2024
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International Workshop
June 30–July 2, 2024IUPAB2024 Hands-on Training Program CHARMM-GUI/GENESIS MD Tutorial
Yuji Sugita (RIKEN), Wonpil Im (Lehigh University), Florence Tama (Nagoya University), Yasuhiro Matsunaga (Saitama University), Kei Moritsugu (Osaka Metropolitan University)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.
2023
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International Workshop
August 9–10, 2023Multi-scale Molecular Dynamics Simulation and Machine Learning of Biomolecular Systems
Yuji Sugita (RIKEN), Kiyoshi Yagi (RIKEN), Yasuhiro Matsunaga (Saitama University), Yuko Okamoto (Nagoya University)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.
2022
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Symposium (The 60th Annual Meeting of the Biophysical Society of Japan)
September 28, 2022, 13:50–16:20Structure and function of “meso-entangled bodies” in the cell
Yuji Sugita (RIKEN), Hayashi Yamamoto (U. Tokyo)Proteins often assemble to form “mesoscopic” complexes – some ordered and some disordered – to exert their functions in the cell. Therefore, elucidating their architectures and physical properties is necessary to understand the molecular mechanisms underlying life phenomena and diseases. In this research area “Cross-Scale Biology”, we particularly focus on mesoscopic structures in the range of 20–500 nm (including LLPS condensates), which we define as “meso-entangled bodies (MEBs)”, because MEBs are thought to be key factors that determine the fate of organisms through the transition from disordered to ordered states at the mesoscale. In this symposium, researchers working on the MEBs will gather to discuss the latest technologies and findings, including In-cell AFM, cryo-EM, chemical biology and LLPS.