PeopleMembers

Technical Scientist Chigusa Kobayashi-Iwahashi

EDUCATION

1996 B.S. Nagoya University, Japan
1998 M.S. Nagoya University, Japan
2000 D.S. Nagoya University, Japan

RESEARCH AND TEACHING EXPERIENCES

2001 JSPS postdoctoral fellowship, Nagoya University, Japan
2001 JSPS postdoctral fellowship for reseach abroad, Univesity of California, San Diego, USA
2003 JSPS postdoctoral fellowship, Kobe University, Japan
2006 Postdoctral fellow, Institute for Molecular Science, Japan
2011 Contract Reseacher, RIKEN Advanced Science Institute, Japan
2013-2018 Reseach Scientist, RIKEN Advanced Institute for Computer Science, Japan
2018-2020 Reseach Scientist, RIKEN Center for Computational Science, Japan
2020-present Technical Scientist (Concurrently), RIKEN Center for Computational Science, Japan

PROFESSIONAL AFFILIATIONS

The chemical society of Japan, The biophysical society of Japan, Japan Society for Molecular Science, BioSuperComputing Research Community, Protein Science Society of Japan

RESEARCH PROJECTS

  1. MD simulations of calcium ion pump
  2. Development of coarse grain models
  3. Development of molecular dymamics program

PUBLICATIONS

  1. Elucidation of interactions regulating conformational stability and dynamics of SARS-Cov-2 S-protein. Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, and Yuji Sugita
  2. New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems. Jaewoon Jung, Chigusa Kobayashi, Kento Kasahara, Cheng Tan, Akiyoshi Kuroda, Kazuo Minami, Shigeru Ishiduki, Tatsuo Nishiki, Hikaru Inoue, Yutaka Ishikawa, Michael Feig, and Yuji Sugita
  3. A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations. Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, and Yuji Sugita
  4. Building a macro-mixing dual-basin Gō model using the Multistate Bennett Acceptance Ratio. Ai Shinobu, Chigusa Kobayashi, Yasuhiro Matsunaga, and Yuji Sugita
  5. Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations. Jaewoon Jung, Wataru Nishima, Marcus Daniels, Gavin Bascom, Chigusa Kobayashi, Adetokunbo Adedoyin, Michael Wall, Anna Lappala, Dominic Phillips, William Fischer, Chang-Shung Tung, Tamar Schlick, Yuji Sugita, and Karissa Y. Sanbonmatsu
  6. Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations. Kioshi Yagi, Kenta Yamada, Chigusa Kobayashi, and Yuji Sugita
  7. Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step. Jaewoon Jung, Chigusa Kobayashi, and Yuji Sugita
  8. Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation. Jaewoon Jung, Chigusa Kobayashi, and Yuji Sugita
  9. GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms. Chigusa Kobayashi*, Jaewoon Jung*, Yasuhiro Matsunaga, Takaharu Mori, Tadashi Ando, Koichi Tamura, Motoshi Kamiya, and Yuji Sugita (*equally contributed)
  10. Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations. Osamu Miyashita, Chigusa Kobayashi, Takaharu Mori, Yuji Sugita, and Florence Tama
  11. Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations. Jaewoon Jung, Akira Naurse, Chigusa Kobayashi, and Yuji Sugita
  12. Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein. Yasuhiro Matsunaga, Yasuaki Komuro, Chigusa Kobayashi, Jaewoon Jung, Takaharu Mori, and Yuji Sugita
  13. Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations. Jaewoon Jung, Chigusa Kobayashi, Toshiyuki Imamura, and Yuji Sugita
  14. Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins. Chigusa Kobayashi, Yasuhiro Matsunaga, Ryotaro Koike, Motonori Ota, and Yuji Sugita
  15. GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations. Jaewoon Jung, Takaharu Mori, Chigusa Kobayashi, Yasuhiro Matsunaga, Takao Yoda, Michael Feig, and Yuji Sugita
  16. Hierarchical domain-motion analysis of conformational changes in sarcoplasmic reticulum Ca2+-ATPase. Chigusa Kobayashi, Ryotaro Koike, Motonori Ota, and Yuji Sugita
  17. CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca2+-ATPase. Yasuaki Komuro, Suyong Re, Chigusa Kobayashi, Eiro Muneyuki, and Yuji Sugita
  18. Relation between conformational heterogeneity and reaction cycle of Ras: Molecular simulation of Ras. Chigusa Kobayashi and Shinji Saito
  19. Quantum Tunneling in Biological Reactions: the Interplay between Theory and Experiments. José N. Onuchic, Chigusa Kobayashi, and Kim K. Baldridge
  20. Protein grabs a ligand by extending anchor residues: Molecular simulation for Ca2+ binding to calmodulin loop. Chigusa Kobayashi and Shoji Takada
  21. Exploring bimolecular machines: energy landscape control of biological reactions. José N. Onuchic, Chigusa Kobayashi, Osamu Miyashita, Patricia Jennings, and Kim K. Baldridge
  22. Multiple versus single pathways in electron transfer in proteins: Influence of protein dynamics and hydrogen bonds. Chigusa Kobayashi, Kim. Baldridge, and José N. Onuchic
  23. Landscape of Water Dynamics and Chemical Reactions. I. Ohmine, M. Matsumoto, S. Saito, A. Baba, Y. Yonekura, S. Ogasawara, H. Inagaki and C. Kobayashi
  24. Mechanism of proton transfer in ice. II.: Hydration, modes, and transport. Chigusa Kobayashi, Shinji Saito, and Iwao Ohmine
  25. Mechanism of fast proton transfer in ice: Potential energy surface and reaction coordinate analyses. Chigusa Kobayashi, Shinji Saito, and Iwao Ohmine
  26. Liquid Water Dynamics; Hydrogen Bond Rearrangement, Phase Space Dynamics and Proton Transfer. Masakazu Matsumoto, Shinji Saito, Chigusa Kobayashi. and Iwao Ohmine
  27. Dynamics of Proton Attachment to Water Cluster; Proton Transfer, Evaporation and Relaxation. C. Kobayashi, Kensuke Iwahashi, Shinji Saito and Iwao Ohmine