{
  "abstract": "We develop a workflow decomposing a molecule into fragments via quantum embedding and simulating them with a heterogeneous quantum-classical (HQC) method. We sample fragment electronic configurations on two 156-qubit quantum processors (ibm$\\_$cleveland, ibm$\\_$kobe), using up to 94 qubits, running 21,006 circuits for over 239 hours, collecting $3.0 \\cdot 10^9$ measurement outcomes -- the most resource-intensive HQC computation for quantum chemistry to date. We compute fragment wavefunctions via optimized subspace diagonalization on supercomputers Fugaku, Miyabi-G, and ROQUO, 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, 12,635 atoms), demonstrate $>40\\times$ increase in system size and up to $210\\times$ improvement in accuracy over previous state-of-the-art, with HQC matching coupled-cluster (CCSD) accuracy in fragment energies. We present the first HQC protein-ligand binding prediction using a mixed-basis set and an automated end-to-end workflow enabling practical HQC calculations of large protein systems.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": "2605.01138",
  "author_total": 24,
  "authors": [
    {
      "name": "Kenneth M. Merz, Jr."
    },
    {
      "name": "Akhil Shajan"
    },
    {
      "name": "Danil Kaliakin"
    },
    {
      "name": "Fangchun Liang"
    },
    {
      "name": "Yuichi Otsuka"
    },
    {
      "name": "Tomonori Shirakawa"
    },
    {
      "name": "Lukas Broers"
    },
    {
      "name": "Han Xu"
    },
    {
      "name": "Miwako Tsuji"
    },
    {
      "name": "Mitsuhisa Sato"
    },
    {
      "name": "Seiji Yunoki"
    },
    {
      "name": "Ryo Wakizaka"
    },
    {
      "name": "Yukio Kawashima"
    },
    {
      "name": "Jun Doi"
    },
    {
      "name": "Hitomi Takahashi"
    },
    {
      "name": "Toshinari Itoko"
    },
    {
      "name": "Hiroshi Horii"
    },
    {
      "name": "Thaddeus Pellegrini"
    },
    {
      "name": "Javier Robledo Moreno"
    },
    {
      "name": "Kevin J. Sung"
    },
    {
      "name": "Ella Fejer"
    },
    {
      "name": "Robert Walkup"
    },
    {
      "name": "Seetharami Seelam"
    },
    {
      "name": "Mario Motta"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/8ch6wp94dwmd8.bib",
  "cited_by": 3,
  "doi": "10.48550/arxiv.2605.01138",
  "fulltext_url": null,
  "id": "8ch6wp94dwmd8",
  "issns": [],
  "landing_url": "https://arxiv.org/abs/2605.01138",
  "language": null,
  "licence": "LicenseRef-arXiv-nonexclusive-1.0",
  "licence_label": "arXiv licence",
  "licence_source": "article",
  "licence_url": "http://arxiv.org/licenses/nonexclusive-distrib/1.0/",
  "metadata_licence": "CC0-1.0",
  "native_subjects": [
    [
      "arxiv",
      "physics.chem-ph"
    ],
    [
      "arxiv",
      "physics.comp-ph"
    ],
    [
      "arxiv",
      "quant-ph"
    ],
    [
      "openalex",
      "1702|Quantum Computing Algorithms and Architecture"
    ]
  ],
  "openalex": "W7160316575",
  "pdf_url": "https://arxiv.org/pdf/2605.01138",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-05",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/8ch6wp94dwmd8.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:48Z",
      "native_id": "2605.01138",
      "source": "arxiv",
      "url": "https://arxiv.org/abs/2605.01138"
    }
  ],
  "subjects": [
    {
      "field": "chemistry",
      "origin": "arxiv:physics.chem-ph",
      "subfield": "physical"
    },
    {
      "field": "physics",
      "origin": "arxiv:physics.comp-ph",
      "subfield": "computational"
    },
    {
      "field": "physics",
      "origin": "arxiv:quant-ph",
      "subfield": "quantum"
    }
  ],
  "title": "Crossing the 12,000-atom barrier with heterogeneous quantum-classical supercomputing: quantum chemistry of protein-ligand complexes",
  "title_text": "Crossing the 12,000-atom barrier with heterogeneous quantum-classical supercomputing: quantum chemistry of protein-ligand complexes",
  "type": "preprint",
  "updated_at": "2026-10-30T12:19:48Z",
  "url": "https://research.draconitic.com/paper/8ch6wp94dwmd8",
  "venue": "arXiv",
  "versions": []
}