論文 - 泰岡　顕治

Mechanism for H<inf>2</inf>diffusion in sII hydrates by molecular dynamics simulations

Hasegawa T., Brumby P.E., Yasuoka K., Sum A.K.

Journal of Chemical Physics （Journal of Chemical Physics）  153 （ 5 ）  2020年08月

ISSN  00219606

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© 2020 Author(s). Among the many different types of molecules that form clathrate hydrates, H2 is unique as it can easily diffuse into and out of clathrate cages, a process that involves the physical-chemical interactions between guest (H2) and host (water) molecules, and is unlike any other molecular system. The dynamic and nano-scale process of H2 diffusion into binary structure II hydrates, where the large cages are occupied by larger molecules, was studied using molecular dynamics simulation. As the H2 molecules diffused from one cage to another, two types of diffusion processes were observed: (i) when moving between a pair of large cages, the H2 molecules pass through the central part of the hexagonal rings; (ii) however, when the H2 molecules move from a large cage to a small one, it requires one of the pentagonal rings to partially break, as this allows the H2 molecule to pass through the widened space. While the diffusion of H2 molecules between large cages was found to occur more frequently, the presence of SF6 molecules in the large cages was found to inhibit diffusion. Therefore, in order to attain higher H2 storage capacities in binary hydrates, it is suggested that there is an optimal number of large cages that should be occupied by SF6 molecules.

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Dataflow programming for the analysis of molecular dynamics with AViS, an analysis and visualization software application

Pua K., Yuhara D., Ayuba S., Yasuoka K.

PLoS ONE （PLoS ONE）  15 （ 4 ）  2020年04月

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© 2020 Pua et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The study of molecular dynamics simulations is largely facilitated by analysis and visualization toolsets. However, these toolsets are often designed for specific use cases and those only, while scripting extensions to such toolsets is often exceedingly complicated. To overcome this problem, we designed a software application called AViS which focuses on the extensibility of analysis. By utilizing the dataflow programming (DFP) paradigm, algorithms can be defined by execution graphs, and arbitrary data can be transferred between nodes using visual connectors. Extension nodes can be implemented in either Python, C++, and Fortran, and combined in the same algorithm. AViS offers a comprehensive collection of nodes for sophisticated visualization state modifications, thus greatly simplifying the rules for writing extensions. Input files can also be read from the server automatically, and data is fetched automatically to improve memory usage. In addition, the visualization system of AViS uses physically-based rendering techniques, improving the 3D perception of molecular structures for interactive visualization. By performing two case studies on complex molecular systems, we show that the DFP workflow offers a much higher level of flexibility and extensibility when compared to legacy workflows.

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A biointerface effect on the self-assembly of ribonucleic acids: A possible mechanism of RNA polymerisation in the self-replication cycle

Arai N., Kobayashi Y., Yasuoka K.

Nanoscale （Nanoscale）  12 （ 12 ） 6691 - 6698 2020年03月

ISSN  20403364

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© 2020 The Royal Society of Chemistry. Despite decades of intensive research, many questions remain on the formation and growth of the first cells on Earth. Here, we used computer simulation to compare the self-assembly process of ribonucleic acids in two environments: Enclosed in a vesicle-cell membrane and in the bulk. The self-assembly was found to be more favoured in the former environment, and the origin of such a biointerface effect was identified. These results will contribute to a better understanding of the origin of life on the primitive Earth.

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The acidic tail of HMGB1 regulates its secondary structure and conformational flexibility: A circular dichroism and molecular dynamics simulation study

Anggayasti W.L., Ogino K., Yamamoto E., Helmerhorst E., Yasuoka K., Mancera R.L.

Computational and Structural Biotechnology Journal （Computational and Structural Biotechnology Journal）  18   1160 - 1172 2020年

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© 2020 The Author(s) High mobility group box 1 (HMGB1) is a damage-associated molecular pattern (DAMP) molecule that triggers the progression of several pro-inflammatory diseases such as diabetes, Alzheimer's disease and cancer, by inducing signals upon interaction with the receptors such as the receptor for advanced glycation end-products (RAGE) and toll-like receptors (TLRs). The acidic C-terminal tail of HMGB1 is an intrinsically disordered region of the protein which is known to determine the interaction of HMGB1 to DNA and histones. This study characterizes its structural properties using a combination of circular dichroism (CD) and molecular dynamics (MD) simulations. The full-length and tail-less forms of HMGB1 were compared to rationalise the role of the acidic tail in maintaining the stability of the entire structure of HMGB1 in atomistic detail. Consistent with experimental data, the acidic tail was predicted to adopt an extended conformation that allows it to make a range of hydrogen-bonding and electrostatic interactions with the box-like domains that stabilize the overall structure of HMGB1. Absence of the acidic tail was predicted to increase structural fluctuations of all amino acids, leading to changes in secondary structure from α-helical to more hydrophilic turns along with increased exposure of multiple amino acids to the surrounding solvent. These structural changes reveal the intrinsic conformational dynamics of HMGB1 that are likely to affect the accessibility of its receptors.

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Crystal Engineering of Bi<inf>2</inf>WO<inf>6</inf> to Polar Aurivillius-Phase Oxyhalides

Morita K., Park J., Kim S., Yasuoka K., Walsh A.

Journal of Physical Chemistry C （Journal of Physical Chemistry C）  123 （ 48 ） 29155 - 29161 2019年12月

ISSN  19327447

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© 2019 American Chemical Society. The Aurivillius phases of complex bismuth oxides have attracted considerable attention because of their lattice polarization (ferroelectricity) and photocatalytic activity. We report a first-principles exploration of Bi2WO6 and the crystal engineering through replacing W6+ by pentavalent (Nb5+ and Ta5+) and tetravalent (Ti4+ and Sn4+) ions, with charge neutrality maintained by the formation of a mixed anion oxyhalide sublattice. We find that Bi2SnO4F2 is thermodynamically unstable, in contrast to Bi2TaO5F, Bi2NbO5F, and Bi2TiO4F2. The electric dipoles introduced by chemical substitutions in the parent compound are found to suppress the spontaneous polarization from 61.55 μC/cm2 to below 15.50 μC/cm2. Analysis of the trends in electronic structure, surface structure, and ionization potentials is reported. This family of materials can be further extended with control of layer thicknesses and choice of compensating halide species.

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Method to implement interaction surfaces with virtual companion particles for molecular dynamics simulations

Koishi T., Yasuoka K., Zeng X.C.

Journal of Chemical and Engineering Data （Journal of Chemical and Engineering Data）  64 （ 9 ） 3693 - 3700 2019年09月

ISSN  00219568

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© 2019 American Chemical Society. We developed a computational method to establish an interaction surface using virtual companion particles. Upon the implementation of this new method, wetting behaviors of liquid droplets on highly textured solid surfaces can be investigated by molecular dynamics (MD) simulations. The interactions between atoms in the liquid droplets and the "interaction surface" depend only on the distance from the atom to the surface. Textured surfaces with nanopillars can be modeled by setting the range of pillars. The interactions with the droplet atoms can be calculated by using the potential function of the virtual particles which are placed interactively on the range of pillars and the bottom surfaces. The positions of the virtual particles are determined so as to minimize the distance from the droplet atoms and can be set independently of the lattice structures of the solid surfaces. Hence, we can design various pillar shapes (e.g., cylindrical, cone, and pyramidal shapes) for the textured surfaces. Such a method can be useful for the MD simulation of wetting behavior on a complex rough surface with a simple and yet effective procedure.

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Detection of molecular behavior that characterizes systems using a deep learning approach

Endo K., Yuhara D., Tomobe K., Yasuoka K.

Nanoscale （Nanoscale）  11 （ 20 ） 10064 - 10071 2019年05月

ISSN  20403364

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© 2019 The Royal Society of Chemistry. Molecular dynamics (MD) simulation is a powerful computational method to observe molecular behavior. Although the detection of molecular behavior that characterizes systems is an important task in the study of MD, it is typically difficult and depends on human expert knowledge. Therefore, we propose a novel analysis scheme for MD data using deep neural networks. A key aspect of our scheme is the estimation of statistical distances between different ensembles that are probability distributions over the possible states of systems. This allows us to build low-dimensional embeddings of ensembles to visualize differences between systems in a compact metric space. Furthermore, the molecular behavior that contributes to the differences between systems can also be detected using the trained function of deep neural networks. The applicability of our scheme is demonstrated using three types of MD data. Our scheme could be a powerful tool to clarify the underlying physics in the molecular systems.

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Cage occupancies, lattice constants, and guest chemical potentials for structure II hydrogen clathrate hydrate from Gibbs ensemble Monte Carlo simulations

Brumby P., Yuhara D., Hasegawa T., Wu D., Sum A., Yasuoka K.

Journal of Chemical Physics （Journal of Chemical Physics）  150 （ 13 ）  2019年04月

ISSN  00219606

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© 2019 Author(s). In this paper, equilibrium properties of structure II hydrates of hydrogen were determined from Monte Carlo simulations in the isothermal-isobaric Gibbs ensemble. Water and hydrogen molecules are described by the TIP4P/Ice and Silvera-Goldman models, respectively. The use of the Gibbs ensemble has many key advantages for the simulation of hydrates. By the separation of hydrogen vapor and hydrate phases into their own domains, coupled with transfer moves of hydrogen molecules between domains, cage occupancies were determined. Furthermore, the choice of this ensemble also allows equilibrium lattice constants and guest molecule chemical potentials to be straightforwardly estimated. Results for hydrogen mass fractions indicate reasonable agreement with prior simulation data and theoretical models, while detailed analysis of cage occupancy distributions and neighboring cage pair occupancy combinations gives valuable insight into the behavior of this hydrate at the inter-cage scale. These results will aid in the construction of theoretical models, for which knowledge of the occupancy of neighboring cages is of great importance. In support of previous experimental and theoretical works, we also find evidence of double occupancy of a few small cages inside of the hydrate stability zone, albeit at very high pressures; approximately 0.1% of small cages are doubly occupied at 300 MPa, for temperatures of 225 K and 250 K.

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Selectivity of Carbon Nanotubes under An Electric Field on Transferring Water - Alcohol Mixtures

Winarto, Yamamoto E., Yasuoka K.

IOP Conference Series: Materials Science and Engineering （IOP Conference Series: Materials Science and Engineering）  494 （ 1 ）  2019年03月

ISSN  17578981

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© Published under licence by IOP Publishing Ltd. Carbon nanotubes (CNTs) have shown a great promise for nanofluidic-based applications such as for separation membranes. Water confined in nanotubes has different properties compared with those in bulk. Therefore, to develop a membrane with CNTs, it is very important to clarify the behavior of water in CNTs. In this study, we show effects of an electric field on water in a CNT by molecular dynamics simulation. An electric field aligns the dipole moment of water molecules and induces formation of an ordered structure in a CNT. As a result, the electrostatic interaction between water molecules within the structure becomes stronger. Strengthening of the electrostatics interaction facilitates water molecules preferring to fill a CNT over alcohol molecules. This indicates a strong separation effect for water-alcohol solutions.

