Updated on 2024/12/07

写真a

 
YOSHIMORI Akira
 
Organization
Academic Assembly Institute of Science and Technology Fundamental Sciences Professor
Faculty of Science Department of Science Professor
Title
Professor
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Degree

  • 理学博士 ( 1991.3   名古屋大学 )

Research Interests

  • 液体

  • 非平衡

  • 密度汎関数理論

  • 非線形

  • 動的密度汎関数法

  • 電子移動

  • time-dependent density functional method

  • 緩和

  • 溶媒和

  • electron transfer

  • relaxation

  • solvation

  • liquids

  • nonequilibrium

  • density functional theory

Research Areas

  • Nanotechnology/Materials / Fundamental physical chemistry

  • Natural Science / Mathematical physics and fundamental theory of condensed matter physics

Research History (researchmap)

  • Niigata University   Professor

    2015.10

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  • Kyushu University   Faculty of Sciences Department of Physics   Associate Professor

    1997.6 - 2015.9

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  • Nagoya University, Assistant Professor

    1993 - 1997

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  • Nagoya University

    1993 - 1997

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  • Hokkaido National Fisheries

    1991 - 1993

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  • Ministry of Agriculture, Forestry and Fisheries

    1991 - 1993

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  • Research Institute, Researcher

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Research History

  • Niigata University   Faculty of Science Department of Science   Professor

    2017.4

  • Niigata University   Abolition organization Condensed Matter Physics   Professor

    2015.10 - 2017.3

Education

  • Nagoya University   理学研究科   物理学専攻

    - 1991

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    Country: Japan

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  • Nagoya University   Graduate School, Division of Natural Science

    - 1991

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  • Nagoya University   School of Science   Department of Physics

    - 1986

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    Country: Japan

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  • Nagoya University   Faculty of Science

    - 1986

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Professional Memberships

 

Papers

  • Theoretical investigation of interaction measurements in liquid systems with viscosity distributions Reviewed

    Takumi Otake, Ryuki Kajita, Ikuma Ogasawara, Mitsuhiro Iwaki, Hiroshi Onishi, Akira Yoshimori, Ken-ichi Amano

    Physica A: Statistical Mechanics and its Applications   129918   2024.6

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.physa.2024.129918

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  • Nonintegral form of the reciprocal relation associated with violation of the fluctuation response relation

    Kotaro Kasuga, Akira Yoshimori

    Physical Review E   2023.9

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    DOI: 10.1103/PhysRevE.108.034109

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  • Effects of Solvent Density Distribution and Dipole–Dipole Interaction on a Polarization Fluctuation near an Electrically Neutral Surface

    Junpei Noji, Akira Yoshimori, Jun Ohnuki, Mitsunori Takano

    Journal of the Physical Society of Japan   2022.11

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    Publishing type:Research paper (scientific journal)  

    DOI: 10.7566/JPSJ.91.114602

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  • Usefulness of higher-order system-size correction for macromolecule diffusion coefficients: A molecular dynamics study

    Tomoya Iwashita, Masaaki Nagao, Akira Yoshimori, Masahide Terazima, Ryo Akiyama

    Chemical Physics Letters   807   140096 - 140096   2022.11

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    DOI: 10.1016/j.cplett.2022.140096

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  • A Microscopic Theory for Preferential Solvation Effects on Viscosity

    Shota Arai, Akira Yoshimori, Yuka Nakamura, Ryo Akiyama

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   91 ( 9 )   2022.9

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    We propose a theory of viscosity derived using the perturbation expansion of microscopic equations describing solvent particle dynamics to study the solvation effects of a two-component solvent in the vicinity of a large solute. The microscopic theory is expanded in powers of the solvent???solute size ratio. Considering the density distribution of the solvent particles around the solute particle, we obtain hydrodynamic equations with the boundary conditions on the solute surface. Solute???solvent radial distribution functions give the boundary condition. The perturbation theory allows us to compare the viscosity of a pure binary solvent with that of a solution including solute particles. On the basis of the theory, we determine the effects of the solute-surface mass density of solvent particles on viscosity using model radial distribution functions. We also examine some realistic distribution functions on the basis of the integral equation theory.

    DOI: 10.7566/JPSJ.91.094602

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  • Dynamic Monte Carlo calculation generating particle trajectories that satisfy the diffusion equation for heterogeneous systems with a position-dependent diffusion coefficient and free energy

    Tetsuro Nagai, Akira Yoshimori, Susumu Okazaki

    JOURNAL OF CHEMICAL PHYSICS   156 ( 15 )   154506 - 154506   2022.4

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    A series of new Monte Carlo (MC) transition probabilities was investigated that could produce molecular trajectories statistically satisfying the diffusion equation with a position-dependent diffusion coefficient and potential energy. The MC trajectories were compared with the numerical solution of the diffusion equation by calculating the time evolution of the probability distribution and the mean first passage time, which exhibited excellent agreement. The method is powerful when investigating, for example, the long-distance and long-time global transportation of a molecule in heterogeneous systems by coarse-graining them into one-particle diffusive molecular motion with a position-dependent diffusion coefficient and free energy. The method can also be applied to many-particle dynamics.& nbsp;Published under an exclusive license by AIP Publishing.

    DOI: 10.1063/5.0086949

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  • Inhomogeneous Effects of Number Density on Polarization Relaxation of a Polar Solvent around an Ion

    Junpei Noji, Akira Yoshimori

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   90 ( 7 )   2021.7

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    We studied the effects of the inhomogeneous density distribution of polar solvent molecules around an ion on the polarization relaxation by using linearized time-dependent density functional theory. This theory, which takes into account the spatial inhomogeneity of the number density of solvent molecules, enabled us to calculate the spatial distribution of the relaxation time under certain initial conditions. The results of our calculations show that the spatial distribution of the relaxation time correlates with that of the number density. The negative correlation becomes positive as the translational diffusion coefficient increases. This dependence on the translational diffusion coefficient is not affected by the initial condition.

    DOI: 10.7566/JPSJ.90.073801

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  • Solvation effects on diffusion processes of a macromolecule: Accuracy required for radial distribution function to calculate diffusion coefficient. International journal

    Yuka Nakamura, Akira Yoshimori, Ryo Akiyama

    The Journal of chemical physics   154 ( 8 )   084501 - 084501   2021.2

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER INST PHYSICS  

    We investigate the dependence of the diffusion coefficient of a large solute particle on the solvation structure around a solute. The diffusion coefficient of a hard-sphere system is calculated by using a perturbation theory of large-particle diffusion with radial distribution functions around the solute. To obtain the radial distribution function, some integral equation theories are examined, such as the Percus-Yevick (PY), hypernetted-chain (HNC), and modified HNC theories using a bridge function proposed by Kinoshita (MHNC) closures. In one-component solvent systems, the diffusion coefficient depends on the first-minimum value of the radial distribution function. The results of the MHNC closure are in good agreement with those of calculation using the radial distribution functions of Monte Carlo simulations since the MHNC closure very closely reproduces the radial distribution function of Monte Carlo simulations. In binary-solvent mixtures, the diffusion coefficient is affected by the larger solvent density distribution in the short-range part, particularly the height and sharpness of the first peak and the depth of the first minimum. Since the HNC closure gives the first peak that is higher and sharper than that of the MHNC closure, the calculated diffusion coefficient is smaller than the MHNC closure result. In contrast, the results of the PY closure are qualitatively and quantitatively different from those of the MHNC and HNC closures.

    DOI: 10.1063/5.0038894

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  • Reentrant crystallization of like-charged colloidal particles in an electrolyte solution: Relationship between the shape of the phase diagram and the effective potential of colloidal particles Reviewed

    Y. Tamura, A. Yoshimori, A. Suematsu, R. Akiyama

    EPL (Europhysics Letters)   129 ( 6 )   66001 - 66001   2020.4

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:IOP Publishing  

    DOI: 10.1209/0295-5075/129/66001

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    Other Link: https://iopscience.iop.org/article/10.1209/0295-5075/129/66001

  • Reduced density profile of small particles near a large particle: Results of an integral equation theory with an accurate bridge function and a Monte Carlo simulation Reviewed

    Yuka Nakamura, Shota Arai, Masahiro Kinoshita, Akira Yoshimori, Ryo Akiyama

    JOURNAL OF CHEMICAL PHYSICS   151 ( 4 )   044506   2019.7

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    Solute-solvent reduced density profiles of hard-sphere fluids were calculated by using several integral equation theories for liquids. The traditional closures, Percus-Yevick (PY) and the hypernetted-chain (HNC) closures, as well as the theories with bridge functions, Verlet, Duh-Henderson, and Kinoshita (named MHNC), were used for the calculation. In this paper, a one-solute hard-sphere was immersed in a one-component hard-sphere solvent and various size ratios were examined. The profiles between the solute and solvent particles were compared with those calculated by Monte Carlo simulations. The profiles given by the integral equations with the bridge functions were much more accurate than those calculated by conventional integral equation theories, such as the Ornstein-Zernike (OZ) equation with the PY closure. The accuracy of the MHNC-OZ theory was maintained even when the particle size ratio of solute to solvent was 50. For example, the contact values were 5.7 (Monte Carlo), 5.6 (MHNC), 7.8 (HNC), and 4.5 (PY), and the first minimum values were 0.48 (Monte Carlo), 0.46 (MHNC), 0.54 (HNC), and 0.40 (PY) when the packing fraction of the hard-sphere solvent was 0.38 and the size ratio was 50. The asymptotic decay and the oscillation period for MHNC-OZ were also very accurate, although those given by the HNC-OZ theory were somewhat faster than those obtained by Monte Carlo simulations.

    DOI: 10.1063/1.5100040

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  • Reciprocal relations associated with linear responses to mechanical and thermal perturbations in nonequilibrium Langevin systems Reviewed

    Yamada Kazuo, Yoshimori Akira

    PHYSICAL REVIEW E   98 ( 4 )   2018.10

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    We study universal relationships in linear responses to instances when mechanical and thermal perturbations are applied to a nonequilibrium steady state. For perturbations in nonequilibrium Langevin systems, we consider a time-dependent external force exerted on a particle along with a time-dependent temperature for the heat bath. In this system, by calculating heat currents and particle velocity, we obtain the kinetic coefficients (Onsager's coefficients) and the time correlation functions using the Fokker-Planck equations. With these quantities, we derive the reciprocal relation associated with the violation of the fluctuation response relation. We obtain the relation by integrating the extent of the violation with respect to the frequency. We also find the reciprocity in the first moment of the frequency integration. These frequency sum rules hold for both overdamped and underdamped regimes for any type of potential and any strength of the external force.

    DOI: 10.1103/PhysRevE.98.042120

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  • Stick boundary condition at large hard sphere arising from effective attraction in binary hard-sphere mixtures Reviewed

    Yuka Nakamura, Akira Yoshimori, Ryo Akiyama, Tsuyoshi Yamaguchi

    JOURNAL OF CHEMICAL PHYSICS   148 ( 12 )   2018.3

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    We have studied the diffusion of a large hard-sphere solute immersed in binary hard-sphere mixtures. We reveal how the boundary condition at the solute surface is affected by the solvent density around the solute. Solving equations for a binary compressible mixture by perturbation expansions, we obtain the boundary condition depending on the size ratio of binary solvent spheres. When the size ratio is 1: 2, the boundary condition lies close to the slip boundary condition. By contrast, when the size ratio becomes large, the boundary condition approaches the stick boundary condition with the addition of larger solvent spheres. We find that the transition to the stick boundary condition is caused by the increase in the solvent density around the solute due to an entropic effect. Published by AIP Publishing.

    DOI: 10.1063/1.5025202

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  • Method for Studying Many-Particle Effects on Nonequilibrium Steady States Reviewed

    Masao Inoue, Akira Yoshimori

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   86 ( 7 )   2017.7

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    (Received June 26, 2016; revised December 26, 2016; accepted May 12, 2017; published online June 22, 2017) On the basis of time-dependent density functional theory (TDDFT), we develop a method for calculating the spatial distribution of interacting particles in a nonequilibrium state. The particles flow around spatially fixed matter. Using this method, we clarify the many-particle effects due to particle interactions on the distribution of flowing hard spheres around a spatially fixed hard sphere (probe particle). We numerically calculate the TDDFT equations assuming axial symmetry, using the discrete Hankel transform. From this numerical calculation, we obtain the forces exerted on the probe particle by the flowing hard spheres. The calculated forces are compared with those due to noninteracting flowing particles at various particle flow velocities and volume fractions. This comparison shows that the force in the interactingparticle case is reduced by the hard-sphere interaction at low velocities and small volume fractions. In contrast, at high velocities and large volume fractions, the force in the hard-sphere system is stronger than that in the noninteracting particle system.

    DOI: 10.7566/JPSJ.86.074604

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  • Reciprocal relation related with the violation of the fluctuation-response relation in a driven diffusive system Reviewed

    K. Yamada, A. Yoshimori

    EPL   117 ( 2 )   2005   2017.1

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:EPL ASSOCIATION, EUROPEAN PHYSICAL SOCIETY  

    We derive the reciprocal relation between the linear mechanical and thermal response functions in a driven diffusive model. In this model, we consider the violation of the fluctuation-response relation (FRR) of the velocity of a particle to the thermal perturbation. In addition, we also consider the FRR violation of the heat current of the system to a mechanical perturbation. We show the equality for the extent of these FRR violations using the Fokker-Planck equation. Copyright (C) EPLA, 2017

    DOI: 10.1209/0295-5075/117/20005

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  • Effects of interactions between depletants in phase diagrams of binary hard-sphere systems Reviewed

    A. Suematsu, A. Yoshimori, R. Akiyama

    EPL   116 ( 3 )   38004   2016.11

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    Fluid-solid phase diagrams for binary hard-sphere systems were calculated to study the effects of interactions between depletants. Two effective potentials between large hard spheres were examined. One was the Asakura-Oosawa (AO) potential, and the other was an effective potential obtained by using an integral equation theory (IE potential). The IE potential has oscillations caused by the interactions between depletants, whereas in the AO potential, the inter-depletant correlation is ignored. The phase diagrams were obtained by using the thermodynamic perturbation theory with the density functional theory. The phase diagrams for the IE potential systems differed from those for the AO potential systems because of the inter-depletant correlation. The differences in the present calculation were caused by the first minimum of the effective potential. Copyright (C) EPLA, 2016

    DOI: 10.1209/0295-5075/116/38004

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  • Dynamics of the entropic insertion of a large sphere into a cylindrical vessel Reviewed

    Ryohei Hara, Ken-ichi Amano, Masahiro Kinoshita, Akira Yoshimori

    JOURNAL OF CHEMICAL PHYSICS   144 ( 10 )   2016.3

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    Insertion of a solute into a vessel comprising biopolymers is a fundamental function in a biological system. The entropy originating from the translational displacement of solvent particles plays an essential role in the insertion. Here we study the dynamics of entropic insertion of a large spherical solute into a cylindrical vessel. The solute and the vessel are immersed in small spheres forming the solvent. We develop a theoretical method formulated using the Fokker-Planck equation. The spatial distribution of solute-vessel entropic potential, which is calculated by the three-dimensional integral equation theory combined with rigid-body models, serves as input data. The key quantity analyzed is the density of the probability of finding the solute at any position at any time. It is found that the solute is inserted along the central axis of the vessel cavity and trapped at a position where the entropic potential takes a local minimum value. The solute keeps being trapped without touching the vessel inner surface. In a significantly long time tau, the solute transfers to the position in contact with the vessel bottom possessing the global potential minimum along the central axis. As the solute size increases, tau becomes remarkably longer. We also discuss the relevance of our result to the functional expression of a chaperonin/cochaperonin in the assistance of protein folding. (C) 2016 AIP Publishing LLC.

    DOI: 10.1063/1.4943394

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  • Microscopic derivation of the Stokes law in the case of anisotropic interaction between solute and solvent particles

    Yoshimori Akira

    Meeting Abstracts of the Physical Society of Japan   71   3112 - 3112   2016

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    Language:Japanese   Publisher:The Physical Society of Japan  

    DOI: 10.11316/jpsgaiyo.71.2.0_3112

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  • 22aPS-69 Re-entrant phase behavior in a charged colloidal particle system

    Uooka Yuusuke, Yoshimori Akira

    Meeting Abstracts of the Physical Society of Japan   71   3281 - 3281   2016

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    Language:Japanese   Publisher:The Physical Society of Japan (JPS)  

    DOI: 10.11316/jpsgaiyo.71.1.0_3281

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  • 22aPS-78 Effects of Particle interactions and Solvents in Microrheology

    Inoue M., Yoshimori A.

