Publications
- Severine Queyroy, Haruki Nakamura, Ikuo Fukuda, "Numerical Examination of the Extended Phase-Space Volume-Preserving Integrator by the Nosé-Hoover Molecular Dynamics Equations", Journal of Computational Chemistry, in press.
- Takashi Imai, Andriy Kovalenko, Fumio Hirata, Akinori Kidera, "Molecular Thermodynamics of Trifluoroethanol-Induced Helix Formation: Analysis of the Solvation Structure and Free Energy by the 3D-RISM Theory", Interdisciplinary Sciences: Computational Life Sciences, in press.
- Yong Zhang, Hiroshi Fujisaki, John E. Straub, "Mode-specific vibrational energy relaxation of amide I' and amide II' modes in N-methylacetamide/water clusters: Intra- and intermolecular energy transfer mechanisms", Journal of Physical Chemistry A, in press.
- Toshiya Takami, Hiroshi Fujisaki, "Resonant Analytic Fields Applied to Generic Multi-state Systems", Journal of Modern Optics, in press.
- Kei Moritsugu, Jeremy C. Smith, "REACH: A Program for Coarse-Grained Biomolecular Simulation", Computer Physics Communications, in press.
- Tadaomi Furuta, Kentaro Shimizu, Tohru Terada, "Accurate prediction of native tertiary structure of protein using molecular dynamics simulation with the aid of the knowledge of secondary structures", Chemical Physics Letters, 472, 134-139 (2009).
- Yong Zhang, Hiroshi Fujisaki, John E. Straub, "Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. I. Five-coordinated ferrous iron porphyrin model", Journal of Chemical Physics, 130, 25102 (2009).
- Yasuhiro Matsunaga, Sotaro Fuchigami, Akinori Kidera, "Multivariate Frequency Domain Analysis of Protein Dynamics", Journal of Chemical Physics, 130, 124104 (2009).
- Takashi Imai, "Roles of Water in Protein Structure and Function Studied by Molecular Liquid Theory", Frontiers in Bioscience, 14, 1387-1402 (2009).
- Norio Yoshida, Takashi Imai, Saree Phongphanphanee, Andriy Kovalenko, Fumio Hirata, "Molecular Recognition in Biomolecules Studied by Statistical-Mechanical Integral-Equation Theory of Liquids", The Journal of Physical Chemistry B, 113, 873-886 (2009).
- Daisuke Yokogawa, Hirofumi Sato, Takashi Imai, Shigeyoshi Sakaki, "A Highly Parallelizable Integral Equation Theory for Three Dimensional Solvent Distribution Function: Application to Biomolecules", The Journal of Chemical Physics, 130, 64111 (2009).
- Yasuomi Kiyota, Ryusuke Hiraoka, Norio Yoshida, Yutaka Maruyama, Takashi Imai, Fumio Hirata, "Theoretical Study of CO Escaping Pathway in Myoglobin with the 3D-RISM Theory", Journal of the American Chemical Society, 131, 3852-3853 (2009).
- Kei Moritsugu, Jeremy C. Smith, "REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Structural Classes", Biophysical Journal, 95, 1639-1648 (2008).
- Tadaomi Furuta, Yoshimi Fujitsuka, George Chikenji, Shoji Takada, "In silico chaperonin-like cycle helps folding of proteins for structure prediction", Biophysical Journal, 94, 2558-2565 (2008).
- Hiroshi Fujisaki, Gerhard Stock, "Dynamic treatment of vibrational energy relaxation in a heterogeneous and fluctuating environment", Journal of Chemical Physics, 129, 134110 (2008).
- Ikuo Fukuda, Yasushige Yonezawa, Haruki Nakamura, "Consistent Molecular Dynamics Scheme Applying the Wolf Summation for Calculating Electrostatic Interaction of Particles", Journal of Physical Society of Japan, 77, 114301 (2008).