Hamamatsu Corporation v. SiOnyx, LLC

I'll research this before writing. Note that the metadata says the "court" is the PTAB — so let me verify the parallel district court litigation as well.

Key correction identified: the PTAB case is Hamamatsu as petitioner against SiOnyx's patent — and the district court case had the parties reversed. Let me get the IPR specifics.

Now let me verify the parallel/related PTAB proceedings and the estoppel ruling that became notable.

Important framing correction before the overview

IPR2016‑01910 is not an infringement action — it is an inter partes review before the PTAB (Paper 22, institution decision, Mar. 30, 2017; Final Written Decision, Mar. 28, 2018), in which Hamamatsu was the petitioner and SiOnyx the patent owner. The infringement litigation in which these same parties fought over the same technology ran in the reverse direction: SiOnyx, LLC and President and Fellows of Harvard College v. Hamamatsu Photonics K.K., Hamamatsu Corp., and Ocean Optics, Inc., No. 1:15‑cv‑13488‑FDS (D. Mass., filed Oct. 1, 2015), before Judge F. Dennis Saylor IV in Boston. The two proceedings are tightly interlocked (the IPR was filed Sept. 30, 2016, just inside the § 315(b) one‑year window), and the district court's estoppel and claim‑narrowing rulings turned on the IPR's progress. Below I treat the D. Mass. action as the infringement litigation and the IPR as its PTAB companion, since that is how the record actually reads.

Parties and technology. SiOnyx, LLC is a venture‑ and DARPA‑backed operating company (not an NPE/PAE and not a university) founded in 2006 by Harvard physics professor Eric Mazur and his former doctoral student James Carey to commercialize laser‑textured "black silicon" photodetectors; it began selling its own photodetector products by 2013. Harvard (President and Fellows of Harvard College) owns the Mazur/Carey patents and exclusively licensed them to SiOnyx. On the other side, Hamamatsu Photonics K.K. (HPK) is a large Japanese photonics manufacturer (photodiodes, APDs, image sensors, spectrometers; ~¥112 billion in net sales per its 2014 corporate profile), and Hamamatsu Corporation (HC) is its New Jersey‑based North American sales/marketing subsidiary and a wholly owned subsidiary of HPK's holding company. The accused products were Hamamatsu's laser‑textured, back‑thinned near‑IR‑enhanced silicon photodiodes and image sensors — principally the S11499‑series IR‑enhanced Si PIN photodiodes and S11510‑series back‑illuminated FFT‑CCD image sensors — plus downstream end products such as the Ocean Optics Maya2000 Pro‑NIR spectrometer that incorporated them. The technical through‑line is "black silicon": femtosecond/nanosecond laser texturing of a silicon surface (optionally with heavy dopant incorporation) that dramatically improves near‑infrared absorption.

Patents. Two patents were actually tried, plus a third that dropped out: (1) U.S. 8,680,591 ("Photosensitive Imaging Devices and Associated Methods," SiOnyx‑owned, inventors Haddad, Jiang, McKee, Miller, Forbes, Palsule) — claims a photosensitive imager device/array having a laser‑textured region on the semiconductor substrate positioned to interact with electromagnetic radiation, integrated circuitry at the planar surface, and an electrical transfer element, plus method claims for making the device (claim 1 device, claim 13 method); all 26 claims were challenged in IPR2016‑01910. (2) U.S. 8,080,467 ("Silicon‑Based Visible and Near‑Infrared Optoelectric Devices," Harvard‑owned, Carey/Mazur) — a method of fabricating a semiconductor wafer by irradiating silicon with temporally short laser pulses and annealing, i.e., the core black‑silicon process; this was the patent on which SiOnyx/Harvard ultimately won willfulness and injunctive relief. (3) U.S. 7,884,446 (Harvard) was pleaded but stipulated out (ECF 422) after its asserted claims were cancelled in an IPR — I was not able to confirm in the sources reviewed which specific IPR cancelled those claims, so treat that detail as unverified.

