<PAGE>


                                                                     Exhibit 4.4


===============================================================================



                      HIGH VOLTAGE ENGINEERING CORPORATION

                                       and

                 STATE STREET BANK AND TRUST COMPANY, as Trustee


                            -------------------------


                          SECOND SUPPLEMENTAL INDENTURE


                          Dated as of December 22, 1999


                                       to


                                    INDENTURE


                           Dated as of August 8, 1997,
                as amended by First Supplemental Indenture dated
                              as of March 19, 1998


                                 by and between


                      HIGH VOLTAGE ENGINEERING CORPORATION

                                       and

                 STATE STREET BANK AND TRUST COMPANY, as Trustee


                            -------------------------


                                  $155,000,000


                          10 1/2% Senior Notes Due 2004


===============================================================================


<PAGE>


         SECOND SUPPLEMENTAL INDENTURE (the "SUPPLEMENTAL INDENTURE"), dated as
of December 22, 1999, by and between HIGH VOLTAGE ENGINEERING CORPORATION, a
Massachusetts corporation (the "COMPANY") and STATE STREET BANK AND TRUST
COMPANY (the "TRUSTEE").

                                    RECITALS


         WHEREAS, the Company and the Trustee have entered into that certain
Indenture dated as of August 8, 1997, as amended by a certain First Supplemental
Indenture dated March 19, 1998 (collectively, the "ORIGINAL INDENTURE")
providing for the issuance and delivery by the Company of its 10 1/2% Senior
Notes due 2004; and

         WHEREAS, the Company is entering into certain financing and related
transactions (the "TRANSACTIONS") which will benefit the Company and its
Subsidiaries; and

         WHEREAS, Article 8 of the Indenture provides a manner by which the
Indenture may be amended, and by which compliance with the provisions of the
Original Indenture may be waived, with the consent of the Holders of a majority
in aggregate principal amount of the then outstanding Notes by written act of
said Holders delivered to the Company and the Trustee; and

         WHEREAS, the Holders of a majority in aggregate principal amount of the
outstanding Notes have delivered said consents to the Trustee and the Company;
and

         WHEREAS, pursuant to and in accordance with Section 8.02 of the
Original Indenture, and with the consent of the Holders of a majority in
aggregate principal amount of the outstanding Notes, the Company and the Trustee
have agreed to enter into this Supplemental Indenture;

         NOW THEREFORE, in consideration of the mutual agreements contained
herein and for other good and valuable consideration, the receipt and adequacy
of which is hereby acknowledged, the parties hereto agree as follows for the
benefit of each other party and for the equal and ratable benefit of the Holders
of the Company's 10 1/2% Senior Notes due 2004:

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                                      -2-


         Section 1. AMENDMENTS AND WAIVER.

         1.1. Subject to Section 2.2 hereof, the following definitions are added
to Section 1.01 of the Original Indenture as follows:

                  "ANSALDO ACQUISITION" means the acquisition, directly or
         indirectly, of all of the issued and outstanding shares of capital
         stock of Ansaldo Sistemi Industriali S.p.A., pursuant to that certain
         Share Purchase Agreement, dated as of October 7, 1999, by and between
         the Company and Ansaldo Invest S.p.A.

                  "ASSET SECURITIZATION" means the sale, loan or contribution of
         certain accounts receivable and receivables assets of certain of the
         Company's Restricted Subsidiaries to the Company, the Company's sale of
         these assets to High Voltage Funding Corporation, an Unrestricted
         Subsidiary and such Unrestricted Subsidiary's sale of an undivided
         interest in these assets to Blue Keel Funding, LLC pursuant to the
         Purchase and Sale Agreement among such Restricted Subsidiaries and the
         Company, the Purchase and Sale Agreement between the Company and such
         Unrestricted Subsidiary and the Receivables Purchase Agreement among
         such Unrestricted Subsidiary, the Company, Blue Keel Funding, LLC,
         Fleet National Bank, and for certain limited purposes, such Restricted
         Subsidiaries, each of which is dated as of December 23, 1999 and as
         each may be amended from time to time; or any replacement or
         supplemental facility pursuant to which the Company or any of its
         Restricted Subsidiaries sells or contributes accounts receivable and
         related assets to an Unrestricted Subsidiary for cash and/or notes or
         other obligations of such Unrestricted Subsidiary; PROVIDED, that the
         aggregate amount of capital investments by Blue Keel Funding, LLC and
         any other purchasers of undivided interests in the receivables assets
         of such Unrestricted Subsidiary shall not exceed $25 million.

