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

• URL: http://arxiv.org/abs/2605.01138v1
• Date: Fri, 01 May 2026 22:30:56 GMT
• Title: Crossing the 12,000-atom barrier with heterogeneous quantum-classical supercomputing: quantum chemistry of protein-ligand complexes
• Abstract summary: Ab initio wavefunction methods provide accurate molecular simulations but their computational scaling restricts applications to small systems.<n>We develop a workflow combining quantum embedding to decompose a molecule into fragments with a heterogeneous quantum-classical (HQC) method to simulate fragments.
• Score: 2.0403796650328854
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• 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.

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