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Research

Research

We develop new theoretical/computational methods for bio-molecular systems by integrating theoretical chemistry and biophysics. Using these methods, we analyze structural dynamics of bio-molecules, which are not accessible from the conventional simulation methods. We aim to understand bio-molecular functions as well as predict/design new functions. To achieve this goal, we actively collaborate with experimental groups inside and outside of RIKEN.

Research Projects

  • Membrane proteins play important roles in transporting ions and molecules across the biological membranes. We use molecular dynamics (MD) simulations and the hybrid quantum mechanics / molecular mechanics (QM/MM) calculations to investigate the transport mechanisms with emphasis on their coupling to ATP hydrolysis as well as proton motive forces.

  • We develop and use enhanced conformational sampling methods, like replica-exchange molecular dynamics (REMD) or other generalized-ensemble simulations, for biological processes that are hardly accessible from experimental studies. Our current topics involve protein folding, association of membrane proteins, protein-ligand recognition, and structural dynamics of oligosaccharides in solution.

  • Biological phenomena consist of a hierarchy of processes spanning a wide range of space and time scales. Therefore, multi-scale/multi-resolution simulations including electronic structure analysis, atomistic simulations, and coarse-grained simulations are required for proper modeling. We develop novel simulation methods and analysis tools for establishing the next-generation theoretical molecular simulations.

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