Yasuoka Laboratory


Publications

  • 2012年 (19 papers)

    • Suh, D. and Yasuoka, K., "Nanoparticle Growth Analysis by Molecular Dynamics: Cubic Seed", J. Phys. Chem. B, 116, 14637-14649(2012). (13 pages.) DOI: 10.1021/jp3044658

    • Hiratsuka, M., Ohmura, R., Sum, A. K., and Yasuoka, K., "Vibrational Modes of Methane in the Structure H Clathrate Hydrate from Ab initio Molecular Dynamics Simulation", J. Chem. Phys., 137, 144306(2012). (6 pages.) DOI: 10.1063/1.4757914

    • Shibuya, T., Yasuoka, K., Mirbt, S. and Sanyal, B., "A systematic study of polarons due to oxygen vacancy formation at the rutile TiO2 (110) surface by GGA+U and HSE06 methods", J. Phys.: Condens. Matter, 24, 435504(2012). (8 pages.) DOI: 10.1088/0953-8984/24/43/435504

    • Takahashi, K. Z., Narumi, T., Suh, D. and Yasuoka, K., "An improved isotropic periodic sum method that uses linear combinations of basis potentials", J. Chem. Theory Comput., 8, 4503-4516(2012). (14 pages.) DOI: 10.1021/ct3003805

    • Feldman, T., Ostrovsky, M., Kholmurodov, K. and Yasuoka, K., "Model of Abnormal Chromophore-Protein Interaction for E181K Rhodopsin Mutation: Computer Molecular Dynamics Study", The Open Biochemistry Journal, 6, 94-102(2012). (9 pages.) DOI: 10.2174/1874091X01206010094

    • Höfinger, S., Acocella, A., Pop, S. C., Narumi, T., Yasuoka, K., Beu, T. and Zerbetto, F., "GPU-Accelerated Computation of Electron Transfer", J. Comput. Chem., 33, 2351-2365(2012). (15 pages.) DOI: 10.1002/jcc.23082

    • Murakami, D. and Yasuoka, K., "Molecular dynamics simulation of quasi-two-dimensional water cluster on ice nucleation protein", J. Chem. Phys., 137, 054303(2012). (5 pages.) DOI: 10.1063/1.4739299

    • Yamamoto, E., Akimoto, T., Shimizu, H., Hirano, Y., Yasui, M. and Yasuoka, K., "Diffusive Nature of Xenon Anesthetic Changes Properties of a Lipid Bilayer: Molecular Dynamics Simulations", J. Phys. Chem. B, 116, 8989-8995(2012). (7 pages.) DOI: 10.1021/jp303330c

    • Kholmurodov, K., Dushanov, E., Yasuoka, K., Khalil, H., Galal, A., Ahmed, S., Sweilam, N., and Moharram, H., "Molecular dynamics study of ethanol solvated by water on the Pt (1 1 1) surface", Chemical Physics, 402, 41-47(2012). (7 pages.) DOI: 10.1016/j.chemphys.2012.04.002

    • Höfinger, S., Yamamoto, E., Hirano, Y., Zerbettoa, F., Narumi, T., Yasuoka, K., and Yasuii, M., "Structural features of aquaporin 4 supporting the formation of arrays and junctions in biomembranes", Biochimica et Biophysica Acta, 1818, 2234-2243(2012). (10 pages.) DOI: 10.1016/j.bbamem.2012.04.009

    • Kholmurodov, K., Dushanov, E., and Yasuoka, K., "Molecular Dynamics Simulations of a DNA Photolyase Protein : High-Mobility and Conformational Changes of the FAD Molecule at Low Temperatures", Advances in Bioscience and Biotechnology, 3, 169-180(2012). (12 pages.) DOI: 10.4236/abb.2012.33025

    • Eremin, R., Kholmurodov, K., Avdeev, M., Petrenko, V. and Yasuoka, K., "Molecular Dynamics Simulations on trans- and cis-Decalins:The Effect of Partial Atomic Charges and Adjustment of "Real Densities"", Int. J. Chem., 4, 14-22(2012). (9 pages.) DOI: 10.5539/ijc.v4n1p14

    • Kaneko, T., Mitsutake, A., and Yasuoka, K., "Multibaric-Multithermal Ensemble Study of Liquid-Solid Phase Transition in Lennard-Jones Particles", J. Phys. Soc. Jpn., 81, SA014(2012). (8 pages.) DOI: 10.1143/JPSJS.81SA.SA014

    • Dushanov, E., Kholmurodov, Kh., and Yasuoka, K., "The diffusion and concentration effects of formamide on a TiO2 surface in the presence of a water solvent", Natural Science, 4, 313-323(2012). (11 pages.) DOI: 10.4236/ns.2012.45044

    • Seki, H., Shibuya, Y., Kobayashi, D., Nohira, H., Yasuoka, K., and Hirose, K., "Estimation of breakdown electric-field strength while reflecting local structures of SiO2 using first-principles molecular orbital calculation technique", Jpn. J. Appl. Phys., 51, 04DA07(2012). (4 pages.) DOI: 10.1143/JJAP.51.04DA07

    • Takahashi, K., Narumi, T., and Yasuoka, K., "Cutoff radius effect of the isotropic periodic sum method for polar molecules in a bulk water system", Molec. Simul., 38, 397-403(2012). (7 pages.) DOI: 10.1080/08927022.2010.547857

    • Kaneko, T., Yasuoka, K., and Zeng, X. C., "Liquid-solid phase transitions of Lennard-Jones particles confined to slit pores: Towards the construction of temperature-pressure-slit width phase diagram", Molec. Simul., 38, 373-377(2012). (5 pages.) DOI: 10.1080/08927022.2010.539216

    • Arai, N., Yasuoka, K., and Zeng, X. C., "Nanochannel with Uniform and Janus Surfaces: Shear Thinning and Thickening in Surfactant Solution", Langmuir, 28, 2866-2872(2012). (7 pages.) DOI: 10.1021/la2034643

    • Hiratsuka, M., Ohmura, R., Sum, A. K., and Yasuoka, K., "Molecular Vibrations of Methane Molecules in the Structure I Clathrate Hydrate from Ab Initio Molecular Dynamics Simulation", J. Chem. Phys., 136, 044508(2012). (6 pages.) DOI: 10.1063/1.3677231


Yasuoka Laboratory