Yasuoka Laboratory


All Publications

  • 2024年 (2 papers)

        • 232. Ishiai, S., Endo, K., Brumby, P. E., Sum, A. K. and Yasuoka, K., "Novel approach for designing order parameters of clathrate hydrate structures by graph neural network", The Journal of Chemical Physics, 160, 064504(2024). (11 pages) DOI: 10.1063/5.0177815

        231. Ishiai, S., Yasuda, I., Endo, K. and Yasuoka, K., "Graph-Neural-Network-Based Unsupervised Learning of the Temporal Similarity of Structural Features Observed in Molecular Dynamics Simulations", Journal of Chemical Theory and Computation, 20, 819-831(2024). (13 pages) DOI: 10.1021/acs.jctc.3c00995

  • 2023年 (12 papers)

        • 230. Furutani, Y., Hirano, Y., Toguchi, M., Higuchi, S., Qin, X.-Y., Yanaka, K., Sato-Shiozaki, Y., Takahashi, N., Sakai, M., Kongpracha, P., Suzuki, T., Dohmae, N., Kukimoto-Niino, M., Shirouzu, M., Nagamori, S., Suzuki, H., Kobayashi, K., Masaki, T., Koyama, H., Sekiba, K., Otsuka, M., Koike, K., Kohara, M., Kojima, S., Kakeya, H. and Matsuura, T., "A small molecule iCDM-34 identified by in silico screening suppresses HBV DNA through activation of aryl hydrocarbon receptor", Cell Death Discovery, 9, 467(2023). (13 pages) DOI: 10.1038/s41420-023-01755-w

        229. Mustali, J., Yasuda, I., Hirano, Y., Yasuoka, K., Gautieri, A. and Arai, N., "Unsupervised deep learning for molecular dynamics simulations: a novel analysis of protein–ligand interactions in SARS-CoV-2 Mpro", RSC Advances, 13, 34249-34261(2023). (13 pages) DOI: 10.1039/D3RA06375E

        228. 太刀野雄介，土居英男，奥脇弘次，平野秀典，望月祐志, "タンパク質に関するFMO-DPDシミュレーション用パラメータ算定と試行", Journal of Computer Chemistry, Japan, in press.

        227. Miwa, K., Guo, Y., Hata, M., Hirano, Y., Yamamoto, N. and Hoshino, T., "In Silico Identification of Inhibitory Compounds for SARS-CoV-2 Papain-Like Protease", Chemical and Pharmaceutical Bulletin, in press.

        226. Pan, Y., Suzuki, T., Sakai, K., Hirano, Y., Ikeda, H., Hattori, A., Dohmae, N., Nishio, K. and Kakeya, H., "Bisabosqual A: A novel asparagine synthetase inhibitor suppressing the proliferation and migration of human non-small cell lung cancer A549 cells", European Journal of Pharmacology, 960, 176156(2023). (12 pages) DOI: 10.1016/j.ejphar.2023.176156

        225. Sakai, S., Hirano, Y., Kobayashi, Y. and Arai, N., "Effect of temperature on the structure and drug-release behaviour of inclusion complex of β-cyclodextrin with cyclophosphamide: a molecular dynamics study", Soft Matter, 19, 2902-2907(2023). (6 pages) DOI: 10.1039/D2SM01542K

        224. Brumby, P. E., Kowaguchi, A., Nozawa T., Yasuoka, K. and Wensink, H., "Pre-Smectic Ordering and the Unwinding Helix in Monte Carlo Simulations of Cholesteric Liquid-Crystals.", The Journal of Physical Chemistry B, 127, 7103-7206(2023). (11 pages) DOI: 10.1021/acs.jpcb.3c02018

        223. Ishiai, S., Endo, K. and Yasuoka, K., "Graph neural networks classify molecular geometry and design novel order parameters of crystal and liquid", The Journal of Chemical Physics, 159, 064103(2023). (16 pages) DOI: 10.1063/5.0156203

        222. Kubota, T., Suzuki, Y., Kobayashi, S., Tran Q., Yamamoto N. and Nakajima K., "Temporal information processing induced by quantum noise", Physical Review Research, 5, 023057(2023). (15 pages) DOI: 10.1103/PhysRevResearch.5.023057

        221. Okada, K., Endo, K., Yasuoka, K. and Kurabayashi S., "Learned pseudo-random number generator: WGAN-GP for generating statistically robust random numbers", PLOS One, 18, e0287025(2023). (19 pages) DOI: 10.1371/journal.pone.0287025

        220. Arai, N., Yamamoto, E., Koishi, T., Hirano, Y., Yasuoka, K. and Ebisuzaki T., "Wetting hysteresis induces effective uni-directional water transport through a fluctuating nanochannel", Nanoscale Horizons, 8, 652-661(2023). (12 pages) DOI: 10.1039/D2NH00563H

        219. Yasuda, I., Kobayashi, Y., Endo, K., Hayakawa, Y., Fujiwara, K., Yajima, K., Arai N. and Yasuoka, K., "Combining molecular dynamics and machine learning to analyze shear thinning for alkane and globular lubricants in the low shear regime", ACS Applied Materials & Interfaces, 15, 7639-8794(2023). (12 pages) DOI: 10.1021/acsami.2c16366

  • 2022年 (10 papers)

        • 218. Kawada, R., Endo, K., Yasuoka, K., Kojima, H. and Matubayasi, N., "Prediction of Water Diffusion in Wide Varieties of Polymers with All-Atom Molecular Dynamics Simulations and Deep Generative Models", Journal of Chemical Information and Modeling, 63, 76-86(2022). (11 pages) DOI: 10.1021/acs.jcim.2c01316

        217. Kawada, R., Endo, K., Yuhara, D. and Yasuoka, K., "MD-GAN with multi-particle input: the machine learning of long-time molecular behavior from short-time MD data", Soft Matter, 18, 8446-8455(2022). (10 pages) DOI: 10.1039/D2SM00852A

        216. Kobayashi, Y., Arai, N. and Yasuoka, K., "Correlation between ordering and shear thinning in confined OMCTS liquids", The Journal of Chemical Physics, 157, 114506(2022). (10 pages) DOI: 10.1063/5.0099473

        215. Ishiyama, M., Yasuoka K. and Asai M., "Impact of free energy of polymers on polymorphism of polymer-grafted nanoparticles", Soft Matter, 18, 6318-6325(2022). (8 pages) DOI: 10.1039/D2SM00311B

        214. Kowaguchi, A., Endo, K., Brumby, P. E., Nomura, K. and Yasuoka, K., "Optimal Replica-Exchange Molecular Simulations in Combination with Evolution Strategies", Journal of Chemical Information and Modeling, 62, 6544-6552(2022). (9 pages) DOI: 10.1021/acs.jcim.2c00608

        213. Yasuda, I., Endo, K., Yamamoto, E., Hirano, Y., and Yasuoka, K., "Differences in ligand-induced protein dynamics extracted from an unsupervised deep learning approach correlate with protein-ligand binding affinities", Communications Biology, 5, 481(2022). (9 pages) DOI: 10.1038/s42003-022-03416-7

        212. Peng, L., Arai, N., and Yasuoka, K., "A stochastic Hamiltonian formulation applied to dissipative particle dynamics", Applied Mathematics and Computation, 426, 127126(2022). (13 pages) DOI: doi.org/10.1016/j.amc.2022.127126

        211. Endo, K., Yuhara, D., and Yasuoka, K., "Efficient Monte Carlo Sampling for Molecular Systems Using Continuous Normalizing Flow", Journal of Chemical Theory and Computation, 18, 1395-1405(2022). (11 pages) DOI: /10.1021/acs.jctc.1c01047

        210. Suzuki, Y., Gao, Q., Pradel, K. C., Yasuoka, K., and Yamamoto, N., "Natural quantum reservoir computing for temporal information processing", Scientific Reports, 12, 1353(2022). (15 pages) DOI: 10.1038/s41598-022-05061-w

        209. Okada, K., Brumby, P. E. and Yasuoka, K., "An Efficient Random Number Generation Method for Molecular Simulation", Journal of Chemical Information and Modeling, 62, 71-78(2022). (8 pages) DOI: 10.1021/acs.jcim.1c01206

  • 2021年 (4 papers)

