Quantum-HPC hybrid computation of biomolecular excited-state energies
Kentaro Yamamoto, Riku Masui, Takahito Nakajima, Miwako Tsuji, Mitsuhisa Sato, Peter Schow, Lukas Heidemann, Matthew Burke, Philipp Seitz, Oliver J. Backhouse, Juan W. Pedersen, John Children, Craig Holliman, Nathan Lysne, Daichi Okuno, Seyon Sivarajah, David Muñoz Ramo, Alex Chernoguzov, Ross Duncan
quant-phSubmitted Jan 22, 2026• Announced Jan 23, 2026• 0 citations
We develop a workflow within the ONIOM framework and demonstrate it on the hybrid computing system consisting of the supercomputer Fugaku and the Quantinuum Reimei trapped-ion quantum computer. This hybrid platform extends the layered approach for biomolecular chemical reactions to accurately treat the active site, such as a protein, and the large and often weakly correlated molecular environment. Our result marks a significant milestone in enabling scalable and accurate simulation of complex biomolecular reactions
We develop a workflow within the ONIOM framework and demonstrate it on the hybrid computing system consisting of the supercomputer Fugaku and the Quantinuum Reimei trapped-ion quantum computer. This hybrid platform extends the layered approach for biomolecular chemical reactions to accurately treat the active site, such as a protein, and the large and often weakly correlated molecular environment. Our result marks a significant milestone in enabling scalable and accurate simulation of complex biomolecular reactions
We describe the Quantum-HPC hybrid system comprising the supercomputer Fugaku, the QPUs Quantinuum Reimei and ibm_kobe, and the Tierkreis hybrid workflow software. We present two demonstrations of the system at work. In the first, we compute the excited states of a biomolecular system using Fugaku and Reimei (simulator) to handle classical and quantum parts of the workflow respectively. In the second, Fugaku coordinates Reimei and ibm_kobe working together in a combined VQE + QPE workflow to compute the ground state energy of a simple system.
A lot of progress has been made in recent times for simulating accurately the ground state energy of small molecules and their potential energy surface, using quantum-classical hybrid computing architecture. While these single point energy calculations are a significant milestone for quantum chemistry simulation on quantum hardware, a similarly important application is to trace accurately the reaction pathway of various chemical transformations. Such computations require accurate determination of the equilibrium or lowest energy molecular geometry, either by computing energy gradients with respect to the molecule's nuclear coordinates or perturbative distortion of the molecular configuration. In this work, we present a modular quantum-classical hybrid framework, to accurately simulate chemical reaction pathway of various kinds of molecular reactions. We demonstrate our framework by accurately tracing the isomerization pathway for small organic molecules. This framework can now be readily applied to study other 'active' molecules from the pharma and chemical industries.
Predicting chemical reactions in biomolecules is challenging because reactive centers are embedded within complex environments that strongly influence their energetics and mechanisms. Here, we present a hybrid quantum-classical workflow that combines molecular dynamics, density functional theory, and correlated wavefunction methods, tightly integrating CPUs, GPUs, and quantum processing units (QPUs) to enable simulations across multiple length and accuracy scales. We apply this approach to ADGRG1 autoproteolysis, a maturation reaction in an adhesion G protein-coupled receptor that has not previously been studied using correlated electronic-structure methods. Our simulations treat a biologically realistic system containing more than one million atoms, including the full-length uncleaved receptor embedded in an endoplasmic-reticulum membrane, while incorporating a 54-qubit IQM quantum processor and up to 1,200 NVIDIA H100 GPUs. These results demonstrate how quantum computers can serve as accelerators within scalable scientific workflows, extending correlated electronic-structure methods to biologically relevant systems.
Free energy calculations are at the heart of physics-based analyses of biochemical processes. They allow us to quantify molecular recognition mechanisms, which determine a wide range of biological phenomena, from how cells send and receive signals to how pharmaceutical compounds can be used to treat diseases. Quantitative and predictive free energy calculations require computational models that accurately capture both the varied and intricate electronic interactions between molecules as well as the entropic contributions from the motions of these molecules and their aqueous environment. However, accurate quantum-mechanical energies and forces can be obtained only for small atomistic models and not for large biomacromolecules. Here, we demonstrate how to consistently link accurate quantum-mechanical data obtained for substructures to the overall potential energy of biomolecular complexes using machine learning in an integrated algorithm. We do so using a two-fold quantum embedding strategy where the innermost quantum cores are treated at a very high level of accuracy. We demonstrate the viability of this approach for the molecular recognition of a ruthenium-based anticancer drug by its protein target by applying traditional quantum chemical methods. As such methods scale unfavorably with system size, we analyze the requirements for quantum computers to provide highly accurate energies that affect the resulting free energies. Once the requirements are met, our computational pipeline, FreeQuantum, is able to make efficient use of the quantum-computed energies, thereby enabling quantum computing-enhanced modeling of biochemical processes. This approach combines the exponential speedups of quantum computers for simulating interacting electrons with modern classical simulation techniques that incorporate machine learning to model large molecules.
We present a large-scale experimental study of quantum-computing-based molecular simulation carried out on IQM's Sirius 24-qubit superconducting processor, utilizing up to 16 operational qubits. The work employs Sample-based Quantum Diagonalization (SQD) together with the Local Unitary Cluster Jastrow (LUCJ) ansatz to estimate ground-state energies for a set of benchmark molecules, including H2, LiH, BeH2, H2O, and NH3. In addition, we introduce a Linear-CNOT variant of the Unitary Coupled-Cluster Singles and Doubles (LCNot-UCCSD) ansatz within the SQD workflow, trading higher circuit depth for reduced classical preprocessing. A comparison between these ansätze is provided, clarifying their respective strengths, limitations, and suitability for near-term quantum hardware. We further explore potential energy landscapes through 1D scans for H2 and HeH+ using both STO-3G and 6-31G basis sets, and for LiH and BeH2 in STO-3G. Extending beyond this, we demonstrate the experimental construction of a full 2D potential energy surface for the water molecule on quantum hardware, mapped over a 32 × 32 grid in bond length and bond angle. To move beyond small benchmark systems, we combine SQD(LUCJ) with Density Matrix Embedding Theory (DMET) to compute active-space energies for a set of ligand-like molecules, as well as the pharmacologically relevant amantadine system. Across all studies, the majority of quantum-computed energies agree with reference FCI results, as well as with DMET-CASCI energies for embedded systems, to within chemical accuracy for the chosen basis sets. These results demonstrate the reliability of sample-based diagonalization approaches and underscore the potential of hybrid embedding strategies for extending quantum simulations to increasingly complex molecular systems, while also highlighting their practicality on current IQM quantum hardware.
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⋅109 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× increase in system size and up to 210× 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.