                  "NICOLE NOTES" means $8.5 million initial principal amount of
         5.0% unsecured notes of Nicole Corporation issued to the Company in
         connection with


<PAGE>
                                      -3-


                  the Ansaldo Acquisition and any additional such notes issued
                  in payment of interest thereon in accordance with the terms
                  thereof.

                  "PHI COLLATERAL" means the first priority security interest in
         all real estate and improvements thereto owned by PHI located in Eden
         Prairie, Minnesota, or any PHI Collateral substituted therefor in
         accordance with the Pledge Agreement.

         1.2. Subject to Section 2.2 hereof, the definition of "Collateral"
contained in Section 1.01 of the Original Indenture is hereby amended to read in
its entirety as follows:

                  "COLLATERAL" means the Intercompany Notes and the Nicole Notes
         in the possession of the Trustee pursuant to the Pledge Agreement.

         1.3. Subject to Section 2.2 hereof, the definition of "Permitted
Investments" contained in Section 1.01 of the Original Indenture is hereby
amended to read in its entirety as follows:

                  "PERMITTED INVESTMENTS" means, for any Person, Investments
         made on or after the date of this Indenture consisting of:

                  (i) Investments by the Company, or by a Restricted Subsidiary
         thereof, in the Company or a Restricted Subsidiary, provided that any
         such Investment is permitted under clauses (a), (b) or (c) of Section
         4.14;

                  (ii) Temporary Cash Investments;

                  (iii) Investments by the Company, or by a Restricted
         Subsidiary thereof, in a Person, if as a result of such Investment (a)
         such Person becomes a Restricted Subsidiary of the Company or (b) such
         Person is merged, consolidated or amalgamated with or into, or
         transfers or conveys substantially all of its assets to, or is
         liquidated into, the Company or a Restricted Subsidiary thereof;

<PAGE>


                                      -4-


                  (iv) Existing Investments in a Restricted Subsidiary which
         becomes an Unrestricted Subsidiary after a Qualified Subsidiary IPO;
         provided, however, that investments by the Company in a Restricted
         Subsidiary in anticipation of a Qualified Subsidiary IPO shall not be
         considered Permitted Investments;

                  (v) reasonable and customary loans made to employees in
         connection with their relocation not to exceed $1,000,000 in the
         aggregate at any one time outstanding;

                  (vi) an Investment that is made by the Company or a Restricted
         Subsidiary thereof in the form of any stock, bonds, notes, debentures,
         partnership or joint venture interests or other securities that are
         issued by a third party to the Company or Restricted Subsidiary solely
         as partial consideration for the consummation of an Asset Sale that is
         otherwise permitted under Section 4.10;

                  (vii) Investments in High Voltage Funding Corporation, or any
         other Unrestricted Subsidiary of the Company formed solely to be the
         purchaser in an Asset Securitization, in connection with an Asset
         Securitization; and

                  (viii) other Investments that do not exceed $1,000,000 at any
         time outstanding plus, the aggregate amount returned in cash on or with
         respect to Investments made pursuant to this clause (vii) not to exceed
         the aggregate amount invested by the Company therein.

         1.4. Subject to Section 2.2 hereof, the definition of "Pledge
Agreement" contained in Section 1.01 of the Original Indenture is hereby amended
to read in its entirety as follows:

                  "PLEDGE AGREEMENT" means, collectively, (i) the Amended and
         Restated Pledge Agreement, between the Company and the Trustee dated
         December 31, 1999 relating to the pledge of the Collateral by the
         Company to secure its Obligations hereunder and (ii) the Pledge
         Agreement among PHI, the Company and the Trustee dated on or before
         January 31, 2000 relating to the pledge of the PHI Collateral by PHI to
         secure the Obligations of the Company hereunder.