        • 208. Okada, K., Brumby, P. E. and Yasuoka, K., "The influence of random number generation in dissipative particle dynamics simulations using a cryptographic hash function", PLoS ONE, 16, e0250593(2021). (8 pages) DOI: 10.1371/journal.pone.0250593

        207. Winarto, Yamamoto, E. and Yasuoka, K., "Water molecules in CNT--Si3N4 membrane: Properties and the separation effect for water--alcohol solution", The Journal of Chemical Physics, 155, 10(2021). (11 pages) DOI: 10.1063/5.0055027

        206. Kowaguchi, A., Brumby, P. E. and Yasuoka, K., "Phase Transitions and Hysteresis for a Simple Model Liquid Crystal by Replica-Exchange Monte Carlo Simulations", Molecules, 26, 1421(2021). (14 pages) DOI: 10.3390/molecules26051421

        205. Muromachi, S., Takeya, S., Yuhara, D. and Yasuoka, K., "On effective radii of dodecahedral cages in semiclathrate hydrates for van der Waals and Platteeuw model", Fluid Phase Equilibria, 527, (2021). (6 pages) DOI: 10.1016/j.fluid.2020.112846

  • 2020年 (5 papers)

        • 205. Hiraide, K., Hirayama, K., Endo, K. and Muramatsu, M., "Application of deep learning to inverse design of phase separation structure in polymer alloy", Computational Material Science, 190, 110278-NULL 9(2020). DOI: 10.1016/j.commatsci.2021.110278

        203. Endo, K., Nakamura, T., Fuji, K., and Yamamoto, N., "Quantum self-learning Monte Carlo and quantum-inspired Fourier transform sampler", Physical Review Research, 2, 043442(2020). (12 pages) DOI: 10.1103/PhysRevResearch.2.043442

        202. Hasegawa, T., Brumby, P. E., Yasuoka, K. and Sum, A. K., "Mechanism for H2 diffusion in sII hydrates by molecular dynamics simulations", The Journal of Chemical Physics, 154, 054706(2020). (10 pages) DOI: 10.1063/5.0017505

        201. Pua, K., Yuhara, D., Ayuba, S. and Yasuoka, K., "Dataflow programming for the analysis of molecular dynamics with AViS, an analysis and visualization software application", PLOS One, 15, e0231714(2020). (13 pages) DOI: 10.1371/journal.pone.0231714

        200. Anggayasti, W.L., Ogino, K., Yamamoto, E., Helmerhorst, E., Yasuoka, K. and Mancera, R.L., "The acidic tail of HMGB1 regulates its secondary structure and conformational flexibility: A circular dichroism and molecular dynamics simulation study", Computational and Structural Biotechnology Journal, 18, 1160-1172(2020). (14 pages) DOI: 10.1016/j.csbj.2020.05.012

  • 2019年 (8 papers)

        • 199. Yuhara, D., Yasuoka, K., Takeya, S. and Muromachi, S., "Anisotropy of dodecahedral water cages for guest gas occupancy in semiclathrate hydrates", Chemical Communications, 55, 10150-10153(2019). (4 pages) DOI: 10.1039/c9cc05009d

        198. Brumby, P. E., Yuhuara, D., Hasegawa, T., Wu, D. T., Sum, A. K. and Yasuoka, K., "Cage occupancies, lattice constants, and guest chemical potentials for structure II hydrogen clathrate hydrate from Gibbs ensemble Monte Carlo simulations", Journal of Chemical Physics, 150, 134503(2019). (15 pages) DOI: 10.1063/1.5084785

        197. Endo, K., Yuhara, D., Tomobe K. and Yasuoka K., "Detection of molecular behavior that characterizes systems using a deep learning approach", Nanoscale, 11, 10064-10071(2019). (8 pages) DOI: 10.1039/C9NR00219G

        196. Koishi, T., Yasuoka, K. and Zeng, X. C., "Method to Implement Interaction Surfaces with Virtual Companion Particles for Molecular Dynamics Simulations", Journal of Chemical and Engineering Data, 64, 3671-4190(2019). (8 pages) DOI: 10.1021/acs.jced.8b01230

        195. Tomobe, K., Yamamoto, E. and Yasuoka, K., "Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs", Methods in Molecular Biology, 1947, 21-30(2019). (10 pages) DOI: 10.1007/978-1-4939-9121-1_2

        194. Nozawa, T., Brumby, P. E., Ayuba, S. and Yasuoka, K., "Ordering in clusters of uniaxial anisotropic particles during homogeneous nucleation and growth", Journal of Chemical Physics, 150, 054903(2019). (13 pages) DOI: 10.1063/1.5064410

        193. Winarto, W., Yamamoto, E. and Yasuoka, K., "Selectivity of Carbon Nanotubes under An Electric Field on Transferring Water - Alcohol Mixtures", Materials Science and Engineering, 494, 012099(2019). (6 pages) DOI: 10.1088/1757-899X/494/1/012099

        192. Winarto, W., Yamamoto, E. and Yasuoka, K., "Separation of water-alcohol mixtures using carbon nanotubes under an electric field", Physical Chemistry Chemical Physics, 21, 15431-15438(2019). (8 pages) DOI: 10.1063/1.5016609

  • 2018年 (11 papers)

        • 191. Hirai, H., Morita, K., Yasuoka, K., Shibuya, T., Tojo, Y., Kamihara, Y., Miura, A., Suzuki, H., Ohno, T., Matsuda, T., Yagi, S., "Oxygen vacancy-originated highly active electrocatalysts for the oxygen evolution reaction", Journal of Material Chemistry A, 6, 15102(2018). (8 pages) DOI: 10.1039/C8TA04697B

        190. Takahashi, K. Z., Nozawa, T., and Yasuoka, K., "A fast and accurate computational method for the linear-combination-based isotropic periodic sum", Scientific Reports, 8, 11880(2018). (10 pages) DOI: 10.1038/s41598-018-30364-2

        189. Nozawa, T., Brumby, P. E., and Yasuoka, K., "Effect of Central Longitudinal Dipole Interaction on Chiral Liquid-Crystal Phases", Int. J. Mol. Sci., 19, 2715(2018). (22 pages) DOI: 10.3390/ijms19092715

        188. Ayuba, S., Nomura, K., Ebisuzuki, T., Yasuoka, K., "Kinetic analysis of homogenrous droplet nucleation using large-scale molecular dynamics simulations", Journal of Chemical Physics, 149, 044504(2018). (9 pages) DOI: 10.1063/1.5037647

        187. Endo, K., Tomobe, K., Yasuoka, K., "Multi-Step Time Series Generator for Molecular Dynamics", Thirty-Seond AAAI Conference on Artificial Intelligence, 32, 2192-2199(2018). (8 pages) DOI: 10.1609/aaai.v32i1.11863

        186. Kaneko, T., Bali J., Akimoto T., Fransisco J. S., Yasuoka K.,and Zeng X. C., "Phase behaviors of deeply supercooled bilayer water unseen in bulk water", Proceedings of the National Academy of Sciences, 19, 4839-4844(2018). (6 pages) DOI: 10.1073/pnas.1802342115

        185. Morita K., and Yasuoka K, "Density functional theory study of atomic and electronic properties of defects in reduced anatase TiO2 nanocrystals", AIP Advances, 8, 035119(2018). (14 pages) DOI: 10.1063/1.5021024

        184. Suh, D., and Yasuoka, K.,, "Heterogeneous cavitation and crystallisation with an impurity by molecular dynamics", Molecular Simulation, 44, 530-533(2018). (4 pages) DOI: 10.1080/08927022.2017.1402308

        183. Acocella, A., Hofinger, S., Haunshmid, E., Pop, C., S., Narumi, T., Yasuoka, K., Yasui, M., Zerbetto, F., "Structural determinants in the bulk heterojunction", Phys. Chem. Chem. Phys., 20, 5708-5720(2018). (13 pages) DOI: 10.1039/C7CP08435H

        182. Tomobe, K., Yasuoka, K., "Detection of Anomalous Dynamics for a Signle Water Molecule", Journal of Chemical Theory and Computation, 14, 3(2018). (9 pages) DOI: 10.1021/acs.jctc.7b01104