    Meeting Abstracts of the Physical Society of Japan   71   3289 - 3289   2016

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    DOI: 10.11316/jpsgaiyo.71.1.0_3289

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  • Theoretical Method of Calculating Solvent Nonequilibrium Effect on Solute Movement Reviewed

    Ryohei Hara, Akira Yoshimori

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   84 ( 12 )   2015.12

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    We formulate a theoretical method for studying the solvent particle dynamics around a moving solute, using time-dependent density functional theory. The theoretical method is applied to the insertion process of a large sphere into a cylindrical vessel immersed in solvent particles. For various velocities of the large sphere, we calculate the nonequilibrium spatial distribution of number density of solvent particles. We find a nonequilibrium effect on the distribution, which is characterized by the total number of solvent particles inside of the vessel. The number is 32.5% larger for a velocity of D-S/2d(S) than for the equilibrium state, where, d(S) and D-S are the diameter and diffusion coefficient of a solvent particle, respectively.

    DOI: 10.7566/JPSJ.84.123601

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  • A Theory of Solvation Effects on Viscosity Reviewed

    Tomofumi Yamakita, Akira Yoshimori

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   84 ( 4 )   2015.4

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    We formulate a theory for calculating the viscosity of a dilute solution, considering the solute-solvent interaction. We consider an inhomogeneous density distribution of solvent particles caused by the interaction, using the equilibrium solute-solvent radial distribution function. The theory is a microscopic extension of Einstein's viscosity formula. We formulate the theory by a perturbation expansion, assuming that a solvent particle is much smaller than a solute particle. From the perturbation theory, we obtain hydrodynamic equations with new boundary conditions on the surface of the solute. The theory is applied to a system with a simple radial distribution function.

    DOI: 10.7566/JPSJ.84.043602

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  • A Unified Expression of Harada-Sasa Equality in Underdamped and Overdamped Langevin Systems of the Field Variable Description Reviewed

    Kazuo Yamada, Akira Yoshimori

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   84 ( 4 )   2015.4

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    We extend the relationship between the fluctuation-response relation (FRR) violation and the stationary energy dissipation rate to the Langevin system expressed by field variable. We propose two methods for extending: the operator method and the multiple-scale analysis. By these methods, we expand the FRR violation for the underdamped field system in power series of epsilon = m/gamma to establish the relationship between underdamped and overdamped systems. Here, gamma and m are the friction coefficient and mass of a Brownian particle, respectively. By the expansion, we obtain a unified expression including the relations in the underdamped and overdamped field systems as special cases. The expression shows that the relations have the same form in the underdamped and overdamped field systems. In addition, we show that the relation also holds in the time region difference from that in the underdamped or overdamped system.

    DOI: 10.7566/JPSJ.84.044008

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  • 24pAQ-6 Derivation of the Stokes Einstein relation from microscopic dynamics

    Yoshimori Akira

    Meeting Abstracts of the Physical Society of Japan   70   3441 - 3441   2015

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    DOI: 10.11316/jpsgaiyo.70.1.0_3441

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  • 22pPSA-24 The effect of inter-perticle interaction of the depletion force on crystallization

    Suematsu A., Yoshimori A., Akiyama R.

    Meeting Abstracts of the Physical Society of Japan   70   3326 - 3326   2015

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    Language:Japanese   Publisher:The Physical Society of Japan (JPS)  

    DOI: 10.11316/jpsgaiyo.70.1.0_3326

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  • 22pPSA-25 Relationship between velocity of probe particles and resistance force in microrheology

    Inoue Masao, Yoshimori Akira

    Meeting Abstracts of the Physical Society of Japan   70   3327 - 3327   2015

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    Language:Japanese   Publisher:The Physical Society of Japan (JPS)  

    DOI: 10.11316/jpsgaiyo.70.1.0_3327

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  • 22pAJ-7 Derivation of the Harada-Sasa equality described by the field variables

    Yamada K., Yoshimori A.

    Meeting Abstracts of the Physical Society of Japan   70   3004 - 3004   2015

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    Language:Japanese   Publisher:The Physical Society of Japan (JPS)  

    DOI: 10.11316/jpsgaiyo.70.1.0_3004

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  • 22pPSA-34 Force that a solute receives from the solvents in inhomogeneous system

    Hara Ryohei, Yoshimori Akira

    Meeting Abstracts of the Physical Society of Japan   70   3336 - 3336   2015

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    DOI: 10.11316/jpsgaiyo.70.1.0_3336

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  • 16aCR-8 Reciprocal relation for the violation of the ctuation-dissipation theorem

    Yamada K., Yoshimori A.

    Meeting Abstracts of the Physical Society of Japan   70   2542 - 2542   2015

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    DOI: 10.11316/jpsgaiyo.70.2.0_2542

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  • 16aCT-10 solvent dynamics effect on the solute insertion into the vessel

    Hara R., Yoshimori A.

    Meeting Abstracts of the Physical Society of Japan   70   2887 - 2887   2015

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    DOI: 10.11316/jpsgaiyo.70.2.0_2887

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  • Effects of interactions between particles on dynamics in microrheology Reviewed

    Masao Inoue, Akira Yoshimori

    JOURNAL OF MOLECULAR LIQUIDS   200   81 - 84   2014.12

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:ELSEVIER SCIENCE BV  

    We have studied the effects of interactions between particles on the dynamics in a colloidal dispersion system using the time-dependent density functional theory. We consider a hard-sphere probe particle fixed at the origin and hard-sphere colloidal particles suspended in a solvent that flows at a constant velocity against the probe particle. We calculated the density fields of colloidal particles, forces acting on the probe particle, and friction coefficients for small volume fractions of colloidal particles. The results show that hard-sphere interactions between colloidal particles decrease the forces and friction coefficients. The effect of the interactions is more significant for small colloidal particles than for large particles. The effect also becomes weak with increasing velocity of the solvent. (C) 2014 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.molliq.2014.05.029

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  • Effects of the solvation structure on diffusion of a large particle in a binary mixture studied by perturbation theory Reviewed

    Y. Nakamura, A. Yoshimori, R. Akiyama

    JOURNAL OF MOLECULAR LIQUIDS   200   85 - 88   2014.12

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    We study the effects of the solvation structure on the diffusion of a large particle in a binary mixture. Using our recently developed perturbation theory, we calculate the diffusion coefficient of a large hard-sphere solute particle immersed in a binary solvent mixture of hard spheres with two different sizes. The calculation results show that the Stokes-Einstein (SE) relation breaks down in the hard-sphere system. When the size ratio of binary solvent spheres is three or more, the deviation from the SE relation increases with the packing fraction of larger solvent spheres. In contrast, at the size ratio of two, the diffusion coefficient approaches the value predicted by the SE relation as larger solvent spheres are added. We show that the large deviation from the SE relation is caused by the high density of larger solvent spheres around the solute sphere. (C) 2014 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.molliq.2014.06.021

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  • Solid phase stability of a double-minimum interaction potential system Reviewed

    Ayumi Suematsu, Akira Yoshimori, Masafumi Saiki, Jun Matsui, Takashi Odagaki

    JOURNAL OF CHEMICAL PHYSICS   140 ( 24 )   244501   2014.6

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    We study phase stability of a system with double-minimum interaction potential in a wide range of parameters by a thermodynamic perturbation theory. The present double-minimum potential is the Lennard-Jones-Gauss potential, which has a Gaussian pocket as well as a standard Lennard-Jones minimum. As a function of the depth and position of the Gaussian pocket in the potential, we determine the coexistence pressure of crystals (fcc and bcc). We show that the fcc crystallizes even at zero pressure when the position of the Gaussian pocket is coincident with the first or third nearest neighbor site of the fcc crystal. The bcc crystal is more stable than the fcc crystal when the position of the Gaussian pocket is coincident with the second nearest neighbor sites of the bcc crystal. The stable crystal structure is determined by the position of the Gaussian pocket. These results show that we can control the stability of the solid phase by tuning the potential function. (C) 2014 AIP Publishing LLC.

    DOI: 10.1063/1.4884021

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  • Perturbation Theory of Large-Particle Diffusion in a Binary Solvent Mixture Reviewed

    Yuka Nakamura, Akira Yoshimori, Ryo Akiyama

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   83 ( 6 )   2014.6

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    We study the diffusion of a large spherical particle immersed in a binary compressive liquid mixture using a perturbation theory. We focus on the breakdown of the Stokes-Einstein (SE) relation caused by the microscopic solvation structure of binary solvent particles around a solute particle. In order to consider the solvation structure, we solve multicomponent generalized Langevin equations by singular perturbation expansion. Then, we assume that solvent particles are much smaller than the solute particle. Solving the equations, we express the diffusion coefficient analytically using the radial distribution functions of a binary mixture. The expression shows the breakdown of the SE relation if the density distribution of a binary solvent is inhomogeneous around a solute particle. Actually, we show that the SE relation breaks down when a large hard sphere diffuses in a binary hard-sphere mixture. We observe the large deviation from the SE relation, which is a result specific to the binary solvent.

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  • A Unified Proof of the Harada-Sasa Equality for Underdamped and Overdamped Langevin Systems Reviewed

    Kazuo Yamada, Akira Yoshimori

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   83 ( 5 )   2014.5

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    A new expression of the Harada-Sasa equality is derived by multiple-scale analysis. The new expression unifies the equality for the underdamped and overdamped Langevin models in special cases. In addition, the expression shows that the equality is available in a new time region, which differs from that in the underdamped or overdamped model. The expression is obtained by the expansion of the fluctuation response relation (FRR) violation in the underdamped model in powers of epsilon=m/gamma, where gamma is the friction coefficient and m is the mass of a Brownian particle. The violation of the FRR is in agreement with the energy dissipation rate up to the second order of epsilon.

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  • Control of solid-phase stability by interaction potential with two minima Reviewed

    A. Suematsu, A. Yoshimori, M. Saiki, J. Matsui, T. Odagaki

    J. Mole. Liquids   200A   12 - 15   2014

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  • Coarse-grained forms for equations describing the microscopic motion of particles in a fluid Reviewed

    Shankar P. Das, Akira Yoshimori

    PHYSICAL REVIEW E   88 ( 4 )   043008   2013.10

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    Exact equations of motion for the microscopically defined collective density (rho) over cap (x, t) and the momentum density (g) over cap (x, t) of a fluid have been obtained in the past starting from the corresponding Langevin equations representing the dynamics of the fluid particles. In the present work we average these exact equations of microscopic dynamics over the local equilibrium distribution to obtain stochastic partial differential equations for the coarse-grained densities with smooth spatial and temporal dependence. In particular, we consider Dean's exact balance equation for the microscopic density of a system of interacting Brownian particles to obtain the basic equation of the dynamic density functional theory with noise. Our analysis demonstrates that on thermal averaging the dependence of the exact equations on the bare interaction potential is converted to dependence on the corresponding thermodynamic direct correlation functions in the coarse-grained equations.

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  • A theoretical framework for calculations of the structural relaxation time on the basis of the free energy landscape theory Reviewed

    Toru Ekimoto, Akira Yoshimori, Takashi Odagaki, Takashi Yoshidome

    CHEMICAL PHYSICS LETTERS   577   58 - 61   2013.7

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    On the basis of the free energy landscape theory, we develop a framework to calculate the structural relaxation time in supercooled liquids and glasses. By the framework, the relaxation time is obtained by an escaping time from a basin in a given free energy surface. In order to demonstrate its usefulness, we apply the framework to monodisperse hard-sphere glass systems. Then we show that the relaxation time increases drastically with the density. Additionally, we discuss an explicit picture of the cooperatively rearranging region by analyzing the spatial distribution of an activation free energy of one particle. (C) 2013 Elsevier B.V. All rights reserved.

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  • Time-Dependent Density Functional Theory of Polarization Relaxation under External Field Reviewed

    Yuichiro Uematsu, Akira Yoshimori

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   82 ( 1 )   2013.1

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    A new inhomogeneous time-dependent density functional theory is proposed to study an effect of external field on the polarization relaxation of molecular liquids. The effect of external field is considered by the number density of solvent molecules, and the homogeneous approximation introduced by many previous studies is not employed. To demonstrate the validity of the theory, the spatial distribution of the relaxation time is calculated in a polar solvent system with an ion. The calculated results show a notable effect of translational diffusion on the spatial distribution of the polarization relaxation time.

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  • Molecular dynamics study of fast dielectric relaxation of water around a molecular-sized ion Reviewed

    Yoji Kubota, Akira Yoshimori, Nobuyuki Matubayasi, Makoto Suzuki, Ryo Akiyama

    JOURNAL OF CHEMICAL PHYSICS   137 ( 22 )   224502   2012.12

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    We have calculated the dielectric relaxation of water around an ion using molecular dynamics simulations. The collective motion of water near the ion showed fast relaxation, whereas the reorientational motion of individual water molecules does not have the fast component. The ratio of the relaxation time for the fast component and the bulk water was consistent with the experimental results, known as hyper-mobile water, for alkali halide aqueous solution. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4769972]

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  • Perturbation Theory of Large-Particle Diffusion Reviewed

    Yuko Inayoshi, Akira Yoshimori, Ryo Akiyama

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   81 ( 11 )   2012.11

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    A new theory is developed to study the effects of the granularity of a liquid on the diffusion of a large particle in the liquid. Inhomogeneous Langevin equations are expanded in powers of the size ratio between the solvent and large particles. From the expansion, we obtain hydrodynamic equations with new boundary conditions on the surface of the large particle in the first order. The new boundary conditions can be obtained from the radial distribution function between diffusing and solvent particles. The present theory is formulated by perturbation expansion and can thus deal with a large particle. In addition, using analytical solutions of hydrodynamic equations, we consider the effects of solvent particles at an infinite distance in contrast to the case for other methods. The theory is applied to a model radial distribution function, a hard-sphere system, and a Kihara potential system.

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  • New Macroscopic Expression Connecting Energy Dissipation with Violation of Fluctuation Response Relation in Colloidal Many-Particle Systems Reviewed

    Akira Yoshimori, Takahiro Harada

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   81 ( 9 )   2012.9

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    We present a new method of deriving the relation between the dissipation of energy and the violation of the fluctuation response relation in nonequilibrium states. The method is obtained using the Fokker-Planck equation in underdamped cases. Using the method, we show that the relation obtained by Harada and Sasa can be derived from an energy balance in nonequilibrium steady states. In addition, applying the method to colloidal many-particle systems, we derive a new expression for the relation using the current and density fields. The new expression has a simple form with a linear response coefficient for a nonconservative external force, in contrast to that in a previous study.

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  • Application of Phase Transition Theory to a Glass-Forming System Reviewed

    Ayumi Suematsu, Akira Yoshimori, Masafumi Saiki, Jun Matsui, Takashi Odagaki

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   81   2012.9

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    We have investigated the crystallization of a monatomic simple liquid in equilibrium, where the constituents interact through the Lennard-Jones-Gauss (LJG) potential. By incorporating a perturbation expansion into a density functional approach, we obtain a phase diagram covering a wide range of the parameter space. The phase diagram agrees qualitatively with that obtained by molecular dynamics (MD) simulations. The MD simulations show that the system cannot be crystallized, even if the temperature is sufficiently low, in a certain region of the parameter space. In this parameter region, we find that the coexisting density of the fcc crystal is unexpectedly high owing to a decrease in the free energy and show that the third-nearest-neighbor site of the fcc crystal coincides with the second minimum in the LJG potential.

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  • A Perturbation Theory for Friction of a Large Particle Immersed in a Binary Solvent Reviewed

    Yuka Nakamura, Akira Yoshimori, Ryo Akiyama

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   81   2012.9

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    A new theory of a binary solvent is developed to study the effects of the density of solvent particles around a large solute particle on friction. To develop the theory, the solvent particles are assumed to be much smaller than the solute particle, and then a perturbation expansion is employed. The expansion allows one to derive hydrodynamic equations with boundary conditions on the surface of a solute. The boundary conditions are calculated from the radial distribution functions of a binary solvent. The hydrodynamic equations with the boundary conditions provide an analytical expression for the friction. The developed theory is applied to a binary hard-sphere system. The present theory shows that the friction in the system has larger values than those predicted by the Stokes law.

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  • A Theory of Hole Transfer in DNA Reviewed

    Takaki Himeno, Akira Yoshimori

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   81 ( 9 )   2012.9

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    A theory, which was previously applied to electron transfer in DNA, is applied to hole transfer between a dye molecule and an electrode coupled through a DNA bridge, because the applicability to such hole transfer has not yet been studied. The results calculated using the theory are compared with the experimental results for the same system. The theory reproduces the dependence of the current between the dye molecule and the electrode on the length of DNA. However, the agreement with experimental results requires that the reorganization energy in the ground state of a dye molecule be larger than that employed in previous studies of electron transfer.