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Ordering in clusters of uniaxial anisotropic particles during homogeneous nucleation and growth

Nozawa T., Brumby P., Ayuba S., Yasuoka K.

Journal of Chemical Physics （Journal of Chemical Physics）  150 （ 5 ）  2019年02月

ISSN  00219606

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© 2019 Author(s). The nucleation process of anisotropic particles often differs from that of their spherically symmetric counterparts. Despite a large body of work on the structure of droplets of anisotropic particles, their formation process remains poorly understood. In this study, homogeneous nucleation of uniaxial anisotropic particles was studied. Through structural analysis of cluster development and the formation free energy during the nucleation stage, it was revealed that the nucleation of uniaxial particles begins from highly ordered states. There is, however, a marked decrease in orientational order within the cluster before critical nucleus size is attained. Further investigation on variations in the molecular interactions demonstrates how droplet elongation and the direction of the nematic ordering director relative to the axis of elongation can both be controlled according to the nature of the molecular anisotropy.

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Separation of water-alcohol mixtures using carbon nanotubes under an electric field

Winarto W., Yamamoto E., Yasuoka K.

Physical Chemistry Chemical Physics （Physical Chemistry Chemical Physics）  21 （ 28 ） 15431 - 15438 2019年

ISSN  14639076

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© the Owner Societies. Carbon nanotubes (CNTs) are a promising candidate for separation membranes because of their ability to transport substances at very high flow rates. However, there is a tradeoff between achieving a high selectivity using small pore sizes and the reduction of water flux. Here, using molecular dynamics simulations, we report that CNTs can effectively separate water-methanol mixtures under an electric field. Without an electric field and under piston pressure, both water and methanol flow through a CNT, resulting in no separation effect. In contrast, under an electric field and high piston pressure, CNTs allow selective water permeation while rejecting the permeation of methanol molecules. This separation effect is caused by the ordered structures of water molecules in the CNT. A high filtering effect is observed under the conditions of high methanol concentration in the solution or even with large-diameter CNTs up to 3.39 nm. As long as the ordered structure of water in the CNTs can be maintained, the strong filtering effect can be maintained.

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Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs

Tomobe K., Yamamoto E., Yasuoka K.

Methods in Molecular Biology （Methods in Molecular Biology）  1947   21 - 30 2019年

ISSN  10643745

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© 2019, Springer Science+Business Media, LLC, part of Springer Nature. Rhodopsin is a light-driven G protein-coupled receptor mediating signal transduction in eyes. The molecular dynamics (MD) simulations are powerful computational tools to investigate molecular behavior of proteins and internal water molecules which are related to the function of proteins; however, the MD simulations of the rhodopsin require several technical setups for accurate calculations. This chapter discusses practical methods for setting up the MD simulations of the rhodopsin [preparation of initial systems, condition files for MD simulation package GROMACS, and data analysis]. The data analysis includes the root mean square deviation (RMSD) and mapping of accessibility of water molecules.

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Anisotropy of dodecahedral water cages for guest gas occupancy in semiclathrate hydrates

Yuhara D., Yasuoka K., Takeya S., Muromachi S.

Chemical Communications （Chemical Communications）  55 （ 68 ） 10150 - 10153 2019年

ISSN  13597345

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© 2019 The Royal Society of Chemistry. Anisotropic dodecahedral (D) water cages found in semiclathrate hydrates have unique gas selectivity due to their varied shapes. Herein, the D cages incorporating ideally isotropic rare gases, i.e., Xe, Kr and Ar, were characterized by crystal structure analyses. Stabilization mechanisms of the semiclathrate hydrates by the D cages are discussed.

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A fast and accurate computational method for the linear-combination-based isotropic periodic sum

Takahashi K., Nozawa T., Yasuoka K.

Scientific Reports （Scientific Reports）  8 （ 1 ）  2018年12月

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© 2018, The Author(s). An isotropic periodic sum (IPS) is a powerful technique to reasonably calculate intermolecular interactions for wide range of molecular systems under periodic boundary conditions. A linear-combination-based IPS (LIPS) has been developed to attain computational accuracy close to an exact lattice sum, such as the Ewald sum. The algorithm of the original LIPS method has a high computational cost because it needs long-range interaction calculations in real space. This becomes a performance bottleneck for long-time molecular simulations. In this work, the combination of an LIPS and fast Fourier transform (FFT) was developed, and evaluated on homogeneous and heterogeneous molecular systems. This combinational approach of LIPS/FFT attained computational efficiency close to that of a smooth particle mesh Ewald while maintaining the same high accuracy as the original LIPS. We concluded that LIPS/FFT has great potential to extend the capability of IPS techniques for the fast and accurate computation of many types of molecular systems.

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Effect of central longitudinal dipole interactions on chiral liquid-crystal phases

Nozawa T., Brumby P., Yasuoka K.

International Journal of Molecular Sciences （International Journal of Molecular Sciences）  19 （ 9 ）  2018年09月

ISSN  16616596

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© 2018 by the authors. Licensee MDPI, Basel, Switzerland. Monte Carlo simulations of chiral liquid-crystals, represented by a simple coarse-grained chiral Gay–Berne model, were performed to investigate the effect of central longitudinal dipole interactions on phase behavior. A systematic analysis of the structural properties and phase behavior of both achiral and chiral systems, with dipole interactions, reveals differing effects; strong dipole interactions enhance the formation of layered structures; however, chiral interactions may prevent the formation of such phases under certain conditions. We also observed a short-ranged smectic structure within the cholesteric phases with strong dipole interactions. This constitutes possible evidence of presmectic ordering and/or the existence of chiral line liquid phases, which have previously been observed in X-ray experiments to occur between the smectic twisted grain boundary and cholesteric phases. These results provide a systematic understanding of how the phase behavior of chiral liquid-crystals changes when alterations are made to the strength of dipole interactions.

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Molecular Dynamics Simulation of Ice Crystal Growth Inhibition by Hexadecyl-trimethyl-ammonium Bromide

Shimazu N., Takaiwa D., Suh D., Kawaguchi T., Fuse T., Kaneko T., Yasuoka K.

Langmuir （Langmuir）  34 （ 31 ） 9330 - 9335 2018年08月

ISSN  07437463

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© 2018 American Chemical Society. Recent experiments have found hexadecyl-trimethyl-ammonium bromide (CTAB) to have superior ice nucleation inhibition properties [J. Phys. Chem. B 121, 6580]. The mechanism of how the inhibition takes place remains unclear. Therefore, molecular dynamics was used to simulate ice crystallization of a water/CTAB/ice system. The ice crystallization rate for a pure water system was compared for the basal [0001], first prism [1010], and secondary prism plane [1120], where the basal plane grew the slowest followed by the first prism plane. When CTAB was added to the ice-liquid water system, crystallization was clearly impeded. Even when ice starts growing away from the CTAB molecule, the hydrophilic head would at some point protrude and get caught in the water/ice interface. Once the head of the CTAB was encapsulated in the advancing interface, the hydrophobic body would wriggle around and disrupt the formation of hydrogen bond networks that are essential for ice growth. When the interface clears the length of the body of the CTAB molecule, ice crystallization resumes at its normal pace. In summary, the inhibition of ice growth is a combination of the hydrophilic head acting as an anchor and the dynamic motion of the hydrophobic tail hindering stable hydrogen bonding for ice growth.

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Kinetic analysis of homogeneous droplet nucleation using large-scale molecular dynamics simulations

Ayuba S., Suh D., Nomura K., Ebisuzaki T., Yasuoka K.

Journal of Chemical Physics （Journal of Chemical Physics）  149 （ 4 ）  2018年07月

ISSN  00219606

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© 2018 Author(s). Studies on homogeneous nucleation have been conducted for decades, but a large gap between experiment and theory persists when evaluating the nucleation rate because the classical nucleation theory (CNT) with all its modifications still cannot fully incorporate the kinetics of homogeneous nucleation. Recent large-scale molecular dynamics (MD) simulations on homogeneous nucleation estimated a nucleation rate around the same order of magnitude as that obtained in experiments. This immensely improved agreement between experiment and theory is exciting because MD can provide detailed information on molecular trajectories. Therefore, a better understanding of the kinetics of homogeneous nucleation can now be obtained. In this study, large-scale MD simulations on homogeneous nucleation were performed. Through kinetic analysis of the simulation results, the nucleation rate, free energy barrier, and critical cluster size were found. Although the nucleation rates directly obtained from the simulations differed from those calculated from the CNT by 8-13 orders of magnitude, when the parameters calculated from the molecular trajectories were substituted into the classical theory, the discrepancy between the nucleation rates decreased to within an order of magnitude. This proves that the fundamental formulation of the theoretical equation is physically sound. We also calculated the cluster formation free energy and confirmed that the free energy barrier decreases with increasing supersaturation ratio. The estimated barrier height was twice that determined by theory, whereas the critical cluster size showed very good agreement between simulation and theory.

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Phase behaviors of deeply supercooled bilayer water unseen in bulk water

Kaneko T., Bai J., Akimoto T., Francisco J., Yasuoka K., Zeng X.

Proceedings of the National Academy of Sciences of the United States of America （Proceedings of the National Academy of Sciences of the United States of America）  115 （ 19 ） 4839 - 4844 2018年05月

研究論文（学術雑誌）, 共著, 査読有り,  ISSN  00278424

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© 2018 National Academy of Sciences. All rights reserved. Akin to bulk water, water confined to an isolated nanoslit can show a wealth of new 2D phases of ice and amorphous ice, as well as unusual phase behavior. Indeed, 2D water phases, such as bilayer hexagonal ice and monolayer square ice, have been detected in the laboratory, confirming earlier computational predictions. Herein, we report theoretical evidence of a hitherto unreported state, namely, bilayer very low density amorphous ice (BL-VLDA), as well as evidence of a strong first-order transition between BL-VLDA and the BL amorphous ice (BL-A), and a weak first-order transition between BL-VLDA and the BL very low density liquid (BL-VLDL) water. The diffusivity of BL-VLDA is typically in the range of 10 −9 cm 2 /s to 10 −10 cm 2 /s. Similar to bulk (3D) water, 2D water can exhibit two forms of liquid in the deeply supercooled state. However, unlike supercooled bulk water, for which the two forms of liquid can coexist and merge into one at a critical point, the 2D BL-VLDL and BL high-density liquid (BL-HDL) phases are separated by the highly stable solid phase of BL-A whose melting line exhibits the isochore end point (IEP) near 220 K in the temperature−pressure diagram. Above the IEP temperature, BL-VLDL and BL-HDL are indistinguishable. At negative pressures, the metastable BL-VLDL exhibits a spatially and temporally heterogeneous structure induced by dynamic changes in the nanodomains, a feature much less pronounced in the BL-HDL.