Procedural posture and why the forum matters. In the PTAB, Hamamatsu (with HPK named as real party‑in‑interest) asserted five grounds: anticipation by Nakashiba; Akahori + Mazur; Mabuchi + Mazur; Mabuchi + Mazur + Uematsu (claim 6); and Mabuchi + Mazur + Furukawa (claim 12). The Board applied its then‑standard partial institution practice (pre‑SAS): it instituted on Mar. 30, 2017 only on Nakashiba and the Mabuchi/Mazur family of grounds, refusing the Akahori ground because Akahori teaches away from texturing the relevant surface, and refusing claims 19–20 for lack of disclosure of dimension‑based selective diffusion/absorption. On rehearing (Paper 28, May 26, 2017) the Board reversed institution as to claims 9, 24 and 25 on Nakashiba (a product‑by‑process issue). The panel was Administrative Patent Judges Braden, Clements and Ullagaddi, with Judge Ullagaddi writing. The **Final Written Decision of Mar. 28, 2018 held claims 1, 2, 4–11, 13–18, 21 and 23

I'll research this. Note upfront: the case metadata describes a PTAB inter partes review (IPR2016-01910), not a district court infringement action — so I'll need to check whether there was a parallel district court suit and map the actual procedural history accurately rather than assuming a Markman/trial track.

This is more layered than the caption suggests: there appears to be both the PTAB IPR and a parallel D. Mass. infringement/ownership suit. Let me pin down both tracks.

Good — this is a two-track dispute. Now let me pin down the district court milestones, the verdict, and the parallel PTAB activity on the other asserted patents.

Threshold point on scope

The docket number in the case metadata — IPR2016-01910 — is a PTAB inter partes review, not an infringement action. The infringement litigation it ran alongside is a separate D. Mass. case: SiOnyx, LLC v. Hamamatsu Photonics K.K., No. 1:15-cv-13488-FDS (D. Mass., Saylor, J.), filed 2015-10-01 (Justia docket). Note the alignment is reversed: Hamamatsu petitioned for the IPR against SiOnyx's '591 patent, while SiOnyx (with Harvard) was the plaintiff in court. Below I track both, because the PTAB proceeding materially reshaped the district court case.

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Track A — D. Mass. infringement/ownership litigation (1:15-cv-13488-FDS)

Filing and pleadings (2015-10-01). SiOnyx and the President and Fellows of Harvard College sued Hamamatsu Photonics K.K. ("HPK"), Hamamatsu Corporation ("HC"), and Ocean Optics. Four claim families: (1) breach of the mutual NDA; (2) unjust enrichment; (3) patent infringement of Harvard's '467 patent (SiOnyx as exclusive licensee) and the '446 patent, plus SiOnyx's

I'll research counsel on both tracks — the D. Mass. plaintiffs (SiOnyx + Harvard) and, because the case metadata's caption is the PTAB proceeding, the petitioner-side counsel in IPR2016-01910.

Good — I've found the core counsel lineup. Now let me verify the specific IPR2016-01910 petitioner-side counsel (the IPR docket filings) and the D. Mass. appearance records, including whether Harvard had separate counsel.

Now let me nail down the full appearance list on the D. Mass. docket (including any later-added or in-house counsel) and confirm current firm affiliations.

Framing (brief, because the earlier sections already established the reversal)

Two different sets of "plaintiff-side" counsel exist in this record, and the question is ambiguous as posed:

• The case in the metadata (IPR2016-01910) is a PTAB trial in which Hamamatsu Corporation is the petitioner — functionally the plaintiff-side role. Its counsel of record were from Panitch Schwarze Belisario & Nadel LLP (Philadelphia).
• The actual patent infringement case — SiOnyx, LLC and President and Fellows of Harvard College v. Hamamatsu Photonics K.K., Hamamatsu Corp., Ocean Optics, Inc., No. 1:15-cv-13488-FDS (D. Mass.) — had SiOnyx and Harvard as plaintiffs, represented by Pepper Hamilton LLP (Boston).

I give both, flagging which is which. All appearances below are from public opinions, PTAB papers, and Federal Circuit materials — none of this is sealed.