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  • A non-perturbative approach to freezing of superfuid 4He in density functional theory Reviewed

    T. Minoguchi, D. E. Galli, M. Rossi, A. Yoshimori

    Journal of Physics: Conference Series   400 ( 1 )   2012

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    Freezing of various classical liquids is successfully described by density functional theory (DFT). On the other hand, so far no report has been published that DFT describes the freezing of superfuid 4He correctly. In fact, DFT gives too stable solid phase and the superfuid phase does not exist at finite positive pressures within a second order perturbation. In this paper we try a non-perturbative version of DFT, that is modified weighted density approximation (MWDA) to go beyond second order perturbation for the freezing of superfuid 4He. Via an exact zero temperature quantum Monte-Carlo (QMC) method we have computed the equation of state and the compressibility of superfuid 4He. By utilizing a recently introduced analytic continuation method (the GIFT method), we have obtained also density response functions at different densities from QMC imaginary time correlation functions. Contrary to second order perturbation, by employing these QMC data as DFT input we find a too stable superfuid phase, preventing freezing around the experimentally observed freezing pressure. We find the same pathological behavior by using another model energy functional of superfuid 4He (Orsay-Trento model). We conclude that the straightforward MWDA calculation gives such a poor result when liquid-gas transition is present. © Published under licence by IOP Publishing Ltd.

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  • Configurational Entropy and Heat Capacity in Supercooled Liquids Reviewed

    Akira Yoshimori, Takashi Odagaki

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   80 ( 6 )   2011.6

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    We establish the general relationship between the configurational entropy and heat capacity in a supercooled liquid within the framework of equilibrium statistical mechanics. The relationship shows that the configurational entropy is different from the entropy obtained by the integration of the glass heat capacity. In addition, the difference shows the correlation between the energy and entropy in liquid structures. Applying the general results to a simple model, we demonstrate that the difference can be too large to neglect. We also discuss new experiments using the present results.

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  • Time-Dependent Density Functional Theory Formulated Using the Interaction-Site Model Reviewed

    Akira Yoshimori

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   80 ( 3 )   2011.3

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    A theory for studying nonlinear dynamics of molecular liquids is developed. The theory is based on the extension of the time-dependent density functional theory to a rigid interaction-site model. From the theory, one can calculate time changes in interaction-site densities using molecular parameters such as the inertial moment of a molecule. The theory has a differential and integral basic equation with a kernel function, which is not included in the time-dependent density functional theory of simple liquids. The application of the theory to diatomic and three-site molecules allows one to obtain explicit expressions of kernel functions.

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  • Studies of Liquid-Solid Transitions Using a Thermodynamic Perturbation Method with Modified Weighted Density Approximation Reviewed

    Ayumi Suematsu, Akira Yoshimori, Takashi Odagaki

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   80 ( 2 )   2011.2

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  • Derivation of the nonlinear fluctuating hydrodynamic equation from the underdamped Langevin equation Reviewed

    Takenobu Nakamura, Akira Yoshimori

    JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL   42 ( 6 )   2009.2

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    We derive the fluctuating hydrodynamic equation for the number and momentum densities exactly from the underdamped Langevin equation. This derivation is an extension of the Kawasaki-Dean formula in the underdamped case. The steady-state probability distribution of the number and momentum densities field can be expressed by the kinetic and potential energies. In the massless limit, the obtained fluctuating hydrodynamic equation reduces to the Kawasaki-Dean equation. Moreover, the derived equation corresponds to the field equation derived from the canonical equation when the friction coefficient is zero.

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  • Free Energy Landscape Theory of Glass Transition and Entropy Reviewed

    T. Odagaki, A. Yoshimori

    J. Non-Crys. Solids   355 ( 10-12 )   681 - 685   2009

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    DOI: 10.1016/j.jnoncrysol.2008.10.018

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  • Free-energy landscape for a tagged particle in a dense hard-sphere fluid Reviewed

    Takashi Yoshidome, Takashi Odagaki, Akira Yoshimori

    PHYSICAL REVIEW E   77 ( 6 )   061503   2008.6

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    Exploiting the thermodynamic potential functional provided by density functional theory, we determine analytically the free-energy landscape (FEL) in a hard-sphere fluid. The FEL is represented in the three-dimensional coordinate space of the tagged particle. We also analyze the distribution of the free-energy barrier between adjacent basins and show that the most provable value and the average of the free-energy barrier are increasing functions of the density. Since the size of the cooperatively rearranging region (CRR) is also increased as the density is raised [Yoshidome , Phys. Rev. E 76, 021506 (2007)], the present result is consistent with the Adam-Gibbs theory in which the increase of the activation energy is due to the increase of the size of the CRR.

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  • Separation of Dynamics in the Free Energy Landscape

    T. Ekimoto, T. Odagaki, A. Yoshimori

    AIP Conference Proceedings, Complex Systems   982   211 - 214   2008

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  • Free energy landscape and cooperatively rearranging region in a hard sphere glass Reviewed

    Takashi Yoshidome, Akira Yoshimori, Takashi Odagaki

    PHYSICAL REVIEW E   76 ( 2 )   021506   2007.8

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    Exploiting the density functional theory, we calculate the free energy landscape (FEL) of the hard sphere glass in three dimensions. From the FEL, we estimate the number of the particles in the cooperatively rearranging region (CRR). We find that the density dependence of the number of the particles in the CRR is expressed as a power law function of the density. Analyzing the relaxation process in the CRR, we also find that the string motion is the elementary process for the structural relaxation, which leads to the natural definition of the simultaneously rearranging region as the particles displaced in the string motion.

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  • A molecular theory of large-solute diffusion Reviewed

    A. Yoshimori

    Condensed Matter Physics   10 ( 4 )   563 - 571   2007

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    The limit of a large solute in the molecular theory of diffusion developed by Yamaguchi et al. [Yamaguchi T. et al., J. Chem. Phys., 2005, 123, 034504] is studied. By the limit, the Stokes approximation to the hydrodynamic equations is derived in the outside region of a diffusing solute. The limit of a large solute also leads to equations in the inside region of the solute. The analytical solution of the inside equation allows one to derive the boundary condition, which is needed on the surface of the solute when the hydrodynamic equations are calculated. The boundary condition includes stick and slip boundary conditions employed by the Stokes law, in the special case. Besides stick and slip conditions, other conditions can be expressed. The boundary condition depends on properties of a solvent. © A.Yoshimori.

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  • Functional analysis of TIMID protein promoting the root-hair elongation in response to touching stimulus of the root.

    Yoshihiro Koshino-Kimura, Haruna Kiriyama, Akira Yoshimori, Miyuki Kubo, Takuji Wada, Taisuke Nishimura, Sumie Ishiguro, Ryuji Tsugeki, Noritaka Matsumoto, Kiyotaka Okada

    PLANT AND CELL PHYSIOLOGY   48   S144 - S144   2007

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  • Nonlinear effects on solvation dynamics in simple mixtures Reviewed

    Shuhei Murata, Akira Yoshimori

    JOURNAL OF CHEMICAL PHYSICS   125 ( 24 )   244501   2006.12

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    The authors applied the time dependent density functional method (TDDFM) and a linear model to solvation dynamics in simple binary solvents. Changing the solute-solvent interactions at t=0, the authors calculated the time evolution of density fields for solvent particles after the change (t > 0) by the TDDFM and linear model. First, the authors changed the interaction of only one component of solvents. In this case, the TDDFM showed that the solvation time decreased monotonically with a mole fraction of the solvent strongly interacting with the solute. The monotonical decreases agreed with experimental results, while the linear model did not reproduce these results. The authors also calculated the solvation time by changing the interaction of both components. The calculation showed that the mole fraction dependence had the peak. The TDDFM presented a much higher peak than the linear model. The difference between the TDDFM and the linear model was caused by a nonlinear effect on an exchange process of solvent particles. (c) 2006 American Institute of Physics.

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  • Free Energy Landscape Approach to Glass Transition Reviewed

    Takashi Odagaki, Takashi Yoshidome, Akira Koyama, Akira Yoshimori

    Journal of Non-Crystalline   352   4843 - 4846   2006.8

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  • Construction of the free energy landscape by the density functional approarch Reviewed

    Takashi Yoshidome, Akira Yoshimori, Takashi Odagaki

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   75 ( 5 )   2006.5

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    We propose a new method to construct the free energy landscape in the configurational space, where the density functional approach to the thermodynamic function is exploited. In order to demonstrate the validity of the method, we construct the free energy landscape for rearrangement of atoms in an FCC crystal of hard spheres. Analyzing the relaxation process, we deduce two concepts of rearranging region, one is the simultaneously rearranging region (SRR) which is defined by the difference between two adjacent regions. The other is the cooperatively rearranging region (CRR) which is the spheres involved in the saddle configuration between two adjacent regions. The latter region corresponds to the region introduced by Adam and Gibbs. We show that the SRR and the CRR can be determined explicitly from the free energy landscape.

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  • Free energy landscape and CRR of glass-forming substance Reviewed

    Takashi Yoshidome, Akira Yoshimori, Takashi Odagaki

    FLOW DYNAMICS   832   188 - +   2006

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    We propose a method to calculate the size of the cooperatively rearranging region (CRR), N-CRR, from the free energy landscape. In the free energy landscape picture, the particles in the CRR correspond to those involved in determinig the saddle point between two adjacent basins. By using this method, we estimate N-CRR of the 3-D random configuration of hard spheres. We also find that the system can transit to the adjacent basin via the lower height of the saddle point by the string motion.

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  • Bandwidth analysis of solvation dynamics in a simple liquid mixture Reviewed

    M. Sakurai, A. Yoshimori

    Journal of Chemical Physics   122 ( 10 )   2005.3

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    The time-dependent energy distribution of solvation dynamics is studied by molecular dynamics simulations of a Lennard-Jones mixture. We calculate the response functions of the average and the variance which correspond to the spectral peak shift and bandwidth. Our calculation shows that the variance relaxation is slower than that of the average. The result agrees qualitatively with the experimental results. Dividing the obtained response functions into subcomponents caused by each solvent, we find that the relaxation is dominated by that solvent which strongly interacts with the solute. Extracting the redistribution component from the response functions, we find that it causes the slower relaxation of the response function. Thus, we conclude that the difference of the slower relaxations between the average and variance is caused by the redistribution process. © 2005 American Institute of Physics.

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  • Microscopic derivation of time-dependent density functional methods Reviewed

    Akira Yoshimori

    Physical Review E - Statistical, Nonlinear, and Soft Matter Physics   71 ( 3 )   031203   2005.3

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    Time-dependent density functional methods (TDDFM) are studied from the microscopic viewpoint using projection operator methods in classical liquids. A density field is denned without averaging, so that a time evolution equation of the density field is derived with a random force. The derived equation includes a free energy functional, which is different from that defined in the TDDFM. The projection operator method provides the exact expression of the free energy functional. Another definition of the density field by an average leads to the equation of the TDDFM. In addition, an equation describing fluctuations is also derived. (c)2005 The American Physical Society.

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  • Microscopic derivation of time-dependent density functional methods Reviewed

    A Yoshimori

    PHYSICAL REVIEW E   71 ( 3 )   2005.3

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    Time-dependent density functional methods (TDDFM) are studied from the microscopic viewpoint using projection operator methods in classical liquids. A density field is defined without averaging, so that a time evolution equation of the density field is derived with a random force. The derived equation includes a free energy functional, which is different from that defined in the TDDFM. The projection operator method provides the exact expression of the free energy functional. Another definition of the density field by an average leads to the equation of the TDDFM. In addition, an equation describing fluctuations is also derived.

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  • A Microscopic Model of Jump Rate Distribution in the Glass Transition Reviewed

    A. Yoshimori, T. Odagaki

    J. Phys. Soc. Jpn.   74 ( 4 )   1206 - 1213   2005

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    We study distribution of jump rates in supercooled liquids and glass by activation theories developed in studies of chemical reactions. Defining jump conditions, we explain the physical origin giving rise to the jump rate distribution. Jump rates distribute if some kinds of relaxation have different time scales. In addition, we express the distribution by the microscopic parameters of liquids using appropriate approximations. The obtained expression is the power law distribution in the limit of small jump rates. We relate the exponents of the power law with the time scale in the mode coupling theory.

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  • Cooling rate dependence of specific heat in systems out of equilibrium Reviewed

    T. Tao, T. Odagaki, A. Yoshimori

    J. Chem. Phys.   122   044505   2005

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  • 特別企画 森肇氏インタビュー

    Yoshimori, Akira, Ishizaki, Ryuji

    80 ( 5 )   631 - 661   2003.8

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  • Selective solvation caused by size effects Reviewed

    M. Sakurai, A. Yoshimori

    Chemical Physics Letters   371 ( 1-2 )   23 - 28   2003.3

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    A simple binary-solvent model is theoretically employed to study the size-effect on selective solvation. We consider multi-component hard-sphere molecules with solute-solvent attraction. We employ the PY approximation to calculate coordination numbers. The calculated coordination number shows that the solute attracts more large solvent molecules than small solvent molecules at a weak attraction. The solute, however, attracts small solvent molecules at strong attraction. To study the selectivity, we divide the size-effect into the exclude effect and the steric hindrance. Attractive strength increases the steric hindrance of large solvent molecules more than that of the small solvent molecules. © 2003 Elsevier Science B.V. All rights reserved.

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  • Specific Heat Anomaly at the Glass Transition Reviewed

    Takashi Odagaki, Takashi Yoshidome, Toshiaki Tao, Akira Yoshimori

    Journal of Chemical Physics   117   10151 - 10155   2002.12

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  • Specific heat in a nonequilibrium system composed of Einstein oscillators Reviewed

    Toshiaki Tao, Akira Yoshimori, Takashi Odagaki

    Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics   66 ( 4 )   5   2002.10

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    In order to understand the behavior of thermodynamic quantities near the glass transition temperature, we put the energy landscape picture and the particle’s jump motion together and calculate the specific heat of a nonequilibrium system. Taking the finite observation time into account, we study the observation time dependence of the specific heat. We assume the Einstein oscillators for the dynamics of each basin in the landscape structure of phase space and calculate the specific heat of a system with 20 basins. For a given observation time, a transition from annealed to quenched system occurs at the temperature when the time scale of jumps exceeds the observation time. The transition occurs at lower temperature and becomes sharper for longer observation time. © 2002 The American Physical Society.

    DOI: 10.1103/PhysRevE.66.041103

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  • Specifie heat in a nonequilibrium system composed of Einstein oscillators Reviewed

    Toshiaki Tao, Akira Yoshimori, Takashi Odagaki

    Physical Review E - Statistical, Nonlinear, and Soft Matter Physics   66 ( 4 )   041103/5   2002.10

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    In order to understand the behavior of thermodynamic quantities near the glass transition temperature, we put the energy landscape picture and the particle's jump motion together and calculate the specific heat of a nonequilibrium system. Taking the finite observation time into account, we study the observation time dependence of the specific heat. We assume the Einstein oscillators for the dynamics of each basin in the landscape structure of phase space and calculate the specific heat of a system with 20 basins. For a given observation time, a transition from annealed to quenched system occurs at the temperature when the time scale of jumps exceeds the observation time. The transition occurs at lower temperature and becomes sharper for longer observation time. © 2002 The American Physical Society.

    DOI: 10.1103/PhysRevE.66.041103

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  • Specific heat in a nonequilibrium system composed of Einstein oscillators Reviewed

    T Tao, A Yoshimori, T Odagaki

    PHYSICAL REVIEW E   66 ( 4 )   2002.10

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    In order to understand the behavior of thermodynamic quantities near the glass transition temperature, we put the energy landscape picture and the particle's jump motion together and calculate the specific heat of a nonequilibrium system. Taking the finite observation time into account, we study the observation time dependence of the specific heat. We assume the Einstein oscillators for the dynamics of each basin in the landscape structure of phase space and calculate the specific heat of a system with 20 basins. For a given observation time, a transition from annealed to quenched system occurs at the temperature when the time scale of jumps exceeds the observation time. The transition occurs at lower temperature and becomes sharper for longer observation time.

    DOI: 10.1103/PhysRevE.66.041103

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  • Spatial mosaic and interfacial dynamics in a Mullerian mimicry system Reviewed

    A Sasaki, Kawaguchi, I, A Yoshimori

    THEORETICAL POPULATION BIOLOGY   61 ( 1 )   49 - 71   2002.2

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    Uncovering why spatial mosaics of mimetic morphs are maintained in a Mullerian mimicry system has been a challenging issue in evolutionary biology. In this article, we analyze the reaction diffusion system that describes two-species Mullerian mimicry in one- and two-dimensional habitats. Due to positive frequency-dependent selection, a local population first approaches the state where one of the comimicking patterns predominates, which is followed by slow movement of boundaries where different patterns meet. We then analyze the interfacial dynamics of the boundaries to find whether a stable cline is maintained and to obtain the wave speed if the cline is unstable. The results are: (1) In a spatially uniform habitat the morph with greater base fitness spreads both in one and two species system. (2) The strength of cross-species interaction determines whether the mimetic morph clines of model and mimic species coalesce into the same geographical region or pass through each other. The joint wave speed of clines decreases by increasing the number of comimicking species in the mimicry ring. (3) In spatial heterogeneous habitats, stable clines can be maintained due to the balance between the base fitness gradient and the biased gene flow by negative curvature of boundary. This allows the persistence of a spatial mosaic even if one of the morphs is in every place advantageous over the other. A balanced cline is also maintained if there is a gradient in the population density. (4) A new advantageous morph occurring at a local region is doomed to go to extinction in a finite time if the "radius" of initial distribution is below a threshold. Possible applications to the heliconiine butterfly mimicry ring, heterozygous disadvantage systems of chromosomal rearrangement and hybrid zone, the third phase of Wright's Shifting Balance theory, and cytoplasmic incompatibility are discussed. (C) 2002 Elsevier Science (USA).