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Analysis of three-phase equilibrium conditions for methane hydrate by isometric-isothermal molecular dynamics simulations

Yuhara D., Brumby P., Wu D., Sum A., Yasuoka K.

Journal of Chemical Physics （Journal of Chemical Physics）  148 （ 18 ） 184501 (9 pages) 2018年05月

研究論文（学術雑誌）, 共著, 査読有り,  ISSN  00219606

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© 2018 Author(s). To develop prediction methods of three-phase equilibrium (coexistence) conditions of methane hydrate by molecular simulations, we examined the use of NVT (isometric-isothermal) molecular dynamics (MD) simulations. NVT MD simulations of coexisting solid hydrate, liquid water, and vapor methane phases were performed at four different temperatures, namely, 285, 290, 295, and 300 K. NVT simulations do not require complex pressure control schemes in multi-phase systems, and the growth or dissociation of the hydrate phase can lead to significant pressure changes in the approach toward equilibrium conditions. We found that the calculated equilibrium pressures tended to be higher than those reported by previous NPT (isobaric-isothermal) simulation studies using the same water model. The deviations of equilibrium conditions from previous simulation studies are mainly attributable to the employed calculation methods of pressure and Lennard-Jones interactions. We monitored the pressure in the methane phase, far from the interfaces with other phases, and confirmed that it was higher than the total pressure of the system calculated by previous studies. This fact clearly highlights the difficulties associated with the pressure calculation and control for multi-phase systems. The treatment of Lennard-Jones interactions without tail corrections in MD simulations also contributes to the overestimation of equilibrium pressure. Although improvements are still required to obtain accurate equilibrium conditions, NVT MD simulations exhibit potential for the prediction of equilibrium conditions of multi-phase systems.

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Density functional theory study of atomic and electronic properties of defects in reduced anatase TiO<inf>2</inf> nanocrystals

Morita K., Yasuoka K.

AIP Advances （AIP Advances）  8 （ 3 ） 035119 (14 pages) 2018年03月

研究論文（学術雑誌）, 共著, 査読有り

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© 2018 Author(s). Anatase TiO2 nanocrystals have received considerable attention owing to their promising applications in photocatalysis, photovoltaics, and fuel cells. Although experimental evidence has shown that the performance of nanocrystals can be significantly improved through reduction, the mechanistic basis of this enhancement remains unclear. To shed a light on the chemistry of reduced anatase TiO2 nanocrystals, density functional theory were used to investigate the properties of defects and excess electrons. We demonstrated that oxygen vacancies are stable both on the surface and at the sub-surface of the nanocrystal, while titanium interstitials prefer sub-surface sites. Different defect locations possessed different excess electron structures, which contributed to deep and shallow states in the band gap of the nanocrystals. Furthermore, valence band tailing was observed, resulting in band gap narrowing. The theoretical results presented here deepen our understanding, and show the potential of defects to considerably change the macroscopic properties of anatase TiO2 nanocrystals.

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Heterogeneous cavitation and crystallisation with an impurity by molecular dynamics

Suh D., Yasuoka K.

Molecular Simulation （Molecular Simulation）  44 （ 7 ） 530 - 533 2018年03月

研究論文（学術雑誌）, 共著, 査読有り,  ISSN  08927022

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© 2017 Informa UK Limited, trading as Taylor & Francis Group. A homogeneous metastable liquid system and a heterogeneous system with an immersed impurity were used to investigate the cavitation and crystallisation characteristics by molecular dynamics. An isochoric quench was conducted to the systems, which initially produced a cavity, where the entire system subsequently crystallised. The systems with the impurities showed an overall increase in the crystal nucleation rate and a modest but clear shape effect was observed. Similar to previous droplet condensation studies, a clear curvature effect was observed to influence the rate of the phenomenon. At the onset of quenching, crystallisation occurred on the faces of the seed, so a flat surface promoted local crystallisation, which propagated the formation of the cavity, and thereafter increased the density of the metastable liquid, so to advance overall crystallisation within the system.

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Critical test of isotropic periodic sum techniques with group-based cut-off schemes

Nozawa T., Yasuoka K., Takahashi K.

Scientific Reports （Scientific Reports）  8 （ 1 ） 4185 (9 pages) 2018年03月

研究論文（学術雑誌）, 共著, 査読有り

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© 2018 The Author(s). Truncation is still chosen for many long-range intermolecular interaction calculations to efficiently compute free-boundary systems, macromolecular systems and net-charge molecular systems, for example. Advanced truncation methods have been developed for long-range intermolecular interactions. Every truncation method can be implemented as one of two basic cut-off schemes, namely either an atom-based or a group-based cut-off scheme. The former computes interactions of "atoms" inside the cut-off radius, whereas the latter computes interactions of "molecules" inside the cut-off radius. In this work, the effect of group-based cut-off is investigated for isotropic periodic sum (IPS) techniques, which are promising cut-off treatments to attain advanced accuracy for many types of molecular system. The effect of group-based cut-off is clearly different from that of atom-based cut-off, and severe artefacts are observed in some cases. However, no severe discrepancy from the Ewald sum is observed with the extended IPS techniques.

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Detection of Anomalous Dynamics for a Single Water Molecule

Tomobe K., Yasuoka K.

Journal of Chemical Theory and Computation （Journal of Chemical Theory and Computation）  14 （ 3 ） 1177 - 1185 2018年03月

研究論文（学術雑誌）, 共著, 査読有り,  ISSN  15499618

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© 2018 American Chemical Society. Water dynamics is of predominant importance in life, and it plays a critical role in chemical and biological systems. Many studies have reported nonbulk and anomalous dynamics of water molecules; however, a general method to detect the anomalous dynamics is yet to be established. Here, we develop a detection approach for the anomalous dynamics of a water molecule. Using a time series of the dipole vector of a water molecule, our approach achieves single-molecule detection of the anomalous dynamics for all water molecules in the system. Moreover, our approach quantifies the anomalous dynamics of a water molecule, which enables users to compare between different systems. In addition to the applicability, our approach has computational efficiency because it never calculates interactions with any other molecules. Experiments on five different systems of molecular dynamics simulations illustrate that our approach successfully detects the change points of water-molecule dynamics. These results demonstrate that our approach is a useful tool and provides a better understanding of dynamics of water molecules.

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Structural determinants in the bulk heterojunction

Acocella A., Höfinger S., Haunschmid E., Pop S., Narumi T., Yasuoka K., Yasui M., Zerbetto F.

Physical Chemistry Chemical Physics （Physical Chemistry Chemical Physics）  20 （ 8 ） 5708 - 5720 2018年02月

研究論文（学術雑誌）, 共著, 査読有り,  ISSN  14639076

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© 2018 the Owner Societies. Photovoltaics is one of the key areas in renewable energy research with remarkable progress made every year. Here we consider the case of a photoactive material and study its structural composition and the resulting consequences for the fundamental processes driving solar energy conversion. A multiscale approach is used to characterize essential molecular properties of the light-absorbing layer. A selection of bulk-representative pairs of donor/acceptor molecules is extracted from the molecular dynamics simulation of the bulk heterojunction and analyzed at increasing levels of detail. Significantly increased ground state energies together with an array of additional structural characteristics are identified that all point towards an auxiliary role of the material's structural organization in mediating charge-transfer and -separation. Mechanistic studies of the type presented here can provide important insights into fundamental principles governing solar energy conversion in next-generation photovoltaic devices.

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Theoretical analyses on water cluster structures in polymer electrolyte membrane by using dissipative particle dynamics simulations with fragment molecular orbital based effective parameters

Okuwaki K., Mochizuki Y., Doi H., Kawada S., Ozawa T., Yasuoka K.

RSC Advances （RSC Advances）  8 （ 60 ） 34582 - 34595 2018年

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© The Royal Society of Chemistry. The mesoscopic structures of polymer electrolyte membrane (PEM) affect the performances of fuel cells. Nafion® with the Teflon® backbone has been the most widely used of all PEMs, but sulfonated poly-ether ether-ketone (SPEEK) having an aromatic backbone has drawn interest as an alternative to Nafion. In the present study, a series of dissipative particle dynamics (DPD) simulations were performed to compare Nafion and SPEEK. These PEM polymers were modeled by connected particles corresponding to the hydrophobic backbone and the hydrophilic moiety of sulfonic acid group. The water particle interacting with Nafion particles was prepared as well. The crucial interaction parameters among DPD particles were evaluated by a series of calculations based on the fragment molecular orbital (FMO) method in a non-empirical way (Okuwaki et al., J. Phys. Chem. B, 2018, 122, 338-347). Through the DPD simulations, the water and hydrophilic particles aggregated, forming cluster networks surrounded by the hydrophobic phase. The structural features of formed water clusters were investigated in detail. Furthermore, the differences in percolation behaviors between Nafion and SPEEK revealed much better connectivity among water clusters by Nafion. The present FMO-DPD simulation results were in good agreement with available experimental data.

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Self-assembly of peptide amphiphiles by vapor pressure osmometry and dissipative particle dynamics

Seki T., Arai N., Suh D., Ozawa T., Shimada T., Yasuoka K., Hotta A.

RSC Advances （RSC Advances）  8 （ 47 ） 26461 - 26468 2018年

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© The Royal Society of Chemistry. Peptide amphiphiles are one of the most promising materials in the biomedical field, so much effort has been devoted to characterizing the mechanism of their self-assembly and thermosensitive gelation. In this work, vapor pressure osmometry measurements were carried out to parameterize the thermosensitivity of interactions between peptide amphiphiles in an aqueous solution. The osmometry measurement verified that the peptides became more hydrophobic as temperature increased, which was quantitatively described with the Flory-Huggins χ parameter. Thereafter, a coarse-grained molecular model was used to simulate peptide amphiphiles dissolved in an aqueous solution. The temperature sensitive coarse-grained parameter aHW, which is the repulsive force between the hydrophilic head of the peptide amphiphile and water was estimated from the aforementioned experimentally obtained χ. Furthermore, the effects of concentration and temperature on the self-assembly behavior of peptide amphiphiles were quantitatively studied by dissipative particle dynamics. The simulation results revealed that aHW plays an important role in self-assembly characteristics and in the resulting microstructure of the peptide amphiphiles, which coincides with previous experimental and computational findings. The methodology in quantitatively linking the coarse-grained parameter from experiment and theory provides a sensible foundation for bridging future simulation studies with experimental work on macromolecules.

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Recent advances in clathrate hydrates research using molecular simulations

Yuhara D., Hiratsuka M., Yasuoka K.

