Crossing the 12,000-atom barrier with heterogeneous quantum-classical supercomputing: quantum chemistry of protein-ligand complexes
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Quantum Physics arXiv:2605.01138 (quant-ph) [Submitted on 1 May 2026] Title:Crossing the 12,000-atom barrier with heterogeneous quantum-classical supercomputing: quantum chemistry of protein-ligand complexes Authors:Kenneth M. Merz Jr., Akhil Shajan, Danil Kaliakin, Fangchun Liang, Yuichi Otsuka, Tomonori Shirakawa, Lukas Broers, Han Xu, Miwako Tsuji, Mitsuhisa Sato, Seiji Yunoki, Ryo Wakizaka, Yukio Kawashima, Jun Doi, Toshinari Itoko, Hiroshi Horii, Thaddeus Pellegrini, Javier Robledo Moreno, Kevin J. Sung, Ella Fejer, Robert Walkup, Seetharami Seelam, Mario Motta View a PDF of the paper titled Crossing the 12,000-atom barrier with heterogeneous quantum-classical supercomputing: quantum chemistry of protein-ligand complexes, by Kenneth M. Merz and 23 other authors View PDF HTML (experimental) Abstract:Ab initio wavefunction methods provide accurate molecular simulations but their computational scaling restricts applications to small systems. We develop a workflow combining quantum embedding to decompose a molecule into fragments with a heterogeneous quantum-classical (HQC) method to simulate fragments. We sample fragment electronic configurations on two 156-qubit quantum processors (ibm$\_$cleveland, ibm$\_$kobe), using up to 94 qubits, running 9,200 circuits for over 100 hours, collecting $1.3 \cdot 10^9$ measurement outcomes - the most resource-intensive HQC computation for quantum chemistry to date. We compute fragment wavefunctions via optimized subspace diagonalization on two supercomputers (Fugaku, Miyabi-G), achieving 72.5$\%$ parallel efficiency with scalable distributed linear algebra kernels. We simulate two protein-ligand complexes spanning dispersion- and electrostatics-dominated regimes (11,608 and 12,635 atoms), demonstrate $>40\times$ increase in system size and up to $210\times$ improvement in accuracy over the previous state-of-the-art, with HQC matching coupled-cluster (CCSD) accuracy in fragment energies, and establish a scalable pathway for systematically improvable biomolecular simulations. Comments: Subjects: Quantum Physics (quant-ph); Chemical Physics (physics.chem-ph); Computational Physics (physics.comp-ph) Cite as: arXiv:2605.01138 [quant-ph] (or arXiv:2605.01138v1 [quant-ph] for this version) https://doi.org/10.48550/arXiv.2605.01138 Focus to learn more arXiv-issued DOI via DataCite (pending registration) Submission history From: Mario Motta [view email] [v1] Fri, 1 May 2026 22:30:56 UTC (4,638 KB) Full-text links: Access Paper: View a PDF of the paper titled Crossing the 12,000-atom barrier with heterogeneous quantum-classical supercomputing: quantum chemistry of protein-ligand complexes, by Kenneth M. Merz and 23 other authorsView PDFHTML (experimental)TeX Source view license Current browse context: quant-ph new | recent | 2026-05 Change to browse by: physics physics.chem-ph physics.comp-ph References & Citations INSPIRE HEP NASA ADSGoogle Scholar Semantic Scholar export BibTeX citation Loading... BibTeX formatted citation × loading... Data provided by: Bookmark Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer (What is the Explorer?) Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are Smart Citations?) Code, Data, Media Code, Data and Media Associated with this Article alphaXiv Toggle alphaXiv (What is alphaXiv?) Links to Code Toggle CatalyzeX Code Finder for Papers (What is CatalyzeX?) DagsHub Toggle DagsHub (What is DagsHub?) GotitPub Toggle Gotit.pub (What is GotitPub?) Huggingface Toggle Hugging Face (What is Huggingface?) ScienceCast Toggle ScienceCast (What is ScienceCast?) Demos Demos Replicate Toggle Replicate (What is Replicate?) Spaces Toggle Hugging Face Spaces (What is Spaces?) Spaces Toggle TXYZ.AI (What is TXYZ.AI?) Related Papers Recommenders and Search Tools Link to Influence Flower Influence Flower (What are Influence Flowers?) Core recommender toggle CORE Recommender (What is CORE?) Author Venue Institution Topic About arXivLabs arXivLabs: experimental projects with community collaborators arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs. Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)