論文 - 泰岡　顕治

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

研究論文（学術雑誌）, 共著, 査読有り

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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

研究論文（学術雑誌）, 共著, 査読有り

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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

研究論文（学術雑誌）, 共著, 査読有り

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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

研究論文（学術雑誌）, 共著, 査読有り

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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

研究論文（学術雑誌）, 共著, 査読有り

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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

研究論文（学術雑誌）, 共著, 査読有り

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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

研究論文（学術雑誌）, 共著, 査読有り

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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

研究論文（学術雑誌）, 共著, 査読有り

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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

研究論文（学術雑誌）, 共著, 査読有り

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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

研究論文（学術雑誌）, 共著, 査読有り

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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

研究論文（学術雑誌）, 共著, 査読有り

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