Review of High Pressure Science and Technology/Koatsuryoku No Kagaku To Gijutsu （Review of High Pressure Science and Technology/Koatsuryoku No Kagaku To Gijutsu）  28 （ 2 ） 102 - 112 2018年

ISSN  0917639X

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© 2018, Japan Society of High Pressure Science and Technology. All rights reserved. The thermodynamic and kinetic properties of clathrate hydrates have been studied for scientific interest and various potential industrial applications. This article highlights recent advances in the hydrate researches using molecular simulations with a focus on formation processes and thermodynamic properties. Subsets of molecular simulations, Molecular Dynamics (MD), Monte Carlo (MC) and ab initio MD simulations have been applied to hydrate systems and provide the fundamental insights at molecular level.

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Oxygen vacancy-originated highly active electrocatalysts for the oxygen evolution reaction

Hirai S., Morita K., Yasuoka K., Shibuya T., Tojo Y., Kamihara Y., Miura A., Suzuki H., Ohno T., Matsuda T., Yagi S.

Journal of Materials Chemistry A （Journal of Materials Chemistry A）  6 （ 31 ） 15102 - 15109 2018年

ISSN  20507488

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© 2018 The Royal Society of Chemistry. The oxygen evolution reaction (OER) is an important reaction in the field of renewable energy and is utilized in electrochemical water splitting for hydrogen fuel production and rechargeable metal-air batteries. Herein, we report a new oxygen evolution reaction mechanism originating from oxygen vacancies, which remarkably enhances the OER activity of oxygen deficient electrocatalysts. The OER activity of Sr 2 VFeAsO 3-δ is drastically enhanced above the lattice oxygen vacancy of δ = 0.5, exhibiting ∼300 mV lower overpotential and 80 times higher specific activity at 1.7 V vs. RHE. Surprisingly, the initially low OER activity of Sr 2 VFeAsO 3-δ (δ < 0.5) is enhanced to the level of state-of-the-art OER catalysts simply by introducing higher concentrations of oxygen vacancies. Density functional theory (DFT) calculations clarify that the oxygen vacancies are initially dominated by one of the crystallographic sites, while two types of crystallographic sites become fully accessible for δ > 0.5. As a result, the distance between OH - coupled oxygen-vacant sites becomes sufficiently short to enable direct O-O bond formation as in photosystem II. Thus, we found that the OER activity of oxygen deficient electrocatalysts is controllable by the variety of lattice oxygen vacancies, which suggests that oxygen deficient layered superconductors are promising OER catalysts for energy conversion technologies.

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Multi-step time series generator for molecular dynamics

Endo K., Tomobe K., Yasuoka K.

32nd AAAI Conference on Artificial Intelligence, AAAI 2018 （32nd AAAI Conference on Artificial Intelligence, AAAI 2018）     2192 - 2199 2018年

ISSN  9781577358008

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Copyright © 2018, Association for the Advancement of Artificial Intelligence (www.aaai.org). All rights reserved. Molecular dynamics (MD) is a powerful computational method for simulating molecular behavior. Deep neural networks provide a novel method of generating MD data efficiently, but there is no architecture that mitigates the well-known exposure bias accumulated by multi-step generations. In this paper, we propose a multi-step time series generator using a deep neural network based on Wasserstein generative adversarial nets. Instead of sparse real data, our model evolves a latent variable z that is densely distributed in a low-dimensional space. This novel framework successfully mitigates the exposure bias. Moreover, our model can evolve part of the system (Feature extraction) with any time step (Step skip), which accelerates the efficient generation of MD data. The applicability of this model is evaluated through three different systems: harmonic oscillator, bulk water, and polymer melts. The experimental results demonstrate that our model can generate time series of the MD data with sufficient accuracy to calculate the physical and important dynamical statistics.

Origin of the blueshift of water molecules at interfaces of hydrophilic cyclic compounds

Tomobe, K., Yamamoto, E., Kojic, D., Sato, Y., Yasui, M., and Yasuoka, K.

Science Advances 3   e1701400 (7 pages) 2017年12月

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Evidence of low-density and high-density liquid phases and isochore end point for water confined to carbon nanotube

Nomura, K., Kaneko, T., Bai, J., Francisco, J. S., Yasuoka, K., and Zemg, X. C.

Proc. Natl. Acad. Sci. USA 114   4066 - 4071 2017年04月

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Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity

Yamamoto, E., Akimoto, T., Kalli, A. C., Yasuoka, K., and Sansom, M. P. S.

Science Advances 3   e1601871 (6 pages) 2017年01月

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Molecular Dynamics Simulations for Resolving Scaling Laws of Polythylene Melts

Takahashi, K. Z., Nishimura, R., Yasuoka, K., and Masubuchi, Y.

Polymers 9   24 (12 pages) 2017年01月

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Onset of static and dynamic universality among molecular models of polymers

Takahashi, K. Z., Nishimura, R., Yamato, N., Yasuoka, K., and Masubuchi, Y.

Scientific Reports 7   12379 (7 pages) 2017年

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Water permeation through the internal water pathway in activated GPCR rhodopsin

Tomobe, K., Yamamoto, E., Kholmurodov, K., and Yasuoka, K.

PLOS ONE 12   e0176876 2017年

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Subsurface Polaron Concentration As a Factor in the Chemistry of Reduced TiO2 (110) Surfaces

Shibuya, T., Yasuoka, K., Mirbt, S., and Sanyal, B.

J. Phys. Chem. C 121   11325 - 11334 2017年

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Effects of temperature, concentration, and isomer on the hydration structure in monosaccharide solutions

Tomobe, K., Yamamoto, E., Yasui, M., and Yasuoka, K.

Phys. Chem. Chem. Phys. 19   15239 - 15246 2017年

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Effects of temperature, concentration, and isomer on the hydration structure in monosaccharide solutions

Tomobe, K., Yamamoto, E., Yasui, M., and Yasuoka, K.

Phys. Chem. Chem. Phys. 19   15239 - 15246 2017年

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Replica exchange molecular simulation of Lennard-Jones particles in a two-dimensional confined system

Doi, H., and Yasuoka, K.

AIP Advances 7   055018 (9 pages) 2017年

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Water Molecules in a Carbon Nanotube under an Applied Electric Field at Various Temperatures and Pressures

Winarto, Yamamoto, E., and Yasuoka, K.

Water 9,   473 (14 pages) 2017年

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Dissipative particle dynamics (DPD) simulations with fragment molecular orbital (FMO) based effective parameters for 1-Parmitoyl-2-oleoyl phosphatidyl choline (POPC) membrane

Doi, H., Okuwaki, K., Mochizuki, Y., Ozawa, T., and Yasuoka, K.

Chem. Phys. Lett. 684   427 - 432 2017年

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Critical test of bead-spring model to resolve the scaling laws of polymer melts: a molecular dynamics study

Takahashi, K. Z., Yamato, N., Yasuoka, K., and Masubuchi, Y.,

Molec. Simul. 43   1196 - 1201 2017年

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Molecular Dymamics Simulation of Water Nanodroplet Bounce Back from Flat and Nanopillared Surface

Koishi, T., Yasuoka, K., and Zeng, X. C.

Langmuir 33   10184 - 10192 2017年

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Aspect ratio effect of nanorods on heterogeneous nucleation rates by molecular dynamics

Suh, D. and Yasuoka, K.

Journal of Thermal Science and Technology 11 （ 3 ） JTST0044 (6 pages) 2016年12月

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Instability of buried hydration sites increases protein subdomains fluctuations in the human prion protein by the pathogenic mutation T188R

Tomobe K., Yamamoto E., Akimoto T., Yasui M., and Yasuoka K.,

AIP Advances 6   055324 2016年05月

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Cage Occupancy of Methane Hydrates from Gibbs Ensemble Monte Carlo Simulations

Brumby, P. E., Yuhara, D., Wu, D. T., Sum, A. K. and Yasuoka, K.

Fluid Phase Equilibria 413   242 - 248 2016年04月

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Stability of Excess Electrons Introduced by Ti Interstitial in Rutile TiO2(110) Surface

Morita, K., Shibuya, T., and Yasuoka, K.

J. Phys. Chem. C 121   1602 - 1607 2016年

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Condensation on Nanorods by Molecular Dynamics

Suh, D. and Yasuoka, K

J. Chem. Phys. 144   244702 2016年

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Interactions of Pleckstrin Homology Domains with Membranes

Yamamoto, E., Kalli, A. C., Yasuoka, K., and Samsom, M. S. P.

Structure 24   1421 - 1431 2016年

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Self-assembly behaviours of primitive and modern lipid membrane solutions: a coarse-grained molecular simulation study

Arai, N., Yoshimoto, Y., Yasuoka, K., and Ebisuzaki, T.

Phys. Chem. Chem. Phys. 18   19426 - 19432 2016年

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Suppression of lattice thermal conductivity by mass-conserving cation mutation in multi-component semiconductors

Shibuya, T., Skelton, J. M., Jackson, A. J., Yasuoka, K., Togo, A., Tanaka, I., and Walsh, A.,

APL Materials 4   104809 2016年

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Self-Assembly of Janus Oligomers into Onion-like Vesicles with Layer-by-Layer Water Discharging Capability: A Minimalist Model

Arai, N., Yasuoka, K., and Zeng, X. C.

ACS Nano 10   8026 - 8037 2016年

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Separation of Water - Ethanol Solution with Carbon Nanotubes and Electric Fields

Winarto, Takaiwa, D., Yamamoto, E., and Yasuoka, K.

Phys. Chem. Chem. Phys. 10   33310 - 33319 2016年

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Comparison of the Accuracy of Periodic Reaction Field Methods in Molecular Dynamics Simulations of a Model Liquid Crystal System

Nozawa, T., Takahashi, K. Z., Narumi, T. and Yasuoka, K.

J. Comput. Chem. 36   2406 - 2411 2015年12月

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Molecular dynamics study of guest-host hydrogen bonding in alcohol clathrate hydrates

Hiratsuka, M., Ohmura, R., Sum, A. K., Alavi, S. and Yasuoka, K.

Phys. Chem. Chem. Phys. 17   12639 - 12647 2015年05月

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Structures of water molecules in carbon nanotubes under electric fields

Winarto, Takaiwa, D., Yamamoto, E., and Yasuoka, K.,

J. Chem. Phys. 142   124701 2015年03月

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Origin of 1/f Noise in Hydration Dynamics on Lipid Membrane Surfaces

Yamamoto, E., Akimoto, T., Yasui, M., and Yasuoka, K.

Sci. Rep. 5   8876 2015年03月

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Velocity auto-correlation function of ions and water molecules in different concentrations, anions, and ion clusters

Tomobe, K., Yamamoto, E., Dusan, K., Yasui, M. and Yasuoka, K.

