Crossing the 12,000-atom barrier with heterogeneous quantum-classical supercomputing: quantum chemistry of protein-ligand complexes

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; Hitomi Takahashi; Toshinari Itoko; Hiroshi Horii; Thaddeus Pellegrini; Javier Robledo Moreno; Kevin J. Sung; Ella Fejer; Robert Walkup; Seetharami Seelam; Mario Motta

arXiv · 2605.01138

Crossing the 12,000-atom barrier with heterogeneous quantum-classical supercomputing: quantum chemistry of protein-ligand complexes

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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.

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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, Hitomi Takahashi, Toshinari Itoko, Hiroshi Horii, Thaddeus Pellegrini, Javier Robledo Moreno, Kevin J. Sung, Ella Fejer, Robert Walkup, Seetharami Seelam, Mario Motta. 2026-05-01. Crossing the 12,000-atom barrier with heterogeneous quantum-classical supercomputing: quantum chemistry of protein-ligand complexes. https://arxiv.org/abs/2605.01138

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