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.
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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Research facilities in our laboratory
