YASUOKA LAB

Papers

  • Shoji, T., Shinojima, A., Kishimoto, T., Sato, K., Ikegami, N., Yumoto, E., Shindo, R., Uchida, Y., Kusumi, S., Koga, D., Yamamoto, E., Hirano, Y., Ogino, R., Shibata, H., Izawa, K., Yasumi, T., Sato, R., Nakayama, J., Higashiyama, S., Hasegawa, J., Kajiho, H., Sasaki, T., Kuchitsu, Y. and Taguchi, T., A PI(3,5)P2/CHMP4B axis on lysosomes is essential for microautophagic degradation of STING, Nature Communications, 17, 4602 (2026). DOI: 10.1038/s41467-026-72828-4

  • Yano, K., Yasuda, I., Hirano, Y. and Yasuoka, K., Allosteric inhibition mechanism of PTP1B by DPM-1001 using molecular dynamics simulation, Biophysical Journal, 125, 1-10 (2026). DOI: 10.1016/j.bpj.2026.02.005

  • Kojima, T., Yasuda, I., Sato, T., Arai, N. and Yasuoka, K., Enhanced premelting at the ice–rubber interface using all-atom molecular dynamics simulation, Langmuir, 42, 2454-2461 (2026). DOI: 10.1021/acs.langmuir.5c04522

  • Arai, N., Yamamoto, E., Koishi, T., Hirano, Y., Yasuoka, K. and Ebisuzaki, T., Frequency-selective enhancement of water permeation through an aquaporin-inspired fluctuating nanochannel, The Bulletin of the Chemical Society of Japan, 99, uoag120 (2026). DOI: 10.1093/bulcsj/uoag120

  • Yoshine, R., Hirano, Y., Doi, H., Kitahara, S., Akisawa, K., Okuwaki, K., Yamamoto, E., Yasuoka, K. and Mochizuki, Y., Residue‑resolved dynamically averaged interaction analysis of direct factor Xa inhibitors by MD‑FMO combination calculations, Journal of Computer-Aided Molecular Design, 40, 132 (2026). DOI: 10.1007/s10822-026-00846-x

  • Winarto, W., Yuliati, L., Anam, K., Brumby, P. E. and Yasuoka, K., A Molecular Dynamics Study of Enhanced CO2 Separation via Boron Nitride Nanotubes Embedded in a Silicon Nitride Membrane, Physical Chemistry Chemical Physics, 27, 14597-14605 (2025). DOI: 10.1039/D5CP01337B

  • Yasuda, I., Bülow, S., Tesei, G., Yamamoto, E., Yasuoka, K. and Lindorff-Larsen, K., Coarse-Grained Model of Disordered RNA for Simulations of Biomolecular Condensates, Jouranl of Chemical Theory and Computation, 21, 2766-2779 (2025). DOI: 10.1021/acs.jctc.4c01646

  • Suzuki, M., Adachi, K., Wiriyasermukul, P., Fukumura, M., Tamura, R., Hirano, Y., Aizawa, Y., Miyamoto, T., Taniguchi, S., Toda, M., Homma, H., Kanekura, K., Yasuoka, K., Kanai, T., Sugimoto, M., Nagamori, S., Yasui, M. and Sasabe, J., D-serine suppresses one-carbon metabolism by competing with mitochondrial L-serine transport, Biochemistry and Chemical Biology (2025). DOI: 10.7554/eLife.108562.1

  • Nishihara, R., Kihara, Y., Yamamoto, E., Hirano, Y. and Kurita, R, Discovery of Pseudo-Luciferase Activity in Immunoglobulin G (IgG) and Its Application to the Detection of IgG Denaturation, Analytical Chemistry, 97, 9935-9943 (2025). DOI: 10.1021/acs.analchem.5c00646

  • Akisawa, K., Sakuma, Y., Tsukamoto, A., Doi, H., Okuwaki, K., Hirano, Y., Yamamoto, E., Yasuoka, K. and Mochizuki, Y., FMO-based interaction analysis on DEET/Icaridin – AgamOBP1 complex, Chemistry Letters, 54, upaf030 (2025). DOI: 10.1093/chemle/upaf030

  • Kato, Y., Muncan, J., Hirano, Y., Yamamoto, H., Tsenkova, R. and Yasui, M., Identification of Redox State Based on the Difference in Solvation Dynamics, Chemistry Open, 14, e202400278 (2025). DOI: 10.1002/open.202400278

  • Doi, H., Nakano, T., Sakakura, K., Akisawa, K., Okuwaki, K., Hirano, Y., Yamamoto, E., Yasuoka, K., Ohshima, S., Katagiri, T. and Mochizuki, Y., Large-Scale FMO-MP2 Calculations of the Spike Protein Droplet Model, Journal of Computational Chemistry, 46, e70052 (2025). DOI: 10.1002/jcc.70052