Molec. Simul. 41   840 2015年

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Vibrational Spectra of Deuterated Methane and Water Molecules in Structure I Clathrate Hydrate from ab initio MD simulation

Hiratsuka, M., Ohmura, R., Sum, A. K. and Yasuoka, K.

Molec. Simul. 41   813 2015年

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A determination of liquid-vapor interfacial properties for methanol using a linear-combination-based isotropic periodic sum

Takahashi, K. Z. and Yasuoka, K.

Molec. Simul. 41   795 2015年

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Application of isotropic periodic sum method for 4-pentyl-4'-cyanobiphenyl liquid crystal

Nozawa, T., Takahashi, K. Z., Kameoka, S., Narumi, T. and Yasuoka, K.

Molec. Simul. 41   927 2015年

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Nucleation rate analysis of methane hydrate from molecular dynamics simulations

Yuhara, D., Barnes, B. C., Suh, D., Knott, B. C., Beckham, G. T., Yasuoka, K., Wu, D. T. and Sum, A. K.

Faraday Discussions 179   463 - 474 2015年

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Molecular Dynamics Simulation of Heterogeneous Nucleation on Nanotubes

Suh, D., Yasuoka, K. and Zeng, X. C.

R. Soc. Chem. Adv 5   40953 - 40963 2015年

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Water-methanol separation with carbon nanotubes and electric fields

Winarto, Takaiwa, D., Yamamoto, E. and Yasuoka, K.

Nanoscale 7   12659 - 12665 2015年

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Approaches for controlling the temperature and pressure range in generalized NPT ensembles

Doi, H. and Yasuoka, K.

J. Chem. Theory Comput. 11   4370 - 4376 2015年

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Anomalous dynamics of a lipid recognition protein on a membrane surface

Yamamoto, E., Kalli, A. C., Akimoto, T., Yasuoka, K. and Sansom, M. S. P.

Sci. Rep. 5   18245 2015年

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Heterogeneous nucleation of bubbles by molecular dynamics

Suh, D., Nakamura, M. and Yasuoka, K.

J. Phys. Conf. Series （IOP Publishing）  656   012037 2015年

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GPU-Accelerated Replica Exchange Molecular Simulation on Solid-Liquid Phase Transition Study of Lennard-Jones Fluids

Nomura K., Oikawa M., Kawai A., Narumi T. and Yasuoka, K.

Molec. Simul. 41   874 2015年

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Analysis of crystal growth of methane hydrate using molecular dynamics simulation

Yuhara, D., Hiratsuka, M., Takaiwa, D. and Yasuoka, K.

Molec. Simul. 41   918 2015年

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Nanoscale Droplet Vaporization by Molecular Dynamics

Suh, D. and Yasuoka, K.

Molec. Simul. 41   896 2015年

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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

老川 稔, 野村 昴太郎, 泰岡 顕治, 成見 哲

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年

研究論文（学術雑誌）, 共著,  ISSN  1882-7829

Poisson property of the occurrence of flip-flops in a model membrane

Arai, N., Akimoto, T., Yamamoto, E., Yasui M., and Yasuoka K.

J. Chem. Phys. 140   064901 2014年

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From kesterite to stannite photovoltaics: stability and band gaps of the Cu2(Zn,Fe)SnS4 alloy

Shibuya, T., Goto, Y., Kamihara, Y., Matoba, M., Yasuoka, K., Burton, L.A., and Walsh, A.

App. Phys. Lett. 104   021912 2014年

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1/f fluctuations of amino acids regulate water transportation in aquaporin 1

Yamamoto, E., Akimoto, T., Hirano, Y., Yasui M., and Yasuoka K.

Phys. Rev. E. 89   022718 2014年

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Origin of subdiffusion of water molecules on cell membrane surfaces

Yamamoto, E., Akimoto, T., Yasui M., and Yasuoka K.

Sci. Rep. 4   4720 2014年

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Bipolaron Formation Induced by Oxygen Vacancy at Rutile TiO2(110) Surfaces

Shibuya, T., Yasuoka, K., Mirbt, S. and Sanyal, B.

J. Phys. Chem. C 118   9429 - 9435 2014年

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Liquid-solid and solid-solid phase transition of monolayer water: High-density rhombic monolayer ice

Kaneko, T., Bai, J., Yasuoka, K., Mitsutake, A., and Zeng, X.,

J. Chem. Phys. 140   184507 2014年

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Effects of the Cu off-stoichiometry on transport properties of wide gap p-type semiconductor, layered oxysulfide LaCuSO

Goto, Y., Tanaki, M., Okusa, Y., Shibuya, T., Yasuoka, K., Matoba, M., and Kamihara, Y.

App. Phys. Lett. 105   022104 2014年

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Observation of Interstitial Molecular Hydrogen in Clathrate Hydrates

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.

Angew. Chem. Int. Ed. 53   10710 - 10713 2014年

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Water confined in the local field of ions

Kojić D., Tsenkova R, Tomobe K, Yasuoka K, and Yasui M.

ChemPhysChem 15   4077 - 4086 2014年

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Common Force Field Thermodynamics of Cholesterol

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.

Sci. World J. 2013   207287 2013年

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Petascale Turbulence Simulation Using a Highly Parallel Fast Multipole Method

Yokota, R., Barba, L. A., Narumi, T. and Yasuoka, K.

Comput. Phys. Comm. 184   445 2013年

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Self-Assembly of Triblock Janus Nanoparticle in Nanotube

Arai, N., Yasuoka, and K., Zeng, X.C.

J. Chem. Theory Comput. 9   179 2013年

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Water Proton Configurations in Structures I, II and H Clathrate Hydrate Unit Cells

Takeuchi, F., Hiratsuka, M., Ohmura, R., Alavi, S., Sum, A. K. and Yasuoka, K.

J. Chem. Phys. 138   124505 2013年

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Phase diagrams of confined solutions of dimyristoylphosphatidylcholine (DMPC) lipid and cholesterol in nanotubes

7. Arai, N., Yasuoka, K., and Zeng, X.C.

Microfluid. Nanofluid 14   995 - 1010 2013年

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Kinetic Analysis on Nanoparticle Condensation by Molecular Dynamics

Suh, D. and Yasuoka, K.

J. Heat Transfer 135   101002 2013年

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Dynamic Interactions of Cations, Water and Lipids Influence on Membrane Fluidity

Kagawa, R., Hirano, Y., Taiji, M., Yasuoka, K., and Yasui, M.

J. Membr. Sci. 435   130 - 136 2013年

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Homogeneous Connectivity of Potential Energy Network in a Solidlike State of Water Cluster

Akimoto, T., Kaneko, T., Yasuoka, K., and Zeng X.C.

J. Chem. Phys. 138   244301 2013年

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Power-Law Trapping of Water Molecules on the Lipid-Membrane Surface Induce Water Retardation

Yamamoto, E., Akimoto, T., Hirano, Y., Yasui M., and Yasuoka K.

Phys. Rev. E 87   052715 2013年

研究論文（学術雑誌）, 共著, 査読有り

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Understanding Molecular Motor Walking along Microtubule: A Themo-sensitive Asymmetric Brownian Motor Driven by Bubble Formation

Arai, N. Yasuoka, K. Koishi, T. Ebisuzaki, T. Zeng, X.C.

J. Am. Chem. Soc. 135   8616 - 8624 2013年

研究論文（学術雑誌）, 共著, 査読有り

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Molecular Insight into Different Denaturing Efficiency of Urea, Guanidinium, and Methanol: A Comparative Simulation Study

Koishi, K., Yasuoka, K., Willow S.Y., Fujikawa S., and Zeng X.C.

J. Chem. Theory Comput. 9   2540 - 2551 2013年

研究論文（学術雑誌）, 共著, 査読有り

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A New Computational Approach to Determine Liquid-Solid Phase Equilibria of Water Confined to Slit Nanopores

Kaneko, T., Bai, J., Yasuoka, K., Mitsutake, A., Zeng, X.C.

J. Chem. Theory Comput. 9   3299 - 3310 2013年

研究論文（学術雑誌）, 共著, 査読有り

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Vesicle Cell under Collision with Janus or Homogeneous Nanoparticle: Translocation Dynamics and Late-Stage Morphology

Arai, N., Yasuoka, K., Zeng, X.C.

Nanoscale 5   9089 - 9100 2013年

研究論文（学術雑誌）, 共著, 査読有り

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Structural and diffusion properties of formamide/water mixture interacting with TiO2 surface

Dushanov, E., Kholmurodov, Kh., Yasuoka, K.

Bioorganic Chemistry 50   11 - 16 2013年

研究論文（学術雑誌）, 共著, 査読有り

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MD studies on conformational behavior of a DNA photolyase enzyme

Dushanov, E., Kholmurodov, K., Yasuoka, K., Krasavin, E.

Physics of Particles and Nuclei Letters 10   597 - 605 2013年

研究論文（学術雑誌）, 共著, 査読有り

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Nanoparticle Growth Analysis by Molecular Dynamics: Cubic Seed

Suh, D. and Yasuoka, K.

J. Phys. Chem. B 116   14637 2012年

研究論文（学術雑誌）, 単著, 査読有り

Molecular Vibrations of Methane Molecules in the Structure I Clathrate Hydrate from Ab Initio Molecular Dynamics Simulation

Hiratsuka, M., Ohmura, R., Sum, A. K., and Yasuoka, K.

J. Chem. Phys. 136   044508 2012年

研究論文（学術雑誌）, 共著, 査読有り

Nanochannel with Uniform and Janus Surfaces: Shear Thinning and Thickening in Surfactant Solution

Arai, N., Yasuoka, K., and Zeng, X. C.

Langmuir 28   2866 2012年

研究論文（学術雑誌）, 共著, 査読有り

Liquid-solid phase transitions of Lennard-Jones particles confined to slit pores: Towards the construction of temperature-pressure-slit width phase diagram

Kaneko, T., Yasuoka, K., and Zeng, X. C.

Molec. Simul. 38   373 2012年

研究論文（学術雑誌）, 共著, 査読有り

Cutoff radius effect of the isotropic periodic sum method for polar molecules in a bulk water system

Takahashi, K., Narumi, T., and Yasuoka, K.

Molec. Simul. 38   397 2012年

研究論文（学術雑誌）, 共著, 査読有り

Estimation of breakdown electric-field strength while reflecting local structures of SiO2 using first-principles molecular orbital calculation technique

Seki, H., Shibuya, Y., Kobayashi, D., Nohira, H., Yasuoka, K., and Hirose, K.

Jpn. J. Appl. Phys. 51   04DA07 2012年

研究論文（学術雑誌）, 共著, 査読有り

The diffusion and concentration effects of formamide on a TiO2 surface in the presence of a water solvent

Dushanov, E., Kholmurodov, Kh., and Yasuoka, K.

