to
arbitration subject to such other person or entity’s agreement.  Judgment upon the award rendered by the
arbitrator may be entered in any court having jurisdiction thereof.  This Section 10 shall be specifically
enforceable. Notwithstanding the foregoing, this Section 10 shall not
preclude either party from pursuing a court action for the sole purpose of
obtaining a temporary restraining order or a preliminary injunction in
circumstances in which such relief is appropriate; provided that any other relief shall be pursued through an
arbitration proceeding pursuant to this Section 10.


 


11.           Consent
to Jurisdiction.  To the extent that
any court action is permitted consistent with or to enforce Section 10 of
this Agreement, the parties hereby consent to the jurisdiction of the Superior
Court of the Commonwealth of Massachusetts and the United States District Court
for the District of Massachusetts. 
Accordingly, with respect to any such court action, the Executive (a) submits
to the personal jurisdiction of such courts; (b) consents to service of
process; and (c) waives any other requirement (whether imposed by statute,
rule of court, or otherwise) with respect to personal jurisdiction or
service of process.


 


12.           Integration.  This Agreement shall constitute the sole and
entire agreement among the parties with respect to the subject matter hereof,
and supersedes and cancels all prior, concurrent and/or contemporaneous
arrangements, understandings, promises, programs, policies, plans, practices,
offers, agreements and/or discussions, whether written or oral, by or among the



 


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parties regarding the subject matter hereof, including, but not limited
to, those constituting or concerning employment agreements, change in control
benefits and/or severance benefits; provided, however, that this Agreement is
not intended to, and shall not, supersede, affect, limit, modify or terminate
any of the following, all of which shall remain in full force and effect in
accordance with their respective terms: (i) any written agreements,
programs, policies, plans, arrangements or practices of the Company that do not
relate to the subject matter hereof; (ii) any written stock or stock
option agreements between Executive and the Company (except as expressly
modified hereby); and (iii) any written agreements between Executive and
the Company concerning noncompetition, nonsolicitation, inventions and/or
nondisclosure obligations.


 


13.           Successor
to the Executive.  This Agreement
shall inure to the benefit of and be enforceable by the Executive’s personal
representatives, executors, administrators, heirs, distributees, devisees and
legatees.  In the event of the Executive’s
death after a Terminating Event but prior to the completion by the Company of
all payments due him or her under Section 4 of this Agreement, the Company
shall continue such payments to the Executive’s beneficiary designated in
writing to the Company prior to his or her death (or to his or her estate, if
the Executive fails to make such designation).


 


14.           Enforceability.  If any portion or provision of this Agreement
shall to any extent be declared illegal or unenforceable by a court of
competent jurisdiction, then the remainder of this Agreement, or the
application of such portion or provision in circumstances other than those as
to which it is so declared illegal or unenforceable, shall not be affected
thereby, and each portion and provision of this Agreement shall be valid and
enforceable to the fullest extent permitted by law.


 


15.           Waiver.
 No waiver of any provision hereof shall
be effective unless made in writing and signed by the waiving party.  The failure of any party to require the
performance of any term or obligation of this Agreement, or the waiver by any
party of any breach of this Agreement, shall not prevent any subsequent
enforcement of such term or obligation or be deemed a waiver of any subsequent
breach.


 


16.           Notices.  Any notices, requests, demands and other
communications provided for by this Agreement shall be sufficient if in writing
and delivered in person or sent by registered or certified mail, postage
prepaid, to the Executive at the last address the Executive has filed in
writing with the Company, or to the Company at its main office, attention of
the Board of Directors.


 


17.           Amendment.  This Agreement may be amended or modified
only by a written instrument signed by the Executive and by a duly authorized
representative of the Company.


 


18.           Effect
on Other Plans.  An election by the
Executive to resign after a Change in Control under the provisions of this
Agreement shall not be deemed a voluntary termination of employment by the
Executive for the purpose of interpreting the provisions of any of the Company’s
benefit plans, programs or policies. 
Nothing in this Agreement shall be construed to limit the rights of the
Executive under the Company’s benefit plans, programs or policies except that
the Executive shall have no rights to any severance benefits under any Company
severance 


 


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pay plan.  In the event that the
Executive is party to an employment agreement with the Company providing for
change in control payments or benefits, the Executive must elect to receive
either the benefits payable under such other agreement or the benefits payable
under this Agreement, but not both.  The
Executive shall make such an election in the event of a Change in Control.


 


19.           Governing
Law.  This is a Massachusetts
contract and shall be construed under and be governed in all respects by the
laws of the Commonwealth of Massachusetts, without giving effect to the
conflict of laws principles of such Commonwealth.  With respect to any disputes concerning
federal law, such disputes shall be determined in accordance with the law as it
would be interpreted and applied by the United States Court of Appeals for the
First Circuit.


 


20.           Successors
to Company.  The Company shall
require any successor (whether direct or indirect, by purchase, merger,
consolidation or otherwise) to all or substantially all of the business or
assets of the Company to expressly assume and agree to perform this Agreement
in the same manner and to the same extent that the Company would be required to
perform if no such succession had taken place. 
Failure of the Company to obtain an assumption of this Agreement at or
prior to the effectiveness of any succession shall be a breach of this
Agreement and shall constitute Good Reason if the Executive elects to terminate
employment.


 


21.           Gender Neutral.  Wherever used herein, a pronoun in the
masculine gender shall be considered as including the feminine gender unless
the context clearly indicates otherwise.


 


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IN
WITNESS WHEREOF, this Agreement has been executed as a sealed instrument by the
Company by its duly authorized officer, and by the Executive, as of the date
first above written.


 


	
   

  	
  HELICOS BIOSCIENCES CORPORATION

  
	
   

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
  By:

  	
  /s/
  Stephen P. Hall

  
	
   

  	
   

  	
  Name:
  Stephen P. Hall

  
	
   

  	
   

  	
  Title:
  Senior Vice President and Chief Financial Officer

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  EXECUTIVE

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  /s/
  Ronald A. Lowy

  
	
   

  	
  Name:
  Ronald A. Lowy