  • Zhang, L., Pan, Y., Uekusa, H., Suzuki, T., Dohmae, N., Hattori, A., Hirano, Y. and Kakeya, H., Natural Lysine-Reactive Meroterpenoids, Stachybenzals A–C, as Covalent Asparagine Synthetase Inhibitors, Journal of Natural Products, 88, 1797-1803 (2025). DOI: 10.1021/acs.jnatprod.5c00572

  • Ono, Y., Yamamoto, E. and Yasuoka, K., Water-ethanol separation with Janus tip charged carbon nanotubes, Physical Chemistry Chemical Physics, 27, 25524-25535 (2025). DOI: 10.1039/D5CP03818A

  • 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). DOI: 10.1021/acs.jctc.3c00995

  • Winarto, Yuliati, L., Purnami, Brumby, P. E., Yasuoka, K., High selectivity of CO2 capture with single- and double-walled carbon nanotubes, Environmental Science: Nano, 12, 1375-1383 (2024). DOI: 10.1039/D4EN00496E

  • Kowaguchi, A., Brumby, P. E. and Yasuoka, K., Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization, Journal of Chemical Information and Modeling, 64, 4673-4686 (2024). DOI: 10.1021/acs.jcim.4c00078

  • Yasuda, I., Endo, K., Arai, N. and Yasuoka, K., In-layer inhomogeneity of molecular dynamics in quasi-liquid layers of ice, Communications Chemistry, 7, 117 (2024). DOI: 10.1038/s42004-024-01197-0

  • 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). DOI: 10.1063/5.0177815

  • Ono Y., Yamamoto E. and Yasuoka K., Water structures in tip-charged carbon nanotubes, The Journal of Chemical Physics, 161, 054702 (2024). DOI: 10.1063/5.0218315

  • 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). DOI: 10.1038/s41420-023-01755-w

  • 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). DOI: 10.1016/j.ejphar.2023.176156

  • 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, 8567-8578 (2023). DOI: 10.1021/acsami.2c16366

  • Nitta, H., Ozawa, T. and Yasuoka, K., Construction of full-atomistic polymer amorphous structures using reverse-mapping from Kremer–Grest models, The Journal of Chemical Physics, 159, 194903 (2023). DOI: 10.1063/5.0159722

  • 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). DOI: 10.1039/D2SM01542K

  • 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). DOI: 10.1063/5.0156203

  • 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, 71, 897-905 (2023). DOI: 10.1248/cpb.c23-00622

  • 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). DOI: 10.1371/journal.pone.0287025

  • 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, 7194-7204 (2023). DOI: 10.1021/acs.jpcb.3c02018

  • 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). DOI: 10.1103/PhysRevResearch.5.023057

  • 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). DOI: 10.1039/D3RA06375E

  • 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). DOI: 10.1039/D2NH00563H

  • 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, 22, 15-17 (2023). DOI: 10.2477/jccj.2023-0019

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

  • 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). DOI: 10.1021/acs.jcim.1c01206

  • 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). DOI: 10.1063/5.0099473

  • 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). DOI: 10.1038/s42003-022-03416-7

  • 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). DOI: 10.1021/acs.jctc.1c01047

  • 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). DOI: 10.1039/D2SM00311B

  • 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). DOI: 10.1039/D2SM00852A

  • 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). DOI: 10.1038/s41598-022-05061-w

  • 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). DOI: 10.1021/acs.jcim.2c00608

  • 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). DOI: 10.1021/acs.jcim.2c01316

  • 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). DOI: 10.1016/j.fluid.2020.112846

  • 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). DOI: 10.3390/molecules26051421

  • 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). DOI: 10.1371/journal.pone.0250593

  • 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). DOI: 10.1063/5.0055027

  • 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

  • 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). DOI: 10.1371/journal.pone.0231714

  • 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). DOI: 10.1063/5.0017505

  • 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). DOI: 10.1103/PhysRevResearch.2.043442

  • 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). DOI: 10.1016/j.csbj.2020.05.012

  • 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). DOI: 10.1039/c9cc05009d

  • 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). DOI: 10.1063/1.5084785

  • 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). DOI: 10.1039/C9NR00219G

  • 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). DOI: 10.1021/acs.jced.8b01230

  • 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). DOI: 10.1007/978-1-4939-9121-1_2

  • 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). DOI: 10.1063/1.5064410

  • 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). DOI: 10.1088/1757-899X/494/1/012099

  • 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). DOI: 10.1039/C9CP01799B

  • 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). DOI: 10.1038/s41598-018-30364-2

  • 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). DOI: 10.1038/s41598-018-22514-3

  • 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). DOI: 10.1063/1.5021024

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

  • 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). DOI: 10.3390/ijms19092715

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

  • 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). DOI: 10.1063/1.5037647

  • 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). DOI: 10.1609/aaai.v32i1.11863

  • 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). DOI: 10.1039/C8TA04697B

  • 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). DOI: 10.1073/pnas.1802342115

  • 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). DOI: 10.1039/C7CP08435H

