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Technical Scientist Chigusa Kobayashi-Iwahashi

EDUCATION

RESEARCH AND TEACHING EXPERIENCES

PROFESSIONAL AFFILIATIONS

RESEARCH PROJECTS

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

PUBLICATIONS

1. Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations. Cheng Tan, Jaewoon Jung, Chigusa Kobayashi,  Diego Ugarte La Torre, Shoji Takada and Yuji Sugita
   PLOS Comput. Biol. 18, e1009578 (2022).
2. The inhderent flexibility of receptor binding domains in SARS-CoV-2 spike protein. Hisham M Dokainish, Suyong Re, Takaharu Mori, Chigusa Kobayashi, Jaewoon Jung and Yuji Sugita
   eLife 11, e75720 (2022).
3. Structural and energetic analysis of metastable intermediate states in the E1P-E2P transition of Ca2+-ATPase. Chigusa Kobayashi, Yasuhiro Matsunaga, Jaewoon Jung and Yuji Sugita
   Proc. Natl. Acad. Sci. USA 118, e2105507118 (2021).
4. Optimized hydrogen mass repartitioning scheme combined with accurate temperature/pressure evaluations for thermodynamic and kinetic properties of biological systems. Jaewoon Jung, Kento Kasahara, Chigusa Kobayashi, Hiraku Oshima, Takaharu Mori and Yuji Sugita
   J. Chem. Theory Comput. 17, 5312-5321 (2021).
5. 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
   Biophysical J., 120, 1060-1071 (2021)
6. 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
   J. Comput. Chem., 42, 231-241 (2021)
7. A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations. Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, and Yuji Sugita
   J. Chem. Phys., 153, 044110 (2020).
8. Building a macro-mixing dual-basin Gō model using the Multistate Bennett Acceptance Ratio. Ai Shinobu, Chigusa Kobayashi, Yasuhiro Matsunaga, and Yuji Sugita
   Biophys. and Physicobiol., 16, 310-321 (2019).
9. 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
   J. Comput. Chem., 40, 1919-1930 (2019).
10. Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations. Kioshi Yagi, Kenta Yamada, Chigusa Kobayashi, and Yuji Sugita
    J. Chem. Theory Comput., 15, 1924-1938 (2019).
11. Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step. Jaewoon Jung, Chigusa Kobayashi, and Yuji Sugita
    J. Chem. Theory Comput., 15, 84-94 (2019).
12. Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation. Jaewoon Jung, Chigusa Kobayashi, and Yuji Sugita
    J. Chem. Phys., 148, 164109 (2018).
13. 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)
    J. Comput. Chem., 38, 2193-2206 (2017).
14. Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations. Osamu Miyashita, Chigusa Kobayashi, Takaharu Mori, Yuji Sugita, and Florence Tama
    J. Comput. Chem., 38, 1447-1461 (2017).
15. Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations. Jaewoon Jung, Akira Naurse, Chigusa Kobayashi, and Yuji Sugita
    J. Chem. Theory Comput., 12, 4947-4958 (2016).
16. 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
    J. Phys. Chem. Lett., 7, 1446-1451 (2016).
17. Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations. Jaewoon Jung, Chigusa Kobayashi, Toshiyuki Imamura, and Yuji Sugita
    Comp. Phys. Comm., 200, 57-65 (2016).
18. Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins. Chigusa Kobayashi, Yasuhiro Matsunaga, Ryotaro Koike, Motonori Ota, and Yuji Sugita
    J. Phys. Chem. B, 119, 14584-14593 (2016).
19. 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
    WIREs Comput. Mol. Sci., 5, 310-323 (2015).
20. Hierarchical domain-motion analysis of conformational changes in sarcoplasmic reticulum Ca²⁺-ATPase. Chigusa Kobayashi, Ryotaro Koike, Motonori Ota, and Yuji Sugita
    Proteins: Struct. Funct. Bioinf., 83, 746-756 (2015).
21. 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
    J. Chem. Theory Comput., 10, 4133-4142 (2014).
22. Relation between conformational heterogeneity and reaction cycle of Ras: Molecular simulation of Ras. Chigusa Kobayashi and Shinji Saito
    Biophys. J., 99, 3726-3734 (2010).
23. Quantum Tunneling in Biological Reactions: the Interplay between Theory and Experiments. José N. Onuchic, Chigusa Kobayashi, and Kim K. Baldridge
    J. Braz. Chem. Soc., 19, 206-210 (2008).
24. Protein grabs a ligand by extending anchor residues: Molecular simulation for Ca²⁺ binding to calmodulin loop. Chigusa Kobayashi and Shoji Takada
    Biophys. J., 90, 3043-3051 (2006).
25. Exploring bimolecular machines: energy landscape control of biological reactions. José N. Onuchic, Chigusa Kobayashi, Osamu Miyashita, Patricia Jennings, and Kim K. Baldridge
    Phil. Trans. R. Soc. B., 361, 1439-1443 (2006).
26. Multiple versus single pathways in electron transfer in proteins: Influence of protein dynamics and hydrogen bonds. Chigusa Kobayashi, Kim. Baldridge, and José N. Onuchic
    J. Chem. Phys., 119, 3550-3558 (2003).
27. Landscape of Water Dynamics and Chemical Reactions. I. Ohmine, M. Matsumoto, S. Saito, A. Baba, Y. Yonekura, S. Ogasawara, H. Inagaki and C. Kobayashi
    In New Kind of Phase Transitions: Transformation in Disordered Substances, edited by V. V. Brazhkin, S.V. Buldyrev, V. N. Ryzov, H. G. Stanley, NATO ASI Series, Kluwer Academic Publisher, London, , 613-622 (2002).
28. Mechanism of proton transfer in ice. II.: Hydration, modes, and transport. Chigusa Kobayashi, Shinji Saito, and Iwao Ohmine
    J. Chem. Phys., 115, 4742-4749 (2001).
29. Mechanism of fast proton transfer in ice: Potential energy surface and reaction coordinate analyses. Chigusa Kobayashi, Shinji Saito, and Iwao Ohmine
    J. Chem. Phys., 113, 9090-9100 (2000).
30. Liquid Water Dynamics; Hydrogen Bond Rearrangement, Phase Space Dynamics and Proton Transfer. Masakazu Matsumoto, Shinji Saito, Chigusa Kobayashi. and Iwao Ohmine
    In The Physics of Complex Liquids, edited by F. Yonezawa, K. Tuji, M. Doi and T. Fujiwara, World Scientific, Singapore, , 324-338 (1998).
31. Dynamics of Proton Attachment to Water Cluster; Proton Transfer, Evaporation and Relaxation. C. Kobayashi, Kensuke Iwahashi, Shinji Saito and Iwao Ohmine
    J. Chem. Phys., 105, 6358-6366 (1996).