    DOI: 10.1006/tpbi.2001.1552

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  • ガラス転移点近傍の比熱の異常について

    小田垣孝, 田尾聡明, 吉森明

    KEK Proceedings   2001-27   1   2002

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  • Specific heat in nonequilibrium systems and glass transition Reviewed

    T. Odagaki, T. Tao, A. Yoshimori

    J. Non-Cryst. Sol.   307-310   407   2002

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    DOI: 10.1016/S0022-3093(02)01501-6

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  • 非平衡系の比熱

    田尾 聡明, 吉森 明, 小田垣 孝

    KEK Proceedings   2001-27   86   2002

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  • Specific heat in nonequilibrium systems Reviewed

    T Tao, A Yoshimori, T Odagaki

    PHYSICAL REVIEW E   64 ( 4 )   046112   2001.10

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    We propose a general framework of calculating the specific heat of the system in nonequilibrium, where the dynamics of the representative point can be separated into fast motion in a basin of energy landscape and the slow stochastic jump motion among basins. We apply this framework to gaseous hydrogen and obtain the observation time (t(obs)) dependence of the specific heat. We find that the specific heat gives the quenched and the annealed one in the limit of t(obs)-->0 and t(obs)--> infinity, respectively. We also investigate the waiting time and the observation time dependence of the specific heat and show that, for shorter waiting time, the observation time must be Ion-er to obtain the same degree of annealing. This tendency is consistent with the observation that the glass transition temperature is higher for faster quenching.

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  • Specific heat in nonequilibrium systems

    T. Tao, A. Yoshimori, T. Odagaki

    Physical Review E - Statistical, Nonlinear, and Soft Matter Physics   64 ( 4 )   461121 - 461125   2001.10

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    The specific heat of the system, where the dynamics of the representative point can be separated into fast motion in a basin of energy landscape, was calculated. The framework was applied to gaseous hydrogen and the observation time dependence of the specific heat was obtained. The waiting time of specific heat was also observed to obtain the degree of annealing. It was observed that the specific heat changes continuously from the quenched one to the annealed one as a function of the observation time and waiting time.

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  • Localization transition in the vitrification process Reviewed

    T. Odagaki, A. Yoshimori

    Physica B   296 ( 1/3 )   174 - 179   2001

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    DOI: 10.1016/S0921-4526(00)00796-1

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  • Microscopic derivation of jump rate distribution and the glass transition Reviewed

    T. Odagaki, A. Yoshimori

    J. Phys.: Condens. Matter   12 ( 29 )   6509 - 6514   2000

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    DOI: 10.1088/0953-8984/12/29/322

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  • Monte Carlo simulation study on the structure and reaction at metal-electrolyte interface Reviewed

    N Goto, A Okada, T Kakitani, A Yoshimori, Y Hatano

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   66 ( 6 )   1825 - 1835   1997.6

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    Monte Carlo simulation calculations were made for investigating the structure and the mechanism of the electron transfer reactions at the metal-electrolyte interface. All the particles are assumed to be spherical with the same radii and the metal was treated as a source of the mirror image force. We obtained a result that many electrolyte ions are directly adsorbed to the metal surface in the presence and absence of the external field, indicating that the structure of the interface is non-uniform and a strong alternating local field is produced. Free energy surfaces for the electron transfer reaction are calculated using the simulation data. We found that the distance fluctuation of a reactant from the metal surface makes significant contribution to the free energy surfaces as well as the orientational and positional fluctuations of solvent and electrolyte ions do, and that the distribution of these fluctuations deviate greatly from the Gaussian, bringing about large nonlinear response effects in the relation between the activation free energy and energy gap of the reaction.

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  • Analysis of the excited-state dynamics of 13-trans-locked-bacteriorhodopsin Reviewed

    R Akiyama, A Yoshimori, T Kakitani, Y Imamoto, Y Shichida, Y Hatano

    JOURNAL OF PHYSICAL CHEMISTRY A   101 ( 4 )   412 - 417   1997.1

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    Optical absorption spectra of 13-trans-locked-bacteriorhodopsin, which contains a chemically modified retinal chromophore inhibiting photoisomerization, were obtained at five temperatures. Analysis of the excited-state dynamics of the time-correlation function (tcf) of the modified wavepacket was made by the Fourier transform of the optical absorption spectra. Even though the photoisomerization of the chromophore was inhibited, the normalized tcf decayed rapidly until the level of about 10(-6) at 200 fs almost independently of the temperature. The ratio of the tcf between 13-trans-locked-bacteriorhodopsin and native bacteriorhodopsin displayed some oscillations. Its mean value was close to 1 until about 100 fs, and it increased, gradually up to the level of 10(0.5)-10(1) at about 200 fs. Namely, the excited-state dynamics of 13-trans-locked-bacteriorhodopsin appears globally quite similar to that of native bacteriorhodopsin up to about 100 fs, and the difference of them becomes slightly evident after 100 fs up to about 200 fs. Those data suggest that the excited-state dynamics of bacteriorhodopsin is not solely determined by the conformation change of the chromophore but also by another factor such as the movement of the microenvironment of the protein.

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  • Variability in timing and magnitude of spring bloom in the Oyashio region, the western subarctic Pacific off Hokkaido, Japan Reviewed

    Hiromi Kasai, Hiroaki Saito, Akira Yoshimori, Satoru Taguchi

    Fisheries Oceanography   6 ( 2 )   118 - 129   1997

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    The spring bloom of phytoplankton is a well-established, regular, seasonal event in the western subarctic Pacific and is considered one of the most important conditions of massive production of pelagic fishes. A series of 12 cruises was conducted from 1990 to 1992 to examine the timing and magnitude of the spring phytoplankton bloom in the Oyashio region, the western subarctic Pacific off Hokkaido, Japan. An interannual variability in the bloom events was also analysed. On the basis of hydrographical characteristics, the study area was divided into three water masses: the Oyashio Water Mass, the Mixed Water Mass, and the Coastal Water Mass. Spring blooms were observed first in April in the Oyashio and the Coastal Water Masses, and continued to May in 1991 and 1992. However, no bloom was recorded in the Mixed Water Mass. High nutrient supply into the surface mixed layer during winter is likely to be one of the factors supporting an intense spring bloom in the Oyashio Water Mass. A significant positive relationship between log-transformed surface chlorophyll a concentration and maximum density gradient (MDG) within the euphotic layer was obtained in April, indicating the importance of vertical stability of the water column in the initiation of spring blooms in the Oyashio and the Coastal Water Masses. The spring blooms in 1991 were much more extensive and lasted longer than in 1990. It is suggested that meteorological conditions and abundance of grazers were responsible for this interannual difference.

    DOI: 10.1046/j.1365-2419.1997.00034.x

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  • Analysis of the temperature dependence of femtosecond excited state dynamics of bacteriorhodopsin by spin-boson model Reviewed

    R Akiyama, A Yoshimori, T Kakitani, Y Imamoto, Y Shichida, Y Hatano

    CHEMICAL PHYSICS LETTERS   256 ( 1-2 )   165 - 171   1996.6

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    The spin-boson model was applied to analyze the temperature dependence of excited state dynamics for the cis-trans photoisomerization of the chromophore in bacteriorhodopsin which was obtained by the Fourier transform of the optical absorption spectrum. The results indicate that the model is valid in the short time region less than about 30 fs and that the excited state dynamics in the time region larger than 30 fs is dominated by the non-harmonic slow vibrational motion, which is temperature independent. It is suggested that this specific vibrational motions might reflect the ultrafast cis-trans isomerization of the chromophore as well as conformation change of the protein environment.

    DOI: 10.1016/0009-2614(96)00434-4

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  • Refraction of active waves in reaction-diffusion media Reviewed

    Hiroyasu Yamada, Chihiro Matsuoka, Akira Yoshimori

    Physics Letters, Section A: General, Atomic and Solid State Physics   210 ( 3 )   189 - 194   1996.1

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    The refraction of active waves is analyzed for a stable-metastable reaction-diffusion system consisting of two regions with different diffusion coefficients. The equations governing the evolution of wavefronts are derived by means of an asymptotic perturbation method for boundary layers. These equations describe non-stationary refraction near the steady state regime. It is shown that the dynamics of wavefronts separates into that in the region near the boundary and that far from the boundary.

    DOI: 10.1016/S0375-9601(96)80008-9

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  • Nonlinear effects of solvation dynamics Reviewed

    Akira Yoshimori

    Studies in Physical and Theoretical Chemistry   83 ( C )   297 - 300   1995.1

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    The nonlinear Smoluchowski-Vlasov equation is calculated to investigate nonlinear effects on solvation dynamics. While a linear response has been assumed for free energy in equilibrium solvent, the equation includes dynamical nonlinear terms. The solvent density function is expanded in terms of spherical harmonics for orientation of solvent molecules, and then only terms for ℓ=0 and 1, and m=0 are taken. The calculated results agree qualitatively with that obtained by many molecular dynamics simulations. In the long-term region, solvent relaxation for a change from a neutral solute to a charged one is slower than that obtained by the linearized equation. Further, in the model, the nonlinear terms lessen effects of acceleration by the translationai diffusion on solvent relaxation. © 1995, Elsevier Ltd. All rights reserved.

    DOI: 10.1016/S0167-6881(06)80794-9

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  • Nonlinear effects of solvation dynamics Reviewed

    Akira Yoshimori

    Journal of Molecular Liquids   65-66 ( C )   297 - 300   1995

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    The nonlinear Smoluchowski-Vlasov equation is calculated to investigate nonlinear effects on solvation dynamics. While a linear response has been assumed for free energy in equilibrium solvent, the equation includes dynamical nonlinear terms. The solvent density function is expanded in terms of spherical harmonics for orientation of solvent molecules, and then only terms for ℓ=0 and 1, and m=0 are taken. The calculated results agree qualitatively with that obtained by many molecular dynamics simulations. In the long-term region, solvent relaxation for a change from a neutral solute to a charged one is slower than that obtained by the linearized equation. Further, in the model, the nonlinear terms lessen effects of aceleration by the translational diffusion on solvent relaxation. © 1995.

    DOI: 10.1016/0167-7322(95)00881-6

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  • EFFECTS OF THE DONOR-ACCEPTOR DISTANCE DISTRIBUTION ON THE ENERGY-GAP LAWS OF CHARGE SEPARATION AND CHARGE RECOMBINATION REACTIONS IN POLAR SOLUTIONS Reviewed

    T KAKITANI, A YOSHIMORI, N MATAGA

    JOURNAL OF PHYSICAL CHEMISTRY   96 ( 13 )   5385 - 5392   1992.6

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    We have investigated energy pp laws of the intermolecular charge separation (CS) and charge recombination (CR) reactions by considering the distance distribution between donor and acceptor molecules. The experimentally obtained energy gap dependence of the CS reaction rate constant, which shows a large width and flat shape, has been theoretically explained as follows. The sharp increase in the normal region is due to the donor-acceptor molecules in close contact which give the energy pp laws with small widths and are located at small energy gaps. The flat shapes of the top region and the inverted region arc due to the donor-acceptor molecules at large mutual distances which give the energy gap laws with large widths and are located at large energy gaps. The experimentally obtained energy gap law of the CR reaction, which is nearly bell-shaped and located at thc rather large energy gap, cannot be explained by assuming thc same distance distribution as in the CS reaction. A narrow distance distribution of the geminate radical ion pair was necessary for the satisfactory interpretation of the energy gap law of thc CR reaction. It was also shown that the energy gap law of the CR reaction can be reproduced rather well by considering a dynamical process of relaxation of the initial distance distribution of the geminate radical ion pair which is produced by the photoinduced CS reaction.

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  • MONTE-CARLO SIMULATION STUDY ON ENERGY-GAP DEPENDENCE OF ELECTRON-TRANSFER REACTIONS IN POLAR SOLUTION - EFFECT OF ELECTRONIC POLARIZABILITY OF SOLVENT Reviewed

    Y ENOMOTO, T KAKITANI, A YOSHIMORI, Y HATANO

    CHEMICAL PHYSICS LETTERS   186 ( 4-5 )   366 - 371   1991.11

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    We conducted Monte Carlo simulations of polar solutions by explicitly treating the effect of electronic polarizability of solvent molecules. Based on these data, we calculated the energy-gap dependence of electron-transfer rates. It was found that a considerable asymmetry of the energy-gap dependence of the charge-separation rate is brought about by the electronic polarizability. It was also found that the inverted region of the charge-recombination reaction shifts considerably to the smaller energy gap from that of the charge-separation reaction, due to the non-linearity of solvent polarization.

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  • Monte carlo simulation study of free energy curves for electron transfer reactions in polar solutions by considering the electronic polarizability Reviewed

    Yasuyo Hatano, Toshiaki Kakitani, Yoshitaka Enomoto, Akira Yoshimori

    Molecular Simulation   6 ( 4-6 )   191 - 198   1991.5

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    We have conducted Monte Carlo simulations of polar solutions with a spherical hard core model by properly taking into account the electronic polarizability of solvent molecules. We have calculated the free energy curve as a function of the reaction coordinate of electron transfer reactions in cases where the reactant is neutral and charged. From the analysis of the free energy curvature ratio between the two cases, we have found that the electronic polarizability contributes to enhance the nonlinear response of solvent polarizations and that this enhancement is greatly strengthened if the translational motion of solvent molecules is frozen. © 1991, Taylor &amp
    Francis Group, LLC. All rights reserved.

    DOI: 10.1080/08927029108022428

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  • MONTE-CARLO SIMULATION STUDY ON REORGANIZATION ENERGY OF ELECTRON-TRANSFER REACTIONS IN POLAR SOLUTION Reviewed

    Y ENOMOTO, T KAKITANI, A YOSHIMORI, Y HATANO, M SAITO

    CHEMICAL PHYSICS LETTERS   178 ( 2-3 )   235 - 240   1991.3

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    The reorganization energy of electron-transfer reactions as a function of the distance between donor and acceptor molecules is calculated by Monte Carlo simulation. It is found that the reorganization energy of charge-separation reactions is appreciably different from that of charge-recombination reactions. The average of these values agrees very well with the value obtained by a mean-spherical-approximation theory.

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  • THEORETICAL-ANALYSIS OF ENERGY-GAP LAWS OF ELECTRON-TRANSFER REACTIONS - DISTRIBUTION EFFECT OF DONOR-ACCEPTOR DISTANCE Reviewed

    T KAKITANI, A YOSHIMORI, N MATAGA

    ADVANCES IN CHEMISTRY SERIES   ( 228 )   45 - 69   1991

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    The electron-transfer rate as a function of the free energy gap (energy-gap law) was formulated by including the solvent nonlinear response effect and averaging over the distribution of donor-acceptor distances. Using the same parameter values, we fit the theoretical energy-gap laws to three independent experimental measurements: the photoinduced charge-separation (CS) rate as measured from fluorescence quenching in the stationary state, the actual photoinduced charge-separation rate as obtained from analysis of the transient effect in the fluorescence decay curve, and the charge-recombination (CR) rate of the geminate radical-ion pair. The different energy-gap laws among those reactions can be reproduced reasonably well by adopting different distributions of the donor-acceptor distance: that of the CS reaction covering those over various distances and more specified ones corresponding to the contact ion-pair (CIP) and solvent-separated ion-pair (SSIP) models for the CR reaction. The nonlinear effect in those homogeneous reactions is small when the CIP model applies and appreciable when the SSIP model applies.

