Ippei Obayashi, “Volume-Optimal Cycle: Tightest Representative Cycle of a Generator in Persistent Homology”, 2018, 2(4), pp.508–534. [D72]
Ippei Obayashi, Yasuaki Hiraoka, Masao Kimura, "Persistence diagrams with linear machine learning models", J Appl. and Comput. Topology,(2018). [D72]
M. Kimura, I. Obayashi, Y. Takeichi, R. Murao, Y. Hiraoka,"Non-empirical identification of trigger sites in heterogeneous processes using persistent homology", Scientific Reports, volume 8, Article number: 3553 (2018). [D72]
T. Yamashita, “Toward rational antibody design: recent advancements in molecular dynamics simulations”, International Immunology, 30(2018)pp.133-140 [D75]
Keisuke Saito*, Takumi Suzuki, and Hiroshi Ishikita, “Absorption-energy calculations of chlorophyll a and b with an explicit solvent model”, J. Photochem. Photobiol. A, Chem. 358(2018) pp.422-431. [D75]
Edgar Avalos, Takashi Teramoto, Hideaki Komiyama, Hiroshi Yabu and Yasumasa Nishiura, ”Transformation of block copolymer nanoparticles from ellipsoids with striped lamellae into onion-like spheres and dynamical control via coupled CahnHilliard equations”, ACS Omega 2018 3 (1), 1304-1314. [D72]
K. Z. Takahashi, R. Nishimura, K. Yasuoka and Y. Masubuchi, “Molecular Dynamics Simulations for Resolving Scaling Laws of Polyethylene Melts”, Polymers, 9(1), 24 (2017). [D71]
P. K. Bhattacharjee, D. A. Nguyen, Y. Masubuchi, and T. Sridhar, “Extensional Step Strain Rate Experiments on an Entangled Polymer Solution”, Macromolecules, 2017, 50 (1), pp 386–395. [D71]
H.J.Zhang, S.Sellaiyan, T.Kakizaki, A.Uedono, Y.Taniguchi, K.Hayashi, Effect of Free-Volume Holes on Dynamic Mechanical Properties of Epoxy Resins for Carbon-Fiber-Reinforced Polymers, Macromolecules, 50, 3933-3942, 2017. [D71]
”Local atomic structure near an Nb atom in aged βTi alloys”, Tokujiro Yamamoto, Kouichi Hayashic, Naohisa Happo, Shinya Hosokawa, Hiroo Tajiri, Acta Materialia, 131, 534-542 (2017).[D72]
”Persistent homology analysis of craze formation”, Takashi Ichinomiya, Ippei Obayashi, and Yasuaki Hiraoka, Physical Review E 95, 012504 (2017).[D72]
Nada, H., Kudo, M., Takahashi, J., Yamamoto, T., Hara, H. and Shizawa, K., Development of Simulation Technology for Production of Porous Polymeric Membranes, Key Engineering Materials, Vol.725, pp.261-266, 2017. [D74]
T. Yamashita and Y. Takamatsu, “An Ensemble Docking Calculation of Lysozyme and HyHEL-10: Insight into the Binding Mechanism” AIP Conf. Proc. 1906, (2017) 030022. [D75]
Hiroshi C. Watanabe, Yuki Yamashita, and Hiroshi Ishikita*, “Molecular dynamics simulations do not provide functionally relevant values of redox potential in MtrF”, Proc. Natl. Acad. Sci. U. S. A. 114 (2017) E10029–E10030. [D75]
Shinnosuke Kishi, Keisuke Saito, Yuki Kato, and Hiroshi Ishikita*, “Redox potentials of ubiquinone, menaquinone, phylloquinone, and plastoquinone in aqueous solution”, Photosynth. Res. 134 (2017) 193-200. [D75]
Hiroshi C. Watanabe*, Maximilian Kubillus, Tomáš Kubař, Robert Stach, Boris Mizaikoff, and Hiroshi Ishikita, “Cation solvation with quantum chemical effects modeled by size-consistent multi-partitioning quantum mechanics/molecular mechanics method”, Phys. Chem. Chem. Phys 19. (2017) 17985-17997. [D75]
Takuya Ikeda, Keisuke Saito, Ryo Hasegawa, and Hiroshi Ishikita*,“The existence of an isolated hydronium ion in the interior of proteins”, Angew. Chem. Int. Ed. Engl. 56 (2017) 9151-9154. [D75]
Naoki Sakashita, Hiroshi C. Watanabe, Takuya Ikeda, Keisuke Saito, and Hiroshi Ishikita*, “Origins of water molecules in the photosystem II crystal structure”, Biochemistry 56 (2017) 3049-3057. [D75]
・Keisuke Kawashima and Hiroshi Ishikita*,“Structural factors that alter the redox potential of quinones in cyanobacterial and plant photosystem I”, Biochemistry 56 (2017) 3019-3028. [D75]
Ryo Hasegawa, Keisuke Saito, Tomohiro Takaoka, and Hiroshi Ishikita*, “pKa of ubiquinone, menaquinone, phylloquinone, plastoquinone, and rhodoquinone in aqueous solution”, Photosynth. Res. 133 (2017) 297-304. [D75]
Hiroshi C. Watanabe, Yuki Yamashita, and Hiroshi Ishikita*, “Electron transfer pathways in a multi-heme cytochrome MtrF”, Proc. Natl. Acad. Sci. U. S. A. 114 (2017) 2916-2921. [D75]
Naoki Sakashita, Hiroshi C. Watanabe, Takuya Ikeda, and Hiroshi Ishikita*, “Structurally conserved channels in cyanobacterial and plant photosystem II”, Photosynth. Res. 133 (2017) 75-85. [D75]
