Masahiro Kinoshita

The hypernetted-chain integral equations are solved on a three-dimensional cubic grid to calculate the spatial distribution of the depletion potential between a big solute of arbitrary geometry and a big sphere immersed in small spheres forming the solvent. By analyzing the potential along a specific trajectory of the big sphere, effects due to the geometric feature of the big solute (step edges, trenches, corners, changing curvature, etc.) can be examined in detail. As an illustration, effects

The molecular origin of the hydrophobic effect is investigated using the angle-dependent integral equation theory combined with the multipolar water model. The thermodynamic quantities of solvation (excess quantities) of a nonpolar solute are decomposed into the translational and orientational contributions. The translational contributions are substantially larger with the result that the temperature dependence of the solute solubility, for example, can well be reproduced by a model simple fluid

We briefly review our studies on the folding/unfolding mechanisms of proteins. In biological self-assembly processes such as protein folding, the number of accessible translational configurations of water in the system increases greatly, leading to a large gain in the water entropy. The usual view looking at only the water in the close vicinity of the protein surface is capable of elucidating neither the large entropic gain upon apoplastocyanin folding, which has recently been found in a novel e

This paper contributes to development of a microscopic approach to predicting stable conformations of proteins in solvent. We report results of the first attempt to combine Monte Carlo simulated annealing, a powerful conformational sampling technique, and the reference interaction site model (RISM) theory, a statistical-mechanical treatment for molecular fluids. In solvent the key function is the total energy defined as the sum of the conformational energy and the solvation free energy, and the

We have developed robust and very efficient algorithms for solving the reference interaction site model (RISM) equations for salt solutions in the bulk and near a solute atom of noble gases. The theory of dielectric consistency recently developed for solutions at finite salt concentrations is employed in the formalism. The change in water structure in the bulk caused by addition of salts have been examined for model 1–1 salt solutions (LiCl, NaCl, KCl, KF, KBr, KI, and CsI). The density and orie

We report results of numerical analyses on the surface (macroparticle) interactions in simple fluids. The singlet Ornstein–Zernike theories with hypernetted-chain closures are employed. With no (or very weak) attraction in the surface–fluid interaction uMS, both the interaction φMM and the force fMM between macroparticles in Lennard-Jones fluids are characterized by monotonically decreasing attraction. With increasing attraction in uMS, however, φMM and fMM become more oscillatory. The force bet

By reviewing the results of our analyses based on statistical-mechanical theories, we point out that the entropic effect arising from the translational motion of water molecules is a principal driving force in a variety of self-assembling and ordering processes in biological systems such as protein folding, molecular recognition, and ordered aggregation of protein molecules. The great entropic loss for the biomolecules accompanying these processes is largely compensated by a great entropic gain

Algorithms, previously reported for solving integral equation theories for fluids of non-spherical particles, are now extended to water-like fluids (bulk fluids and fluids near a macroparticle and a planar wall) modelled as hard spheres embedded with point dipoles and tetrahedral quadrupoles. Alternative algorithms are reviewed in detail, and the unique advantages of the present methods are emphasized. These advantages include compactness of the analytically derived expressions for the Jacobian

An efficient algorithm, a hybrid of the Picard-type and Newton-Raphson (NR) methods, is developed for solving the reference hypernetted-chain (RHNC) theory for non-spherical particles near a uniform planar wall. The basic idea of the algorithm is also applicable to non-spherical particles near a large macroparticle at infinite dilution. The problem of dipolar hard spheres near a hard wall is chosen here as an example system. A feature of the algorithm is that the Jacobian matrix is determined in

We report results of theoretical calculations for the interaction between two isolated, structureless spherical macroparticles immersed in aqueous electrolytes comprising waterlike molecules (hard spheres embedded with point dipoles and tetrahedral quadrupoles), 1:1 cations and anions (the diameter of cations is equal to that of anions). The reference hypernetted-chain (RHNC) theory with hard-sphere bridge functions is employed in the calculations. The fluid structure and the potential of mean f