Multi-scale Molecular Dynamics Simulation and Machine Learning of Biomolecular Systems

Aug.9 (Wed)-10(Thu), 2023, RIKEN


Understanding the relationship between function and structure of biomolecules such as proteins and nucleic acids requires not only simulations by molecular dynamics, but also a deep understanding of various physical chemical theories such as solution theory and molecular vibrational theory, as well as information science such as machine learning and Bayesian statistics. In this workshop, experts in these fields are invited to give lectures to discuss state-of-the-art techniques/results and to understand their interrelationships. In addition, experts are invited from one of the Programs for Promoting Research on the Supercomputer “Fugaku” to discuss the cutting-edge computational science research.


RIKEN Wako Campus Suzuki Umetaro Hall Please refer to the access map for more information on the location. Suzuki Umetaro Hall is numbered as “S01” in the campus map.


The registration is closed.

Invited Speakers

  • Giovanni Brandani (Kyoto University, Japan)
  • Bernard Brooks (NIH, USA)
  • Fumio Hirata (IMS, Japan)
  • Jaewoon Jung (RIKEN R-CCS, Japan)
  • Akio Kitao (Tokyo Institute of Technology, Japan)
  • Juyong Lee (Seoul National University, Korea)
  • Mai Suan Li (Polish Academy of Science, Poland)
  • Yasuhiro Matsunaga (Saitama University, Japan)
  • Osamu Miyashita (RIKEN R-CCS, Japan)
  • Toshifumi Mori (Kyushu University, Japan)
  • Ai Niitsu (RIKEN CPR, Japan)
  • John Straub (Boston University, USA)
  • Cheng Tan (RIKEN R-CCS, Japan)
  • Kiyoshi Yagi (RIKEN CPR, Japan)


Aug. 9th

Opening Remarks

12:55 – 13:00

Yuji Sugita (RIKEN CPR)

Session 1: Molecular Dynamics Simulations of Biomolecules (Chair: Yuji Sugita)

13:00 – 13:40

Scalable Electrostatics via Spherical Grids and Treecode Summation, and other Recent Computational Methods for Biophysics
Bernard Brooks (NIH)

13:40 – 14:20

The Role of Structural Heterogeneity in the Homodimerization of Transmembrane Proteins
John Straub (Boston University)

Coffee Break and Group Photo

14:50 – 15:30

Protein Folding and Dimerization on Ribosomes
Mai Suan Li (Polish Academy of Science)

Session 2: Chemical Theory of Complex Systems (Chair: Yuko Okamoto)

15:30 – 16:00

Regulation of Biomolecular Condensation Studied with Large-Scale Coarse-Grained Molecular Dynamics Using GENESIS
Cheng Tan (RIKEN R-CCS)

Coffee Break

16:30 – 17:00

Bridging the Gap between Static and Dynamic Mechanisms in Enzyme Catalysis
Toshifumi Mori (Kyushu University)

17:00 – 17:30

Mechanisms of Bacterial Flagellar Rotation and Roles of Water as Lubricant
Akio Kitao (Tokyo Institute of Technology)

17:30 – 18:00

On Linearity of the Structural Fluctuation of Protein in Water
Fumio Hirata (IMS)


18:30 – 20:00

Aug. 10th

10:00 – 10:30

Acceleration of QM/MM-MD and Free-Energy Calculations of Enzymatic Reactions
Kiyoshi Yagi (RIKEN CPR)

Session 3: Machine Learning and Molecular Design (Chair: Yasuhiro Matsunaga)

10:30 – 11:10

Accurate Protein-Ligand Interaction Prediction using Graph Neural Network and Physics-based Scoring Functions
Juyong Lee (Seoul National University)

11:10 – 11:40

Transmembrane Peptide Design towards Functional and Dynamic Channels
Ai Niitsu (RIKEN CPR)


Session 4: Simulations on Fugaku (Chair: Kiyoshi Yagi)

13:00 – 13:30

Integrative Modeling of Biomolecular Dynamics from Molecular Dynamics Simulations and Single-Molecule Experiments
Yasuhiro Matsunaga (Saitama University)

13:30 – 14:00

Development of GENESIS on Fugaku for Large-Scale MD Simulations
Jaewoon Jung (RIKEN R-CCS)

Coffee Break

14:30 – 15:00

Integrating Hi-C Data into Polymer Simulations to Study the Principles of Enhancer-Promoter Communication
Giovanni Brandani (Kyoto University)

15:00 – 15:30

Integrative/Hybrid Modeling Approaches for Dynamic Structural Biology
Osamu Miyashita (RIKEN R-CCS)

Closing Remarks

Yuko Okamoto (Nagoya University)


Yuji Sugita (RIKEN Cluster for Pioneering Research)
Kiyoshi Yagi (RIKEN Cluster for Pioneering Research)
Yasuhiro Matsunaga (Saitama University)
Yuko Okamoto (Nagoya University)