Natural Science 4   313 2012年

研究論文（学術雑誌）, 共著, 査読有り

Multibaric-Multithermal Ensemble Study of Liquid-Solid Phase Transition in Lennard-Jones Particles

Kaneko, T., Mitsutake, A., and Yasuoka, K.

J. Phys. Soc. Jpn. 81   SA014 2012年

研究論文（学術雑誌）, 共著, 査読有り

Molecular Dynamics Simulations on trans- and cis-Decalins:The Effect of Partial Atomic Charges and Adjustment of "Real Densities"

Eremin, R., Kholmurodov, K., Avdeev, M., Petrenko, V. and Yasuoka, K.

Int. J. Chem. 4   14 2012年

研究論文（学術雑誌）, 共著, 査読有り

Molecular Dynamics Simulations of a DNA Photolyase Protein : High-Mobility and Conformational Changes of the FAD Molecule at Low Temperatures

Kholmurodov, K., Dushanov, E., and Yasuoka, K.

Advances in Bioscience and Biotechnology 3   169 2012年

研究論文（学術雑誌）, 共著, 査読有り

Structural features of aquaporin 4 supporting the formation of arrays and junctions in biomembranes

Höfinger, S., Yamamoto, E., Hirano, Y., Zerbettoa, F., Narumi, T., Yasuoka, K., and Yasuii, M.

Biochimica et Biophysica Acta 1818   2234 2012年

研究論文（学術雑誌）, 共著, 査読有り

Molecular dynamics study of ethanol solvated by water on the Pt (1 1 1) surface

Kholmurodov, K., Dushanov, E., Yasuoka, K., Khalil, H., Galal, A., Ahmed, S., Sweilam, N., and Moharram, H.

Chemical Physics 402   41 2012年

研究論文（学術雑誌）, 共著, 査読有り

Diffusive Nature of Xenon Anesthetic Changes Properties of a Lipid Bilayer: Molecular Dynamics Simulations

Yamamoto, E., Akimoto, T., Shimizu, H., Hirano, Y., Yasui, M. and Yasuoka, K.

J. Phys. Chem. B 116   8989 2012年

研究論文（学術雑誌）, 共著, 査読有り

Molecular dynamics simulation of quasi-two-dimensional water cluster on ice nucleation protein

Murakami, D. and Yasuoka, K.

J. Chem. Phys. 137   054303 2012年

研究論文（学術雑誌）, 共著, 査読有り

GPU-Accelerated Computation of Electron Transfer

Höfinger, S., Acocella, A., Pop, S. C., Narumi, T., Yasuoka, K., Beu, T. and Zerbetto, F.

J. Comput. Chem. 33   2351 2012年

研究論文（学術雑誌）, 共著, 査読有り

Model of Abnormal Chromophore-Protein Interaction for E181K Rhodopsin Mutation: Computer Molecular Dynamics Study

Feldman, T., Ostrovsky, M., Kholmurodov, K. and Yasuoka, K.

The Open Biochemistry Journal, 6   94 2012年

研究論文（学術雑誌）, 共著, 査読有り

An improved isotropic periodic sum method that uses linear combinations of basis potentials

Takahashi, K. Z., Narumi, T., Suh, D. and Yasuoka, K.

J. Chem. Theory Comput. 8   4503 2012年

研究論文（学術雑誌）, 共著, 査読有り

A systematic study of polarons due to oxygen vacancy formation at the rutile TiO2 (110) surface by GGA+U and HSE06 methods

Shibuya, T., Yasuoka, K., Mirbt, S. and Sanyal, B.

J. Phys.: Condens. Matter 24   435504 2012年

研究論文（学術雑誌）, 共著, 査読有り

Vibrational Modes of Methane in the Structure H Clathrate Hydrate from Ab initio Molecular Dynamics Simulation

Hiratsuka, M., Ohmura, R., Sum, A. K., and Yasuoka, K.

J. Chem. Phys. 137   144306 2012年

研究論文（学術雑誌）, 共著, 査読有り

Molecular Dynamics Simulation of the Interaction of Ethanol - Water Mixture with a Pt Surface

Kholmurodov, K., Dushanov, E., Yasuoka, K., Khalil, H., Galal, A., Ahmed, A., Sweilam, N. and Moharram, H.

Natural Science 3   1011 2011年

研究論文（学術雑誌）, 共著, 査読有り

Fast quasi double-precision method with single-precision hardware to accelerate scientific applications

Narumi, T., Hamada, T., Nitadori, K., Sakamaki, R., and Yasuoka, K.

Int. J. Comput. Meth. 8   561 2011年

研究論文（学術雑誌）, 共著, 査読有り

Molecular dynamics simulations of vapor/liquid coexistence using the nonpolarizable water models

Sakamaki, R., Sum, A. K., Narumi, T., and Yasuoka, K.

J. Chem. Phys. 134   124708 2011年

研究論文（学術雑誌）, 共著, 査読有り

Thermodynamic Properties of Methane/Water Interface Predicted by Molecular Dynamics Simulations

Sakamaki, R., Sum, A. K., Narumi, T., Ohmura, R., and Yasuoka, K.

J. Chem. Phys. 134   144702 2011年

研究論文（学術雑誌）, 共著

Cutoff radius effect of the isotropic periodic sum and Wolf method in liquid-vapor interfaces of water

Takahashi, K. Z., Narumi, T., and Yasuoka, K.

J. Chem. Phys. 134   174112 2011年

研究論文（学術雑誌）, 共著, 査読有り

An Analysis of Natural Convection Using the Thermal Finite Element Discrete Boltzmann Equation

Seino, M., Tanahashi, T., Yasuoka, K.

Computers and Fluids 40   113 2011年

研究論文（学術雑誌）, 共著, 査読有り

Nanoparticle Growth Analysis by Molecular Dynamics: Spherical Seed

Suh, D., and Yasuoka, K.

J. Phys. Chem. B 115   10631 2011年

研究論文（学術雑誌）, 共著, 査読有り

Measurement of Contact-Angle Hysteresis for Droplets on Nanopillared Surface and in the Cassie and Wenzel States: A Molecular Dynamics Simulation Study

Koishi, T., Yasuoka, K., Fujikawa, S., and Zeng, X. C.

ACS Nano 5   6834 2011年

研究論文（学術雑誌）, 共著, 査読有り

MD Simulations of the P53 Oncoprotein Structure: the Effect of the Arg273-->His Mutation on the DNA Binding Domain

Kholmurodov, K., Dushanov, E., and Yasuoka, K.

Advances in Bioscience and Biotechnology 2   330 2011年

研究論文（学術雑誌）, 共著, 査読有り

Non-Gaussian Fluctuations Resulting from Power-Law Trapping in a Lipid Bilayer

Akimoto, T., Yamamoto, E., Yasuoka, K., Hirano, Y., and Yasui, M.

Phys. Rev. Lett. 107   178103 2011年

研究論文（学術雑誌）, 共著, 査読有り

Size Dependent Phase Changes in Water Clusters

Kaneko, T., Akimoto, T., Yasuoka, K., Mitsutake, A., and Zeng, X. C.

J. Chem. Theory Comput. 7   3083 2011年

研究論文（学術雑誌）, 共著, 査読有り

A combination of the tree-code and IPS method to simulate large scale systems by molecular dynamics

Takahashi, K. Z., Narumi, T., and Yasuoka, K.

J. Chem. Phys. 135   174108 2011年

研究論文（学術雑誌）, 共著, 査読有り

Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3

Narumi, T., Yasuoka, K., Taiji, M., Zerbetto, F., and Hoefinger, S.

Comput. J. on line 2010年

研究論文（学術雑誌）, 共著, 査読有り

Molecular mechanisms how mercury inhibits water permeation through aquaporin-1: understanding by molecular dynamics simulaiton

Hirano, Y., Okimoto, N., Kadohira, I., Suematsu, M., Yasuoka, K, and Yasui, M.

Biopys. J. 98   1512 2010年

研究論文（学術雑誌）, 共著, 査読有り

Phase Diagram of Lennard-Jones Fluid Confined in Slit Pores

Kaneko, T., Mima, T., and Yasuoka, K.

Chem. Phys. Lett. 490   165 2010年

研究論文（学術雑誌）, 共著, 査読有り

Molecular dynamics simulations of the interaction of carbon nanotube and a carbon disulfide solvent

Kholmurodov, K., Aru, G., and Yasuoka, K.

Natural Science 2   902 2010年

研究論文（学術雑誌）, 共著, 査読有り

Molecular Dynamics Study of the Effect of Electrostatic Interactions on the Biphenyl Structure in the Active HNO3 Solvent

Kholmurodov, K., Chulkova A., and Yasuoka, K.

The Open Physical Chemistry Journal 4   10 2010年

研究論文（学術雑誌）, 共著, 査読有り

Cutoff radius effect of isotropic periodic sum method in homogeneous system. II . Water

Takahashi, K., Narumi, T., and Yasuoka, K

J. Chem. Phys. 133   014109 2010年

研究論文（学術雑誌）, 共著, 査読有り

Molecular dynamics simulations of urea‒water binary droplets on flat and pillared hydrophobic surfaces

Koishi, T., Yasuoka, K., Zeng, X. C., and Fujikawa, S.

Faraday Disc. 146   185 2010年

研究論文（学術雑誌）, 共著, 査読有り

Molecular dynamics simulations of valinomycin interactions with potassium and sodium ions in water solvent

Kholmurodov, K., Abasheva, M., and Yasuoka, K.

Advances in Bioscience and Biotechnology 1   216 2010年

研究論文（学術雑誌）, 共著, 査読有り

Asymmetric Brownian motor driven by bubble formation in a hydrophobic channel

Arai, N., Yasuoka, K., Koishi, T., and Ebisuzaki, T.

ACS Nano 4   5905 2010年

研究論文（学術雑誌）, 共著, 査読有り

Accelerating molecular dynamics simulation using graphics processing unit

Myung, H., J., Sakamaki, R., Oh, K., J., Narumi, T., Yasuoka, K., and Lee, S.

Bull. Korean Chem. Soc. 31   3639 2010年

研究論文（学術雑誌）, 共著, 査読有り

JINR CICC in Computational Chemistry and Nanotechnology Problems: DL_POLY Performance for Different Communication Architectures

Dushanov, E., Kholmurodov, Kh., Aru, G., Korenkov, V., Smith, W., Ohno, Y., Narumi, T., Morimoto, G., Taiji, M., and Yasuoka, K.

Physics of Particles and Nuclei Letters 6   251 2009年

研究論文（学術雑誌）, 共著, 査読有り

Formation of Nuclear ''Pasta'' in Supernovae

Watanabe, G., Sonoda, H., Maruyama, T., Sato, K., Yasuoka, K., and Ebisuzaki, T.

