- 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).