        181. Nozawa, T., Yasuoka, K., and Takahashi, K. Z., "Critical test of isotropic periodic sum techniques with group-based cut-off schemes", Scientific Reports, 8, 4185(2018). (9 pages) DOI: 10.1038/s41598-018-22514-3

  • 2017年 (15 papers)

        • 181. Yuhara, D., Brumby, P. E., David, T., W., Sum, A. K., Yasuoka, K., "Analysis of three-phase equilibrium conditions for methane hydrate by isometric-isothermal molecular dynamics simulations", The Journal of Chemical Physics, 148, 184501(2017). (9 pages) DOI: 10.1063/1.5016609

        180. Tomobe, K., Yamamoto, E., Kojic, D., Sato, Y., Yasui, M., and Yasuoka, K., "Origin of the blueshift of water molecules at interfaces of hydrophilic cyclic compounds", Science Advances, 3, e1701400(2017). (7 pages) DOI: 10.1126/sciadv.1701400

        179. Suh, D., and Yasuoka, K., "Heterogeneous cavitation and crystallisation with an impurity by molecular dynamics", Molec. Simul., 44, 530-533(2017). (4 pages) DOI: 10.1080/08927022.2017.1402308

        178. Takahashi, K. Z., Nishimura, R., Yamato, N., Yasuoka, K., and Masubuchi, Y., "Onset of static and dynamic universality among molecular models of polymers", Scientific Reports, 7, 12379(2017). (7 pages) DOI: 10.1038/s41598-017-08501-0

        177. Koishi, T., Yasuoka, K., and Zeng, X. C., "Molecular Dynamics Simulation of Water Nanodroplet Bounce Back from Flat and Nanopillared Surface", Langmuir, 33, 10184-10192(2017). DOI: 10.1021/acs.langmuir.7b02149

        176. Takahashi, K. Z., Yamato, N., Yasuoka, K., and Masubuchi, Y., "Critical test of bead-spring model to resolve the scaling laws of polymer melts: a molecular dynamics study", Molec. Simul., 43, 1196-1201(2017). DOI: 10.1080/08927022.2017.1334883

        175. Doi, H., Okuwaki, K., Mochizuki, Y., Ozawa, T., and Yasuoka, K., "Dissipative particle dynamics (DPD) simulations with fragment molecular orbital (FMO) based effective parameters for 1-Parmitoyl-2-oleoyl phosphatidyl choline (POPC) membrane", Chem. Phys. Lett., 684, 427-432(2017). DOI: 10.1016/j.cplett.2017.07.032

        174. Winarto, Yamamoto, E., and Yasuoka, K., "Water Molecules in a Carbon Nanotube under an Applied Electric Field at Various Temperatures and Pressures", Water, 9, 473(2017). (14 pages) DOI: 10.3390/w9070473

        173. Doi, H., and Yasuoka, K., "Replica exchange molecular simulation of Lennard-Jones particles in a two-dimensional confined system", AIP Advances, 7, 055018(2017). (9 pages) DOI: 10.1063/1.4984815

        172. Tomobe, K., Yamamoto, E., Yasui, M., and Yasuoka, K., "Effects of temperature, concentration, and isomer on the hydration structure in monosaccharide solutions", Phys. Chem. Chem. Phys., 19, 15239-15246(2017). DOI: 10.1039/C7CP02392H

        171. Shibuya, T., Yasuoka, K., Mirbt, S., and Sanyal, B., "Subsurface Polaron Concentration As a Factor in the Chemistry of Reduced TiO2 (110) Surfaces", J. Phys. Chem. C, 121, 11325-11334(2017). DOI: 10.1021/acs.jpcc.7b00935

        170. Tomobe, K., Yamamoto, E., Kholmurodov, K., and Yasuoka, K., "Water permeation through the internal water pathway in activated GPCR rhodopsin", PLOS ONE, 12, e0176876(2017). DOI: 10.1371/journal.pone.0176876

        169. Nomura, K., Kaneko, T., Bai, J., Francisco, J. S., Yasuoka, K., and Zeng, X. C., "Evidence of low-density and high-density liquid phases and isochore end point for water confined to carbon nanotube", PNAS, 114, 4066-4071(2017). DOI: 10.1073/pnas.1701609114

        168. Yamamoto, E., Akimoto, T., Kalli, A. C., Yasuoka, K., and Sansom, M. S. P., "Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity", Science Advances, 3, e1601871(2017). (6 pages) DOI: 10.1126/sciadv.1601871

        167. Takahashi, K. Z., Nishimura, R., Yasuoka, K., and Masubuchi, Y., "Molecular Dynamics Simulations for Resolving Scaling Laws of Polythylene Melts", Polymers, 9, 24(2017). (12 pages) DOI: 10.3390/polym9010024

  • 2016年 (10 papers)

        • 166. Morita, K., Shibuya, T., and Yasuoka, K., "Stability of Excess Electrons Introduced by Ti Interstitial in Rutile TiO2(110) Surface", J. Phys. Chem. C , 121, 1602-1607(2016). (6 pages) DOI: 10.1021/acs.jpcc.6b09669

        165. Winarto, Takaiwa, D., Yamamoto, E., and Yasuoka, K., "Separation of Water - Ethanol Solution with Carbon Nanotubes and Electric Fields", Phys. Chem. Chem. Phys., 10, 33310-33319(2016). (10 pages) DOI: 10.1039/C6CP06731J

        164. Arai, N., Yasuoka, K., and Zeng, X. C., "Self-Assembly of Janus Oligomers into Onion-like Vesicles with Layer-by-Layer Water Discharging Capability: A Minimalist Model", ACS Nano, 10, 8026-8037(2016). (12 pages) DOI: 10.1021/acsnano.6b04087

        163. Suh, D. and Yasuoka, K., "Aspect ratio effect of nanorods on heterogeneous nucleation rates by molecular dynamics", Journal of Thermal Science and Technology, 11, JTST0044(2016). (6 pages) DOI: 10.1299/jtst.2016jtst0044

        162. Shibuya, T., Skelton, J. M., Jackson, A. J., Yasuoka, K., Togo, A., Tanaka, I., and Walsh, A., "Suppression of lattice thermal conductivity by mass-conserving cation mutation in multi-component semiconductors", APL Materials, 4, 104809(2016). (7 pages) DOI: 10.1063/1.4955401

        161. Arai, N., Yoshimoto, Y., Yasuoka, K., and Ebisuzaki, T., "Self-assembly behaviours of primitive and modern lipid membrane solutions: a coarse-grained molecular simulation study", Phys. Chem. Chem. Phys., 18, 19426-19432(2016). (7 pages) DOI: 10.1039/C6CP02380K

        160. Yamamoto, E., Kalli, A. C., Yasuoka, K., and Sansom, M. S. P., "Interactions of Pleckstrin Homology Domains with Membranes", Structure, 24, 1421-1431(2016). (11 pages) DOI: 10.1016/j.str.2016.06.002

        159. Suh, D. and Yasuoka, K., "Condensation on Nanorods by Molecular Dynamics", J. Chem. Phys., 144, 244702-7(2016). DOI: 10.1063/1.4954240

        158. Tomobe K., Yamamoto E., Akimoto T., Yasui M., and Yasuoka K., "Instability of buried hydration sites increases protein subdomains fluctuations in the human prion protein by the pathogenic mutation T188R", AIP Advances, 6, 055324-10(2016). DOI: 10.1063/1.4953061

        157. Brumby, P. E., Yuhara, D., Wu, D. T., Sum, A. K. and Yasuoka, K., "Cage Occupancy of Methane Hydrates from Gibbs Ensemble Monte Carlo Simulations", Fluid Phase Equilibria, 413, 242-248(2016). (7 pages) DOI: 10.1016/j.fluid.2015.10.005

  • 2015年 (18 papers)

        • 156. Suh, D., Nakamura, M. and Yasuoka, K., "Heterogeneous nucleation of bubbles by molecular dynamics", J. Phys. Conf. Series, 656, 012037(2015). (4 pages) DOI: 10.1088/1742-6596/656/1/012037

        155. Nozawa, T., Takahashi, K. Z., Narumi, T. and Yasuoka, K., "Comparison of the Accuracy of Periodic Reaction Field Methods in Molecular Dynamics Simulations of a Model Liquid Crystal System", J. Comput. Chem., 36, 2406-2411(2015). (6 pages) DOI: 10.1002/jcc.24222