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  • THEORETICAL-ANALYSIS OF ENERGY-GAP LAWS OF ELECTRON-TRANSFER REACTIONS - DISTRIBUTION EFFECT OF DONOR-ACCEPTOR DISTANCE Reviewed

    T KAKITANI, A YOSHIMORI, N MATAGA

    ELECTRON TRANSFER IN INORGANIC, ORGANIC, AND BIOLOGICAL SYSTEMS   228   45 - 69   1991

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  • THEORETICAL-STUDY OF DIELECTRIC SATURATION IN MOLECULAR SOLUTIONS BY THE MONTE-CARLO SIMULATION Reviewed

    Y HATANO, T KAKITANI, A YOSHIMORI, M SAITO, N MATAGA

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   59 ( 3 )   1104 - 1116   1990.3

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  • 液体・溶液の動的性質に関する統計力学的研究

    吉森 明

    [九州大学]  2003 

MISC

  • Diffusion coefficient of a large particle calculated by radial distribution functions in hard-sphere systems

    Y. Nakamura, A. Yoshimori, S. Arai, M. Kinoshita, R. Akiyama

    The 12th Mini-Symposium on Liquids (MSL2018)   2018.6

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  • Radial distribution functions for hard sphere fluid calculated by MC and by an integral equation theory with a bridge function

    Y. Nakamura, S. Arai, A. Yoshimori, M. Kinoshita, R. Akiyama

    The 12th Mini-Symposium on Liquids (MSL2018)   2018.6

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  • 7pAM-4 Application of the time-dependent density functional theory to microrheology

    Inoue Masao, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   69 ( 2 )   193 - 193   2014.8

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  • 7pAM-2 Effective attraction between like-charged colloidal particles in an electrolyte solution : Decomposition to the indirect effect using integral equation theory

    Fujihara Shingo, Sawayama Takuto, Yoshimori Akira, Akiyama Ryo

    Meeting abstracts of the Physical Society of Japan   69 ( 2 )   192 - 192   2014.8

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  • 8pPSB-43 A large particle diffusion and breakdown of the Stokes-Einstein relation : Effects of solute size and solvent density on diffusion coefficient

    Nakamura Yuka, Yoshimori Akira, Akiyama Ryo

    Meeting abstracts of the Physical Society of Japan   69 ( 2 )   214 - 214   2014.8

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  • 7pAM-10 A solvent dynamic effect in entropic insertion of a big sphere into an even bigger cylindrical vessel

    Hara Ryohei, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   69 ( 2 )   194 - 194   2014.8

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  • 7pAM-8 Effective potential of the depletion force and crystallization

    Suematsu A., Yoshimori A., Akiyama R., Nakamura Y.

    Meeting abstracts of the Physical Society of Japan   69 ( 2 )   194 - 194   2014.8

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  • 27aAB-9 Studies of crystallization due to depletion effects using effective potential

    Suematsu Ayumi, Yoshimori Akira, Akiyama Ryo, Nakamura Yuka

    Meeting abstracts of the Physical Society of Japan   69 ( 1 )   389 - 389   2014.3

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  • 27aAB-2 Theory of diffusion for studying effects of solvent granularity

    Nakamura Yuka, Yoshimori Akira, Akiyama Ryo

    Meeting abstracts of the Physical Society of Japan   69 ( 1 )   388 - 388   2014.3

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  • 27aAB-1 A theory of viscosity for including granularity of solvents

    Yamakita Tomofumi, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   69 ( 1 )   387 - 387   2014.3

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  • 30aPS-124 Time-Dependent Density Functional Theory in the Interaction-Site Model

    Okatsugi Satoshi, Yoshimori Akira, Yoshida Norio

    Meeting abstracts of the Physical Society of Japan   69 ( 1 )   428 - 428   2014.3

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  • 30aPS-123 Microrheology in colloidal dispersion system

    Inoue Masao, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   69 ( 1 )   428 - 428   2014.3

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  • The effects of packing fraction of solvent particles on large-particle diffusion

    Nakamura Yuka, Yoshimori Akira, Akiyama Ryo

    Meeting abstracts of the Physical Society of Japan   68 ( 2 )   322 - 322   2013.8

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  • Depletion effects on phase transition

    Suematsu Ayumi, Yoshimori Akira, Akiyama Ryo, Nakamura Yuka

    Meeting abstracts of the Physical Society of Japan   68 ( 2 )   337 - 337   2013.8

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  • 29pXM-8 Relationship of Harada-Sasa relation between the overdamped and underdamped limits

    Yamada Kazuo, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   68 ( 1 )   407 - 407   2013.3

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  • 27aXC-7 Perturbation theory of large-particle diffusion : Comparison with non-perturbative theory

    Nakamura Yuka, Yoshimori Akira, Akiyama Ryo

    Meeting abstracts of the Physical Society of Japan   68 ( 1 )   427 - 427   2013.3

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  • 27aXC-1 A study of phase transition using a interaction potential with two minima

    Suematsu A., Yoshimori A., Saiki M., Matsui J., Odagaki T.

    Meeting abstracts of the Physical Society of Japan   68 ( 1 )   426 - 426   2013.3

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  • 27aXC-8 Extension of Einstein's viscosity formula for including the solvation of the solute

    Yamakita Tomofumi, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   68 ( 1 )   428 - 428   2013.3

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  • 29aPS-8 Numerical Research on Microrheology

    Inoue Masao, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   68 ( 1 )   448 - 448   2013.3

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  • 19aPSA-45 The second law in general compound systems and mechanics

    Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   67 ( 2 )   254 - 254   2012.8

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  • 21aPSA-21 Extension of Einstein's viscosity formula

    Yamakita Tomofumi, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   67 ( 2 )   347 - 347   2012.8

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  • 19aAB-8 Molecular dynamics study in fast dielectric relaxation of water around a solute molecule

    Kubota Yoji, Yoshimori Akira, Matubayasi Nobuyuki, Suzuki Makoto, Akiyama Ryo

    Meeting abstracts of the Physical Society of Japan   67 ( 2 )   329 - 329   2012.8

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  • 19aAB-1 Slip and Stick Boundary Conditions for Diffusion Coefficient and Radial Distribution Function

    Nakamura Yuka, Yoshimori Akira, Akiyama Ryo

    Meeting abstracts of the Physical Society of Japan   67 ( 2 )   327 - 327   2012.8

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  • 26pAH-2 A new theory of large-particle diffusion : Comparison with another theory

    Inayoshi Yuko, Nakamura Yuka, Yoshimori Akira, Akiyama Ryo

    Meeting abstracts of the Physical Society of Japan   67 ( 1 )   411 - 411   2012.3

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  • 26pAH-3 Effects of a small amount of co-solvent to diffusion of a large particle

    Nakamura Yuka, Inayoshi Yuko, Yosimori Akira, Akiyama Ryo

    Meeting abstracts of the Physical Society of Japan   67 ( 1 )   412 - 412   2012.3

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  • 24pBF-8 A study of liquid-solid transition in a Lennard-Jones-Gauss system using a thermo-dynamic perturbation theory

    Suematsu A., Yoshimori A., Saiki M., Matsui J., Odagaki T.

    Meeting abstracts of the Physical Society of Japan   67 ( 1 )   398 - 398   2012.3

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  • A solvent effect on insertion path of a solute particle into a cylindrical vessel

    R. Hara, K. Amano, M. Kinoshita, A. Yoshimori

    6-th Mini-Symposium on Liquid,Kyushu University, Hakozaki Campus,2012.6.23   2012

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  • A Perturbation Theory for Friction of a Large Particle Immersed in a Binary Solvent (Proceedings of the 5th Mini-Symposium on Liquids : Fundamental Problems on Liquids and Related Topics)

    Journal of the Physical Society of Japan   81   SA026 - 1-7   2012

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  • Application of Phase Transition Theory to a Glass-Forming System (Proceedings of the 5th Mini-Symposium on Liquids : Fundamental Problems on Liquids and Related Topics)

    Journal of the Physical Society of Japan   81   SA020 - 1-7   2012

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  • 21pJF-6 Theory of friction of a large particle from a binary solvent and the application

    Nakamura Yuka, Yoshimori Akira, Akiyama Ryo

    Meeting abstracts of the Physical Society of Japan   66 ( 2 )   308 - 308   2011.8

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  • 22pPSB-52 Study of Harada-Sasa formula using Fokker-Planck equation

    Yamada Kazuo, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   66 ( 2 )   259 - 259   2011.8

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  • 26pPSB-21 Theory of friction of a large particle from multi-component solvents

    Nakamura Yuka, Yoshimori Akira, Akiyama Ryo

    Meeting abstracts of the Physical Society of Japan   66 ( 1 )   399 - 399   2011.3

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  • 26aTD-1 Dynamics of hard sphere systems based on the free energy landscape picture

    Ekimoto Toru, Yoshimori Akira, Yoshidome Takashi, Odagaki Takashi

    Meeting abstracts of the Physical Society of Japan   65 ( 2 )   293 - 293   2010.8

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  • 26aPS-17 Solid-liquid phase transition of a Coulomb hard-sphere system

    Yoshidome Takashi, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   65 ( 2 )   343 - 343   2010.8

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  • 24aTG-7 Faster rotational relaxation of solvents around an ion

    Uematsu Y., Yoshimori A.

    Meeting abstracts of the Physical Society of Japan   65 ( 2 )   320 - 320   2010.8

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  • 24pPSA-41 Absence of self-averaging linear response and using urn model

    Noguchi S., Yoshimori A., odagaki T., Matsui J.

    Meeting abstracts of the Physical Society of Japan   65 ( 2 )   256 - 256   2010.8

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  • 23aPS-115 friction to a large particle from multi-component solvents

    Chaen Yutaka, Akiyama Ryo, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   65 ( 1 )   405 - 405   2010.3

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  • 23aPS-114 Rotational relaxation of solvents around an ion

    Uematsu Y., Yoshimori A.

    Meeting abstracts of the Physical Society of Japan   65 ( 1 )   405 - 405   2010.3

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  • 26pPSA-36 Energy Dissipation Structural in a colloidal suspension and Violation of the Fluctuation-Response Relation

    Yoshimori Akira, Harada Takahiro

    Meeting abstracts of the Physical Society of Japan   64 ( 2 )   277 - 277   2009.8

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  • 25pQE-7 Liquid-solid transitions in systems of an inter-particle potential with two minima

    Suematsu A., Yoshimori A., Odagaki T.

    Meeting abstracts of the Physical Society of Japan   64 ( 2 )   251 - 251   2009.8

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  • Yamaguchi theory and Van der Waals picture :

    91 ( 6 )   713 - 715   2009

  • 21aVA-12 Configurational entropy and heat capacity in glass transition

    Yoshimori Akira, Odagaki Takashi, Okubo Tsuyoshi

    Meeting abstracts of the Physical Society of Japan   63 ( 2 )   308 - 308   2008.8

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  • 20aPS-112 Diffusion of a large solute and radial distribution function

    Inayoshi Yuko, Akiyama Ryo, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   63 ( 2 )   290 - 290   2008.8

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  • New conditions for validity of the centroid molecular dynamics and ring polymer molecular dynamics

    Akira Yoshimori

    JOURNAL OF CHEMICAL PHYSICS   128 ( 23 )   234105   2008.6

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    Validity of the centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD) in quantum liquids is studied on an assumption that momenta of liquid particles relax fast. The projection operator method allows one to derive the generalized Langevin equation including a memory effect for the full-quantum canonical (Kubo-transformed) correlation function. Similar equations for the CMD and RPMD correlation functions can be derived too. The comparison of these equations leads to conditions under which the RPMD and CMD correlation functions agree approximately with the full-quantum canonical correlation function. The condition for the RPMD is that the memory effects of the full-quantum and RPMD equations vanish quickly with the same time constants. The CMD correlation function requires additional conditions concerning static correlation. (C) 2008 American Institute of Physics.

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  • 21aPS-59 The relation between the over-damped evolution equation and the under-damped evolution equation for the density field II

    Nakamura Takenobu, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   62 ( 1 )   312 - 312   2007.2

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  • 20aTC-10 Distribution of the height of the saddle point in the free energy lanndscape

    Yoshidome T., Yoshimori A., Odagaki T.

    Meeting abstracts of the Physical Society of Japan   62 ( 1 )   349 - 349   2007.2

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  • 20aTC-9 Relaxation processes in the Free Energy Landscape

    Yoshidome T., Yoshimori A., Odagaki T.

    Meeting abstracts of the Physical Society of Japan   62 ( 1 )   349 - 349   2007.2

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  • 25aRC-4 Density dependence of the size of the cooperatively rearranging region for the hard sphere glass

    Yoshidome T., Yoshimori A., Odagaki T.

    Meeting abstracts of the Physical Society of Japan   61 ( 2 )   270 - 270   2006.8

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  • 20aXG-6 Free energy landscape and string motion

    Yoshidome T., Yoshimori A., Odagaki T.

    Meeting abstracts of the Physical Society of Japan   60 ( 2 )   228 - 228   2005.8

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  • 24pYW-5 Free energy landscape of the glass-forming sustance

    Yoshidome T., Yoshimori A., Odagaki T.

    Meeting abstracts of the Physical Society of Japan   60 ( 1 )   350 - 350   2005.3

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  • 25pYW-4 The width of transient hole burning spectra calculated by MD Simulations of solvation dynamics

    Sakurai Masashi, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   60 ( 1 )   357 - 357   2005.3

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  • 12pTH-5 Identification of CRR and SRR from the free energy landscape

    Yoshidome T., Yoshimori A, Odagaki T.

    Meeting abstracts of the Physical Society of Japan   59 ( 2 )   294 - 294   2004.8

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  • 27aWE-5 Simulation of solvation dynamics in mixture : contribution of the redistribution process to Time Resolved Fluorescence

    Sakurai Masashi, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   59 ( 1 )   347 - 347   2004.3

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  • 28aWE-3 A basis of centroid molecular dynamics methods

    Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   59 ( 1 )   358 - 358   2004.3

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  • 28aWE-4 Free energy landscape and CRR with Density functional theory

    Yoshidome T., Yoshimori A., Odagaki T.

    Meeting abstracts of the Physical Society of Japan   59 ( 1 )   359 - 359   2004.3

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  • Time dependent density functional methods and their application to chemical physics

    Akira Yoshimori

    Journal of Theoretical and Computational Chemistry   3 ( 1 )   117 - 143   2004.3

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    This article reviews microscopic development of time dependent functional method and its application to chemical physics. It begins with the formulation of density functional theory. The time dependent extension is discussed after the equilibrium formulation. Its application is explained by solvation dynamics. In addition, it reviews studies of nonlinear effects on polar liquids and simple mixtures.

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  • Study of Viscosity by the Mode Coupling Theory

    Terada Takeshi, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   58 ( 2 )   299 - 299   2003.8

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  • Density functional theory for glass transition

    Yoshidome T., Yoshimori A., Odagaki T.

    Meeting abstracts of the Physical Society of Japan   58 ( 2 )   310 - 310   2003.8

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  • Spectral Width of Time-Resolved Fluorescence Spectroscopy Calculated by Simulation of Solvation Dynamics

    Sakurai Masashi, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   58 ( 1 )   370 - 370   2003.3

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  • Specific heat anomaly at the glass transition

    Yoshidome T, Tao T, Yoshimori A, Odagaki T

    Meeting abstracts of the Physical Society of Japan   57 ( 2 )   248 - 248   2002.8

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  • On the specific heat anomaly near the glass transition

    T. Odagaki, T. Tao, A. Yoshimori

    KEK Proceedings   2001-27   1   2002

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  • Specific heat in non-equilibrium systems

    T. Tao, A. Yoshimori, T. Odagaki

    KEK Proceedings   2001-27   86   2002

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  • Specific heat in nonequilibrium systems (2)

    Tao T., Yoshimori A., Odagaki T.

    Meeting abstracts of the Physical Society of Japan   56 ( 2 )   276 - 276   2001.9

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  • Nonlinear distribution dynamics of solvation

    A Yoshimori

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   70 ( 6 )   1833 - 1841   2001.6

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    Dynamics of distributions in a solvation process is studied using the Smoluchowski equation. Time evolution of distributions is calculated on a two-dimensional nonlinear free energy surface. The number density of solvent molecules is considered as well as the polarization density. The calculations show that widths of the distribution relax more slowly than peak shifts for slow relaxation of the number density. The result agrees qualitatively with that obtained by time-resolved fluorescence spectroscopy.

    DOI: 10.1143/JPSJ.70.1833

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  • A time dependent density functional method for the interaction site model

    A Yoshimori

    JOURNAL OF MOLECULAR LIQUIDS   90 ( 1-3 )   29 - 33   2001.2

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    A new method is developed to study nonlinear dynamics of molecular liquids. It is a time dependent density functional method for the interaction site model. The nonlinear Langevin theory provides the formulation of the method. An approximation is introduced to calculate the reversible term. (C) 2001 Elsevier Science B.V. All rights reserved.

    DOI: 10.1016/S0167-7322(00)00177-X

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  • Solvation dynamics in mixed solvents

    Murata Shuhei, Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   55 ( 2 )   285 - 285   2000.9

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  • Selective coordination of hard-sphere mixture

    Sakurai M., Yoshimori A.