Phys. Rev. Lett. 103   121101 2009年

研究論文（学術雑誌）, 共著, 査読有り

Statistical-thermodynamics modeling of clathrate hydrate forming systems suitable as working media of a hydrate-based refrigeration system

Takeuchi, F., Ohmura, R., and Yasuoka, K.

Int. J. Thermophys. 30   1838 2009年

研究論文（学術雑誌）, 共著, 査読有り

Fast Multipole Methods on a Cluster of GPUs for the Meshless Simulation of Turbulence

Yokota, R., Narumi, T., Sakamaki, R., Kameoka, S., Obi, S., and Yasuoka, K.

Comput. Phys. Commun. 180   2066 2009年

研究論文（学術雑誌）, 共著, 査読有り

Microscopic insights into nucleation in a sulfuric acid-water vapor mixture based on molecular dynamics simulation

Matsubara, H., Ebisuzaki, T., and Yasuoka, K.

J. Chem. Phys. 130   104705 2009年

研究論文（学術雑誌）, 共著, 査読有り

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

坂牧隆司，成見哲，泰岡顕治

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年

研究論文（学術雑誌）, 共著, 査読有り

Current Performance Gains from Utilizing the GPU or the ASIC MDGRAPE-3 within an Enhanced Poisson Boltzmann Approach

Narumi, T., Yasuoka, K., Taiji, M., and Höfinger, S.

J. Comput Chem. 30   2351 2009年

研究論文（学術雑誌）, 共著, 査読有り

Coexistence and transition between Cassie and Wenzel state on pillared hydrophobic surface

Koishi, T., Yasuoka, K., Fujikawa, S., Ebisuzaki, T., and Zeng, X.C.

Proceedings of the National Academy of Sciences of the United States of America 106   8435 2009年

研究論文（学術雑誌）, 共著, 査読有り

Cell size dependence of orientational order of uniaxial liquid

Mima, T., Narumi, T., Kameoka, S., Yasuoka, K.

Molecular Simulation 34   761-773 2008年

研究論文（学術雑誌）, 共著, 査読有り

Interfacial anisotropy in the transport of liquid crystals confined between flat, structureless walls: A molecular dynamics simulation approach

Mima T. and Yasuoka K.

Phys. Rev. E 77   011705 2008年

研究論文（学術雑誌）, 共著, 査読有り

Liquid-vapor nucleation simulation of Lennard-Jones fluid by molecular dynamics method

Sekine, M., Yasuoka, K., Kinjo, T., and Matsumoto, M.

Fluid Dynamics Research 40   597-605 2008年

研究論文（学術雑誌）, 共著, 査読有り

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

松原裕樹, 泰岡顕治, 戎崎俊一

Thermal Science and Engineering 16   71-77 2008年

研究論文（学術雑誌）, 共著, 査読有り

The study of colliding vortex rings using a special-purpose computer and FMM

Sheel, T. K., Yokota, R., Yasuoka, K., Obi, S.

Transactions of the Japan Society for Computational Engineering and Science    20080003 2008年

研究論文（学術雑誌）, 共著, 査読有り

Phase diagram of nuclear “pasta” and its uncertainties in supernova cores

Sonoda, H., Watanabe, G., Sato, K., Yasuoka, K., and Ebisuzaki, T.,

Phys. Rev. C 77   035806 2008年

研究論文（学術雑誌）, 共著, 査読有り

Self-Assembly of Surfactants and Polymorphic Transition in Nanotubes

Arai, N., Yasuoka, K., and Zeng, X. C.

Journal of American Chemical Society, 130   7916-7920 2008年

研究論文（学術雑誌）, 共著, 査読有り

Accelerating Molecular Dynamics Simulations on PLAYSTATION 3 Platform using “Virtual-Grape”Programming Model

Narumi, T., Kameoka, S., Taiji, M., and Yasuoka, K.

SIAM Journal on Scientific Computing 30   3108-3125 2008年

研究論文（学術雑誌）, 共著, 査読有り

Extended study of molecular dynamics simulation of homogeneous vapor-liquid nucleation of water

Matsubara, H., Koishi, T., Ebisuzaki, T., and Yasuoka, K.

J. Chem. Phys. 127   214507 2007年

研究論文（学術雑誌）, 共著

Molecular understanding of dynamical properties of the vapor/ethanol-aqueous-solution interface

Andoh, Y., Yasuoka, K.

Molecular Simulation 33   139-145 2007年

研究論文（学術雑誌）, 共著, 査読有り

Molecular Dynamics Simulations of Structure-H Hydrates Formed with Methane and 3,3-Dimethylpentane or 2,2-Dimethylpentane

Miyoshi, T., Ohmura, R., Yasuoka, K.

Molecular Simulation 33   65-69 2007年

研究論文（学術雑誌）, 共著, 査読有り

Molecular Dynamics Simulation of Time-irreversibility of Stationary Heat Flux

Mima, T., Yasuoka, K., Nose, S.

Molecular Simulation 33   109-113 2007年

研究論文（学術雑誌）, 共著, 査読有り

Predicting thermodynamic stability of clathrate hydrates based on molecular-dynamics simulations and its confirmation by phase-equilibrium measurements

Miyoshi, T., Ohmura, R., Yasuoka, K.

Journal of Physical Chemistry C 111   3799-3802 2007年

研究論文（学術雑誌）, 共著, 査読有り

Fast Vortex method calculation using a special-purpose computer

Sheel, T.K., Yasuoka, K., Obi, S.

Computers and Fluids 36   1319−1326 2007年

研究論文（学術雑誌）, 共著, 査読有り

Molecular dynamics of homogeneous nucleation in the vapor phase of Lennard-Jones. III. Effect of carrier gas pressure

Yasuoka, K. and Zeng, X.C.

Journal of Chemical Physics 126   124320 2007年

研究論文（学術雑誌）, 共著, 査読有り

Thermodynamic stability of type-I and II clathrate hydrates depending on the chemical species of the guest substances

Miyoshi, T., Imai, M., Ohmura, R., Yasuoka, K.

Journal of Chemical Physics 126   234506 2007年

研究論文（学術雑誌）, 共著, 査読有り

Spontaneous self-assembly process for threadlike micelles

Arai, N., Yasuoka, K., Masubuchi, Y.

Journal of Chemical Physics 126   244905 2007年

研究論文（学術雑誌）, 共著, 査読有り

Phase equilibrium calculation for clathrate hydrates based on a statistical thermodynamics model: An attempt to optimize the Kihara parameters for methane and ethane

Sato, E., Miyoshi, T., Ohmura, R., and Yasuoka K.,

Japanese Journal of Applied Physics 46   5944-5950 2007年

研究論文（学術雑誌）, 共著, 査読有り

Cutoff radius effect of isotropic periodic sum method for transport coefficients of Lennard-Jones liquid

Takahashi, K., Yasuoka, K., Narumi T.

Journal of Chemical Physics 127   114511 2007年

研究論文（学術雑誌）, 共著, 査読有り

Impact of nuclear “pasta” on neutrino transport in collapsing stellar cores

Sonoda,H., Watanabe, G., Sato, K., Takiwaki, T., Yasuoka, K., and Ebisuzaki T.

Physical Review C 75   042801(R) 2007年

研究論文（学術雑誌）, 共著, 査読有り

Anisotropic molecular clustering in liquid ethanol induced by a charged fully hydroxylated silicon dioxide (SiO2) surface

Andoh, Y., Kurahashi, K., Sakuma, H., Yasuoka, K., Kurihara, K.

Chem. Phys. Lett. 448   253-257 2007年

研究論文（学術雑誌）, 共著, 査読有り

Hydrogen-bonded clusters on the vapor/ethanol-aqueous-solution interface

Andoh Y, Yasuoka K

Journal of Physical Chemistry B 110   23264-23273 2006年

研究論文（学術雑誌）, 共著, 査読有り

Free-energy calculation of structure-H hydrates

Okano Y, Yasuoka K

Journal of Chemical Physics 124   024510 2006年

研究論文（学術雑誌）, 共著, 査読有り

Simulation of transitions between "pasta" phases in dense matter

Watanabe G, Maruyama T, Sato K, Yasuoka K, Ebisuzaki T

Physical Review Letters 94   031101 2005年

研究論文（学術雑誌）, 共著, 査読有り

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

Tsuji H, Kobayashi T, Okano Y, Ohmura R, Yasuoka K, Mori YH

Energy & Fuels 19   1587-1597 2005年

研究論文（学術雑誌）, 共著, 査読有り

Two-dimensional supercritical behavior of an ethanol monolayer: A molecular dynamics study

Andoh Y, Yasuoka K

Langmuir 21   10885-10894 2005年

研究論文（学術雑誌）, 共著, 査読有り

Large-scale molecular-dynamics simulation of nanoscale hydrophobic interaction and nanobubble formation

Koishi T, Yasuoka K, Ebisuzaki T, Yoo S, Zeng XC

Journal of Chemical Physics 123   204707 2005年

研究論文（学術雑誌）, 共著, 査読有り

Tyr-317 phosphorylation increases shc structural rigidity and reduces coupling of domain motions remote from the phosphorylation site as revealed by molecular dynamics simulations

Suenaga A, Kiyatkin AB, 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 JB, Konagaya A, Kholodenko BN

Journal of Biological Chemistry 279   4657-4662 2004年

研究論文（学術雑誌）, 共著, 査読有り

Simulations of magnetic materials with MDGRAPE-2

Elmegreen BG, Koch RH, Schabes ME, Crawford T, Ebisuzaki T, Furusawa H, Narumi T, Susukita R, Yasuoka K

IBM Journal of Research and Development 48   199-207 2004年

研究論文（学術雑誌）, 共著, 査読有り

Phases of hot nuclear matter at subnuclear densities

Watanabe G, Sato K, Yasuoka K, Ebisuzaki T

Physical Review C 69   055805 2004年

研究論文（学術雑誌）, 共著, 査読有り

Nanoscale hydrophobic interaction and nanobubble nucleation

Koishi T, Yoo S, Yasuoka K, Zeng XC, Narumi T, Susukita R, Kawai A, Furusawa H, Suenaga A, Okimoto N, Futatsugi N, Ebisuzaki T

Physical Review Letters 93   185701 2004年

研究論文（学術雑誌）, 共著, 査読有り

Molecular Dynamics Simulations of Prion Proteins - Effect of Ala117->Val mutation -

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

Chem-Bio Informatics Journal 3 （ 1 ） 1-11 2003年

研究論文（学術雑誌）, 共著, 査読有り

Microscopic study of nuclear "pasta": Quantum molecular dynamics approach

Watanabe G, Sato K, Yasuoka K, Ebisuzaki T

Nuclear Physics A 718   700C-702C 2003年

研究論文（学術雑誌）, 共著, 査読有り

Statistical study of clathrate-hydrate nucleation in a water/hydrochlorofluorocarbon system: Search for the nature of the "memory effect"

