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Modern GPUs are massively-parallel processors, offering substantial amount of computational power in energy-efficient package. We discuss the benefits of utilizing this computing power for modeling problems in bio-informatics, such as molecular dynamics, quantum chemistry and sequence analysis.

Protein-protein interactions are of central importance for virtually every process in living matter. Modeling the dynamics of protein association is crucial for understanding their functionality. This paper proposes novel simulation software ProKSim (Protein Kinetics Simulator) for modeling of protein interactions by means of the multi-particle Brownian Dynamics. Effect of long-range electrostatic interactions on the process of transient encounter complex formation is numerically estimated. Investigation of transient encounter complex formation was performed for three pairs of proteins: ferredoxin and ferredoxin:NADP⁺-redustase, plastocyanin and cytochrome f, barnase and barstar.

The models of liquid heptane and cyclohexane has been developed. The properties of model liquids appear to be in a good agreement with a properties of real liquids. X-Ray diffraction spectra of model liquids were also in a good agreement with experimental ones. Radial distribution functions analysis allows us to reveal a crucial molecular feature of cyclohexane. Isometric molecules of cyclohexane are packed more tightly and regular. Tight packing lead to the free volume deficiency, which could explain increased viscosity and melting temperature of cyclohexane.

In this paper, the structure of a shock wave in a binary gas mixture is studied on the basis of direct solution of the Boltzmann kinetic equation. The conservative projection method is used to evaluate the collision integral in the kinetic equation. The applied evaluation formulas and numerical methods are described in detail. The model of hard spheres is used as an interaction potential of molecules. Numerical simulation is performed using the developed simulation environment software, which makes it possible to study both steady and non-steady flows of gas mixtures in various flow regimes and for an arbitrary geometry of the problem. Modeling is performed on a cluster architecture. Due to the use of code parallelization technologies, a significant acceleration of computations is achieved. With a fixed accuracy controlled by the simulation parameters, the distributions of macroscopic characteristics of the mixture components through the shock wave front were obtained. Computations were conducted for various ratios of molecular masses and Mach numbers. The total accuracy of at least 1% for the local values of molecular density and temperature and 3% for the shock front width was achieved. The obtained results were compared with existing computation data. The results presented in this paper are of theoretical significance, and can serve as a test computation, since they are obtained using the exact Boltzmann equation.

In various areas of science, technology, environment protection, construction, it is very important to study processes of porous materials interaction with different substances in different aggregation states. From the point of view of ecology and environmental protection it is particularly actual to investigate processes of porous materials interaction with water in liquid and gaseous phases. Since one mole of water contains 6.022140857 · 10²³ molecules of H₂O, macroscopic approaches considering the water vapor as continuum media in the framework of classical aerodynamics are mainly used to describe properties, for example properties of water vapor in the pore. In this paper we construct and use for simulation the macroscopic two-dimensional diffusion model [Bitsadze, Kalinichenko, 1980] describing the behavior of water vapor inside the isolated pore. Together with the macroscopic model it is proposed microscopic model of the behavior of water vapor inside the isolated pores. This microscopic model is built within the molecular dynamics approach [Gould et al., 2005]. In the microscopic model a description of each water molecule motion is based on Newton classical mechanics considering interactions with other molecules and pore walls. Time evolution of “water vapor – pore” system is explored. Depending on the external to the pore conditions the system evolves to various states of equilibrium, characterized by different values of the macroscopic characteristics such as temperature, density, pressure. Comparisons of results of molecular dynamic simulations with the results of calculations based on the macroscopic diffusion model and experimental data allow to conclude that the combination of macroscopic and microscopic approach could produce more adequate and more accurate description of processes of water vapor interaction with porous materials.

An approach to evaluation of a parametric portrait of integral equations of the theory of liquids in the RISM approximation was proposed. To obtain all associated solutions the continuation method was used. The equations reduced to a two-centered molecule model for symmetry reasons were deduced for molecular liquids. For molecular liquids, some equations were obtained which could be reduced, for symmetry reasons, to a two-center molecular model. To avoid critical points we changed the dependence of RISM-equations on reverse compressibility. The suggested method was used to perform numerical computations of methane reverse compressibility isotherms with three closures. No bifurcation of solutions was observed in the case of the partially linearized hypernetted chain closure. For other closures bifurcations of solutions were obtained and the model behavior nontypical for simple liquids was observed. In the case of Percus-Yevick closure nonphysical solutions were obtained at low temperature and density. Additional solution branch with a kink in the bifurcation point was obtained in the case of hypernetted chain closure at temperature above the critical point.