        154. Yamamoto, E., Kalli, A. C., Akimoto, T., Yasuoka, K. and Sansom, M. S. P., "Anomalous dynamics of a lipid recognition protein on a membrane surface", Sci. Rep., 5, 18245(2015). (12 pages) DOI: 10.1038/srep18245

        153. 山本詠士, 秋元琢磨, 泰岡顕治, "分子動力学シミュレーションによる細胞膜表面での水分子の異常拡散の解明", 生物物理, 55, 242-245(2015). (4 pages) DOI: 10.2142/biophys.55.242 :Selected as a cover

        152. Doi, H. and Yasuoka, K., "Approaches for controlling the temperature and pressure range in generalized NPT ensembles", J. Chem. Theory Comput., 11, 4370-4376(2015). (7 pages) DOI: 10.1021/acs.jctc.5b00195

        151. Winarto, Takaiwa, D., Yamamoto, E. and Yasuoka, K., "Water-methanol separation with carbon nanotubes and electric fields", Nanoscale, 7, 12659-12665(2015). (7 pages) DOI: 10.1039/C5NR02182K

        150. Suh, D., Yasuoka, K. and Zeng, X. C., "Molecular Dynamics Simulation of Heterogeneous Nucleation on Nanotubes", R. Soc. Chem. Adv., 5, 40953-40963(2015). (11 pages) DOI: 10.1039/C5RA04398K

        149. Hiratsuka, M., Ohmura, R., Sum, A. K., Alavi, S. and Yasuoka, K., "Molecular dynamics study of guest-host hydrogen bonding in alcohol clathrate hydrates", Phys. Chem. Chem. Phys., 17, 12639-12647(2015). (9 pages) DOI: 10.1039/C4CP05732E

        148. Winarto, Takaiwa, D., Yamamoto, E. and Yasuoka, K., "Structures of water molecules in carbon nanotubes under electric fields", J. Chem. Phys., 142, 124701(2015). (9 pages) DOI: 10.1063/1.4914462 :Selected as a cover

        147. Yamamoto, E., Akimoto, T., Yasui, M. and Yasuoka, K., "Origin of 1/f Noise in Hydration Dynamics on Lipid Membrane Surfaces", Sci. Rep., 5, 8876(2015). (6 pages) DOI: 10.1038/srep08876

        146. Yuhara, D., Barnes, B. C., Suh, D., Knott, B. C., Beckham, G. T., Yasuoka, K., Wu, D. T. and Sum, A. K., "Nucleation rate analysis of methane hydrate from molecular dynamics simulations", Faraday Discussions, 179, 463-474(2015). (12 pages) DOI: 10.1039/C4FD00219A

        145. Nozawa, T., Takahashi, K. Z., Kameoka, S., Narumi, T. and Yasuoka, K., "Application of isotropic periodic sum method for 4-pentyl-4'-cyanobiphenyl liquid crystal", Molec. Simul., 41, 927-935(2015). (9 pages) DOI: 10.1080/08927022.2014.998210

        144. Takahashi, K. Z. and Yasuoka, K., "A determination of liquid-vapor interfacial properties for methanol using a linear-combination-based isotropic periodic sum", Molec. Simul., 41, 795-800(2015). (6 pages) DOI: 10.1080/08927022.2014.913791

        143. Hiratsuka, M., Ohmura, R., Sum, A. K. and Yasuoka, K., "Vibrational Spectra of Deuterated Methane and Water Molecules in Structure I Clathrate Hydrate from ab initio MD simulation", Molec. Simul., 41, 813-817(2015). (5 pages) DOI: 10.1080/08927022.2014.929125

        142. Tomobe, K., Yamamoto, E., Dusan, K., Yasui, M. and Yasuoka, K., "Velocity auto-correlation function of ions and water molecules in different concentrations, anions, and ion clusters", Molec. Simul., 41, 840-844(2015). (5 pages) DOI: 10.1080/08927022.2014.940500

        141. Nomura K., Oikawa M., Kawai A., Narumi T. and Yasuoka, K., "GPU-accelerated replica exchange molecular simulation on solid-liquid phase transition study of Lennard-Jones fluids", Molec. Simul., 41, 874-880(2015). (7 pages) DOI: 10.1080/08927022.2014.954572


        139. Yuhara, D., Hiratsuka, M., Takaiwa, D. and Yasuoka, K., "Analysis of crystal growth of methane hydrate using molecular dynamics simulation", Molec. Simul., 41, 918-922(2015). (5 pages) DOI: 10.1080/08927022.2014.978313

  • 2014年 (10 papers)

        • 138. 老川 稔, 野村 昴太郎, 泰岡 顕治, 成見 哲,, "1,024GPUを使用したレプリカ交換分子動力学シミュレーションの並列化", 情報処理学会論文誌コンピューティングシステム（ACS）, 4, 1-14(2014). DOI: http://id.nii.ac.jp/1001/00107483/

        137. Kojić D., Tsenkova R, Tomobe K, Yasuoka K, and Yasui M., "Water confined in the local field of ions", ChemPhysChem, 15, 4077-4086(2014). (10 pages) DOI: 10.1002/cphc.201402381

        136. Grim, R. G., Barnes, B. C., Lafond, P. G., Kockelmann, W. A., Keen, D. A., Soper, A. K., Hiratsuka, M., Yasuoka, K., Koh, C. A. and Sum A. K., "Observation of Interstitial Molecular Hydrogen in Clathrate Hydrates", Angew. Chem. Int. Ed., 53, 10710-10713(2014). (4 pages) DOI: 10.1002/anie.201406546

        135. Goto, Y., Tanaki, M., Okusa, Y., Shibuya, T., Yasuoka, K., Matoba, M., and Kamihara, Y., "Effects of the Cu off-stoichiometry on transport properties of wide gap p-type semiconductor, layered oxysulfide LaCuSO", App. Phys. Lett., 105, 022104(2014). (4 pages) DOI: 10.1063/1.4890302

        134. Kaneko, T., Bai, J., Yasuoka, K., Mitsutake, A., and Zeng, X., "Liquid-solid and solid-solid phase transition of monolayer water: High-density rhombic monolayer ice", J. Chem. Phys., 140, 184507(2014). (7 pages) DOI: 10.1063/1.4874696

        133. Shibuya, T., Yasuoka, K., Mirbt, S. and Sanyal, B., "Bipolaron Formation Induced by Oxygen Vacancy at Rutile TiO2(110) Surfaces", J. Phys. Chem. C, 118, 9429-9435(2014). (7 pages) DOI: 10.1021/jp410596d

        132. Yamamoto, E., Akimoto, T., Yasui M., and Yasuoka K., "Origin of subdiffusion of water molecules on cell membrane surfaces", Sci. Rep., 4, 4720(2014). (7 pages) DOI: 10.1038/srep04720 :Selected as a featured article in Nature Japan

        131. Yamamoto, E., Akimoto, T., Hirano, Y., Yasui M., and Yasuoka K., "1/f fluctuations of amino acids regulate water transportation in aquaporin 1", Phys. Rev. E., 89, 022718(2014). (6 pages) DOI: 10.1103/PhysRevE.89.022718

        130. Shibuya, T., Goto, Y., Kamihara, Y., Matoba, M., Yasuoka, K., Burton, L.A., and Walsh, A., "From kesterite to stannite photovoltaics: stability and band gaps of the Cu2(Zn,Fe)SnS4 alloy", App. Phys. Lett., 104, 021912(2014). (4 pages) DOI: 10.1063/1.4862030

        129. Arai, N., Akimoto, T., Yamamoto, E., Yasui M., and Yasuoka K., "Poisson property of the occurrence of flip-flops in a model membrane", J. Chem. Phys., 140, 064901(2014). (8 pages) DOI: 10.1063/1.4863330 :Selected as a cover

  • 2013年 (15 papers)

        • 128. Giangreco, F., Yamamoto, E., Hirano, Y., Hodoscek, M., Knecht, V., di Giosia, M., Calvaresi, M., Zerbetto, F., Yasuoka, K., Narumi, T., Masato Y., and Höfinger, S., "Common Force Field Thermodynamics of Cholesterol", Sci. World J., 2013, 207287(2013). (7 pages) DOI: 10.1155/2013/207287