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A. Plaintiffs in the infringement action (D. Mass. 1:15-cv-13488-FDS): SiOnyx, LLC and President and Fellows of Harvard College

All of-record counsel came from a single firm, Pepper Hamilton LLP, 125 High Street, 19th Floor, High Street Tower, Boston, MA 02110 (617-204-5100). Both plaintiffs — SiOnyx and Harvard — were represented by the same Pepper team; no separate Harvard Office of the General Counsel appearance is reflected in the published opinions.

Firm-name note (important for citation hygiene): Pepper Hamilton LLP merged with Troutman Sanders effective July 1, 2020, becoming Troutman Pepper Hamilton Sanders LLP — the Federal Circuit certificate of interest filed January 21, 2021 expressly reads "Troutman Pepper Hamilton Sanders, LLP (Formerly Pepper Hamilton, LLP)." That firm subsequently combined with Locke Lord (2025) to form Troutman Pepper Locke LLP; the Locke Lord combination is general firm knowledge rather than something I confirmed in a case document, so cite the 2020 merger (which is documented in the Fed. Cir. filing) rather than the 2025 one.

In-house counsel: No SiOnyx or Harvard in-house attorney entered an appearance in the published record. SiOnyx's CEO Stephen Saylor and founder James Carey appear only as witnesses/parties, not counsel.

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B. Petitioner-side counsel in IPR2016-01910 (Hamamatsu Corporation): Panitch Schwarze Belisario & Nadel LLP

Firm: Panitch Schwarze Belisario & Nadel LLP, One Commerce Square, 2005 Market Street, Suite 2200, Philadelphia, PA 19103.

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C. Cross-check: who was adverse to plaintiffs (for completeness only)

Hamamatsu's D. Mass. defense team was Panitch Schwarze (Keith A. Jones, John D. Simmons, Stephen E. Murray, pro hac vice), Koichiro Minamino, Minamino Law Office, PLLC (Washington, D.C.), and local counsel Stevenson McKenna & Callanan LLP, Hingham, MA (Alan E. McKenna; Christopher A. Callanan). Ocean Optics was represented by Minamino.

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D. Gaps, caveats, and one inference I am flagging explicitly

1. SiOnyx's PTAB-side counsel in IPR2016-01910 is inferred, not directly confirmed. The IPR papers I could retrieve on the public docket show Pepper Hamilton's Thomas J. Engellenner (Reg. No. 28,711) as SiOnyx's lead counsel and Reza Mollaaghababa as back-up in the companion SiOnyx IPR (IPR2017-00909, on the '467 patent), by mandatory notice dated March 1, 2017. Because the same Pepper trial team (Belanger, Tawresey) handled the appeal from IPR2016-01910, it is highly likely Engellenner and Mollaaghababa were also the registered practitioners of record in -01910 — but I did not retrieve the -01910 mandatory notice itself, so do not state that as established. Same caution for any suggestion that Belanger was PTAB counsel of record (registered practitioners must handle PTAB appearances; Belanger's documented appearance is at the Federal Circuit).
2. Nothing here was sealed. Counsel appearances in both tracks are public; the sealing/redaction issues in this litigation concerned trial exhibits and damages material, not the identity of counsel.
3. Appearance lists changed over the case's four-year life. The names above are those appearing in the substantive opinions (2018, 2019), the Federal Circuit filings (2019–2021), and the PTAB papers. A full PACER pull of every ECF appearance/withdrawal would be needed to date-stamp each attorney's start and end of record; I did not have direct PACER access, so individual appearance dates are not verified except where a filing is cited.

I'll research counsel on both tracks, since "defendant" means different parties in the IPR (SiOnyx, as patent owner) versus the D. Mass. infringement suit (the Hamamatsu entities). Let me start.

Good leads. Now let me pin down the D. Mass. defendants' counsel and verify firm affiliations.

Let me confirm the IPR-specific mandatory notices and check Ocean Optics' separate counsel and the local counsel details.

