研究者詳細 - 泰岡　顕治

論文 - 泰岡　顕治

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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

© 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

© 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

© 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

© 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

© 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

© 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

© 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

© 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

© 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

© 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

© 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

© 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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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

© 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

© 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

© 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

© 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

© 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

© 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

© 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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