Molecular dynamics simulation using the embedded-atom method is applied to study the structural evolution of the particle diameter of 40 Å during the quenching process. Was carried comparative analysis of the structural reconstruction for the particle and the bulk models. Was a reduction in temperature of the beginning and end of the transformation of the particle. In formation of a percolation cluster from interpenetrating and contacting icosahedrons, for model of the particle, it is involved for 10 percent of atoms more, than for model of a bulk.

Molecular dynamics (MD) simulations of rigid water model TIP4P-EW at ambient conditions were carried out. Delaunay’s simplexes were considered as structural elements of liquid water. Topological criterion which allows to identify the water microstructure in snapshot of MD cell was used to allocate its dense part. Geometrical analysis of water Delaunay’s simplexes indicates their strong flatness in comparison with a regular tetrahedron that is fundamentally different from the results for dense part of simple liquids. The statistics of TIP4P-EW water clusters was investigated depending on their cardinality and connectivity. It is similar to the statistics for simple liquids and the structure of this dense part is also a fractal surface consisting of the free edges of the Delaunay’s simplexes.

The study tested correctness of three interatomic potentials available in the scientific literature in reproducing a vacancy diffusion in concentrated Fe–Cr alloys by molecular dynamic simulations. It was necessary for further detailed study of vacancy diffusion mechanism in these alloys with Cr content 5–25 at.% at temperatures in the range of 600–1000 K. The analysis of the potentials was performed on alloys models with Cr content 10, 20, 50 at.%. The consideration of the model with chromium content 50 at.% was necessary for further study of diffusion processes in chromium-rich precipitates in these alloys. The formation energies and the atomic mobilities of iron and chromium atoms were calculated and analyzed in the alloys via an artificially created vacancy for all used potentials. A time dependence of mean squared displacement of atoms was chosen as а main characteristic for the analysis of atomic mobilities. The simulation of vacancy formation energies didn’t show qualitative differences between the investigated potentials. The study of atomic mobilities showed a poor reproduction of vacancy diffusion in the simulated alloys by the concentration-dependent model (CDM), which strongly underestimated the mobility of chromium atoms via vacancy in the investigated range of temperature and chromium content. Also it was established, that the two-band model (2BM) of potentials in its original and modified version doesn’t have such drawbacks. This allows one to use these potentials in simulations of vacancy diffusion mechanism in Fe–Cr alloys. Both potentials show a significant dependence of the ratio of chromium and iron atomic mobilities on temperature and Cr content in simulated alloys. The quantitative data of the diffusion coefficients of atoms obtained by these potentials also differ significantly.

The effect of the nonlinear supratransmission in crystal of A₃B stoichiometry is studied by molecular dynamics on the example of Pt₃Al alloy. This effect is the transfer of energy at frequencies outside the phonon spectrum of the crystal. Research of the mechanisms of energy transport from the material surface to the interior is the important task, both from the theoretical point of view and from the prospects for practical application in the modification of near-surface layers by treatment with intense external influence of various types. The model was a three-dimensional face-centered cubic crystal whose atoms interact by means of the multiparticle potential obtained by the embedded atom method, which provides greater realism of the model in comparison with the use of pair potentials. Various forms of oscillation of the external influence region are considered. The possibility of energy transport from the crystal surface to the interior is shown by excitation of quasi-breathers near the region of influence and their subsequent destruction in the crystal and scattering of the energy stored on them. The quasibreathers are high-amplitude nonlinear atoms' oscillations of the alloy lightweight component at frequencies outside the phonon spectrum of the crystal. This effect was observed not with every oscillation's form of the region of influence. Quasi-breathers appeared most intensely near the region of influence with sinusoidal form oscillations. The results obtained indicate that the contribution of quasi-breathers to the energy transfer through the crystal increases with increasing amplitude of the influence. The range of amplitudes from 0.05 to 0.5 Å is considered. The frequency of the influence varied from 0.2 to 15 THz, which ensured the coverage of the entire spectrum of lowamplitude oscillations for this crystal's model. The minimum magnitude of the external effect amplitude at which this effect was observed was found to be 0.15 Å. At amplitudes greater than 0.5 Å, the cell rapidly decays for frequencies close to the optical branch of the phonon spectrum. The results of the study can be useful for laser processing of materials, surface treatment by low-energy plasma, and also in radiation materials science.