Kowaguchi, Akie

写真a

Affiliation

School of Medicine, Department of Pharmacology ( Shinanomachi )

Position

Instructor
Scopus Paper Info  
Paper Count: 7 Citation Count: 20 h-index: 2

Click to view the Scopus page. The data was downloaded from Scopus API in October 18, 2026, via http://api.elsevier.com and http://www.scopus.com .

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Papers 【 Display / hide 】

  • Structure-resolved free-energy estimation of the 38-atom Lennard-Jones cluster via population annealing

    Kowaguchi A., Hukushima K.

    Journal of Chemical Physics 164 ( 21 )  2026.06

    ISSN  00219606

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    We systematically investigate the thermodynamic landscape of the 38-atom Lennard-Jones cluster LJ<inf>38</inf> using Population Annealing (PA), a method suited for systems with challenging double-funnel energy landscapes. By employing an adaptive temperature schedule, we demonstrate that thermodynamic observables, such as internal energy and heat capacity, converge robustly when the population size is sufficiently large. To gain deeper insights into the competing basins, we introduce an integrated framework that combines PA reweighting factors with structure-resolved analysis. Using quenched configurations characterized by potential energy and Steinhardt’s bond-orientational order parameters, we identify three structural basins, face-centered cubic-like, icosahedral, and liquid-like, via dimensionality reduction and clustering. This framework enables the direct computation of structure-resolved free energy differences from population fractions, providing a quantitative mapping of the thermodynamic competition between the funnels. The resulting structural crossovers are consistent with the heat-capacity peak, demonstrating PA as a promising and scalable framework for structure-resolved thermodynamics in complex molecular systems.

  • A patchy-particle three-dimensional octagonal quasicrystal

    Kowaguchi A., Mehta S., Doye J.P.K., Noya E.G.

    Journal of Chemical Physics 163 ( 24 )  2025.12

    ISSN  00219606

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    We devise an ideal three-dimensional octagonal quasicrystal that is based upon the two-dimensional Ammann–Beenker tiling and that is potentially suitable for realization with patchy particles. Based on an analysis of its local environments, we design a binary system of five- and eight-patch particles that in simulations assembles into a three-dimensional octagonal quasicrystal. The local structure is subtly different from the original ideal quasicrystal possessing a narrower coordination-number distribution; in fact, the eight-patch particles are not needed and a one-component system of the five-patch particles assembles into an essentially identical octagonal quasicrystal. We also consider a one-component system of the eight-patch particles; this assembles into a cluster with a number of crystalline domains, which, because of the coherent boundaries between the crystallites, has approximate eightfold order. We envisage that these systems could be realized using DNA origami or protein design.

  • Navigating Phase Transitions with Path-Finding Algorithms: A Strategic Approach to Replica Exchange Monte Carlo

    Kowaguchi A., Endo K., Nomura K., Kurabayashi S., Brumby P.E., Yasuoka K.

    Journal of Chemical Information and Modeling 65 ( 21 ) 11818 - 11825 2025.11

    ISSN  15499596

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    The replica exchange method is a powerful tool for overcoming slow relaxation in molecular simulations, but its efficiency depends strongly on the choice of the number and interval of replicas and their exchange probabilities. Here, we propose a new optimization scheme based on the Dijkstra algorithm that constructs an optimal exchange path by representing replicas and their exchange probabilities on a graph. Inspired by path-finding techniques widely used in computer science, including applications in game algorithms, our approach ensures that transitions follow a minimum entropy gradient path and effectively speeds up sampling even in systems exhibiting slow relaxation near critical points or phase transition regions. The method provides a systematic way to improve replica exchange efficiency and offers new insights into the control of relaxation dynamics, as demonstrated through applications to the solid–liquid phase transition of the Lennard-Jones bulk system.

  • Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization

    Kowaguchi A., Brumby P.E., Yasuoka K.

    Journal of Chemical Information and Modeling 64 ( 12 ) 4673 - 4686 2024.06

    ISSN  15499596

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    The phenomenon of hysteresis in simulations, in which a system’s current state is correlated to previous states and inhibits the transition to a more stable phase, may often lead to misleading results in physical chemistry. In this study, in addition to the replica exchange method (REM), a novel approach was taken by combining an evolution strategy based on the evolutionary principles of nature to predict phase transitions for the Hess-Su liquid-crystal model. In this model, an anisotropy term is added to the simple 6-12 Lennard-Jones model to intuitively reproduce the behavior of liquid crystals. We first applied the pressure-temperature REM to the Hess-Su model and optimized the replica spacing for the energy distribution to gain the maximum advantage from the REM. We then used the same approach as for the Hamiltonian REM, seeking to optimize the replica spacing in the same way. Based on both results, we attempted to predict this coarse-grained liquid-crystal model’s exact phase transition point. In the Hamiltonian REM, replicas were prepared with different molecular aspect ratios corresponding to the values of the anisotropy terms in the potential function. The Hess-Su liquid-crystal model, which undergoes a direct transition from the nematic to the solid phase without going through a smectic phase, is a challenging research target for understanding phase transitions. Despite the tremendous computational difficulty in overcoming the strong hysteresis present in this system, our method could predict the phase transition point clearly and significantly reduce the extent of hysteresis. Our approach is beneficial when simulating more complex systems and, above all, shows great potential for more accurate and efficient phase transition predictions in the field of molecular simulation in the future.

  • Pre-Smectic Ordering and the Unwinding Helix in Monte Carlo Simulations of Cholesteric Liquid-Crystals

    Brumby P.E., Kowaguchi A., Nozawa T., Yasuoka K., Wensink H.H.

    Journal of Physical Chemistry B 127 ( 32 ) 7194 - 7204 2023.08

    ISSN  15206106

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    In this paper, molecular chirality is studied for liquid-crystal fluids represented by hard rods with the addition of an attractive chiral dispersion term. Chiral forces between molecular pairs are assumed to be long-ranged and are described in terms of the pseudotensor of Goossens [W. J. A. Goossens, Mol. Cryst. Liq. Cryst. 1971, 12, 237-244]. Following Varga and Jackson [S. Varga and G. Jackson, Chem. Phys. Lett. 2003, 377, 6-12], this is combined with a hard-spherocylinder core. We investigate the relationship between molecular chirality and the helical pitch of the system, which occurs in the absence of full three-dimensional periodic boundary conditions. The dependence of the wavenumber of this pitch on the thermodynamic variables, temperature, and density is measured. We also explore the use of a novel surface boundary interaction model. As a result of this approach, we are able to lower the temperature of the system without the occurrence of nematic droplets, which would interfere with the formation of a uniaxial pitch. Regarding the theoretical predictions of Wensink and Jackson [H. H. Wensink and G. Jackson, J. Chem. Phys. 2009, 130, 234911], on the one hand, we have qualitative agreement with the observed non-monotonic density dependence of the wavenumber. Initially increasing with density, the wavenumber reaches a maximum, before falling as the density moves toward the point of phase transition from cholesteric to smectic. However, further analysis for shorter rods, in the presence of novel boundary conditions, reveals some disagreement with the theory, at least in this case; the unwinding of the cholesteric helix in the cholesteric phase occurs simultaneously with subtle increases in smectic ordering. These pre-smectic fluctuations have not been accounted for so far in theories on cholesterics but turn out to play a key role in controlling the pitch of cholesteric phases of rod-shaped mesogens with a small to moderate aspect ratio.

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Courses Taught 【 Display / hide 】

  • PHARMACOLOGY

    2026

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