Workshop2012 – 2021

Molecular dynamics (MD) simulation is an indispensable tool for biological science, which provides molecular-level details of dynamical processes of complex biomolecular systems. This workshop is intended for those interested in running and analyzing the MD simulations of biomolecules. The participants will learn how to model, simulate, and analyze complex biomolecular systems using GENESIS (GENeralized-Ensemble SImulation System), MINT (Motif Identifier for Nucleic acids Trajectory), and RedMDStream.

The computer simulations using supercomputer like K (RIKEN AICS) plays an important role in “life science”. In this workshop, we invite domestic as well as overseas leading researchers in the field computational biophysics and biochemistry and discuss future direction. The major topics are free-energy calculations, folding and aggregations, protein-protein interactions, cellular-scale simulations, and so on. We also organize a tutorial session for young researchers and students to learn molecular dynamics software. In the tutorial, we use our in-house software GENESIS for learning basic/advanced MD, free-energy calculations based on REMD and string method. The workshop/tutorial are mainly supported by discretionary expenses of the President in RIKEN and is also positioned as a preparation for developing future software center.

After ICMS2013, we would like to hold a one-day workshop on molecular simulations on biophysics and biochemistry. Here we invite 7 professors (all of them are the invited speakers of ICMS2013) and 6 young researchers in Japan. At workshop, we hope to have fruitful discussion about both simulation applications and methodological developments in this field.

The overall aim of this workshop is to bring together a mix of computational and experimental researchers to discuss current challenges in developing comprehensive views of cellular environments. More specifically, there are three main themes: 1) What are the biophysical consequences of cellular environments on protein stability and dynamics beyond simple volume exclusion effects? 2) What are the details of the structure and dynamics of genomic DNA and its transcriptional regulation? 3) How can we develop realistic structural and dynamic models of interacting biomolecules at cellular levels? In this workshop, we invite 20 researchers from abroad and from Japan and would like to have fruitful discussion about this new research topics.

Cellular nucleus is also a crowded environment where long DNA chains are packed with high densities. Recently, the highly packed DNA structures with DNA binding proteins have been investigated using X-ray crystallography, cyoelectron microscopy, and small-angle X-ray scattering (SAXS). These updated experimental information encourages multi-scale computational modeling of nucleosomes or chromatin fibers. In the symposium, both experimental and computational scientists show the latest data and discuss about the structures and dynamics of genomic DNA in chromosome or nucleus.

K computer (the ten Peta FLOPS supercomputer installed in Kobe) provides an enormous enhancement of the capability in computational life science. This symposium intends to bring forth the possibility of supercomputing in life science fully utilizing K computer. Particularly, it focuses on the multi-scale descriptions of molecular networks and cellular dynamics by integrating the molecular and the cellular simulation methods.