In this laboratory, we study various chemical and biological systems to investigate their dynamic processes using theoretical/computational chemistry. Multi-scale simulation methods, which include hybrid quantum mechanics/molecular mechanics (QM/MM), all-atom molecular dynamics (AAMD), and coarse-grained MD (CGMD) methods, are required for this purpose. We have developed GENESIS (GENeralized-Ensemble SImulation System) for molecular dynamics and introduced new computational methods into GENESIS, in collaboration with Computational Biophysics Research Team, RIKEN R-CCS, and Laboratory for Biomolecular Function Simulation, RIKEN BDR. This laboratory, Theoretical Molecular Science Laboratory, RIKEN CPR focuses on the development of hybrid QM/MM methods and data-driven simulation methods.
In addition to the developments, we have actively collaborated with experimental biologists and chemists for understanding the relationship between structure, dynamics, and function in various molecular systems. Among many applications, biomolecular dynamics and functions in crowded cellular environments is one of the most important, but difficult research targets. We are now working this subject with many domestic and international collaborators.
(Theoretical Molecular Science Laboratory)