技師 小林(岩橋) 千草
学歴
1996年 |
名古屋大学 理学部 卒業 |
1998年 |
名古屋大学 理学研究科 博士課程前期課程 修了 |
2000年 |
名古屋大学 理学研究科 博士課程後期課程 修了(博士(理学)) |
研究・教育歴
2001年 |
日本学術振興会特別研究員(名古屋大学) |
2001年 |
日本学術振興会海外特別研究員(カルフォルニア大学サンディエゴ校) |
2003年 |
日本学術振興会特別研究員(神戸大学) |
2006年 |
分子科学研究所 専門研究職員 |
2011年 |
理化学研究所 基幹研究所 協力研究員 |
2013年 |
理化学研究所 計算科学研究機構 研究員 |
2018年 |
理化学研究所 計算科学研究センター 研究員 |
2020年 |
理化学研究所 計算科学研究センター 技師 (兼務)(現在に至る) |
所属学会
日本化学会、日本生物物理学会、分子科学会、バイオスーパーコンピューティング研究会、日本蛋白質科学会
研究テーマ
- 膜輸送タンパク質における反応機構解析
- 粗視化モデルの開発
- 分子動力学法プログラムの開発
出版物
- Building a macro-mixing dual-basin Gō model using the Multistate Bennett Acceptance Ratio.
Ai Shinobu, Chigusa Kobayashi, Yasuhiro Matsunaga, and Yuji Sugita
- 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
- Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations.
Kioshi Yagi, Kenta Yamada, Chigusa Kobayashi, and Yuji Sugita
- Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step.
Jaewoon Jung, Chigusa Kobayashi, and Yuji Sugita
- Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation.
Jaewoon Jung, Chigusa Kobayashi, and Yuji Sugita
- 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)
- Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations.
Osamu Miyashita, Chigusa Kobayashi, Takaharu Mori, Yuji Sugita, and Florence Tama
- Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations.
Jaewoon Jung, Akira Naurse, Chigusa Kobayashi, and Yuji Sugita
- 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
- Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations.
Jaewoon Jung, Chigusa Kobayashi, Toshiyuki Imamura, and Yuji Sugita
- Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins.
Chigusa Kobayashi, Yasuhiro Matsunaga, Ryotaro Koike, Motonori Ota, and Yuji Sugita
- 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
- Hierarchical domain-motion analysis of conformational changes in sarcoplasmic reticulum Ca2+-ATPase.
Chigusa Kobayashi, Ryotaro Koike, Motonori Ota, and Yuji Sugita
- 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
- Relation between conformational heterogeneity and reaction cycle of Ras: Molecular simulation of Ras.
Chigusa Kobayashi and Shinji Saito
- Quantum Tunneling in Biological Reactions: the Interplay between Theory and Experiments.
José N. Onuchic, Chigusa Kobayashi, and Kim K. Baldridge
- Protein grabs a ligand by extending anchor residues: Molecular simulation for Ca2+ binding to calmodulin loop.
Chigusa Kobayashi and Shoji Takada
- Exploring bimolecular machines: energy landscape control of biological reactions.
José N. Onuchic, Chigusa Kobayashi, Osamu Miyashita, Patricia Jennings, and Kim K. Baldridge
- Multiple versus single pathways in electron transfer in proteins: Influence of protein dynamics and hydrogen bonds.
Chigusa Kobayashi, Kim. Baldridge, and José N. Onuchic
- Landscape of Water Dynamics and Chemical Reactions.
I. Ohmine, M. Matsumoto, S. Saito, A. Baba, Y. Yonekura, S. Ogasawara, H. Inagaki and C. Kobayashi
- Mechanism of proton transfer in ice. II.: Hydration, modes, and transport.
Chigusa Kobayashi, Shinji Saito, and Iwao Ohmine
- Mechanism of fast proton transfer in ice: Potential energy surface and reaction coordinate analyses.
Chigusa Kobayashi, Shinji Saito, and Iwao Ohmine
- Liquid Water Dynamics; Hydrogen Bond Rearrangement, Phase Space Dynamics and Proton Transfer.
Masakazu Matsumoto, Shinji Saito, Chigusa Kobayashi. and Iwao Ohmine
- Dynamics of Proton Attachment to Water Cluster; Proton Transfer, Evaporation and Relaxation.
C. Kobayashi, Kensuke Iwahashi, Shinji Saito and Iwao Ohmine