Ohmura R, Ogawa M, Yasuoka K, Mori YH

Journal of Physical Chemistry B 107   5289-5293 2003年

研究論文（学術雑誌）, 共著, 査読有り

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

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

Journal of Physical Chemistry B 107   10274-10283 2003年

研究論文（学術雑誌）, 共著, 査読有り

Hardware accelerator for molecular dynamics: MDGRAPE-2

Susukita R, Ebisuzaki T, Elmegreen BG, Furusawa H, Kato K, Kawai A, Kobayashi Y, Koishi T, McNiven GD, Narumi T, Yasuoka K

Computer Physics Communications 155   115-131 2003年

研究論文（学術雑誌）, 共著, 査読有り

Large scale molecular dynamics simulation of nucleation in supercooled NaCl

Koishi T, Yasuoka K, Ebisuzaki T

Journal of Chemical Physics 119   11298-11305 2003年

研究論文（学術雑誌）, 共著, 査読有り

Structure of cold nuclear matter at subnuclear densities by quantum molecular dyna

Watanabe G, Sato K, Yasuoka K, Ebisuzaki T

Physical Review C 68   035806 2003年

研究論文（学術雑誌）, 共著, 査読有り

Microscopic study of nuclear "pasta" by quantum molecular dynamics

Watanabe G, Sato K, Yasuoka K, Ebisuzaki T

Progress of Theoretical Physics Supplement 146   638-639 2002年

研究論文（学術雑誌）, 共著, 査読有り

Molecular dynamics study of the solidification process in alkali halide cluster

Koishi T, Yasuoka K, Narumi T, Susukita R, Furusawa H, Ebisuzaki T

Journal of Non-Crystalline Solids 312   332-336 2002年

研究論文（学術雑誌）, 共著, 査読有り

Microscopic study of slablike and rodlike nuclei: Quantum molecular dynamics approach

Watanabe G, Sato K, Yasuoka K, Ebisuzaki T

Physical Review C 66   012801 2002年

研究論文（学術雑誌）, 共著, 査読有り

Numerical simulations of magnetic materials with MD-GRAPE: curvature induced anisotropy

Elmegreen BG, Koch R, Yasuoka K, Furusawa H, Narumi T, Susukita R, Ebisuzaki T

Journal of Magnetism and Magnetic Materials 250   39-48 2002年

研究論文（学術雑誌）, 共著, 査読有り

MD simulation of cluster-surface impacts for metallic phases: soft landing, droplet spreading and implantation

Kholmurodov K, Puzynin I, Smith W, Yasuoka K, Ebisuzaki T

Computer Physics Communications 141   1-16 2001年

研究論文（学術雑誌）, 共著, 査読有り

Molecular dynamics simulation of supersaturated vapor nucleation in slit pore. II. Thermostatted atomic-wall model

Kholmurodov KT, Yasuoka K, Zeng XC

Journal of Chemical Physics 114   9578-9584 2001年

研究論文（学術雑誌）, 共著, 査読有り

1.34Tflops Molecular Dynamic simulation for NaCl with a Special Purpose Computer: MDM,

T. Narumi, R. Susukita, T. Koishi, K. Yasuoka, H. Furusawa, A. Kawai, and T. Ebisuzaki

SC2000, Dallas, U.S.A. (2000): Winner of the Gordon Bell Prizes (Peak Performance Category). 2000年11月

研究論文（学術雑誌）, 共著, 査読有り

Molecular Dynamics Simulation of Supersaturated Vapor Nucleation in Slit Pore

K. Yasuoka, G. T. Gao, and X. C. Zeng

The Journal of Chemical Physics 112   4279-4285 2000年03月

研究論文（学術雑誌）, 共著

Molecular Dynamics Simulation of the Homogeneous Nucleation of UF6 Molecules: Configurations and Infrared Spectra of the Excited Hot Clusters

S. Tanimura, K. Yasuoka, and T. Ebisuzaki

The Journal of Chemical Physics 112   3812-3819 2000年02月

研究論文（学術雑誌）, 共著, 査読有り

A Highly Vectorised 'Link-Cell' Fortran Code for the DL_POLY Molecular Dynamics Simulation Package

K. Kholmurodov, W. Smith, K. Yasuoka, and T. Ebisuzaki

Computer Physics Communications 124 2000年01月

研究論文（学術雑誌）, 共著, 査読有り

　概要を見る

分子動力学シミュレーション用ソフトウエアにおけるベクトル化について議論した。

Molecular dynamics simulation of dissociation process for methane hydrate

K. Yasuoka and S. Murakoshi

Annals of the New York Academy of Sciences 912   678-684 2000年

研究論文（学術雑誌）, 共著

A smooth-particle mesh ewald method for DL_POLY molecular dynamics simulation package on the Fujitsu VPP700

K. Kholmurodov, W. Smith, K. Yasuoka, T. Darden, T. Ebisuzaki

Journal of Computational Chemistry 21   1187-1191 2000年

研究論文（学術雑誌）, 共著

Molecular Mechanism of Vapor-Liquid Nucleation

K. Ohguchi, K. Yasuoka, and M. Matsumoto

Progress of Theoretical Physics Supplement 138   257-258 2000年

研究論文（学術雑誌）, 共著

Molecular Processes of Cluster Formation in Supersaturated Vapor

M. Matsumoto, K. Yasuoka, and K. Ohguchi

Thermal Science & Engineering 7   75-80 1999年11月

研究論文（学術雑誌）, 共著, 査読有り

Computer Simulation of Fluid Phase Change: Vapor Nucleation and Bubble Formation Dynamics,

金城友之、大口晃司、泰岡顕治、松本充弘

Computational Materials Science 14   138-141 1999年02月

研究論文（学術雑誌）, 共著, 査読有り

　概要を見る

均一核生成の例として気相均一核生成と泡生成過程に関して議論した。

Molecular Dynamics of Homogeneous Nucleation in the Vapor Phase II. Water

泰岡顕治、松本充弘

Journal of Chemical Physics 109   8463-8470 1998年11月

研究論文（学術雑誌）, 共著, 査読有り

　概要を見る

水の系において気相均一核生成を分子動力学シミュレーションを用いて研究した。単純液体の場合と比較した。

Molecular Dynamics of Homogeneous Nucleation in the Vapor Phase I. Lennard-Jones Fluid

泰岡顕治、松本充弘

Journal of Chemical Physics 109   8451-8462 1998年11月

研究論文（学術雑誌）, 共著, 査読有り

　概要を見る

Lennard-Jones 流体の系において気相均一核生成を分子動力学シミュレーションを用いて研究した。核生成速度を求め、古典理論の問題点を明らかにした。また、核生成の自由エネルギーをクラスター分布から見積もった。

Molecular Dynamics Simulations of the Homogeneous Nucleation of UF6 and SF6 Molecules: Effects of the Intramolecular Vibrational Relaxations on the Nucleation Rates

谷村志乃夫、泰岡顕治、戎崎俊一

Journal of Chemical Physics 109   4492-4497 1998年09月

研究論文（学術雑誌）, 共著, 査読有り

　概要を見る

均一核生成の現象において、分子内振動のような分子内自由度が重要になる場合を明らかにした。

Molecular Dynamics Simulation of Homogeneous Nucleation in Supersaturated Water Vapor

泰岡顕治、松本充弘

Fluid Phase Equilbria 144   369-376 1998年02月

研究論文（学術雑誌）, 共著, 査読有り

　概要を見る

水の気相均一核生成現象について、水素結合などの観点から詳細な解析を行った。

Molecular Mechanism of Evaporation and Condendation,

松本充弘、泰岡顕治、片岡洋右

Thermal Science & Engineering 3   27-31 1996年07月

研究論文（学術雑誌）, 共著, 査読有り

　概要を見る

蒸発凝縮に関する温度依存性について議論した。

Dynamics near a Liquid Surface: Mechanisms of Evaporation and Condensation

泰岡顕治、松本充弘、片岡洋右

Journal of Molecular Liquid 65/66   329-332 1995年11月

研究論文（学術雑誌）, 共著, 査読有り

　概要を見る

水、メタノール、アルゴンの３種類の系に関して蒸発・凝縮の分子レベルでのシミュレーションを行った。水・メタノールの水素結合の影響を議論した。

Molecular Simulation of Evaporation and Condensation

松本充弘、泰岡顕治、片岡洋右

Fluid Phase Equilibria 104   431-439 1995年03月

研究論文（学術雑誌）, 共著, 査読有り

　概要を見る

蒸発・凝縮過程における分子動力学シミュレーションの結果を速度分布などの観点から議論した。

Evaporation and Condensation at a Liquid Surface. II. Methanol

松本充弘、泰岡顕治、片岡洋右

Journal of Chemical Physics 101   7912-7917 1994年11月

研究論文（学術雑誌）, 共著, 査読有り

　概要を見る

メタノールを例にして会合性液体に関して、蒸発凝縮の解析を行い、単純液体とは違い分子交換による非凝縮の割合が大きいことを見いだした。

Evaporation and Condensation at a Liquid Surface. I. Argon

泰岡顕治、松本充弘、片岡洋右

Journal of Chemical Physics 101   7904-7911 1994年11月

研究論文（学術雑誌）, 共著, 査読有り

　概要を見る

単純液体の蒸発・凝縮に関して分子レベルで解析を行った。単分子過程における凝縮と分子交換を伴う凝縮を見いだした。

Evaporation and Condensation at a Liquid Methanol Surface

松本充弘、泰岡顕治、片岡洋右

THEOCHEM - Journal of Molecular Structure 318   161-168 1994年07月

研究論文（学術雑誌）, 共著, 査読有り

　概要を見る

メタノール表面における蒸発・凝縮現象を表面構造を中心に解析した。

Evaporation and Condensation as a Unimolecular Chemical Reaction: Does the Potential Barrier Exist at a Molecular Liquid Surface?

泰岡顕治、松本充弘、片岡洋右

Bulletin of the Chemical Society of Japan 67   859ミ862 1994年03月

研究論文（学術雑誌）, 共著, 査読有り

　概要を見る

蒸発・凝縮過程における化学反応過程をもとにした従来の単分子過程モデルの是非について表面付近のポテンシャルバリアの観点から議論した。

Microscopic Features of Evaporation and Condensation at Liquid Surfaces: Molecular Dynamics Simulation

松本充弘、泰岡顕治、片岡洋右

Thermal Science & Engineering 2   64-69 1994年01月

研究論文（学術雑誌）, 共著, 査読有り

　概要を見る

蒸発・凝縮の現象を分子動力学シミュレーションを用いて解析し、実験結果との比較からシミュレーションの可能性を見いだした。