        127. Dushanov, E., Kholmurodov, K., Yasuoka, K., Krasavin, E., "MD studies on conformational behavior of a DNA photolyase enzyme", Physics of Particles and Nuclei Letters, 10, 597-605(2013). (9 pages) DOI: 10.1134/S1547477113060101

        126. Dushanov, E., Kholmurodov, Kh., Yasuoka, K., "Structural and diffusion properties of formamide/water mixture interacting with TiO2 surface ", Bioorganic Chemistry, 50, 11-16(2013). (6 pages) DOI: 10.1016/j.bioorg.2013.07.002

        125. Arai, N., Yasuoka, K., Zeng, X.C., "Vesicle Cell under Collision with Janus or Homogeneous Nanoparticle: Translocation Dynamics and Late-Stage Morphology", Nanoscale, 5, 9089-9100(2013). (12 pages) DOI: 10.1039/C3NR02024J

        124. Kaneko, T., Bai, J., Yasuoka, K., Mitsutake, A., Zeng, X.C., "A New Computational Approach to Determine Liquid-Solid Phase Equilibria of Water Confined to Slit Nanopores", J. Chem. Theory Comput., 9, 3299-3310(2013). (12 pages) DOI: 10.1021/ct400221h

        123. Koishi, K., Yasuoka, K., Willow S.Y., Fujikawa S., and Zeng X.C., "Molecular Insight into Different Denaturing Efficiency of Urea, Guanidinium, and Methanol: A Comparative Simulation Study", J. Chem. Theory Comput., 9, 2540-2551(2013). (12 pages) DOI: 10.1021/ct3010968 :Selected as a cover

        122. Arai, N. Yasuoka, K. Koishi, T. Ebisuzaki, T. Zeng, X.C., "Understanding Molecular Motor Walking along Microtubule: A Themo-sensitive Asymmetric Brownian Motor Driven by Bubble Formation", J. Am. Chem. Soc., 135, 8616-8624(2013). (14 pages) DOI: 10.1021/ja402014u

        121. Yamamoto, E., Akimoto, T., Hirano, Y., Yasui M., and Yasuoka K., "Power-Law Trapping of Water Molecules on the Lipid-Membrane Surface Induce Water Retardation", Phys. Rev. E, 87, 052715(2013). (6 pages) DOI: 10.1103/PhysRevE.87.052715

        120. Akimoto, T., Kaneko, T., Yasuoka, K., and Zeng X.C., "Homogeneous Connectivity of Potential Energy Network in a Solidlike State of Water Cluster", J. Chem. Phys., 138, 244301(2013). (7 pages) DOI: 10.1063/1.4811289

        119. Kagawa, R., Hirano, Y., Taiji, M., Yasuoka, K., and Yasui, M., "Dynamic Interactions of Cations, Water and Lipids Influence on Membrane Fluidity", J. Membr. Sci., 435, 130-136(2013). (7 pages) DOI: 10.1016/j.memsci.2013.02.006

        118. Suh, D. and Yasuoka, K., "Kinetic Analysis on Nanoparticle Condensation by Molecular Dynamics", J. Heat Transfer, 135, 101002(2013). (4 pages) DOI: 10.1115/1.4024495

        117. Arai, N., Yasuoka, K., and Zeng, X.C., "Phase diagrams of confined solutions of dimyristoylphosphatidylcholine (DMPC) lipid and cholesterol in nanotubes", Microfluid. Nanofluid., 14, 995-1010(2013). (16 pages) DOI: 10.1007/s10404-012-1107-3

        116. Takeuchi, F., Hiratsuka, M., Ohmura, R., Alavi, S., Sum, A. K. and Yasuoka, K., "Water Proton Configurations in Structures I, II and H Clathrate Hydrate Unit Cells", J. Chem. Phys., 138, 124504(2013). (12 pages) DOI: 10.1063/1.4795499

        115. Arai, N., Yasuoka, and K., Zeng, X.C., "Self-Assembly of Triblock Janus Nanoparticle in Nanotube", J. Chem. Theory Comput., 9, 179-187(2013). (9 pages) DOI: 10.1021/ct3007748

        114. Yokota, R., Barba, L. A., Narumi, T. and Yasuoka, K., "Petascale Turbulence Simulation Using a Highly Parallel Fast Multipole Method", Comput. Phys. Comm., 184, 445-455(2013). (11 pages) DOI: 10.1016/j.cpc.2012.09.011

  • 2012年 (19 papers)

        • 113. 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

        112. 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

        111. 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

        110. 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

        109. 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

        108. 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

        107. 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

        106. 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

        105. 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

        104. 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

        103. 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

        102. 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

        101. 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

        100. 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

        99. 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

        98. 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

        97. 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

        96. 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

        95. 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

  • 2011年 (13 papers)

        • 94. Kholmurodov, K., Dushanov, E., Yasuoka, K., Khalil, H., Galal, A., Ahmed, A., Sweilam, N. and Moharram, H., , "Molecular Dynamics Simulation of the Interaction of Ethanol - Water Mixture with a Pt Surface", Natural Science, 3, 1011-1021(2011). (11 pages) DOI: 10.4236/ns.2011.312126

        93. Takahashi, K. Z., Narumi, T., and Yasuoka, K., "A combination of the tree-code and IPS method to simulate large scale systems by molecular dynamics", J. Chem. Phys., 135, 174108(2011). (9 pages) DOI: 10.1063/1.3658640

        92. Kaneko, T., Akimoto, T., Yasuoka, K., Mitsutake, A., and Zeng, X. C., "Size Dependent Phase Changes in Water Clusters", J. Chem. Theory Comput., 7, 3083-3087(2011). (5 pages) DOI: 10.1021/ct200458m

        91. Akimoto, T., Yamamoto, E., Yasuoka, K., Hirano, Y., and Yasui, M., "Non-Gaussian Fluctuations Resulting from Power-Law Trapping in a Lipid Bilayer", Phys. Rev. Lett., 107, 178103(2011). DOI: 10.1103/PhysRevLett.107.178103

        90. Kholmurodov, K., Dushanov, E., and Yasuoka, K., "MD Simulations of the P53 Oncoprotein Structure: the Effect of the Arg273-->His Mutation on the DNA Binding Domain", Advances in Bioscience and Biotechnology, 2, 330(2011). DOI: 10.4236/abb.2011.25048

        89. Koishi, T., Yasuoka, K., Fujikawa, S., and Zeng, X. C., "Measurement of Contact-Angle Hysteresis for Droplets on Nanopillared Surface and in the Cassie and Wenzel States: A Molecular Dynamics Simulation Study", ACS Nano, 5, 6834(2011). DOI: 10.1021/nn2005393

        88. Suh, D., and Yasuoka, K., "Nanoparticle Growth Analysis by Molecular Dynamics: Spherical Seed", J. Phys. Chem. B, 115, 10631(2011). DOI: 10.1021/jp201964h

        87. Seino, M., Tanahashi, T., Yasuoka, K., "An Analysis of Natural Convection Using the Thermal Finite Element Discrete Boltzmann Equation", Computers and Fluids, 40, 113(2011). DOI: 10.1016/j.compfluid.2010.08.016

        86. Takahashi, K. Z., Narumi, T., and Yasuoka, K., "Cutoff radius effect of the isotropic periodic sum and Wolf method in liquid-vapor interfaces of water", J. Chem. Phys., 134, 174112(2011). DOI: 10.1063/1.3578473

        85. Sakamaki, R., Sum, A. K., Narumi, T., Ohmura, R., and Yasuoka, K., "Thermodynamic Properties of Methane/Water Interface Predicted by Molecular Dynamics Simulations", J. Chem. Phys., 134, 144702(2011). DOI: 10.1063/1.3579480

        84. Sakamaki, R., Sum, A. K., Narumi, T., and Yasuoka, K., "Molecular dynamics simulations of vapor/liquid coexistence using the nonpolarizable water models ", J. Chem. Phys., 134, 124708(2011). DOI: 10.1063/1.3574038