    Meeting abstracts of the Physical Society of Japan   55 ( 1 )   268 - 268   2000.3

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  • 25aP-12 Time dependent density functional method with the interaction site model

    YOSHIMORI Akira

    Meeting abstracts of the Physical Society of Japan   54 ( 2 )   304 - 304   1999.9

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  • Nonlinear Langevin equations and the time dependent density functional method

    A Yoshimori

    PHYSICAL REVIEW E   59 ( 6 )   6535 - 6540   1999.6

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    To study the time dependent density functional method (TDDFM), two streaming velocity (reversible) terms are reformulated in the nonlinear Langevin equation. Mori's [Prog. Theor. Phys. 33, 423 (1965)] projection operator method shows a variety of nonlinear Langevin equations. This is because the equations depend on the choice of phase space functions employed in the projection. If phase space functions include particular functions, however, the streaming velocity term has an invariable form. The form is independent of the choice of other phase space functions. Since the invariable streaming velocity term does not introduce the TDDFM, the second viewpoint is presented. In this, the linearization of the streaming velocity term agrees with the frequency term in the linear Langevin equation. Since only the second streaming velocity term introduces the TDDFM, one needs to be cautious in the derivation of the TDDFM. [S1063-651X(99)10506-3].

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  • 29a-XC-6 Derivation of jump rate distribution in supercooled liquids and glass states

    Yoshimori A., Matsui J., Odagaki T.

    Meeting abstracts of the Physical Society of Japan   54 ( 1 )   706 - 706   1999.3

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  • Comparisons of semiclassical approximations by expansion in Planck's constant

    A Yoshimori

    JOURNAL OF CHEMICAL PHYSICS   109 ( 20 )   8790 - 8800   1998.11

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    Fermi's golden rule is expanded in Planck's constant to study quantum effects of nuclear baths on transitions between electronic states. For six approximations, the second-order expansion of the transition rates is compared with the exact expansion. The comparison provides the conditions for agreement between the exact and approximate rate constants in the second order. Two of the conditions show that the change in electronic states of the solute does not affect solvent structure much. The other concerns linearity of the reaction coordinate. Besides the comparison of analytical expressions, the expansion of approximations is numerically compared, using a simple model. Most approximations show similar values for a parameter set. The values approximate the value obtained by quantum molecular simulations. (C) 1998 American Institute of Physics. [S0021-9606(98)00844-7].

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  • Dynamics of distribution widths in solvation

    YOSHIMORI Akira

    Meeting abstracts of the Physical Society of Japan   53 ( 2 )   819 - 819   1998.9

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  • Theory of ion solvation dynamics in mixed dipolar solvents

    A Yoshimori, TJF Day, GN Patey

    JOURNAL OF CHEMICAL PHYSICS   109 ( 8 )   3222 - 3231   1998.8

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    Time dependent density functional theory in its "extended linear" or "surrogate" form is used to investigate the dynamics of selective ion solvation in binary dipolar solvents. It is shown that simple analytical approximations that trap the basic physics of the solvation process can be obtained. In particular, it is found that the relaxation of:the solvent number densities about a charged solute is governed by two distinct modes clearly associated with electrostriction and redistribution processes. This is consistent with the physical picture suggested by molecular dynamics (MD) simulations. The solvent polarization relaxation is also dominated by two modes associated with the-two rotational diffusion constants of the binary solvent. In addition to the analytical approximations, full numerical solutions of the extended linear theory are obtained and the dependence of the relaxation on solvent density and solute charge is discussed. Detailed comparisons of the theory with MD simulations for a closely related model indicate that the theory is qualitatively correct, but quantitatively poor generally predicting relaxation rates which are too fast. This is due mainly to the neglect of inertial or non-Markovian effects in the theoretical approach. (C) 1998 American Institute of Physics. [S0021-9606(98)50132-8]

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  • Mathematical models of population dynamics of the kelp Laminaria religiosa, with emphasis on temperature dependence

    A Yoshimori, T Kono, H Iizumi

    FISHERIES OCEANOGRAPHY   7 ( 2 )   136 - 146   1998.6

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    Theoretical and numerical models were developed to investigate the effects of water temperature on the population dynamics of the kelp, Laminaria religiosa. The models describe seasonal changes in the biomass of kelp by calculation of growth and grazing rates of sea urchins, Strongylocentrotus nudus. Using the theoretical model, conditions were obtained to satisfy the statistical analysis of a relationship between water temperature and kelp harvests from a fishery census. The conditions require the negative second derivative Of the growth rate with respect to temperatures, or the positive second derivative of the grazing rate. By using the numerical model, harvests of kelp were calculated for a change in water temperature over a given period. The period of a temperature change giving the maximum effects an the harvest was determined primarily by temperature dependence on the growth rate. Grazing by sea urchins had large effects on the harvest of kelp. A value of 10(4) was obtained for a ratio between harvests at the higher and the lower temperatures differing by +/- 1 degrees C.

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  • An investigation of dynamical density functional theory for solvation in simple mixtures

    A Yoshimori, TJF Day, GN Patey

    JOURNAL OF CHEMICAL PHYSICS   108 ( 15 )   6378 - 6386   1998.4

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    Linear and nonlinear versions of time dependent density functional theory are solved for a single solute particle in a simple binary solvent. All particles interact with Lennard-Jones potentials. The theoretical results are compared with molecular dynamics calculations. It is shown that the nonlinear theory is necessary in order to obtain a good quantitative description of selective solvation dynamics. The linear theory is only of qualitative value. Also, attention is drawn to a previously little appreciated problem which arises when one attempts to compare time dependent density functional theory with computer simulation or experimental results. The difficulty involves matching the theoretical and absolute time scales and is discussed in detail in this paper. (C) 1998 American Institute of Physics. [S0021-9606(98)50615-0].

    DOI: 10.1063/1.476044

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  • Dynamical density functional method and nonlinear Langevin equation

    YOSHIMORI Akira

    Meeting abstracts of the Physical Society of Japan   53 ( 1 )   700 - 700   1998.3

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  • Non-linear quantum effects on electron transfer reactions

    A. Yoshimori

    Journal of Electroanalytical Chemistry   438 ( 1-2 )   21 - 26   1997.11

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    To study nuclear quantum effects on electron transfer reactions, the non-adiabatic rate constant is expanded in terms of Planck's constant. The expansion to the second order reproduces well the quantum correction in the activation free energy for a quantum Monte Carlo simulation of water. In addition, the spin-boson model is discussed using the expansion. The validity of the rate constant given by the spin-boson model is investigated in non-linear systems. Conditions for obtaining exact values of the rate constant are established in the second order of Planck's constant. In liquids, the conditions are satisfied if the one-body distribution function does not change during the electron transfer reaction. © 1997 Elsevier Science S.A.

    DOI: 10.1016/S0022-0728(96)04997-2

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  • 5p-YL-5 Why does the spin-boson model agree?

    Yoshimori Akira

    Meeting abstracts of the Physical Society of Japan   52 ( 2 )   738 - 738   1997.9

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  • 28p-F-10 Solvation dynamics in mixture

    Yoshimori A., Day T.J.F., Patey G.N.

    Meeting abstracts of the Physical Society of Japan   52 ( 1 )   678 - 678   1997.3

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  • Nonlinear effects of number density of solvent molecules on solvation dynamics

    A Yoshimori

    JOURNAL OF CHEMICAL PHYSICS   105 ( 14 )   5971 - 5978   1996.10

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    For the number density of solvent molecules, nonlinear effects on solvation dynamics are studied using the dynamical density functional method. The present method includes nonlinear coupling between the number density and a polarization field only in the free energy functional. By means of the nonlinear free energy functional, nonlinear differential-integral equations are developed for the polarization field and number density. Numerical calculations show that solvent molecules relax more slowly around an ion than around a neutral solute. This result agrees qualitatively with nonlinear effects observed in many molecular dynamics simulations. In addition, the nonlinear dynamics of hydrogen bonds can be understood, by considering the slow relaxation of the number density of solvent molecules. (C) 1996 American Institute of Physics.

    DOI: 10.1063/1.472454

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  • Dynamics of Thin-Jet Sheets in Ocean

    YAMADA Hiroyasu, YOSHIMORI Akira

    Abstracts of the meeting of the Physical Society of Japan. Sectional meeting   1996 ( 4 )   111 - 111   1996.9

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  • Femtosecond Excited State Dynamics of Bacteriorhodopsin.

    Akiyama R., Yoshimori A., Kakitani T., Imamoto Y., Shichda Y., Hatano Y.

    Abstracts of the meeting of the Physical Society of Japan. Sectional meeting   1996 ( 3 )   788 - 788   1996.9

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  • Nonlinear terms due to many-particle correlation in the density functional theory

    A Yoshimori

    JOURNAL OF CHEMICAL PHYSICS   104 ( 23 )   9586 - 9592   1996.6

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    A method of calculating nonlinear terms in free energy is studied for the density functional theory of a molecular system with orientational freedoms. In the method, a free energy functional is expanded into Taylor series of density fields, and then the coefficients are calculated from the cumulant expansion. Using the method, expansion coefficients of third and forth orders are explicitly derived by the three-point and four-point coefficients of the cumulant expansion. For the third-order coefficient, two approximations are compared by calculations of the triplet direct correlation function. The approximation obtained by expansion in terms of pair correlation functions gives abrupt changes in the triplet direct correlation function. The simplified Kirkwood superposition approximation gives slow changes in the function, though its value should be scaled down by a small parameter. (C) 1996 American Institute of Physics.

    DOI: 10.1063/1.471700

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  • 1a-G-4 Optical Absorption Spectra and Excited State Dynamics of Bacteriorhodopsin

    Akiyama R., Yoshimori A., Kakitani T., Imamoto Y., Shichda Y., Hatano Y.

    Abstracts of the meeting of the Physical Society of Japan. Annual meeting   51 ( 3 )   751 - 751   1996.3

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  • 1a-P-12 Effects of diffusion on geminate charge recombination

    Yoshimori A., Watanabe K., Kakitani T., Mizuno N.

    Abstracts of the meeting of the Physical Society of Japan. Annual meeting   51 ( 3 )   605 - 605   1996.3

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  • 1a-P-11 Monte Carlo Simulation Study of the Electrode Interaction

    Goto N., Hatano Y., Kakitani T., Yosimori A.

    Abstracts of the meeting of the Physical Society of Japan. Annual meeting   51 ( 3 )   604 - 604   1996.3

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  • EFFECTS OF DIFFUSION ON GEMINATE CHARGE RECOMBINATION

    A YOSHIMORI, K WATANABE, T KAKITANI

    CHEMICAL PHYSICS   201 ( 1 )   35 - 46   1995.12

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    Diffusion effects on geminate charge recombination are investigated for intermolecular electron transfer system. Analytical and numerical calculations are presented for reaction-diffusion equations. In some limiting cases of the equations, a condition is established where the population of geminate ion pairs decreases exponentially by charge recombination. This condition is that the ion pairs are produced inside the zone of recombination and charge recombination takes place before ion pairs diffuse into separated ions. Numerical calculations are made in realistic cases where reorganization energy in the expression of the rate constant depends on the reactant distance. As a result, we found that the population of ion pairs has both components of exponential decrease and a root inverse tail (t(-1/2)). The component of exponential decrease is large when the recombination rate is fast.

    DOI: 10.1016/0301-0104(95)00305-3

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  • Nonlinear effects of number density for solvent molecules on solvation dynamics

    Yoshimori Akira

    Abstracts of the meeting of the Physical Society of Japan. Sectional meeting   1995 ( 3 )   670 - 670   1995.9

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  • Monte Carlo Simulation Study of Ions and Solvents at the Electrode Interface

    Goto N., Hatano Y., Kakitani T., Yoshimori A.

    Abstracts of the meeting of the Physical Society of Japan. Sectional meeting   1995 ( 3 )   688 - 688   1995.9

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  • Recommendation of Chemical Physics

    Yoshimori Akira

    50 ( 7 )   570 - 571   1995.7

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  • Modeling of spring bloom in the western subarctic Pacific (off Japan) with observed vertical density structure

    A. Yoshimori, J. Ishizaka, T. Kono, H. Kasai, H. Saito, M. J. Kishi, S. Taguchi

    Journal of Oceanography   51 ( 4 )   471 - 488   1995.7

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    Effects of vertical stability on spring blooms of phytoplankton were investigated for the western subarctic Pacific ocean using a one-dimensional (depth) ecosystem model. In the model, vertical stability was expressed by diffusion constants calculated from observed density distribution. Dynamics of phytoplankton in blooms was calculated by the model using the vertical diffusion. Then, the calculated results were compared with the Coastal Zone Color Scanner (CZCS) data. The comparison shows that the shallow surface mixed layer causes early start days of spring blooms at inshore (northern) stations. In addition, spring blooms continue long at inshore (northern) stations since a water column has weak stability. This is because weak stability of a water column causes large nutrient supply from a deep layer and large diffusive transport of phytoplankton biomass from the subsurface maximum. © 1995 Journal of the Oceanographic Society of Japan.

    DOI: 10.1007/BF02286393

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  • Theoretical study on solvation dynamics

    Yoshimori Akira

    Abstracts of the meeting of the Physical Society of Japan. Annual meeting   50 ( 3 )   663 - 663   1995.3

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  • NONLINEAR QUANTUM EFFECTS ON ELECTRON-TRANSFER REACTIONS

    A YOSHIMORI

    CHEMICAL PHYSICS LETTERS   235 ( 3-4 )   303 - 308   1995.3

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    An approximate expression is developed for a nonadiabatic electron transfer rate to estimate quantum effects of nuclear rearrangements. The time-dependent formula for Fermi's golden rule is expanded by Plank's constant to the second order, using the Wigner transformation. The method of ($) over bar h-expansion is applicable to systems with nonlinear potentials or many degrees of freedom. Using a continuum approximation, from the expansion, a rate expression is obtained, including sizes of reactants and a distance between reactants explicitly. The ratio of the obtained rate to the classical rate agrees well with a ratio by a quantum Monte Carlo simulation.

    DOI: 10.1016/0009-2614(95)00109-H

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  • SYMMETRY OF A FREE-ENERGY CURVE IN POLAR SOLUTION

    A YOSHIMORI

    CHEMICAL PHYSICS LETTERS   225 ( 4-6 )   494 - 498   1994.8

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    Two kinds of symmetry causing a symmetric shape of the free energy curve are presented in a Hamiltonian of a neutral reactant state for Polar solution. They are the symmetry for inversion of solvent molecules and a reactant molecule. In addition, the deviation from the symmetry is formulated using a perturbation method. The antisymmetric part of the free energy curve is expressed by the symmetric part using a thermal average of the deviation in the Hamiltonian and the reaction coordinate.

    DOI: 10.1016/0009-2614(94)87117-5

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  • EFFECTS OF INTERACTION BETWEEN 2 WARM-CORE RINGS ON PHYTOPLANKTON DISTRIBUTION

    A YOSHIMORI, MJ KISHI

    DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS   41 ( 7 )   1039 - 1052   1994.7

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    A modeling study was conducted to investigate the effects of interaction between two warm-core rings on the phytoplankton distribution. Using a quasi-geostrophic reduced-gravity model, the interaction between two vortices was calculated to reproduce the partial vortex merger between two warm-core rings, 86B and OR. On the calculated flow field, the three-dimensional model of plankton dynamics generated high phytoplankton biomass at the edge of the merged vortex. In the model, phytoplankton grew due to nutrient transport into the euphotic zone by upward motion of water caused by meanders of the current followed by the partial vortex merger. Further, the model reproduced the horizontal distribution of phytoplankton observed in 86B.

    DOI: 10.1016/0967-0637(94)90017-5

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  • HORIZONTAL DIVERGENCE CAUSED BY MEANDERS OF A THIN JET

    A YOSHIMORI

    JOURNAL OF PHYSICAL OCEANOGRAPHY   24 ( 2 )   345 - 352   1994.2

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    To study horizontal divergence, the thin jet model is applied to meanders of a continuous potential vorticity front in a 1 1/2-layer (divergent barotropic) model. The distributions of the depth of the layer and the velocity component normal to the front are calculated on a coordinate system along the front. The distributions of the horizontal divergence are also investigated for some values of the Rossby number. In the model, divergence appears on the front from the cyclonic curve to the anticyclonic curve, and convergence appears on the front from the anticyclonic curve to the cyclonic curve. Further, a large Rossby number is found to cause an asymmetrical distribution of the horizontal divergence. The calculated values of the divergence are compared with the observational data.

    DOI: 10.1175/1520-0485(1994)024<0345:HDCBMO>2.0.CO;2

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  • Rossby number dependence on meander dynamics of a potential vorticity front

    Akira Yoshimori

    Journal of Oceanography   49 ( 5 )   521 - 533   1993.9

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    Semi-geostrophic dynamics of jets are studied using a potential vorticity front in an equivalent barotropic model. Meandering processes of the front are examined in the thin-jet limit on a β-plane by a curvilinear coordinate system. For calculated along-front velocity fields, asymmetrical profiles are caused by meandering. This asymmetry of the velocity profile is enhanced as the Rossby number becomes large. Using the along-front velocity fields, the normal velocity of front is expressed so that the Rossby number is explicitly included. This expression can be rewritten in the form of the mKdV equation. © 1993 Journal of the Oceanographic Society of Japan.

