Rchr
J-GLOBAL ID：201801007668388348   Update date: Feb. 05, 2025

Sugita Yuji

スギタ ユウジ | Sugita Yuji
Affiliation and department：
RIKEN

About RIKEN


Other affiliations (2)：
  • 理化学研究所計算科学研究センター  チームリーダー
  • 理化学研究所生命機能科学研究センター  チームリーダー
Homepage URL  (2)： https://tms.riken.jp/ ,  https://tms.riken.jp/en/
Research field  (3)： Basic physical chemistry ,  Computational science ,  Biophysics
Research keywords  (4)： Ion Pump ,  Biomolecular Dynamics in Cellular Environments ,  Enhanced Conformational Sampling Method ,  Molecular Dynamics Simulation
Research theme for competitive and other funds  (24)：
  • 2021 - 2026 Cross-scale data-driven modeling of biomolecular dynamics in the cells
  • 2021 - 2026 Cross-scale biology
  • 2019 - 2024 Multi-scale molecular dynamics simulation on biomolecular dynamics in crowded cellular environments
  • 2019 - 2020 「動的構造生命科学を拓く新発想測定技術」の成果取りまとめを目指した組織活動
  • 2016 - 2019 Development and application of a conformational search model to predict three-dimensional structural ensembles of glycans
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Papers (291)：
  • Masahiro Motohashi, Mao Oide, Chigusa Kobayashi, Jaewoon Jung, Eiro Muneyuki, Yuji Sugita. The distortion-push mechanism for the γ-subunit rotation in F1-ATPase. 2025
  • Mirco Dindo, Jakob Metson, Weitong Ren, Michalis Chatzittofi, Kiyoshi Yagi, Yuji Sugita, Ramin Golestanian, Paola Laurino. Enzymes can activate and mobilize the cytoplasmic environment across scales. 2025
  • Debora Monego, Matthias Brosz, Johanna Buck, Vsevolod Viliuga, Jaewoon Jung, Torsten Stuehn, Matthias Schmies, Yuji Sugita, Frauke Gräter. ColBuilder: Flexible structure generation of crosslinked collagen fibrils. 2024
  • Soundhararajan Gopi, Giovanni B Brandani, Cheng Tan, Jaewoon Jung, Chenyang Gu, Azuki Mizutani, Hiroshi Ochiai, Yuji Sugita, Shoji Takada. In siliconanoscope to study the interplay of genome organization and transcription regulation. 2024
  • Yao-Kun Lei, Kiyoshi Yagi, Yuji Sugita. Efficient Training of Neural Network Potentials for Chemical and Enzymatic Reactions by Continual Learning. 2024
ｍore...
MISC (95)：
  • Chigusa KOBAYASHI, Yasuhiro MATSUNAGA, Jaewoon JUNG, Yuji SUGITA. Analyses of Structure Changes and Free Energy of Sarco/Endoplasmic Reticulum Ca<sup>2+</sup>-ATPase. Seibutsu Butsuri. 2022. 62. 5. 298-300
  • Hisham M. Dokainish, Suyong Re, Takaharu Mori, Chigusa Kobayashi, Jaewoon Jung, Yuji Sugita. Unraveling SARS-CoV-2 spike protein activation pathway reveals unprecedented cryptic pockets. BIOPHYSICAL JOURNAL. 2022. 121. 3. 457A-457A
  • Free-energy Calculation of Protein-Ligand Binding Using Molecular Dynamics Simulation Software "GENESIS". 2021. 40. 1. 22-28
  • ANDO Toshio, ITO Yutaka, SUGITA Yuji, NANGO Eriko, YASUNAGA Takuo, OKADA Yasushi, KANDA Genki N. New Technologies that Propel Biophysics. Seibutsu Butsuri. 2021. 61. 2. 111-118
  • 森貴治, 的場一晃, 野田展生, 杉田有治, 杉田有治, 杉田有治. オートファゴソーム形成に関与する膜タンパク質Atg9の膜中配向予測. 分子シミュレーション討論会講演要旨集. 2020. 34th (CD-ROM)
ｍore...
Books (1)：
  • 計算科学のためのHPC技術
    大阪大学出版会 2017 ISBN:9784872595864
Education (2)：
  • 1993 - 1998 Kyoto University Graduate School of Science Department of Chemistry
  • 1989 - 1993 Kyoto University Faculty of Science
Professional career (1)：
  • 博士(理学) (京都大学)
Work history (5)：
  • 2012/04 - 現在 RIKEN Theoretical Molecular Science Laboratory Chief Scientist
  • 2007/04 - 2012/03 RIKEN Theoretical Biochemistry Laboratory Associate Chief Scientist
  • 2002/04 - 2007/03 The University of Tokyo Institute of Molecular and Cellular Biosciences Lecturer
  • 1998/09 - 2002/03 Institute for Molecular Science Research Associate
  • 1998/04 - 1998/08 RIKEN Postdoctoral Fellow
Association Membership(s) (6)：
Biophysical Society ,  American Chemical Society ,  PROTEIN SCIENCE SOCIETY OF JAPAN ,  THE PHYSICAL SOCIETY OF JAPAN ,  THE MOLECULAR SIMULATION SOCIETY OF JAPAN ,  THE BIOPHYSICAL SOCIETY OF JAPAN
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