        83. Narumi, T., Hamada, T., Nitadori, K., Sakamaki, R., and Yasuoka, K., "Fast quasi double-precision method with single-precision hardware to accelerate scientific applications", Int. J. Comput. Meth., 8, 561(2011). DOI: 10.1142/S0219876211002708

        82. Narumi, T., Yasuoka, K., Taiji, M., Zerbetto, F., and Hoefinger, S., "Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3", Comput. J., 54, 1181(2011). DOI: 10.1093/comjnl/bxq079

    • 2010年 (9 papers)


          • 80. Arai, N., Yasuoka, K., Koishi, T., and Ebisuzaki, T., "Asymmetric Brownian motor driven by bubble formation in a hydrophobic channel", ACS Nano, 4, 5905(2010). DOI: 10.1021/nn101855d

          79. Kholmurodov, K., Abasheva, M., and Yasuoka, K., "Molecular dynamics simulations of valinomycin interactions with potassium and sodium ions in water solvent", Advances in Bioscience and Biotechnology, 1, 216(2010). DOI: 10.4236/abb.2010.13030

          78. Koishi, T., Yasuoka, K., Zeng, X. C., and Fujikawa, S., "Molecular dynamics simulations of urea‒water binary droplets on flat and pillared hydrophobic surfaces", Faraday Disc., 146, 185(2010). DOI: 10.1039/b926919c

          77. Takahashi, K., Narumi, T., and Yasuoka, K., "Cutoff radius effect of isotropic periodic sum method in homogeneous system. II . Water", J. Chem. Phys., 133, 014109(2010). DOI: 10.1063/1.3462241

          76. Kholmurodov, K., Chulkova A., and Yasuoka, K., "Molecular Dynamics Study of the Effect of Electrostatic Interactions on the Biphenyl Structure in the Active HNO3 Solvent", The Open Physical Chemistry Journal, 4, 10(2010). DOI: 10.2174/1874067701004010010

          75. Kholmurodov, K., Aru, G., and Yasuoka, K., "Molecular dynamics simulations of the interaction of carbon nanotube and a carbon disulfide solvent", Natural Science, 2, 902(2010). DOI: 10.4236/ns.2010.28111

          74. Kaneko, T., Mima, T., and Yasuoka, K., "Phase Diagram of Lennard-Jones Fluid Confined in Slit Pores", Chem. Phys. Lett., 490, 165(2010). DOI: 10.1016/j.cplett.2010.03.048

          73. Hirano, Y., Okimoto, N., Kadohira, I., Suematsu, M., Yasuoka, K, and Yasui, M., "Molecular mechanisms how mercury inhibits water permeation through aquaporin-1: understanding by molecular dynamics simulaiton", Biopys. J., 98, 1512(2010). DOI: 10.1016/j.bpj.2009.12.4310

      • 2009年 (8 papers)

            • 72. Dushanov, E., Kholmurodov, Kh., Aru, G., Korenkov, V., Smith, W., Ohno, Y., Narumi, T., Morimoto, G., Taiji, M., and Yasuoka, K., "JINR CICC in Computational Chemistry and Nanotechnology Problems: DL_POLY Performance for Different Communication Architectures", Phys. Part. Nucl. Lett., 6, 251(2009). DOI: 10.1134/S154747710903011X

            71. Takeuchi, F., Ohmura, R., and Yasuoka, K., "Statistical-thermodynamics modeling of clathrate hydrate forming systems suitable as working media of a hydrate-based refrigeration system", Int. J. Thermophys., 30, 1838(2009). DOI: 10.1007/s10765-009-0661-8

            70. Watanabe, G., Sonoda, H., Maruyama, T., Sato, K., Yasuoka, K., and Ebisuzaki, T., "Formation of Nuclear ''Pasta'' in Supernovae", Phys. Rev. Lett., 103, 121101(2009). DOI: 10.1103/PhysRevLett.103.121101

            69. Yokota, R., Narumi, T., Sakamaki, R., Kameoka, S., Obi, S., and Yasuoka, K., "Fast Multipole Methods on a Cluster of GPUs for the Meshless Simulation of Turbulence Computer Physics Communications", Comput. Phys. Commun., 180, 2066(2009). DOI: 10.1016/j.cpc.2009.06.009

            68. Koishi, T., Yasuoka, K., Fujikawa, S., Ebisuzaki, T., and Zeng, X.C., "Coexistence and transition between Cassie and Wenzel state on pillared hydrophobic surface", PNAS, 106, 8435(2009). DOI: 10.1073/pnas.0902027106

            67. Narumi, T., Yasuoka, K., Taiji, M., and Höfinger, S., "Current Performance Gains from Utilizing the GPU or the ASIC MDGRAPE-3 within an Enhanced Poisson Boltzmann Approach", J. Comput Chem., 30, 2351(2009). DOI: 10.1002/jcc.21257

            66. 坂牧隆司，成見哲，泰岡顕治, "グラフィックカードを用いた水表面張力の高速分子動力学シミュレーション", 情報処理学会論文誌.コンピューティングシステム, 2, 89-97(2009). DOI: http://id.nii.ac.jp/1001/00060774/

            65. Matsubara, H., Ebisuzaki, T., and Yasuoka, K., "Microscopic insights into nucleation in a sulfuric acid-water vapor mixture based on molecular dynamics simulation", J. Chem. Phys., 130, 104705(2009). DOI: 10.1063/1.3082079

      • 2008年 (8 papers)

            • 64. Mima, T., Narumi, T., Kameoka, S., Yasuoka, K., "Cell size dependence of orientational order of uniaxial liquid", Molecular Simulation, 34, 761-773(2008). DOI: 10.1080/08927020802256058

            63. Narumi, T., Kameoka, S., Taiji, M., and Yasuoka, K., "Accelerating Molecular Dynamics Simulations on PLAYSTATION 3 Platform using “Virtual-Grape”Programming Model", SIAM Journal on Scientific Computing, 30, 3108-3125(2008). DOI: 10.1137/070692054

            62. Arai, N., Yasuoka, K., and Zeng, X. C., "Self-Assembly of Surfactants and Polymorphic Transition in Nanotubes", Journal of American Chemical Society, 130, 7916-7920(2008). DOI: 10.1021/ja7108739

            61. Sonoda, H., Watanabe, G., Sato, K., Yasuoka, K., and Ebisuzaki, T., "Phase diagram of nuclear “pasta” and its uncertainties in supernova cores", Phys. Rev. C, 77, 035806(2008). DOI: 10.1103/PhysRevC.77.035806

            60. Sheel, T. K., Yokota, R., Yasuoka, K., Obi, S., "The study of colliding vortex rings using a special-purpose computer and FMM", Transactions of the Japan Society for Computational Engineering and Science, 2008, 20080003(2008). DOI: 10.11421/jsces.2008.20080003

            59. 松原裕樹, 泰岡顕治, 戎崎俊一, "少量の硫酸分子を含む不均質核生成の分子動力学シミュレーション", Thermal Science and Engineering, 16, 71-77(2008). DOI: 10.11368/tse.16.71

            58. Sekine, M., Yasuoka, K., Kinjo, T., and Matsumoto, M., "Liquid-vapor nucleation simulation of Lennard-Jones fluid by molecular dynamics method", Fluid Dynamics Research, 40, 597-605(2008). DOI: 10.1016/j.fluiddyn.2007.12.012

            57. Mima T. and Yasuoka K., "Interfacial anisotropy in the transport of liquid crystals confined between flat, structureless walls: A molecular dynamics simulation approach", Phys. Rev. E, 77, 011705(2008). DOI: 10.1103/PhysRevE.77.011705

      • 2007年 (13 papers)

            • 56. Matsubara, H., Koishi, T., Ebisuzaki, T. and Yasuoka, K., "Extended study of molecular dynamics simulation of homogeneous vapor-liquid nucleation of water", J. Chem. Phys., 127, 214507(2007). DOI: 10.1063/1.2803899

            55. Andoh, Y., Kurahashi, K., Sakuma, H., Yasuoka, K. and Kurihara, K., "Anisotropic molecular clustering in liquid ethanol induced by a charged fully hydroxylated silicon dioxide (SiO2) surface", Chem. Phys. Lett., 448, 253-257(2007). DOI: 10.1016/j.cplett.2007.10.008

