Ivan Vyalov

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We combined molecular dynamics simulation and DBSCAN algorithm (Density Based Spatial Clustering of Application with Noise) in order to characterize the local density inhomogeneity distribution in supercritical fluids. The DBSCAN is an algorithm that is capable of finding arbitrarily shaped density domains, where domains are defined as dense regions(More)
We develop an efficient method to extract site-site bridge functions from molecular simulations. The method is based on the inverse solution of the reference site interaction model. Using the exact long-range asymptotics of site-site direct correlation functions defined by the site-site Ornstein-Zernike equations, we regularize the ill-posed inverse(More)
In this work we present the results of the extensive molecular simulations of solute-solvent cavity and bridge functions. The mixtures of Lennard-Jones solvent with Lennard-Jones solute at infinite dilution are considered for different solute-solvent size ratios-up to 4:1. The Percus-Yevick and hypernetted chain closures deviate substantially from(More)
We investigate local phase transitions of the solvent in the neighborhood of a solvophobic polymer chain which is induced by a change of the polymer-solvent repulsion and the solvent pressure in the bulk solution. We describe the polymer in solution by the Edwards model, where the conditional partition function of the polymer chain at a fixed radius of(More)
Voronoi polyhedra (VP) analysis of mixtures of acetone and methanol is reported on the basis of molecular dynamics computer simulations, performed at 300 K and 1 bar. The composition of the systems investigated covers the entire range from neat acetone to neat methanol. Distribution of the volume, reciprocal volume and asphericity parameter of the VP as(More)
Combining infrared spectroscopy and molecular dynamics simulations, we have investigated the structural and dynamical properties of ammonia from liquid state (T = 220 and 303 K) up to the supercritical domain along the isotherm T = 423 K. Infrared spectra show that the N-H stretching and bending modes are significantly perturbed which is interpreted as a(More)
We report results of molecular dynamics simulations and detailed analysis of the local structure of sub- and supercritical ammonia in the range of temperature between 250 and 500 K along the 135 bar isobar. This analysis is based on the behavior of distributions of metric and topological properties of the Voronoi polyhedra (VP). We show that by increasing(More)
Solvation is a fundamental contribution in many biological processes and especially in molecular binding. Its estimation can be performed by means of several computational approaches. The aim of this review is to give an overview of existing theories and methods to estimate solvent effects giving a specific focus on the category of implicit solvent models(More)
Binary mixtures of CO(2) with ethanol and with acetone are studied by computer simulation, including extensive free energy calculations done by the method of thermodynamic integration, at 313 K, i.e., above the critical point of CO(2) in the entire composition range. The calculations are repeated with three different models of acetone and ethanol, and two(More)
The nearest neighbor approach was used to characterize the local structure of CO(2) fluid along its coexistence curve (CC) and along the critical isochore (CI). The distributions of the distances, orientations, and interaction energies between a reference CO(2) molecule and its subsequent nearest neighbors were calculated. Our results show that the local(More)