Hybrid Quantum-Supercomputer System Completes First Biomolecular Simulation Workflow

A full scientific workflow has been executed for the first time across Fugaku, one of the world's most powerful supercomputers, and Reimei, a trapped-ion quantum computer, marking a transition from infrastructure development to practical deployment. The system explored chemical reactions that occur inside biomolecules such as proteins, reactions found throughout biology from enzyme functions to drug interactions.

Quantinuum installed its Reimei quantum computer at a facility in Japan operated by RIKEN, the country's largest comprehensive research institution. The system was integrated with the supercomputer Fugaku as part of a national project commissioned by the New Energy and Industrial Technology Development Organization (NEDO), the national research and development entity under the Ministry of Economy, Trade and Industry.

The team extended computational chemistry's layered approaches into the hybrid computing era by combining classical supercomputing with quantum computing. The supercomputer Fugaku handled geometry optimization and baseline electronic structure calculations. The quantum computer Reimei was used to enhance the treatment of the most difficult electronic interactions in the active site, those that are known to challenge conventional approximate methods. The entire process was coordinated through Quantinuum's workflow system Tierkreis, which allows jobs to move efficiently between machines.

Simulating biomolecular reactions accurately is extremely challenging. The region where the chemical reaction occurs—the "active site"—requires very high precision, because subtle electronic effects determine the outcome. At the same time, this active site is embedded within a much larger molecular environment that must also be represented, though typically at a lower level of detail.

The researchers designed the algorithm to specifically exploit the strengths of both the quantum and the classical hardware. First, the classical computer constructs an approximate description of the molecular system. Then, the quantum computer is used to model the detailed quantum mechanics that the classical computer can't handle. Together, this improves accuracy, extending the utility of the classical system.

Although the present study uses simplified systems to focus on methodology, it lays the groundwork for future applications in drug design, enzyme engineering, and photoactive biological systems. Accurate simulation of biomolecular reactions remains one of the major challenges in biochemistry.

In the near term, the most plausible gains from quantum technology in biomedicine stem from hybrid quantum-classical computational chemistry for drug discovery, specifically de novo design and lead optimization that can be rigorously benchmarked against classical baselines. Quantum chemistry allows researchers to explore molecular reaction pathways and binding behaviors that are classically intractable, including hypotheses concerning neurodegenerative diseases and the blood-brain barrier.

While fully fault-tolerant, large-scale quantum computers are still under development, hybrid approaches allow today's quantum hardware to augment powerful classical systems to explore meaningful applications. As quantum technology matures, the same workflows can scale accordingly.

High-performance computing centers worldwide are actively exploring how quantum devices might integrate into their ecosystems. By demonstrating coordinated job scheduling, direct hardware access, and workflow orchestration across heterogeneous architectures, this work offers a concrete example of how such integration can be achieved. For Japan's research ecosystem, this first application milestone signals that hybrid quantum–supercomputing is moving from ambition to implementation.