            54. Takahashi, K., Yasuoka, K. and Narumi, T., "Cutoff radius effect of isotropic periodic sum method for transport coefficients of Lennard-Jones liquid", J. Chem. Phys., 127, 114511(2007). DOI: 10.1063/1.2775929

            53. Sato, E., Miyoshi, T., Ohmura, R. and Yasuoka K., "Phase Equilibrium Calculation for Clathrate Hydrates based on a Statistical Thermodynamics Model: An Attempt to Optimize the Kihara Parameters for Methane and Ethane", Jpn. J. Appl. Phys., 46, 5944-5950(2007). DOI: 10.1143/JJAP.46.5944

            52. Sonoda,H., Watanabe, G., Sato, K., Takiwaki, T., Yasuoka, K., Ebisuzaki T., "Impact of nuclear “pasta” on neutrino transport in collapsing stellar cores", Phys. Rev. C, 75, 042801(R)(2007). DOI: 10.1103/PhysRevC.75.042801

            51. Arai, N., Yasuoka, K., Masubuchi, Y. , "Spontaneous self-assembly process for threadlike micelles", J. Chem. Phys., 126, 244905(2007). DOI: 10.1063/1.2747240

            50. Miyoshi, T., Imai, M., Ohmura, R., Yasuoka, K., "Thermodynamic stability of type-I and II clathrate hydrates depending on the chemical species of the guest substances", J. Chem. Phys., 126, 234506(2007). DOI: 10.1063/1.2746324

            49. Sheel, T.K., Yasuoka, K., Obi, S., "Fast Vortex method calculation using a special-purpose computer", Computers and Fluids, 36, 1319-1326(2007). DOI: 10.1016/j.compfluid.2007.01.006

            48. Yasuoka, K., Zeng, X.C., "Molecular dynamics of homogeneous nucleation in the vapor phase of Lennard-Jones. III. Effect of carrier gas pressure", J. Chem. Phys., 126, 124320(2007). DOI: 10.1063/1.2712436

            47. Miyoshi, T., Ohmura, R., Yasuoka, K., "Predicting thermodynamic stability of clathrate hydrates based on molecular-dynamics simulations and its confirmation by phase-equilibrium measurements", J. Phys. Chem. C, 111, 3799(2007). DOI: 10.1021/jp068244e

            46. Andoh, Y., Yasuoka, K., "Molecular understanding of dynamical properties of the vapor/ethanol-aqueous-solution interface", Molecular Simulation, 33, 139(2007). DOI: 10.1080/08927020601075337

            45. Miyoshi, T., Ohmura, R., Yasuoka, K., "Molecular Dynamics Simulations of Structure-H Hydrates Formed with Methane and 3,3-Dimethylpentane or 2,2-Dimethylpentane", Molecular Simulation, 33, 65(2007). DOI: 10.1080/08927020601059885

            44. Mima, T., Yasuoka, K., Nose, S., "Molecular Dynamics Simulation of Time-irreversibility of Stationary Heat Flux", Molecular Simulation, 33, 109(2007). DOI: 10.1080/08927020601067565

      • 2006年 (2 papers)

            • 43. Andoh, Y., Yasuoka, K., "Hydrogen-bonded clusters on the vapor/ethanol-aqueous-solution interface", Journal of Physical Chemistry B, 110, 23264(2006). DOI: 10.1021/jp061150k

            42. Okano, Y., Yasuoka, K., "Free-energy calculation of structure-H hydrates", Journal of Chemical Physics, 124, 024510(2006). DOI: 10.1063/1.2150430

      • 2005年 (4 papers)

            • 41. Watanabe, G., Maruyama, T., Sato, K., Yasuoka, K., Ebisuzaki, T., "Simulation of transitions between "pasta" phases in dense matter", Physical Review Letters, 94, 031101(2005). DOI: 10.1103/PhysRevLett.94.031101

            40. Tsuji, H., Kobayashi, T., Okano, Y., Ohmura, R., Yasuoka, K., Mori, Y.H., "Thermodynamic simulations of isobaric hydrate-forming operations: Formulation of computational scheme and its application to hydrate formation from a methane plus ethane plus propane mixture", Energy & Fuels, 19, 1587-1597(2005). DOI: 10.1021/ef050009s

            39. Andoh, Y., Yasuoka, K., "Two-dimensional supercritical behavior of an ethanol monolayer: A molecular dynamics study", Langmuir, 21, 10885-10894(2005). DOI: 10.1021/la051384f

            38. Koishi, T., Yasuoka, K., Ebisuzaki, T., Yoo, S., Zeng, X.C., "Large-scale molecular-dynamics simulation of nanoscale hydrophobic interaction and nanobubble formation", Journal of Chemical Physics, 123, 204707(2005). DOI: 10.1063/1.2102906

      • 2004年 (4 papers)

            • 37. Suenaga, A., Kiyatkin, A.B., Hatakeyama, M., Futatsugi, N., Okimoto, N., Hirano, Y., Narumi, T., Kawai, A., Susukita, R., Koishi, T., Furusawa, H., Yasuoka, K., Takada, N., Ohno, Y., Taiji, M., Ebisuzaki, T., Hoek, J.B., Konagaya, A., Kholodenko, B.N., "Tyr-317 phosphorylation increases shc structural rigidity and reduces coupling of domain motions remote from the phosphorylation site as revealed by molecular dynamics simulations", Journal of Biological Chemistry, 279, 4657-4662(2004). DOI: 10.1074/jbc.M310598200

            36. Elmegreen, B.G., Koch, R.H., Schabes, M.E., Crawford, T., Ebisuzaki, T., Furusawa, H., Narumi, T., Susukita, R., Yasuoka, K., "Simulations of magnetic materials with MDGRAPE-2", IBM Journal of Research and Development, 48, 199-207(2004). DOI: 10.1147/rd.482.0199

            35. Watanabe, G., Sato, K., Yasuoka, K., Ebisuzaki, T., "Phases of hot nuclear matter at subnuclear densities", Physical Review C, 69, 055805(2004). DOI: 10.1103/PhysRevC.69.055805

            34. Koishi, T., Yoo, S., Yasuoka, K., Zeng, X.C., Narumi, T., Susukita, R., Kawai, A., Furusawa, H., Suenaga, A., Okimoto, N., Futatsugi, N., Ebisuzaki, T., "Nanoscale hydrophobic interaction and nanobubble nucleation", Physical Review Letters, 93, 185701(2004). DOI: 10.1103/PhysRevLett.93.185701

      • 2003年 (7 papers)

            • 33. Watanabe, G., Sato, K., Yasuoka, K., Ebisuzaki, T., "Microscopic study of nuclear "pasta": Quantum molecular dynamics approach", Nuclear Physics A, 718, 700C-702C(2003). DOI: 10.1016/S0375-9474(03)00893-5

            32. Ohmura, R., Ogawa, M., Yasuoka, K., Mori, Y.H., "Statistical study of clathrate-hydrate nucleation in a water/hydrochlorofluorocarbon system: Search for the nature of the "memory effect"", Journal of Physical Chemistry B, 107, 5289-5293(2003). DOI: 10.1021/jp027094e

            31. Fujii, Y., Okimoto, N., Hata, M., Narumi, T., Yasuoka, K., Susukita, R., Suenaga, A., Futatsugi, N., Koishi, T., Furusawa, H., Kawai, A., Ebisuzaki, T., Neya, S., Hoshino, T., "Molecular dynamics study on class A beta-lactamase: Hydrogen bond network among the functional groups of penicillin G and side chains of the conserved residues in the active site", Journal of Physical Chemistry B, 107, 10274-10283(2003). DOI: 10.1021/jp034536t

            30. Okimoto, N., Yamanaka, K., Suenaga, A., Hirano, Y., Futatsugi, N., Narumi, T., Yasuoka, K., Susukita, R., Koishi, T., Furusawa, H., Kawai, A., Hata, M., Hoshino, T., Ebisuzaki, T., "Molecular Dynamics Simulations of Prion Proteins - Effect of Ala117->Val mutation -", Chem-Bio Informatics Journal, 3, 1-11(2003). DOI: 10.1273/cbij.3.1

