Research Projects
Project 1: Development of GENESIS for high performance MD
We have developed GENESIS with an efficient parallelization scheme on K and various computational platforms. We further develop GENESIS with better performance for next-generation supercomputers and new hardware architectures.
Project 2: Cellular-scale simulations using multi-resolution methods
Inside the cell, macromolecules such as proteins, nucleic acids, and lipids interact with each other. In order to understand intercellular biological function, we develop multi resolution methods which integrate molecular models with different resolutions, with the aim to perform a cellular-scale simulation using supercomputers.
Project 3: Elucidating dynamic processes related to biological function in proteins
We study processes accompanying biologically relevant large-scale structure changes in proteins. Developing extended-ensemble methods and machine learning methods, we analyze dynamics which reproduces experimental data.
Gallery
Movies and figures in our research activity
Facilities
Research facilities in our laboratory
Software
Project 1: Development of GENESIS for high performance MD
Collaborators
Yoshitsugu Shiro (University of Hyogo)
Project 2：Data-driven simulations to understand protein dynamics
Collaborators
Osamu Miyashita (RIKEN R-CCS)、Florence Tama (RIKEN R-CCS)
Project 3：Molecular crowding in the cell
Collaborators
Michael Feig (Michigan State University)