J. Jung, C. Kobayashi, Y. Sugita., "Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation"J. Chem. Phys., 148, 164109 (2018)
C. Kobayashi*, J. Jung*, Y. Matsunaga, T. Mori, T. Ando, K. Tamura, M. Kamiya, Y. Sugita. "GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms", J. Comput. Chem. (2017) 38, 2193-2206 (*equally contributed)
O. Miyashita, C. Kobayashi, T. Mori, Y. Sugita, F. Tama "Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations", J. Comput. Chem. (2017) 38, 1447-1461
J. Jung, A. Naruse, C. Kobayashi, Y. Sugita, "Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations", J. Chem. Theory Comput. (2016) 12, 4947-4958
Y. Matsunaga, Y. Komuro, C. Kobayashi, J. Jung, T. Mori, Y. Sugita, "Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein", J. Phys. Chem. Lett. (2016) 7, 1446-1451
J. Jung, C. Kobayashi, T. Imamura, Y. Sugita, "Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations.", Comput. Phys. Comm. (2016) 200, 57-65.
C. Kobayashi, Y. Matsunaga, R. Koike, M. Ota, and Y. Sugita , "Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins", J. Phys. Chem. B, (2015) 119 (46), 14584-14593.
J. Jung, T. Mori, C. Kobayashi, Y. Matsunaga, T. Yoda, M. Feig, and Y. Sugita, "GENESIS: a hybrid‐parallel and multi‐scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations", WIREs Comput. Mol. Sci. (2015) 5, 310-323.
Y. Komuro, S. Re, C. Kobayashi, E. Muneyuki, and Y. Sugita , " CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca2+-ATPase.", J. Chem. Theory Comput.,(2014) 10, 4133-4142.
C. Kobayashi, and S. Saito , " Reaction between conformational heterogeneity and reaction cycle of Ras: Molecular simulation of Ras.", Biophys. J., (2010) 99, 3726-3734.
J. N. Onuchic, C. Kobayashi, and K. K. Baldridge, "Quantum Tunneling in Biological Reactions: the Interplay between Theory and Experiments", J. Braz. Chem. Soc., (2008), 19, 206-210.
C Kobayashi, and S. Takada, " Protein grabs a ligand by extending anchor residues: Molecular simulation for Ca2+ binding to calmodulin loop.", Biophys. J., (2006) 90, 3043-3051.
J. N. Onuchic, C. Kobayashi, O. Miyashita, P. Jennings and K. K. Baldridge, " Exploring bimolecular machines: energy landscape control of biological reactions", Phil. Trans. R. Soc. B.,(2006), 361, 1439 - 1443.
C. Kobayashi, K. Baldridge, and J. N. Onuchic, "Multiple versus single pathways in electron transfer in proteins: Influence of protein dynamics and hydrogen bonds", J. Chem. Phys.,(2003), 119, 3550-3558.
I. Ohmine, M. Matsumoto, S. Saito, A. Baba, Y. Yonekura, S. Ogasawara, H. Inagaki and C. Kobayashi, "Landscape of Water Dynamics and Chemical Reactions",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).
C. Kobayashi,S. Saito, and I. Ohmine, "Mechanism of fast proton transfer in ice: Potential energy surface and reaction coordinate analyses", J. Chem. Phys.,(2000), 113, 9090-9100.
M. Matsumoto, S. Saito, C. Kobayashi. and I. Ohmine, "Liquid Water Dynamics; Hydrogen Bond Rearrangement, Phase Space Dynamics and Proton Transfer" in "The Physics of Complex Liquids", edited by F. Yonezawa, K. Tuji, M. Doi and T. Fujiwara, World Scientific, Singapore,(1998), pp 324-338.
C. Kobayashi, K. Iwahashi, S. Saito and I. Ohmine, "Dynamics of Proton Attachment to Water Cluster; Proton Transfer, Evaporation and Relaxation", J. Chem. Phys.,(1996), 105, 6358-6366.