Kento Motoyama, Hideaki Unno, Ai Hattori, Tomohiro Takaoka, Hiroshi Ishikita, Hiroshi Kawaide, Tohru Yoshimura, and Hisashi Hemmi*, “A single amino acid mutation converts (R)-5-diphosphomevalonate decarboxylase into a kinase”, J. Biol. Chem. 292 (2017) 2457-2469. [D75]
Y. Masubuchi and H. Watanabe, “Stress-Optical Relationship in Bead-Spring Simulations for Entangled Polymers under Start-up Shear Flows”, Nihon Reoroji Gakkaishi (J. Soc. Rheol. Jpn.), 44(1), 65-68 (2016). [D71]
Y. Masubuchi, “Molecular Modeling for Polymer Rheology”, Reference Module in Materials Science and Materials Engineering 2016. [D71]
Y. Masubuchi and Y. Amamoto, “Orientational Cross-Correlation in Entangled Binary Blends in Primitive Chain Network Simulations”, Macromolecules,2016, 49 (23), pp 9258–9265, [D71]
Y. Masubuchi, M. Langeloth, M. C. Böhm, T. Inoue, and F. Müller-Plathe, “A Multichain Slip-Spring Dissipative Particle Dynamics Simulation Method for Entangled Polymer Solutions”, Macromolecules, 2016, 49 (23), pp 9186–9191. [D71]
Y. Masubuchi and Y. Amamoto,“Effect of osmotic force on orientational cross-correlation in primitive chain network simulation”, Nihon Reoroji Gakkaishi (J Soc Rheol Jpn), 44(4), 219-222 (2016).[D71]
Y. Masubuchi,“PASTA and NAPLES: Rheology Simulator”, Computer Simulation of Polymeric Materials: Applications of the OCTA System, Ed. by Japan Association for Chemical Innovation, Springer, pp101-127 (2016). [D71]
”Frustrated phases under three-dimensional confinement simulated by a set of coupled Cahn–Hilliard equations”, Edgar Avalos, Takeshi Higuchi, Takashi Teramoto, Hiroshi Yabu and Yasumasa Nishiura, Soft Matter, 12, 5905-5914 (2016).[D72]
”Hierarchical structures of amorphous solids characterized by persistent homology”, Yasuaki Hiraoka, Takenobu Nakamura, Akihiko Hirata, Emerson G. Escolar, Kaname Matsue, and Yasumasa Nishiura, Proceedings of the National Academy of Sciences of the United States of America, 113(26), 7035-40 (2016) [D72]
”X-ray Fluorescence Holography for a Ti–Nb Binary Alloy Consisting of the Martensite, Austenite and Omega Phase”, Tokujiro Yamamoto, Kouichi Hayashi, Naohisa Happo, and Shinya Hosokawa, Z. Phys. Chem. 230(4), 509–517 (2016). [D72]
Tsuge, Y. and Aoyagi, Y., Molecular Dynamics Simulation on Microscopic Plastic Deformation Behavior of Crystalline Phase of Polypropylene, Proceedings of International Conference on Asia-Pacific Conference on Fracture and Strength 2016 (APCFS2016), pp. 465-466, 2016. [D74]
T. Yamashita “On the Accurate Molecular Dynamics Analysis of Biological Molecules” AIP Conf. Proc. 1790 (2016) pp. 020026. [D75]
T. Sakano, Md. Iqbal Mahmood, T. Yamashita, and H. Fujitani, Molecular dynamics analysis to evaluate docking pose prediction, Biophys. Physicobiol. 13 (2016), pp. 181–194. [D75]
T. Yamashita. Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories. Biomedical Sciences. 2 (2016) pp. 34-47. [D75]
Keisuke Saito*, Naoki Sakashita, and Hiroshi Ishikita, “Energetics of the proton transfer pathway for tyrosine D in photosystem II”, Aust. J. Chem. 69 (2016) 991-998. [D75]
Tomohiro Takaoka, Naoki Sakashita, Keisuke Saito, and Hiroshi Ishikita*, “pKa of a proton conducting water chain in photosystem II”, J. Phys. Chem. Lett. 7 (2016) 1925-1932. [D75]
Y. Masubuchi, “Effects of degree of freedom below entanglement segment on relaxation of polymer configuration under fast shear in multi-chain slip-spring simulations”, J. Chem. Phys., 143, [224905-1] – [224905-6] (2015). [D71]
”Persistent homology and many-body atomic structure for medium-range order in the glass”, Takenobu Nakamura, Yasuaki Hiraoka, Akihiko Hirata,Emerson G. Escolar and Yasumasa Nishiura, Nanotechnology, 26, 304001 (2015). [D72]
”Visualization of topological landscape in shear-flow dynamics of amorphous solids”, Takeshi Fujita, Koji Ohara, Keiji Miura, Akihiko Hirata, Motoko Kotani, Yasumasa Nishiura and Mingwei Chen, EPL, 110, 38002 (2015).[D72]
T. Yamashita, Improvement in Empirical Potential Functions for Increasing the Utility of Molecular Dynamics Simulations, JPS Conf. Proc., 5 (2015), pp. 010003. [D75]
Keisuke Saito, A. William Rutherford, and Hiroshi Ishikita*, “Energetics of proton release on the first oxidation step in the water oxidizing enzyme”, Nat. Commun. 6:8488 (2015). [D75]
Keisuke Saito and Hiroshi Ishikita*, “Influence of the Ca2+ ion on the Mn4Ca conformation and the H-bond network arrangement in Photosystem II”, Biochim. Biophys. Acta 1837 (Bioenergetics) (2014) 159-166. [D75]
Hiroshi Ishikita* and Keisuke Saito, “Proton transfer reactions and hydrogen-bond networks in protein environments”, J. R. Soc. Interface 11 (2014) 20130518. [D75]