  • 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). DOI: 10.1063/1.5016609

  • 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

  • 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

  • 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). DOI: 10.1126/sciadv.1601871

  • 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

  • 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

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

  • 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

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

  • 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). DOI: 10.1038/s41598-017-08501-0

  • 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). DOI: 10.1126/sciadv.1701400

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

  • 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

  • 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). DOI: 10.3390/w9070473

  • 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

  • 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). DOI: 10.1299/jtst.2016jtst0044

  • 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). DOI: 10.1016/j.fluid.2015.10.005

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

  • 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

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

  • 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). DOI: 10.1039/C6CP02380K

  • 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). DOI: 10.1021/acsnano.6b04087

  • 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). DOI: 10.1039/C6CP06731J

  • 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). DOI: 10.1021/acs.jpcc.6b09669

  • 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). DOI: 10.1063/1.4955401

  • 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). DOI: 10.1080/08927022.2014.913791

  • 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). DOI: 10.1080/08927022.2014.978313

  • 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). DOI: 10.1038/srep18245

  • 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). DOI: 10.1080/08927022.2014.998210

  • 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). DOI: 10.1021/acs.jctc.5b00195

  • 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). DOI: 10.1002/jcc.24222

  • 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). DOI: 10.1080/08927022.2014.954572

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

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

  • 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). DOI: 10.1039/C4CP05732E

  • Suh, D. and Yasuoka, K., Nanoscale Droplet Vaporization by Molecular Dynamics, Molec. Simul., 41, 896-904 (2015). DOI: 10.1080/08927022.2014.968851

  • 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). DOI: 10.1039/C4FD00219A

  • 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). DOI: 10.1038/srep08876

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

  • 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). DOI: 10.1080/08927022.2014.940500

  • 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). DOI: 10.1080/08927022.2014.929125

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

  • 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). DOI: 10.2142/biophys.55.242 Selected as a cover

  • 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).

  • 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). DOI: 10.1103/PhysRevE.89.022718

  • 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). DOI: 10.1021/jp410596d

  • 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). DOI: 10.1063/1.4890302

  • 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). DOI: 10.1063/1.4862030

  • 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). DOI: 10.1063/1.4874696

  • 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). DOI: 10.1002/anie.201406546

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

  • 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). DOI: 10.1063/1.4863330 Selected as a cover

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

  • 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). DOI: 10.1021/ct400221h

  • 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). DOI: 10.1155/2013/207287

  • 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). DOI: 10.1016/j.memsci.2013.02.006

  • 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). DOI: 10.1063/1.4811289

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

  • 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). DOI: 10.1134/S1547477113060101

  • 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). DOI: 10.1021/ct3010968 Selected as a cover

  • 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). DOI: 10.1016/j.cpc.2012.09.011

  • 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). DOI: 10.1007/s10404-012-1107-3

  • 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). DOI: 10.1103/PhysRevE.87.052715

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

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

  • 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). DOI: 10.1021/ja402014u

  • 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). DOI: 10.1039/C3NR02024J

  • 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). DOI: 10.1063/1.4795499

  • 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). 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). DOI: 10.1021/ct3003805

  • 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). DOI: 10.1080/08927022.2010.547857

  • 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). DOI: 10.1021/jp303330c

  • 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). DOI: 10.1143/JJAP.51.04DA07

  • 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). DOI: 10.1002/jcc.23082

  • 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). DOI: 10.1080/08927022.2010.539216

  • 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). DOI: 10.2174/1874091X01206010094

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

  • 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). 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). DOI: 10.5539/ijc.v4n1p14

  • 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). DOI: 10.1016/j.chemphys.2012.04.002

  • 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). DOI: 10.1063/1.3677231

  • 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). DOI: 10.1143/JPSJS.81SA.SA014

  • 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). DOI: 10.1021/la2034643

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

  • 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). DOI: 10.1016/j.bbamem.2012.04.009

  • 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). DOI: 10.4236/ns.2012.45044

  • 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). DOI: 10.1063/1.4757914

  • 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). DOI: 10.1063/1.3658640

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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). DOI: 10.4236/ns.2011.312126

  • 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

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

  • 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

  • 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). DOI: 10.1021/ct200458m

  • 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

  • Myung, H., J., Sakamaki, R., Oh, K., J., Narumi, T., Yasuoka, K., and Lee, S., Accelerating molecular dynamics simulation using graphics processing unit, Bull. Korean Chem. Soc., 31, 3639 (2010). DOI: 10.5012/bkcs.2010.31.12.3639

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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).

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

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

  • 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

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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • Kholmurodov, K., Smith, W., Yasuoka, K., Darden, T., Ebisuzaki, T., A smooth-particle mesh ewald method for DL_POLY molecular dynamics simulation package on the Fujitsu VPP700, Journal of Computational Chemistry, 21, 1187-1191 (2000). DOI: 10.1002/1096-987X(200010)21:133.0.CO;2-7

  • 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

  • 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

  • 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

  • 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

  • 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

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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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