    DOI: 10.1007/BF02237459

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  • ENERGY-GAP DEPENDENCE OF THE SOLVENT DYNAMICS EFFECT ON ELECTRON-TRANSFER RATES IN NONLINEAR RESPONSE SYSTEMS

    A YOSHIMORI, T KAKITANI

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   61 ( 7 )   2577 - 2592   1992.7

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    Energy gap dependences of solvent dynamics effects on the electron transfer rate in polar solutions are investigated by solving the diffusion-reaction equation. New points in this study are that (1) we treat non-linear response systems where the translational motion couples non-linearly with the rotational motion and (2) we investigate systematically the energy gap dependence of the solvent dynamics effect for the charge separation (CS) and charge recombination (CR) reactions. The non-linear free energy functions are characterized, based on the Monte Carlo simulation data for model systems where solvent translational positions are either allowed to move or fixed. The calculated results are that so far as the non-linear coupling is substantial, the energy gap law of the CS reaction is little affected by the solvent dynamics, while that of the CR reaction is greatly modified.

    DOI: 10.1143/JPSJ.61.2577

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  • NONLINEAR EFFECTS ON SOLVATION DYNAMICS

    A YOSHIMORI

    CHEMICAL PHYSICS LETTERS   184 ( 1-3 )   76 - 80   1991.9

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    We study the non-linear effects on the dynamical process of the solvation in a polar solvent. On the basis of the non-linear generalized Smoluchowski equation with the linear-response free energy, we calculate the time dependence of the solvent-solute interaction. It is shown that the solvation process becomes slow in the long-time region where the non-linear coupling between the dynamics of the solvent number density and the orientational relaxation is significant.

    DOI: 10.1016/0009-2614(91)87166-9

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  • 26p-B-3 Evaluation of Reorganization Energy in Electron Transfer Reactions

    Kakitani T., Yoshimori A., Hatano Y.

    1991 ( 3 )   529 - 529   1991.3

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  • THEORETICAL-STUDY OF THE FREE-ENERGY CURVE AS A FUNCTION OF REACTION COORDINATE OF ELECTRON-TRANSFER BY THE CUMULANT EXPANSION METHOD

    A YOSHIMORI, T KAKITANI

    JOURNAL OF CHEMICAL PHYSICS   93 ( 7 )   5140 - 5146   1990.10

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    DOI: 10.1063/1.458651

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  • Theoretical Study of Energy Gap Law of Electron Transfer

    Yoshimori Akira, Kakitani Toshiaki

    45 ( 3 )   457 - 457   1990.3

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  • SHAPES OF THE ELECTRON-TRANSFER RATE VS ENERGY-GAP RELATIONS IN POLAR SOLUTIONS

    A YOSHIMORI, T KAKITANI, Y ENOMOTO

    JOURNAL OF PHYSICAL CHEMISTRY   93 ( 26 )   8316 - 8323   1989.12

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    DOI: 10.1021/j100363a009

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  • TRANSFER-COEFFICIENT IN ELECTROCHEMICAL REACTIONS

    A YOSHIMORI, T KAKITANI, N MATAGA

    JOURNAL OF PHYSICAL CHEMISTRY   93 ( 9 )   3694 - 3702   1989.5

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    DOI: 10.1021/j100346a064

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  • 29a-X-3 The Theory of Electron Transfer in Polar Solvent

    Yoshimori Akira, Kakitani Toshiaki

    44 ( 3 )   454 - 454   1989.3

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Works

  • Interfacial Dynamics in M(]E88DB[)llerian Mimicry System

    2000

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  • ちょうの生息域の境界のダイナミックス

    2000

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  • くり込み群を使ったKuramoto-Sivansky方程式の導出

    1999

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  • Derivation of the Kuramoto-Sivansky Equation

    1999

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  • 溶媒和ダイナミックスの研究

    1996
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    1997

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  • Study of Solvation Dynamics

    1996
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    1997

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Research Projects

  • Anomalous change of diffusion coefficient of protein and reconsideration for meaning of hydrodynamic radius

    Grant number:19H01863

    2019.4 - 2023.3

    System name:Grants-in-Aid for Scientific Research

    Research category:Grant-in-Aid for Scientific Research (B)

    Awarding organization:Japan Society for the Promotion of Science

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    Grant amount:\17290000 ( Direct Cost: \13300000 、 Indirect Cost:\3990000 )

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  • Microscopic theory of Stokes resistance

    Grant number:16K05512

    2016.4 - 2021.3

    System name:Grants-in-Aid for Scientific Research

    Research category:Grant-in-Aid for Scientific Research (C)

    Awarding organization:Japan Society for the Promotion of Science

    Akira Yoshimori

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    Grant amount:\4550000 ( Direct Cost: \3500000 、 Indirect Cost:\1050000 )

    Stokes' law describes the force exerted on a macroscopic solute from flowing solvent particles using the hydrodynamic equations with a boundary condition on the solute surface. In the present study, the boundary condition is exactly derived from Hamiltonian equations even at a high solvent density, such as a liquid state. It is derived from the large-solute particle limit in regions far from and near the solute particle. From the limit near the solute, the slip boundary condition is always obtained if the solute-solvent particle interaction depends solely on the distance between particles. In addition, the deviation from the slip boundary condition is obtained by perturbation expansion in solute-solvent size ratio.

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  • Roles of solvent particles in effective interactions between charged protein and phase behavior under weak coupling condition

    Grant number:15K05249

    2015.4 - 2019.3

    System name:Grants-in-Aid for Scientific Research

    Research category:Grant-in-Aid for Scientific Research (C)

    Awarding organization:Japan Society for the Promotion of Science

    Akiyama Ryo, Suematsu Ayumi

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    Grant amount:\4550000 ( Direct Cost: \3500000 、 Indirect Cost:\1050000 )

    The effective interactions between like-charged macromolecules in an electrolyte solution has been investigated using the linearized Poisson-Boltzmann equation (ex. the Debye-Huckel theory). In the present study, the integral equation theory of the liquid (HNC-OZ theory) was used to determine the effective interaction between like-charged macromolecules under conditions where the Debye-Huckel theory becomes worse, namely the Intermediate region. We found that when the ion intensity is the same and the valence number of the coions is different, the distance property is different. These results are qualitatively different from the results in the Debye Huckel region above. Also, this result corresponds qualitatively to the experimental result.

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  • 生命現象に対する水分子の動的効果

    2013 - 2015

    System name:科学研究費基盤研究(C)

    吉森 明

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    Authorship:Principal investigator  Grant type:Competitive

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  • 溶質分子が作り出す水の状態変化と水からの反作用

    2009 - 2012

    System name:科学研究費新学術領域研究 (計画研究) 「水を主役としたATPエネルギー変換」

    吉森 明

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  • 大きな疎水性物質の拡散

    2009 - 2011

    System name:科学研究費基盤研究(C)

    吉森 明

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    Authorship:Principal investigator  Grant type:Competitive

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  • Free energy landscape theory for unified understanding of glass transition

    Grant number:19540405

    2007 - 2009

    System name:Grants-in-Aid for Scientific Research

    Research category:Grant-in-Aid for Scientific Research (C)

    Awarding organization:Japan Society for the Promotion of Science

    ODAGAKI Takashi, YOSHIMORI Akira, MATSUI Jun

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    Grant amount:\4550000 ( Direct Cost: \3500000 、 Indirect Cost:\1050000 )

    I constructed a unified theoretical framework to understand various phenomena related to vitrification process. First, I reformulated the equilibrium statistical mechanics on the basis of the free energy landscape (FEL) and showed that anomalous behaviors of the specific heat and structural entropy near the glass transition can be explained by the theory. This framework was extended to non-equilibrium systems by exploiting the Langevin equation for the dynamics on the FEL and slow dynamics observed near the glass transition are shown to be attributed to stochastic dynamics on the FEL. I also succeeded in producing a long-lived glassy state for a monatomic simple system.

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  • イオン液体の統計力学

    2006 - 2008

    System name:科学研究費基盤研究(C)

    吉森 明

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    Authorship:Principal investigator  Grant type:Competitive

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  • 溶液中の拡散に対する溶質と溶媒分子の相互作用の効果

    Grant number:18031027

    2006 - 2007

    System name:科学研究費助成事業

    Research category:特定領域研究

    Awarding organization:日本学術振興会

    吉森 明

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    Grant amount:\4500000 ( Direct Cost: \4500000 )

    1.大きな溶質分子の拡散(溶質の大きさ無限大の極限)
    最近山口らが開発した理論(J.^~Chem.^~Phys.,123,034504 2005)の木きな溶質の極限を調べた。その極限により、流体力学のストークス近似を溶質粒子の外側で導いた。大きな溶質の極限は、また、溶質粒子の内側に対する方程式も導く。この内側方程式の解析解を求め、溶質粒子の表面における境界条件を導いた。この境界条件は、流体力学を計算するとき、必要になる。導いた境界条件は、ストークス則に使われるスティックやスリップ等の境界条件を特別な場合として含む。スティックやスリップ境界条件に加え、他の境界条件も含まれる。この境界条件は、溶媒の性質で決まる。
    2.大きな溶質分子の拡散(摂動理論)
    Stokes Einstein則に、溶媒-溶質の動径分布関数$g(r)$を含めた理論を開発した。Stokes近似により定常の速度場を計算し、Einsteinの関係式から拡散係数を計算する。最終的に拡散係数をずり粘性率、体積粘性率、温度、ボルツマン定数、溶質の半径、動径分布関数で表す事が出来た。
    3.剛体球ガラスにおける自由エネルギーランドスケープと協調的再配向領域
    密度汎関数法を使って、3次元剛体球ガラスの自由エネルギーランドスケープ(FEL)を計算した。FELから協調的再配向領域(CRR)にある粒子の数を見積もった。CRRの粒子の数の密度依存性を求め、それを密度のベキの形で表した。CRRの緩和過程から、さらに、計算機シミュレーションで見られているstring motionが、構造緩和の素過程になっている事を見いだした。

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  • First-principle determination of landscape and the unifying concept for glass transition

    Grant number:15340139

    2003 - 2005

    System name:Grants-in-Aid for Scientific Research

    Research category:Grant-in-Aid for Scientific Research (B)

    Awarding organization:Japan Society for the Promotion of Science

    ODAGAKI Takashi, YOSHIMORI Akira, MATSUI Jun

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    Grant amount:\14900000 ( Direct Cost: \14900000 )

    1.A unifying concept for understanding glass transition was found on the basis of the free energy landscape which plays the same role as the free energy in the Landau theory of phase transitions.
    2.A novel method to calculate the free energy landscape was found using the density functional of the grand potential. Analyzing the free energy landscape obtained, we showed that the string motion is a common elementary process of the slow relaxation and that there are two kinds of the cooperatively rearranging regions.
    3.The principal component analysis was utilized to calculate the free energy landscape from the molecular simulation data.
    4.An interactive molecular dynamics simulation and a fast method to construct the Voronoi tessellation were developed. These methods were exploited to calculate the temperature dependence of the cooperatively rearranging region.
    5.Using a microscopic theory we showed that the jump rate distribution obeys a power law function.
    6.The temperature dependence of the specific heat of a model glass former was obtained within the frame work of the free energy landscape and it was shown that the cooling rate dependence of the glass transition can be explained by the landscape picture.
    7.On the basis of the free energy landscape picture, the first and second order frequency-dependent (complex) specific heats were defined and their anomalous behavior was found around the glass transition point and the Vogel-Fulcher temperature.
    8.Packing fraction of binary hard discs was obtained in the entire parameter space and it was found that the packing fraction has a minimum as a function of the ratio of radii.

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  • Theory of glass transition in the energy landscape picture and nonequilibrium statistical physics

    Grant number:13640389

    2001 - 2002

    System name:Grants-in-Aid for Scientific Research

    Research category:Grant-in-Aid for Scientific Research (C)

    Awarding organization:Japan Society for the Promotion of Science

    ODAGAKI Takashi, MATSUI Jun, YOSHIMORI Akira

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    Grant amount:\3500000 ( Direct Cost: \3500000 )

    1. First observation of the cooperatively rearranging region was made for the supercooled liquid of soft-core discs.
    2. Using the newly developed frame work to obtain the specific heat of non-equilibriun system described by the energy landscape picture, the temperature dependence of the specific heat was obtained for various cooling process for a model energy landscape and it was shown that the anomaly at the glass transition point is explained by the transition from the annealed to the quenched average.
    3. A new order parameter, the degree of annealing, was introduced and was shown to be effective in describing the glass transition.
    4. Employing the power law distribution for the jump rate between basins in the energy landscape, we showed that the specific heat anomaly at the glass transition is comoatible with experiments.
    5. Relaxation process in the supercooled state of various modes of diatomic molecule were investigated by the molecular dynamics simulation and it was shown that coupling between rotational, bibrational and translational motions gives rise to the Johari-Goldstein process and the high frequency wing.
    6. A non-Gaussian parameter in the frequency domain was introduced and its behavior near the glass transition was investigated. Using the wave number dependence of the relaxation time we developed a new method to distinguish the homogeneous and non-homogeneous pictures for the slow relaxation.

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  • Statistical physics of liquids an solution

    Grant number:12640378

    2000 - 2002

    System name:Grants-in-Aid for Scientific Research

    Research category:Grant-in-Aid for Scientific Research (C)

    Awarding organization:Japan Society for the Promotion of Science

    YOSHIMORI Akira

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    Grant amount:\1500000 ( Direct Cost: \1500000 )

    1. The extension of time-dependent density functional methods to molecular liquids.
    Time-dependent density functional methods were extended to interaction site models, employed in computer simulations of molecular liquids. One can calculate density fields of interaction sites if one has free energy functional of interaction site density fields. Many equilibrium theories, such as RISM, can give the free energy functionals.
    2. Dynamics of distribution widths in solvation.
    Nishiyama and Okada have recently found that time-dependent fluorescence spectral widths relax more slowly than peaks in solvation dynamics. Previous theories cannot explain their results because the relaxation rates of the peak and width are exactly the same in the theories. To understand the phenomena, a simple model was considered where nonlinear effects of density fields were included as well as the rotational relaxation of molecules. The dynamics of distribution widths was calculated using the model. The results show that the relaxation of widths is slower than that of peaks if the density field relaxes slowly enough. We are calculating molecular dynamics simulations to confirm the model at the present.
    3. Studies of supercooled liquids and the glass transition
    (1) The trapping diffusion model was derived from microscopic viewpoints. The jump rate distribution was microscopically derived using the chemical reaction theory. The results show that the jump rate is distributed when particles have some motions with different relaxation rates. In addition, an explicit expression of the distribution was obtained. In the small rate region, the distribution was a power law.
    (2) Specific heats in the glass transition were studied. To explain a drastic change in specific heats, some models were calculated using a new definition of a nonequilibrium specific heat.