Preliminary point: "defendant" is doing double duty here

Following the metadata's framing (Hamamatsu = plaintiff/petitioner, SiOnyx = defendant/patent owner), there are two different defense-side teams, and they sat on opposite sides of the two proceedings:

Both are set out below, with sourcing and verification caveats.

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A. IPR2016-01910 — counsel for Patent Owner SiOnyx ("defendant" in this docket)

SiOnyx's IPR team was Pepper Hamilton LLP, 125 High Street, 19th Floor, High Street Tower, Boston, MA 02110.

Verification caveat: the Engellenner/Mollaaghababa lead/back-up designation is documented directly in the IPR2017-00909 mandatory notice (same patent family, same patent owner, same counsel, filed five months after this IPR was instituted). I did not retrieve the Paper 3/4 mandatory notice in IPR2016-01910 itself, so the designation is a well-supported inference rather than a quotation from this docket. Belanger and Tawresey are confirmed as SiOnyx's appellate counsel on this IPR from the Federal Circuit's Rule 36 judgment in SiOnyx LLC v. Hamamatsu Corporation, No. 2018-2019 (Apr. 3, 2019) ("WILLIAM D. BELANGER, Pepper Hamilton LLP, Boston, MA, argued for appellant. Also represented by GWENDOLYN TAWRESEY.").

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B. Petitioner Hamamatsu's IPR counsel (the "plaintiff" side in this docket, but the defendant side in the district court)

Panitch Schwarze Belisario & Nadel LLP, Philadelphia, PA:

• John David Simmons — lead; argued for Hamamatsu as appellee in the 18-2019 appeal.
• Keith Aaron Jones — of counsel on the appeal.
• Stephen Emerson Murray — of counsel on the appeal.

(Same three attorneys, per the Fed. Cir. 18-2019 judgment.)

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C. D. Mass. 1:15-cv-13488-FDS — counsel for the Hamamatsu defendants and Ocean Optics

This is the infringement action in which the Hamamatsu entities were defendants. Per the appearances recited in SiOnyx, LLC v. Hamamatsu Photonics K.K., 540 F. Supp. 3d 85 (D. Mass. May 18, 2021) (Saylor, C.J.):

Caveats: (1) Ocean Optics' appearance is documented only through Minamino in the 2021 costs opinion; I could not confirm whether it had separate trial counsel earlier or was dismissed/settled before the May 2019 trial. (2) I did not access the PACER docket sheet directly, so initial appearance dates and any withdrawn appearances are unverified; the above is drawn from the court's own recitation of appearances plus the Federal Circuit opinions.

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D. Cross-reference: SiOnyx/Harvard's counsel in the district court (the plaintiff side there)

For completeness, since the two tracks are mirror images: William D. Belanger, Anthony H. Cataldo, Gwendolyn E. Tawresey, Miranda Hooker, and Maia H. Harris — Pepper Hamilton LLP (later Troutman Pepper Hamilton Sanders LLP), Boston. Belanger argued the Dec. 7, 2020 Federal Circuit appeal, SiOnyx LLC v. Hamamatsu Photonics K.K., 981 F.3d 1339 (Fed. Cir. 2020).

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E. Flagged naming/verification issues

• Firm-name drift. Pepper Hamilton merged into Troutman Pepper in 2020; the same attorneys appear as "Pepper Hamilton LLP" in the 2018–2019 IPR/appeal papers and as "Troutman Pepper Hamilton Sanders LLP" from 2020 onward. The IPR-era filings in this case use Pepper Hamilton.
• Spelling. Board papers in the SiOnyx IPRs alternate between "Engellenner" and "Engellener" (e.g., the IPR2017-00909 mandatory notice spells it "Engellener" in the signature block). The USPTO registered name is Thomas J. Engellenner, Reg. No. 28,711.
• Not verified: Hamamatsu's IPR-specific power of attorney/lead-back-up designations in IPR2016-01910 (Paper 2/3); whether Hamamatsu used in-house counsel of record; and whether Ocean Optics had separate counsel in the district court.
• No sealed-counsel issue identified — all appearances above are from public opinions and public PTAB filings.