<PAGE>
                                      -5-


         1.5. Subject to Section 2.2 hereof, the definition of "Unrestricted
Subsidiary" contained in Section 1.01 of the Original Indenture is hereby
amended to read in its entirety as follows:

                  "UNRESTRICTED SUBSIDIARY" means (a) any Subsidiary of an
         Unrestricted Subsidiary, (b) Nicole Corporation and (c) any Subsidiary
         of the Company which is classified after the Issue Date as an
         Unrestricted Subsidiary by a vote adopted by the Board of Directors of
         the Company; PROVIDED that, other than a Restricted Subsidiary which
         may be classified as an Unrestricted Subsidiary upon consummation of a
         Qualified Subsidiary IPO in compliance with Section 4.22, a Subsidiary
         may be so classified as an Unrestricted Subsidiary only if (x) the
         Restricted Subsidiary to be so designated has total assets of $1,000 or
         less or (y) immediately after giving effect to such designation, the
         Company could incur at least $1.00 of additional Indebtedness pursuant
         to the first paragraph of Section 4.06; and PROVIDED, FURTHER, that the
         Company could make a Restricted Payment in an amount equal to the
         greater of the fair market value (as determined by the Board of
         Directors in good faith) and book value of such Restricted Subsidiary
         pursuant to Section 4.09 and such amount is thereafter treated as a
         Restricted Payment for the purpose of calculating the aggregate amount
         available for Restricted Payments thereunder. The Trustee shall be
         given prompt notice by the Company of each resolution adopted by the
         Board of Directors of the Company under this provision, together with a
         copy of each such resolution adopted.

         1.6. Subject to Section 2.2 hereof, Section 4.09 of the Original
Indenture is hereby amended to read in its entirety as follows:

         Section 4.09. LIMITATION ON RESTRICTED PAYMENTS.

                  The Company shall not make, and shall not permit any of its
         Restricted Subsidiaries to, directly or indirectly, make, any
         Restricted Payment, unless:

                           (a) no Default or Event of Default shall have
                  occurred and be continuing at the time of or immediately after
                  giving effect to such Restricted Payment;

<PAGE>
                                      -6-


                           (b) immediately after giving pro forma effect to such
                  Restricted Payment, the Company could incur $1.00 of
                  additional Indebtedness (other than Permitted Indebtedness)
                  under Section 4.06; and

                           (c) immediately after giving effect to such
                  Restricted Payment, the aggregate of all Restricted Payments
                  declared or made after the Issue Date does not exceed the sum
                  of (1) 50% of the Company's cumulative Consolidated Net Income
                  after the Issue Date (or minus 100% of any cumulative deficit
                  in Consolidated Net Income during such period), (2) 100% of
                  the aggregate Net Proceeds and the fair market value of
                  securities or other property received by the Company as a
                  capital contribution to the common equity of the Company after
                  the Issue Date and from the issue or sale, after the Issue
                  Date, of Capital Stock (other than Disqualified Capital Stock
                  or Capital Stock of the Company issued to any Subsidiary of
                  the Company) of the Company or any Indebtedness or other
                  securities of the Company convertible into or exercisable or
                  exchangeable for Capital Stock (other than Disqualified
                  Capital Stock) of the Company which has been so converted or
                  exercised or exchanged, as the case may be and (3) $350,000.
                  For purposes of determining under this clause (c) the amount
                  expended for Restricted Payments, cash distributed shall be
                  valued at the face amount thereof and property other than cash
                  shall be valued at its fair market value.

