Workshop2011 –


  • Symposium (The 60th Annual Meeting of the Biophysical Society of Japan)
    September 29 (13:50~16:20)

    High-performance computational biophysics with supercomputer

    Yasuhiro Matsunaga (Saitama University), Ai Shinobu (RIKEN)

    Computational approaches are becoming increasingly important in biophysics, not only for simulations but also for the detailed interpretation of various measurement data. In particular, with the recent launch of modern supercomputers such as Fugaku, enormous computational resources have become available, and new computational methods and applications that were not computationally feasible in the past are becoming possible. In this symposium, we invite researchers who conduct cutting-edge high-performance computations. We discuss current computational research using supercomputers as well as future directions of computational biophysics.

  • Workshop (The 22th Annual Meeting of the Protein Science Society of Japan)
    June 9 (8:45~11:15)

    Molecular simulations in the era of AlphaFold

    Song-ho Chong (RIKEN), Hiraku Oshima (RIKEN)

    Machine learning approaches such as AlphaFold are imparting significant impacts on various scientific fields. Molecular simulations are no exception. In this workshop, we will argue “what is and will be true progress that cannot be achieved without machine learning approaches” and “how AlphaFold will impact the future of molecular simulations.


  • Symposium
    November 18 – 19

    “Symposium on Computer Simulations and Cryo-ET/EM of Complex Biomolecular Systems”

    Chen Song (Peking University), Shoji Takada (Kyoto University), Yuji Sugita (RIKEN)
  • Workshop
    January 6 – 7

    “The 1st Fugaku Bio-supercomputing Workshop on Cellular-scale Molecular Dynamics Simulations”

    Yuji Sugita (RIKEN), Shoji Takada (Kyoto University)


  • Workshop
    November 20 – 22

    “Workshop on molecular dynamics based binding free energy calculations, post-processing of trajectories and force field development”

    Yuji Sugita (RIKEN), Joanna Trylska (University of Warsaw)


  • Workshop
    November 21

    “Workshop on Molecular Simulations of Biophysics and Biochemistry”

    Yuji Sugita (RIKEN), Yuko Okamoto(Nagoya Univ.)

    Official Site

    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.

  • Workshop
    October 31 – November 1

    “Workshop on Modeling Biomolecular Systems in Cellular Environment”

    Yuji Sugita (RIKEN), Shoji Takada (Kyoto Univ.), Koichi Takahashi (RIKEN), Michael Feig (Michigan State Univ.)

    Official Site

    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.

  • Symposium (The 51st Annual Meeting of the Biophysical Society of Japan)
    October 29 (16:15-18:45)

    “Structure, dynamics, and function of nucleosomes and chromatin in nuclear crowded environment”

    Yuji Sugita (RIKEN), Koichi Takahashi (RIKEN)

    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.


  • Symposium (The 50th Annual Meeting of the Biophysical Society of Japan)
    September 23 (9:00-11:30)

    “Supercomputing in Molecular Network to Cellular Dynamics”

    Akinori Kidera (Yokohama City Univ.), Yuji Sugita (RIKEN)

    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.


  • Workshop
    November 7 (13:00-18:00)


    Koichi Takahashi (RIKEN, Keio Univ.), Masahiro Ueda (RIKEN, Osaka Univ.) Yuji Sugita (RIKEN)

    JSBi Applied System Biology Workshop

    細胞は、1ピコリットル程度の極微小の空間に、その一つ一つが複雑な複合デ バイスであるタンパク質分子や核酸などの巨大分子を数万種類詰め込んだ、人類 が知る最も複雑なシステムです。これまでは、細胞内の分子の働きは試験管中の ような均一な希薄溶液や真空中などの理想的な環境を念頭にモデル化され、理解 される事が多く行われて来ました。しかし、現実の細胞内空間は1ミリリットル あたり数百ミリグラム以上に逹するいわゆる分子混雑の状況にあるだけでなく、 細胞膜や細胞骨格、細胞内小器官、ゲノムなどにより高度に構造化されている事 が知られています。近年、1分子レベルの観察技術が急速に発展し、このような 特異な「細胞環境」の中で、細胞内分子が動的に時空間パターンを変化させなが ら、いかに高次の細胞機能を実現しているか、その様を直接観測する事が可能に なってきました。多方、「京」をはじめとする高性能計算機の実用化や新たな 計算手法の開発で、細胞環境を露わに考慮した細胞内分子ダイナミクスのシミュ レーションに道筋が付きつつあります。
    本ワークショップでは、細胞レベルおよび分子レベルでのモデリングに取り組む 研究者と1分子計測の一線で活躍される実験科学者を講師にお招きし、今後大き く発展するであろう細胞環境の研究にどのように取り組んでゆくべきか、参加者 の皆様と実験、理論、計算の多方面から幅広く議論したいと思います。