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) DOI: 10.1002/jcc.24874
M. Kamiya and S. Hayashi, "Photoactivation Intermediates of a G-Protein Coupled Receptor Rhodopsin Investigated by a Hybrid Molecular Simulation", J. Phys. Chem. B 121, 3842-3852 (2017).
C. Cheng, M. Kamiya, Y. Uchida, and S. Hayashi, "Molecular Mechanism of Wide Photoabsorption Spectral Shifts of Color Variants of Human Cellular Retinol Binding Protein II", J. Am. Chem. Soc. 137, 13362-13370 (2015).
H. E. Kato, M. Kamiya, S. Sugo, J. Ito, R. Taniguchi, A. Orito, K. Hirata, A. Inutsuka, A. Yamanaka, A. D. Maturana, R. Ishitani, Y. Sudo, S. Hayashi, and O. Nureki, "Atomistic design of microbial opsin-based blue-shifted optogenetics tools", Nature Comm. 6, 7177 (2015).
M. Kamiya, H. E. Kato, R. Ishitani, O. Nureki, and S. Hayashi, “Structural and spectral characterizations of C1C2 channelrhodopsin and its mutants by molecular simulations”,
Chem. Phys. Lett. , 556, 266-271 (2013).
N. Kishi, M. Akita, M. Kamiya, S. Hayashi, H.-F. Hsu, and M. Yoshizawa, “Facile Catch and Release of Fullerenes Using a Photoresponsive Molecular Tube”, J. Am. Chem. Soc., 135, 12976-12979 (2013).
Y. Sudo, A. Okazaki, H. Ono, J. Yagasaki, S. Sugo, M. Kamiya, L. Reissig, K. Inoue, K. Ihara, H. Kandori, S. Takagi, and S. Hayashi, “A Blue-shifted Light-driven Proton Pump for Neural Silencing”, J. Biol. Chem., 288, 20624-20632 (2013).
S. Hayashi, H. Ueno, A. R. Shaikh, M. Umemura, M. Kamiya, Y. Ito, M. Ikeguchi, Y. Komoriya, R. Iino, H. Noji, “Molecular Mechanism of ATP Hydrolysis in F1-ATPase Revealed by Molecular Simulations and Single-Molecule Observations”,J. Am. Chem. Soc., 134, 8447-8454 (2012).
M. Kamiya, S. Saito, and I. Ohmine, “A Molecular Dynamics Study for the Structure Determination of the Signaling State in the Photocycle of Photoactive Yellow Protein”, J. Phys. Chem. B, 114, 6594-6600 (2010).
M. Kamiya, S. Saito, and I. Ohmine, “Proton Transfer and Associated Molecular Rearrangements in the Photocycle of Photoactive Yellow Protein: Role of Water Molecular Migration on the Proton Transfer Reaction”, J. Phys. Chem. B, 111, 2948-2956 (2007).