                  The provisions of this covenant shall not prohibit (i) the
         payment of any distribution within 60 days after the date of
         declaration thereof, if at such date of declaration such payment would
         comply with the provisions of this Indenture, (ii) the retirement of
         any shares of Capital Stock of the Company or subordinated Indebtedness
         by conversion into, or by or in exchange for, shares of Capital


<PAGE>
                                      -7-


         Stock (other than Disqualified Capital Stock), or out of, the Net
         Proceeds of the substantially concurrent sale (other than to a
         Subsidiary of the Company) of other shares of Capital Stock of the
         Company (other than Disqualified Capital Stock), (iii) the redemption
         or retirement of Indebtedness of the Company subordinated to the Notes
         in exchange for, by conversion into, or out of the Net Proceeds of, a
         substantially concurrent sale or incurrence of Indebtedness (other than
         any Indebtedness owed to a Subsidiary) of the Company that is
         contractually subordinated in right of payment to the Notes to at least
         the same extent as the Subordinated Indebtedness being redeemed or
         retired, (iv) the retirement of any shares of Disqualified Capital
         Stock by conversion into, or by exchange for, shares of Disqualified
         Capital Stock, or out of the Net Proceeds of the substantially
         concurrent sale (other than to a Subsidiary of the Company) of other
         shares of Disqualified Capital Stock, (v) so long as no Default or
         Event of Default shall have occurred and be continuing, the payment of
         cash dividends on the Series A Preferred Stock when such dividends are
         required to be paid in cash in accordance with the Restated Articles,
         (vi) payment, from the net proceeds of the Offerings, of up to
         $2,250,000 to Parent to be used to repurchase from the High Voltage
         Engineering Corporation Retirement Plan shares of the common stock of
         Parent within 60 days of the Issue Date for not more than $2,250,000,
         and fund a proportional accrual relating to the Subordinated Notes
         Warrants of up to $150,000, (vii) so long as no Default or Event of
         Default shall have occurred and be continuing, the exchange of Warrants
         for Subsidiary Warrants or Common Shares for Subsidiary Shares in the
         event of a Qualified Subsidiary IPO, (viii) payments required to effect
         the reclassification of an Unrestricted Subsidiary as a Restricted
         Subsidiary in compliance Section 4.22, (ix) the payment of management
         fees for services provided by Parent or its employees in an aggregate
         annual amount not to exceed $750,000 and (x) payment for the Nicole
         Notes; PROVIDED, HOWEVER, that any amounts paid by the Company pursuant
         to clauses (i), (v), (vi), (vii) and (x) shall reduce amounts otherwise
         available for Restricted


<PAGE>
                                      -8-


         Payments, except that, in the case of clause (x) above, the amounts
         otherwise available for Restricted Payments shall be reduced only by
         the principal amount of the Nicole Notes outstanding on the Restricted
         Payment determination date, subject to a maximum of $8.5 million.

                  Not later than the date of making any Restricted Payment, the
         Company shall deliver to the Trustee an Officers' Certificate stating
         that such Restricted Payment is permitted and setting forth the basis
         upon which the calculations required by this Section 4.09 were
         computed, which calculations may be based upon the Company's latest
         available financial statements, and that no Default or Event of Default
         exists and is continuing and no Default or Event of Default will occur
         immediately after giving effect to any Restricted Payments.

         1.7. Subject to Section 2.2 hereof, Section 6.01 of the Original
Indenture is hereby amended to read in its entirety as follows:


         Section 6.01. EVENTS OF DEFAULT.

         An "Event of Default" occurs if

                  (1) there is a default in payment of any principal of, or
         premium, if any, on the Notes when the same becomes due and payable at
         maturity, upon acceleration or otherwise;

                  (2) there is a default in the payment of any interest on any
         Note when the same becomes due and payable and the Default continues
         for a period of 30 days;

                  (3) there is a default by the Company or any Guarantor in the
         observance or performance of any other covenant in the Notes or this
         Indenture for 60 days after written notice from the Trustee or the
         holders of not less than 25% in aggregate principal amount of the Notes
         then outstanding;

<PAGE>
                                      -9-


                  (4) there is a default in the payment when due of principal,
         interest or premium in an aggregate amount of $3,000,000 or more with
         respect to any Indebtedness of the Company or any Restricted Subsidiary
         thereof, or the acceleration of any such Indebtedness aggregating
         $3,000,000 or more which default shall not be cured, waived or
         postponed pursuant to an agreement with the holders of such
         Indebtedness within 60 days after written notice of such Default to the
         Company by the Trustee or to the Company and the Trustee by any Holder,
         or such acceleration shall not be rescinded or annulled within 20 days
         after written notice of such Default to the Company by the Trustee or
         to the Company and the Trustee by any Holder;

