The 1st Fugaku Bio-supercomputing Workshop on Cellular-scale Molecular Dynamics Simulations
January 6 (Wed.) – 7 (Thr.), 2021
Online using Zoom

General Information

Molecular dynamics (MD) simulation is widely used for understanding structure-dynamics-function relationships of various biomolecules. Recent developments of conformational sampling algorithms, force-fields, and multi-scale molecular models have allowed us to study essential biological processes in the cell. In this workshop, we discuss these methodological advances in bio-supercomputing as well as the latest application studies on protein-DNA dynamics in cell nuclear systems, membrane dynamics and membrane protein systems, and disorder, disease, and drug discovery.

Scientific Program

January 6 (Wednesday)

9:30 – 9:35 Opening Remarks by Yuji Sugita (RIKEN)
Session 1 Methods and algorithms in Bio-supercomputing (Chair: Akio Kitao (Tokyo Institute of Technology))
9:35 – 10:05 Xuhui Huang (Hong Kong University of Science and Technology)
Memory Kernels of Protein Dynamics
10:05 – 10:35 Juyong Lee (Kangwon National University)
Finding multiple transition pathways with QM potentials using the least action principle and the Gaussian process
10:35 – 11:05 Yuji Sugita (RIKEN)
Multi-scale MD simulations using GENESIS on Fugaku
<< Break >>
Session 2 Protein-DNA dynamics in cell nuclear systems (Chair: Hidetoshi Kono (National Institute of Quantum and Radiological Science and Technology))
11:20 – 11:50 Yi Qin Gao (Peking University)
Coding of the high order 3D chromatin structure in 1D sequence
11:50 – 12:20 Jejoong Yoo (Sungkyunkwan University)
Friction-controlled diffusion of DNA-binding proteins along DNA
12:20 – 12:50 Shoji Takada (Kyoto University)
Nucleosome and transcription factor dynamics

January 7 (Thursday)

Session 3 Membrane dynamics and membrane protein systems (Chair: Keiko Shinoda (University of Tokyo))
9:30 – 10:00 Peter Bond (A*STAR)
Understanding how viral envelopes “sense” their surroundings
10:00 – 10:30 Yi Wang (Chinese University of Hong Kong)
Membrane permeability of beyond-rule-of-five drugs and 3D cell spreading in host-guest decorated hydrogels
10:30 – 11:00 Wataru Shinoda (Nagoya University)
Computer simulations of biomacromolecular self-assembly using the SPICA coarse-grained model
<< Break >>
Session 4 Disorder, disease, and drug (Chair: Yasuhiro Matsunaga (Saitama University))
11:15 – 11:45 Wenning Wang (Fudan University)
Interactions Between Intrinsically Disordered Proteins: Structures and Dynamics
11:45 – 12:15 Shigeyuki Matsumoto (RIKEN)
Challenges in Large-scale MD-based Docking Study Targeting SARS-CoV-2 Proteins on Fugaku
12:15 – 12:45 Wei Han (Peking University Shenzhen Graduate School)
Understanding Peptide Self-Assembly with Multiscale Molecular Simulations for Design of Nanomaterials
12:45 – 12:50 Closing Remarks by Shoji Takada (Kyoto University)


The workshop is open to anyone registered at and is free of charge. If you can’t access the web site, please send e-mail indicating your name, affiliation, and e-mail address to (biocompws[at] Please replace “[at]” as “@”.
Once registered, you will receive the link to the Zoom meeting a few days before the workshop. Please do not distribute the Zoom link you receive, instead every attendee must register at this page to get the link. Recoding the workshop talks are prohibited. By registering at this page, you are supposed to agree with the above statements.

Organizing Committee

Yuji Sugita RIKEN CPR, BDR, and R-CCS
Shoji Takada Department of Biophysics, Kyoto University

For any questions regarding the workshop, please send an email to Dr. Yuji Sugita (sugita[at] or Prof. Shoji Takada (takada[at]