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  • 電子移動反応における溶媒効果の分子論

    Grant number:12042262

    2000 - 2001

    System name:科学研究費助成事業

    Research category:特定領域研究(A)

    Awarding organization:日本学術振興会

    吉森 明

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    Grant amount:\1600000 ( Direct Cost: \1600000 )

    電子移動反応における溶媒の動的効果を研究する目的で、溶媒のダイナミックス自身に対する分子論の整備と電子移動に対する影響を考察した。具体的には、1.動的密度汎関数法の分子液体への拡張を行った。分子液体のモデルは剛体相互作用点モデルを使った。今年度は、近似に改良を加え、可逆項の扱いについてはほぼ完成した。この改良により、時間無限大で正しい平衡状態を保障するH定理が、拡散極限を取らなくても成り立つようになった。また、自由エネルギー汎関数に対数項がある場合も単純液体と同様に取り扱えるようになった。
    2.溶媒の緩和が分布するとき、その幅のダイナミックスを記述する分子論的な方程式を導出した。北原のオメガ展開の方法を単純液体の動的密度汎関数法に応用して、具体的な表式を得た。この式により分布が非平衡な時の密度場の分散を求めることが出来る。これを使えば、溶媒和ダイナミックスにおける分布の幅の緩和を、分子シミュレーションよりは簡単に計算することが出来る。
    3.溶媒の緩和における分布が、電子移動にどういう影響を及ぼすか、簡単なモデルで調べた。始状態と終状態のエネルギー差を反応座標とし、その分布関数の時間変化を与える反応拡散方程式を考える。反応が起こらないときのグリーン関数をガウス型に近似して、幅とピークに違った緩和時間を与える。このモデルに対して、数値計算を行ったところ、活性化エネルギーが小さい時は、ピークの緩和が速くても幅の緩和が遅ければ、電子移動速度は遅くなることが分かった。

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  • Mode Coupling Theory and Trapping Model of Glass Transition

    Grant number:11640379

    1999 - 2000

    System name:Grants-in-Aid for Scientific Research

    Research category:Grant-in-Aid for Scientific Research (C)

    Awarding organization:Japan Society for the Promotion of Science

    ODAGAKI Takashi, MATSUI Jun, YOSHIMORI Akira

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    Grant amount:\3400000 ( Direct Cost: \3400000 )

    1. It was shown that the jump rate distribution function of atoms in supercooled liquids is given by a power law function and that the power is determined by the ratio of the contribution of slow and fast relaxation modes.
    2. Using the wave number dependence of the relaxation time for a hard sphere system derived by Fuchs et al with the mode coupling theory, the mobility edges between fast and slow modes were determined for a given attempt frequency. The relation between the mobility edges and the key parameter in the trapping model was exploited to determine the glass transition temperature and the Vogel-Fulcher temperature and it was shown that the glass transition occurs before the mobility edges are closed and the temperature at which the mobility edges are closed corresponds to the Vogel-Fulcher temperature.
    3. The specific heat of fragile glass formers near the glass transition temperature was shown to be scaled by [TSc(T)-TgSc(Tg)] which is the same parameter chracterizing the relaxation of atomic dynamics.
    4. The relaxation process of diatomic molecules in the supercooled state was analyzed theoretically and it was shown that the susceptibility for the density fluctuation can be written as sum of the contributions due to the motion of the center of mass and the motion of the internal degree of freedom.
    5. By the molecular dynamics simulation, the rotational relaxation of a diatomic molecular supercooled liquid was shown to separate from the relaxation of the translational motion, giving rise to the Johari-Goldstein process of the Arrhenius type.
    6. The theoretical frame work was established to calculate the specific heat of non-equilibrium systems described by the energy landscape picture. The frame work was applied to the hydrogen gas which has two energy basins and the temperature dependence of the specific heat was obtained as a function of the observation time. It was shown that annealed and quenched averages are obtained depending on the jump rate between two basins and the relation between the cooling rate and the degree of annealing are obtained.

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  • 溶液分子の動的性質に対する統計力学的な研究

    Grant number:10740193

    1998 - 1999

    System name:科学研究費助成事業

    Research category:奨励研究(A)

    Awarding organization:日本学術振興会

    吉森 明

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    Grant amount:\2100000 ( Direct Cost: \2100000 )

    溶液分子の動的性質を統計力学を使って、理論的に研究した。具体的には、
    1.(1)溶媒和における非線形応答について現在分かっている知見をまとめた。その結果、静的な場合に非線形応答が小さいのは、溶媒分子の数密度の緩和が重要であることが分かった。つまり、溶質の電荷が増えると誘電飽和が起こるが、溶媒分子が溶質分子に近づくことにより、溶質分子の周りの数密度が増え、分極率は大きくなる。これと誘電飽和が互いに相殺して、非線形応答が弱くなる。この静的な場合の事から、動的な場合には、数密度の緩和が分極の緩和より遅い時に、強い非線形応答が期待できる。実際、小さい溶質の計算機シミュレーションはこの様な非線形応答を示している。
    (2)以上の知見を基に実際の実験で非線形応答が測定される可能性を吟味した。特に、溶媒和の分布に関して非線形応答がどの様な効果を持つかを考えた。最近の分光学的な実験で得られているスペクトルのバンド幅がピークより遅く緩和するという結果を、昨年つくったモデルと比較検討した。その結果、数密度と分極の非線形効果が充分強く、さらにスペクトルと溶媒和の分布が一致していれば、この実験は非線形応答を示していると言えることがわかった。
    2.昨年研究した非線形ランジュバン方程式と動的密度汎関数法の関係を使って、動的密度汎関数法を分子液体に拡張した。分子液体は、原子間距離や角度が変わらない剛体の相互作用点モデルを使った。特に2原子分子について具体的な表式を得た。さらに、得られた表式が、充分時間が経った所で正しい平衡状態を与える事を、H定理を証明することにより示した。また、原子間距離の制限をなくして、分子をバラバラにする極限を取ると、単純液体の動的密度汎関数法と一致することも確かめた。

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  • ブランク定数による展開を使った半古典近似の研究

    Grant number:10120227

    1998

    System name:科学研究費助成事業

    Research category:特定領域研究(A)

    Awarding organization:日本学術振興会

    吉森 明

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    Grant amount:\300000 ( Direct Cost: \300000 )

    2つ以上の電子状態間の遷移における原子集団のトンネル効果を調べるために、プランク定数展開を使って、これまでよく使われている近似理論を検討した。各々の近似理論の物理的な意味を明らかにして、適応範囲をはっきりさせた。ここで考える遷移は、電子状態間の(Hamiltonianの非対角項)結合が小さくて、遷移速度が摂動論(golden rule)で与えられる場合に限る。この様な遷移が起こる時は、系に含まれる原子集団は、エネルギーの保存からエネルギー的に不安定な配置を要求される。この原子集団の活性化は、熱的にも起こり得るが、水やタンパク質の場合、トンネル効果も強い。
    具体的には、以下の6つの近似について、その遷移速度をプランク定数で展開し、厳密な式と比べた。
    1.Spin-bosonモデル。2.Cumulant展開の方法(古典)。3.Cumulant展開の方法(量子)。4.Warshelの方法(半古典軌道近似)。5.Frozen Gaussianの方法。6.Frozen Gaussian+local harmonics近似。これらの近似のプランク定数による展開を比較する事により、プランク定数が2次のオーダーで近似が厳密になる条件を見つけた。条件のうち2つは、反応体の電子状態が溶媒の構造にあまり影響を与えないというもので、他の条件は、反応座標の線形性に関係している。解析的な式の比較に加えて、数値的な比較もした。検討したパラメーターでは、ほとんどの近似が同じ値を与えたが、5のFrozen Gaussianは、全く違った値を与えた。

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  • 配向を持った分子液体の個別運動と集団運動

    Grant number:09212215

    1997

    System name:科学研究費助成事業

    Research category:重点領域研究

    Awarding organization:日本学術振興会

    吉森 明

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    Grant amount:\800000 ( Direct Cost: \800000 )

    混合系の溶媒和ダイナミックスを拡張された線形理論を使って研究した。溶媒和ダイナミックスとは、光などによって起こる溶質分子の電子状態の変化に対する溶媒分子の応答である。拡張された線形理論と共に、reference hypemetted-chainという近似を使うことにより、溶質分子周りの第一殻の溶媒分子の数を数えることが出来た。加えて、溶質分子と溶媒分子の相互作用も計算した。拡張された線形応答の理論では、溶媒分子の密度場の時間変化が、波数空間で幾つかの指数関数の和で表される。これを2種類の溶媒からなる混合系に適応すると、最初の2つの指数関数は、2種類の溶媒分子の総数の時間変化と、異種分子間の交換過程を表す事がわかった。これらの緩和の時定数は、小さな波数で遅くなるので、集団運動が遅いことがわかった。3番目と4番目の指数関数は、分極場の緩和に関係している事がわかった。特に3番目の指数関数は、波数の小さい方が時定数が速く、集団運動の方が速いことがわかった。また、混合比の依存性も調べた。大きな双極子モーメントを持った溶媒分子の濃度を減らすと、小さな双極子モーメントを持った溶媒分子の数の時間変化に大きな影響があることがわかった。さらに、溶質の電荷の依存性も調べた。電荷を半分にすると交換過程の影響が小さくなった。これにより、小さな双極子モーメントを持った溶媒分子数が、早い時間で急激に増加した。

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  • Dynamical Property of Oriented Molecular Solution

    Grant number:08640482

    1996 - 1997

    System name:Grants-in-Aid for Scientific Research

    Research category:Grant-in-Aid for Scientific Research (C)

    Awarding organization:Japan Society for the Promotion of Science

    KAKITANI Toshiaki, YOSHIMORI Akira

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    Grant amount:\2200000 ( Direct Cost: \2200000 )

    Dynamical behavior of molecular solution with orientation was investigated by means of Monte Calro simulation of the electrolyte solution at the electrode interface and dynamical density functional method of reorientation of solvent due to a rarid change of electronic state of a solue molecule. The result of the simulation study is as follows. The adsorbed, layred structure of electrolyte ions is formed just in touch with the electrode surface and its layred structure is deformed when external field is applied. this layr is considered to be the Helmholtz double layr as expected before. The energy gap dependence of the electrode reaction rate (energy gap law) is calculated. It is not a bell shaped one which is expected by the linear response theory, but like trapezoid with broad width, suggesting a strong nonlinear contribution in the solvent fluctuation at the electrode interface. The result of the analysis by dynamical density functional method is as follows. A large nonlinear phenomenon was observed in the reorientational dynamics of the mixed solvents of two kinds. It was clearified that the origin of this nonlinearity is the coupling between the reorientational motion and the translational motion of the two kind of solvent molecules. Combinng those results, we can say that a large nonlinear phenomenon exists in the oriented molecular solutions.

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  • 配向をもった分子液体の個別運動と集団運動のダイナミックス

    Grant number:07236221

    1995

    System name:科学研究費助成事業

    Research category:重点領域研究

    Awarding organization:日本学術振興会

    吉森 明

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    Grant amount:\1200000 ( Direct Cost: \1200000 )

    基底状態と励起状態で電荷分布が大きく変わる分子を分子液体に溶かし、光をあて励起状態にする。励起直後はまわりを取り囲む溶媒分子は非平衡な不安定な状態にあるが、時間が経つと安定な平衡状態に緩和する。この緩和が溶媒和ダイナミックスである。この研究では、配向を持った分子液体の個別運動における非線形効果を、動的密度汎関数法で調べた。特に、溶媒和ダイナミックスに注目して、分子動力学シミュレーション(MD)で得られている非線形効果の物理的な機構を明らかにした。
    動的密度汎関数法では、溶媒分子の分布関数の時間変化を自由エネルギーの汎関数微分で計算する。ここでは非線形の効果を調べるために、自由エネルギーの汎関数微分は溶媒分子の分布関数について非線形の項まで含んだものを使う。さらに、溶媒分子の分布関数を、配向の自由度について球関数で展開して、数密度と分極場だけを取った。これらの2つの量は、線形のモデルでは全く独立に運動するが、非線形効果が強くなると、数密度の遅い緩和が分極場の緩和に強く影響すると考えられる。
    数密度を考慮した計算結果は、MDの結果と定性的に一致した。すなわち、イオンの周りの溶媒分子の緩和は、中性の溶質分子の周りより緩和が遅かった。この結果は、配向を持った分子液体の、分極に関する個別運動の非線形効果に、数密度のゆらぎが重要な役割を果たしている事を示唆している。また、数密度の効果で重要な点は、分極場との結合が溶質の電荷分布によって変わる事である。溶質が中性の時、分極場は数密度と独立なので速く緩和する事が出来る。一方、溶質が電荷を持っている場合、分極場は数密度と独立ではないので、数密度の緩和を待たなければ分極場は緩和できない。そのために緩和が遅くなると考えられる。

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  • 溶液中の電子移動反応におけるダイナミックスの効果

    Grant number:06740441

    1994

    System name:科学研究費助成事業

    Research category:奨励研究(A)

    Awarding organization:日本学術振興会

    吉森 明

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    Grant amount:\900000 ( Direct Cost: \900000 )

    電子移動反応における反応体の拡散の効果を、特に電荷再結合反応に注目して調べた。光誘起分子間電子移動反応では電荷分離反応が起きたあとイオン対が出来るが、このイオン対が無限遠方に離れる前に、再結合反応するものがある。この再結合反応は常に拡散過程と競争して起り、電荷分離反応とは違った特別な考慮を必要とする。Burshteinらは、反応体同士が接触しないと電子移動が起こらないモデルにおいて、イオン対の濃度は時間の平方根の逆数で減衰することを示した。ところが実験的にはイオン対の濃度は時間とともに指数関数的に減衰することが確かめられている。そこで本研究では。電子移動速度の反応体間の距離依存性をより現実に近いモデルを使うことにより、指数的な減衰が得られる条件を調べた。まず、電子移動速度が反応体間の距離について、ある領域では定数になり、それ以外の所では、0になる簡単なモデルをたてた。このモデルについては、解析解を得ることに成功したので、その解から指数関数的に減衰するためには、反応速度kと反応が起る領域の幅Lと拡散係数DのあいだにkL^2/D>>1の関係がなければならないことを示した。また、イオン対が指数関数的に減衰する割合が多い場合には量子収率が少なくなることも得られた。更に、電子移動速度のより現実的な距離の依存性について反応拡散方程式を数値的に解いた。電子移動速度の距離依存性についてはMarcusの式に従って、再配向エネルギーにも距離依存性を含めた。このモデルを使って、指数関数的な減衰がどのパラメータで起るかを調べた。

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  • 不均一系における電子移動速度のエネルギー・ギャップ則

    Grant number:06219213

    1994

    System name:科学研究費助成事業

    Research category:重点領域研究

    Awarding organization:日本学術振興会

    垣谷 俊昭, 吉森 明

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    Grant amount:\900000 ( Direct Cost: \900000 )

    本研究では電極反応における電子移動速度のエネルギー・ギャップ依存性(エネルギー・ギャップ則という)が均一系のものに比べてどのように変わるかをモンテカルロシミュレーション計算により調べた。その結果次のことが明らかにされた。電極表面に電荷が存在するときに、始状態(反応体の電荷が0)の自由エネルギー曲線の曲率は終状態(反応体の電荷が+I)の自由エネルギー曲線の曲率の約1.5倍になった。均一系反応ではこの比が約1.1であるので、電極界面では誘導飽和のために非線形性が増大していると考えられる。このことを確かめるために電解質イオンと溶媒分子の電極表面からの分布を求めた。その結果、半径23Aの電極表面の円内に、28個の負イオンと11個の正イオンと49個の溶媒分子が吸着していることが明らかになった。これはいわゆるヘルムホルツ層を構成しており、非線形現象を生み出している。吸着層の外側は電解質イオンの濃度勾配のゆるやかな変化があり、グイ-チャップマン層を構成する。また、電極表面に電荷が存在しないときには電解質イオンの電極表面への吸着量は少なく、均一系と余り変わった分子環境を作っていないことも明らかにされた。備品で購入したパーソナルコンピュータはモンテカルロシミュレーションに役立てた。本年度の研究だけではまだ十分成果を得ておらず来年度以後の研究の基礎としての意味があると思われる。

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  • 動的密度汎関数法の研究

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  • Theoretical study of electron transfer reactionsin solution.

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  • Theoretical study of solvation dynamics

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    Grant type:Competitive

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  • Study of time dependent density functional methods

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    Grant type:Competitive

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  • 溶液中の電子移動反応の理論的研究

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  • 溶媒和ダイナミックスの理論的研究

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Teaching Experience

  • 海外研修

    2024
    Institution name:新潟大学

  • 海外英語研修

    2024
    Institution name:新潟大学

  • 理学基礎演習

    2023
    Institution name:新潟大学

  • 統計物理学I

    2022
    Institution name:新潟大学

  • 物理学特論III

    2021
    Institution name:新潟大学

  • 不規則系物理学I

    2021
    Institution name:新潟大学

  • 理学スタディ・スキルズ

    2021
    Institution name:新潟大学

  • 現代物理学セミナーB

    2020
    Institution name:新潟大学

  • 物理学への招待B

    2020
    Institution name:新潟大学

  • 現代物理学セミナーA

    2020
    Institution name:新潟大学

  • 先端科学技術総論

    2020
    Institution name:新潟大学

  • 統計力学IIIA

    2017
    Institution name:新潟大学

  • 統計力学IIIB

    2017
    Institution name:新潟大学

  • 波動とフーリエ解析

    2017
    Institution name:新潟大学

  • 理学スタディ・スキルズ

    2017
    -
    2021
    Institution name:新潟大学

  • 物質の世界

    2017
    -
    2018
    Institution name:新潟大学

  • 自然科学総論Ⅰ

    2017
    Institution name:新潟大学

  • 統計物理学Ⅰ

    2016
    -
    2020
    Institution name:新潟大学

  • 物性物理学I

    2016
    -
    2017
    Institution name:新潟大学

  • 現代物理学への招待(物理学学習法)

    2016
    Institution name:新潟大学

  • 統計力学演習I

    2016
    Institution name:新潟大学

  • 不規則系物理学Ⅰ

    2015
    -
    2017
    Institution name:新潟大学

  • 統計力学演習II

    2015
    -
    2016
    Institution name:新潟大学

  • 振動・波動

    2015
    -
    2016
    Institution name:新潟大学

▶ display all