                  (5) the entry of a final judgment or judgments which can no
         longer be appealed for the payment of money in excess of $3,000,000
         shall be rendered against the Company or any Restricted Subsidiary
         thereof, and shall not be discharged for any period of 60 consecutive
         days during which a stay of enforcement shall not be in effect;

                  (6) the Company or any Significant Restricted Subsidiary
         pursuant to or within the meaning of any Bankruptcy Law:

                           (A) commences a voluntary case,

                           (B) consents to the entry of an order for relief
                  against it in an involuntary case,

                           (C) consents to the appointment of a Custodian of it
                  or for all or substantially all of its property,

                           (D) makes a general assignment for the benefit of its
                  creditors, or

                           (E) generally is not paying its debts as they become
                  due;

                  (7) a court of competent jurisdiction enters an order or
         decree under any Bankruptcy Law that:

<PAGE>
                                      -10-


                           (A) is for relief against either of the Company or
                  any Restricted Subsidiary in an involuntary case,

                           (B) appoints a Custodian of either of the Company or
                  any Restricted Subsidiary or for all or substantially all of
                  the property of either of the Company or any Restricted
                  Subsidiary, or

                           (C) orders the liquidation of either of the Company
                  or any Restricted Subsidiary,

         and the order or decree remains unstayed and in effect for 60 days;

                  (8) the Company fails to cause up to $2,250,000 of the
         proceeds from the Issue Date Offerings to be applied, as completely as
         possible, to the repurchase of the common stock of Parent held by the
         High Voltage Engineering Corporation Retirement Plan within 60 days of
         the Issue Date;

                  (9) the Company fails to cause the Foreign Realignment to
         occur on or before May 31, 1998; or

                  (10) the Company fails to cause PHI to provide a valid and
         effective first priority security interest in the PHI Collateral as
         provided for the in the Company's Supplement to Consent Solicitation
         Statement dated December 21, 1999, supplementing the Company's Consent
         Solicitation Statement dated November 30, 1999, on or prior to January
         31, 2000.

                  The term "BANKRUPTCY LAW" means Title 11, U.S. Code or any
         similar Federal or state law for the relief of debtors. The term
         "Custodian" means any receiver, trustee, assignee, liquidator or
         similar official under any Bankruptcy Law.

                  Subject to Sections 7.01 and 7.02, the Trustee shall not be
         charged with knowledge of any Default, Event of Default, Change of
         Control or Asset Sale or the requirement for payment of Additional
         Interest unless written notice thereof shall have been given to a
         Responsible Officer at the Corporate Trust Office of the Trustee by the
         Company or any other Person.

<PAGE>
                                      -11-


         1.8. Subject to Section 2.2 hereof, the following Section 4.26 is
hereby added to the Indenture:

         Section 4.26. TEMPORARY ADDITIONAL INTEREST

                  In addition to the Interest required to be paid by the Company
         under the Notes, from and after December 23, 1999 and until such time
         as the Company is able to incur $1.00 of additional Indebtedness (other
         than Permitted Indebtedness) under Section 4.06 (giving pro forma
         effect to the expiration of the Company's obligations under this
         Section 4.26 in making such calculation), the Company shall pay, as
         additional Interest on the Notes, and in accordance with all of the
         terms and conditions of the Notes, additional interest on the principal
         amount thereof at a rate of 0.25% per annum.

         1.9. Subject to Section 2.2 hereof, compliance by the Company with
Sections 4.09, 4.11, 4.13, 5.01 and 5.02 of the Original Indenture are hereby
waived to the extent any default would occur under such Sections as a result of
the transactions contemplated by the Ansaldo Acquisition (as defined in the
Consent Soliciation Statement of the Company dated November 30, 1999, as
supplemented on December 21, 1999, relating to certain waivers and amendments as
contemplated herein relating to the Company's 10 1/2% Senior Notes due 2004 (the
"Consent Solicitation Statement")), the purchase by the Company of $8.5 million
initial principal amount of Nicole Notes or entrance into the Asset
Securitization (as defined in the Consent Solicitation Statement). In addition,
in accordance with Section 6.04 of the Indenture, any default arising under
Section 6.01(3) of the Indenture as a result of the completion of the Ansaldo
Acquisition, the Asset Securitization and such purchase of the Nicole Notes, and
any other default arising under any other convenant of the Indenture that may
be, or may have been, inadvertently breached as a result of the Ansaldo
Acquisition, the Asset Securitization or such purchase of the Nicole Notes are
hereby waived.