            29. Susukita, R., Ebisuzaki, T., Elmegreen, B.G., Furusawa, H., Kato, K., Kawai, A., Kobayashi, Y., Koishi, T., McNiven, G.D., Narumi, T., Yasuoka, K., "Hardware accelerator for molecular dynamics: MDGRAPE-2", Computer Physics Communications, 155, 115-131(2003). DOI: 10.1016/S0010-4655(03)00349-7

            28. Koishi, T., Yasuoka, K., Ebisuzaki, T., "Large scale molecular dynamics simulation of nucleation in supercooled NaCl", Journal of Chemical Physics, 119, 11298-11305(2003). DOI: 10.1063/1.1622371

            27. Watanabe, G., Sato, K., Yasuoka, K., Ebisuzaki,T., "Structure of cold nuclear matter at subnuclear densities by quantum molecular dynamics", Physical Review C, 68, 035806(2003). DOI: 10.1103/PhysRevC.68.035806

      • 2002年 (4 papers)

            • 26. Watanabe, G., Sato, K., Yasuoka, K., Ebisuzaki, T., "Microscopic study of slablike and rodlike nuclei: Quantum molecular dynamics approach", Physical Review C, 66, 012801(2002). DOI: 10.1103/PhysRevC.66.012801

            25. Elmegreen, B.G., Koch, R., Yasuoka, K., Furusawa, H., Narumi, T., Susukita, R., Ebisuzaki, T., "Numerical simulations of magnetic materials with MD-GRAPE: curvature induced anisotropy", Journal of Magnetism and Magnetic Materials, 250, 39-48(2002). DOI: 10.1016/S0304-8853(02)00344-X

            24. Koishi, T., Yasuoka, K., Narumi, T., Susukita, R., Furusawa, H., Ebisuzaki, T., "Molecular dynamics study of the solidification process in alkali halide cluster", Journal of Non-Crystalline Solids, 312, 332-336(2002). DOI: 10.1016/S0022-3093(02)01710-6

            23. Watanabe, G., Sato, K., Yasuoka, K., Ebisuzaki. T., "Microscopic study of nuclear "pasta" by quantum molecular dynamics", Progress of Theoretical Physics Supplement, 146, 638-639(2002). DOI: 10.1143/PTPS.146.638

      • 2001年 (2 papers)

            • 22. Kholmurodov, K.T., Yasuoka, K., Zeng, X.C., "Molecular dynamics simulation of supersaturated vapor nucleation in slit pore. II. Thermostatted atomic-wall model", Journal of Chemical Physics, 114, 9578-9584(2001). DOI: 10.1063/1.1370057

            21. Kholmurodov, K., Puzynin, I., Smith, W., Yasuoka, K., Ebisuzaki, T., "MD simulation of cluster-surface impacts for metallic phases: soft landing, droplet spreading and implantation", Computer Physics Communications, 141, 1-16(2001). DOI: 10.1016/S0010-4655(01)00292-2

      • 2000年 (6 papers)

            • 20. Yasuoka, K. , Gao, G. T. , Zeng, X. C., "Molecular Dynamics Simulation of Supersaturated Vapor Nucleation in Slit Pore", Journal of Chemical Physics, 112, 4279-4285(2000). DOI: 10.1063/1.480973

            19. Tanimura, S., Yasuoka, K., Ebisuzaki, T., "Molecular Dynamics Simulation of the Homogeneous Nucleation of UF6 Molecules: Configurations and Infrared Spectra of the Excited Hot Clusters", Journal of Chemical Physics, 112, 3812-3819(2000). DOI: 10.1063/1.480530

            18. Kholmurodov, K., Smith, W., Yasuoka, K., Ebisuzaki, T., "A Highly Vectorised 'Link-Cell' Fortran Code for the DL_POLY Molecular Dynamics Simulation Package", Computer Physics Communications, 125, 167-192(2000). DOI: 10.1016/S0010-4655(99)00485-3


            16. Ohguchi, K., Yasuoka, K., Matsumoto, M., "Molecular Mechanism of Vapor-Liquid Nucleation", Progress of Theoretical Physics Supplement, 138, 257-258(2000). DOI: 10.1143/PTPS.138.257

            15. Yasuoka, K., Murakoshi, S., "Molecular dynamics simulation of dissociation process for methane hydrate", Annals of the New York Academy of Sciences, 912, 678-684(2000). DOI: 10.1111/j.1749-6632.2000.tb06823.x

      • 1999年 (2 papers)

            • 14. Kinjo, T., Ohguchi, K., Yasuoka, K., Matsumoto, M., "Computer Simulation of Fluid Phase Change: Vapor Nucleation and Bubble Formation Dynamics", Computational Materials Science, 14, 138-141(1999). DOI: 10.1016/S0927-0256(98)00088-3

            13. M. Matsumoto, Yasuoka, K. and Ohguchi K., "Molecular Processes of Cluster Formation in Supersaturated Vapor", Thermal Science & Engineering, 7, 75-80(1999).in press.

      • 1998年 (4 papers)

            • 12. Tanimura, S., Yasuoka, K., Ebisuzaki, T., "Molecular Dynamics Simulations of the Homogeneous Nucleation of UF6 and SF6 Molecules: Effects of the Intramolecular Vibrational Relaxations on the Nucleation Rates", Journal of Chemical Physics, 109, 4492-4497(1998). DOI: 10.1063/1.477052

            11. Yasuoka, K., Matsumoto, M., "Molecular Dynamics Simulation of Homogeneous Nucleation in Supersaturated Water Vapor", Fluid Phase Equilbria, 44, 369-376(1998). DOI: 10.1016/S0378-3812(97)00281-1

            10. Yasuoka K., Matsumoto M., "Molecular Dynamics of Homogeneous Nucleation in the Vapor Phase I. Lennard-Jones Fluid", Journal of Chemical Physics, 109, 8451-8462(1998). DOI: 10.1063/1.477509

            9. Yasuoka K., Matsumoto M., "Molecular Dynamics of Homogeneous Nucleation in the Vapor Phase II. Water", Journal of Chemical Physics, 109, 8463-8470(1998). DOI: 10.1063/1.477510

      • 1996年 (1 paper)

            • 8. Matsumoto, M., Yasuoka, K., Kataoka, Y., "Molecular Mechanism of Evaporation and Condendation", Thermal Science & Engineering, 3, 27-31(1996). DOI: 10.1016/0167-7322(95)00892-0

      • 1995年 (2 papers)

            • 7. Matsumoto, M., Yasuoka, K., Kataoka, Y., "Molecular Simulation of Evaporation and Condensation", Fluid Phase Equilibria, 104, 431-439(1995). DOI: 10.1016/0378-3812(94)02667-P

            6. Yasuoka, K., Matsumoto, M., Kataoka, Y., "Dynamics near a Liquid Surface: Mechanisms of Evaporation and Condensation", Journal of Molecular Liquid, 65, 329-332(1995). DOI: 10.1016/0167-7322(95)00892-0

      • 1994年 (5 papers)

            • 5. Matsumoto, M., Yasuoka, K., Kataoka, Y., "Evaporation and Condensation at a Liquid Methanol Surface", THEOCHEM - Journal of Molecular Structure, 318, 161-168(1994). DOI: 10.1016/S0166-1280(09)80094-8

            4. Yasuoka, K., Matsumoto, M., Kataoka, Y., "Evaporation and Condensation as a Unimolecular Chemical Reaction: Does the Potential Barrier Exist at a Molecular Liquid Surface?", Bulletin of the Chemical Society of Japan, 67, 859-862(1994). DOI: 10.1246/bcsj.67.859

            3. Matsumoto, M., Yasuoka, K., Kataoka, Y., "Microscopic Features of Evaporation and Condensation at Liquid Surfaces: Molecular Dynamics Simulation", Thermal Science & Engineering, 2, 64-69(1994). DOI: 10.1080/08927029608024075

            2. Matsumoto, M., Yasuoka, K., Kataoka, Y., "Evaporation and Condensation at a Liquid Surface. II. Methanol", Journal of Chemical Physics, 101, 7912-7917(1994). DOI: 10.1063/1.468217

            1. Yasuoka, K., Matsumoto, M., Kataoka, Y., "Evaporation and Condensation at a Liquid Surface. I. Argon", Journal of Chemical Physics, 101, 7904-7911(1994). DOI: 10.1063/1.468216


Yasuoka Laboratory