arXiv subjects

Ryo Akiyama

Publications and source records attributed to Ryo Akiyama.

7 recordsLinked to original sources

arXiv2026

Solvent Mixing Effect on Free-Energy Barrier and Stability for Molecular Recognition Driven by the Translational Motion of Solvent Molecules

We calculated the potentials of mean force (PMFs) between a ring-like host and a spherical guest in a solvent mixture. We adopted hard-body interactions between particles to discuss the effects of solvent-particle translational motion. The PMFs were obtained using the three-dimensional Ornstein-Zernike equation coupled with the modified hypernetted-chain closure (3D-MHNC-OZ theory). The entropic stabilization at the recognition site is confirmed, and a free-energy barrier wall is observed surrounding it. The free-energy barrier for the solvent mixture is much lower than that for the one-component solvent. Similar barrier reduction for the association of two spherical solute molecules has also been reported, and the mixing effect also reduced the dimerization stability. By contrast, the mixing effect does not significantly reduce recognition stability in the present study. In this respect, the behavior of the host-guest association is different from that of the association of two spherical solute molecules.

cond-mat.soft↗

arXiv2024

Decomposition of Friction Coefficients to Analyze Hydration Effects on a C$_{60}$(OH)$_{\rm n}$

To analyze hydration effects on macromolecular diffusion, the friction coefficients of macromolecules were examined using molecular dynamics simulations with an all-atom model. In the present study, a method was introduced to decompose the molecular friction coefficient into the contributions for each site on the macromolecule. The method was applied to several fullerenols in ambient water. The friction coefficients for the hydrophilic part, such as the OH group, were larger than those for the hydrophobic part, such as the C. The hydration effect did not depend only on the kind of functional group but also on surface roughness. This approach would be useful in explaining the experimentally observed large changes in diffusion coefficients of proteins that were accompanied by conformation changes.

physics.bio-ph↗

arXiv2023

Spatial distribution of reduced density of hard spheres near a hard-sphere dimer: Results from three-dimensional Ornstein-Zernike equations coupled with several different closures and from grand canonical Monte Carlo simulation

We calculated the spatial distribution of reduced density and pair distribution function (PDF) of solvent hard spheres near a solute using three-dimensional Ornstein-Zernike (OZ) equations coupled with closures in which Percus-Yevick (PY) and hypernetted-chain (HNC) approximations were employed or bridge functions (BFs) proposed by Verlet, Duh and Henderson, and Kinoshita were incorporated. The solute was formed by two solvent hard spheres in contact with each other, with the result that the system is not radial-symmetric, necessitating the extension of Verlet, Duh-Henderson, and Kinoshita BFs to three-variable functions considered in the Cartesian coordinate system. The results were compared with those from grand canonical Monte Carlo (MC) simulation. In terms of the PDF, HNC is superior to PY in the sense that the results from the former are closer to those from MC. The incorporation of the three BFs makes the results further closer to those from MC. The three BFs share almost the same performance for a solute immersed in a one-component solvent at the infinite-dilution limit. Analyses on the triplet distribution function (TDF) were also performed. It was found that in terms of the TDF the incorporation of the BFs does not necessarily lead to improvement.

cond-mat.soft↗

arXiv2022

Collision-induced torque mediates transition of chiral dynamic patterns formed by active particles

It is still challenging to control dynamic self-organization patterns of self-propelled particles. Although varieties of patterns associated with chirality have been observed, essential control factors determining patterns remain unclear. Here, we explore numerically how torque upon particle collision affects dynamic self-organization. Based on the particle-based model with both collision-induced torque and torque in self-propulsion, we find that introducing collision-induced torque turns homogeneous bi-polar orientation templated by bi-directional alignment into rotating mono-polar flocks.

cond-mat.soft↗

arXiv2022

Integral equation study of effective attraction between like-charged particles mediated by cations: Comparison between IPY2 and HNC closures

Effective interactions between like-charged particles immersed in an electrolyte solution were calculated using two integral equation theories, hypernetted-chain (HNC)-Ornstein--Zernike (OZ) and ionic Percus--Yevick 2 (IPY2)-OZ. When the HNC-OZ theory was adopted, the electrolyte concentration dependence of the effective interaction showed a reentrant behavior. By contrast, the IPY2-OZ theory did not indicate the behavior. Monte Carlo simulations were performed for one of the model systems, and the results agreed qualitatively with those calculated using the HNC-OZ theory.

cond-mat.soft↗

arXiv2022

Usefulness of Higher Order of System-Size Correction for Diffusion Coefficients of Macromolecules: A Molecular Dynamics Study

Yeh and Hummer's simplified estimation method has often been adopted to obtain diffusion coefficients for solute molecules using molecular dynamic simulation. However, the simplified formula is not necessarily valid when a small basic cell is used. Therefore, we conducted molecular dynamics simulations of aqueous protein solution to estimate the diffusion coefficient for the infinite dilution limit. We confirmed a deviation from the simplified formula in the simulation data and rationalized the discrepancy based on the unsimplified formula.

physics.chem-ph↗

arXiv2020

Lateral depletion effect on two-dimensional ordering of bacteriorhodopsins in a lipid bilayer: A theoretical study based on a binary hard-disk model

The two-dimensional ordering of bacteriorhodopsins in a lipid bilayer was studied using a binary hard-disk model. The phase diagrams were calculated, taking into account the lateral depletion effects. The critical concentrations of the protein ordering for the monomers and the trimers were obtained from the phase diagrams. The critical concentration ratio agreed well with the experiment when the repulsive core interaction between the depletants, namely the lipids, was taken into account. The results suggest that the depletion effect plays an important role in the association behaviors of transmembrane proteins.

cond-mat.soft↗