<PAGE>
                                      -12-


         Section 2. MISCELLANEOUS.


         2.1. GOVERNING LAW. THIS SUPPLEMENTAL INDENTURE SHALL BE GOVERNED BY
AND CONSTRUED IN ACCORDANCE WITH THE LAWS OF THE COMMONWEALTH OF MASSACHUSETTS,
AS APPLIED TO CONTRACTS MADE AND PERFORMED WITHIN THE COMMONWEALTH OF
MASSACHUSETTS, WITHOUT REGARD TO PRINCIPLES OF CONFLICTS OF LAW. EACH OF THE
PARTIES HERETO AGREES TO SUBMIT TO THE JURISDICTION OF THE COURTS OF THE
COMMONWEALTH OF MASSACHUSETTS IN ANY ACTION OR PROCEEDING ARISING OUT OF OR
RELATING TO THIS SUPPLEMENTAL INDENTURE.

         2.2. OPERATIVE TIME. Upon the execution and delivery of this
Supplemental Indenture by the Company and the Trustee, the Indenture shall be
supplemented in accordance herewith, and this Supplemental Indenture shall form
a part of the Original Indenture for all purposes, and every Holder of Notes
heretofore or hereafter authenticated and delivered under the Original Indenture
shall be bound hereby and thereby; PROVIDED, however, that Section 1 hereof
shall become operative upon the satisfaction of the Acquisition Condition (as
defined in the Consent Solicitation Statement); PROVIDED, in the event that the
Acquisition Condition is not satisfied on or prior to January 31, 2000, this
Supplemental Indenture shall become null and void. Upon the receipt by the
Trustee of (i) an Officers' Certificate certifying that such conditions have
been satisfied, or waived by the Company, and (ii) an Opinion of Counsel to the
effect set forth in Section 8.06 of the Original Indenture, the amendments set
forth herein shall become operative.

         2.3. CONFIRMATION OF THE ORIGINAL INDENTURE. Except as amended hereby,
the Original Indenture shall remain in full force and effect and is hereby
ratified and confirmed in all respects.

         2.4. MULTIPLE COUNTERPARTS. The parties may sign multiple counterparts
of this Supplemental Indenture. Each signed counterpart shall be deemed an
original, but all of them together represent one and the same agreement.


         2.5. SEPARABILITY. Each provision of this Supplemental Indenture shall
be considered separable and if for any reason any provision which is not
essential to the effectuation of the basic purpose of this Supplemental
Indenture shall be invalid, illegal or unenforceable, the validity, legality and
enforceability of the remaining provisions shall not in any way be affected or
impaired thereby.


<PAGE>
                                      -13-


         2.6. HEADINGS. The captions of the various section headings of this
Supplemental Indenture have been inserted for convenience of reference only, are
not to be considered a part hereof, and shall in no way modify or restrict any
of the terms or provisions hereof.


         2.7. THE TRUSTEE. The Trustee shall not be responsible in any manner
whatsoever for or in respect of the validity or sufficiency of this Supplemental
Indenture or for or in respect of the recitals contained herein, all of which
recitals are made solely by the Company.


         2.8. DEFINITIONS. All terms defined in the Original Indenture shall
have the same meaning in this Supplemental Indenture unless otherwise defined
herein.


<PAGE>


         IN WITNESS WHEREOF, the parties hereto caused this Supplemental
Indenture to be duly executed as of this 22nd day of December, 1999.

                                HIGH VOLTAGE ENGINEERING CORPORATION


                                By:  __________________________________________
                                     Name:
                                     Title:


                                STATE STREET BANK AND TRUST COMPANY,
                                    as Trustee


                                By:  __________________________________________
                                     Name:
                                     Title: