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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.

Pattern formation described by the scalar Fisher–Kolmogorov–Petrovsky–Piscounov equation with nonlocal competition loses and convection linear on coordinates is considered numerically. Initial function localized around a point is shown to transform in a function localized around a ring with symmetrically sited local maxima. The ring radius and number of maxima depend on convection.

Тhe new test-signals forming method for correlation identification of a nonlinear system based on Lee–Shetzen cross-correlation approach is developed and tested. Numerical Gauss–Newton algorithm is applied to correct autocorrelation functions of test signals. The achieved test-signals have length less than 40 000 points and allow to measure the 2nd order Wiener kernels with a linear resolution up to 32 points, the 3rd order Wiener kernels with a linear resolution up to 12 points and the 4th order Wiener kernels with a linear resolution up to 8 points.

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.

We investigated numerically the dynamics of kinks of modified sine-Gordon equation in the model with localized spatial modulation of a periodic potential (or impurity). We considered the case of two identical impurities. We showed the possibility of collective effects of the influence of impurities, which are heavily dependent on the distance between them. We demonstrated the existence of a certain critical value of the distance between impurities, which has two qualitatively different scenarios of the dynamic behavior of kink.

Stochastically forced discrete dynamical systems are considered. Using first approximation systems, we study dynamics of deviations of stochastic solutions from deterministic equilibria. Necessary and sufficient conditions of the existence of stable stationary solutions of equations for mean-square deviations are derived. Stationary values of these mean-square deviations are used for the estimations of the dispersion of random states nearby stable equilibria and analysis of noise-induced transitions. Constructive application of the suggested technique to the analysis of various stochastic regimes in Ricker population model with Allee effect is demonstrated.

In the context of problems of hydrogen and thermonuclear power engineering intensive research of the hydrogen isotopes properties is being conducted. Mathematical models help to specify physical-chemical ideas about the interaction of hydrogen isotopes with structural materials, to discover the limiting factors. Classical diffusion models are often insufficient. The paper is devoted to the models and numerical solution of the boundary-value problems of hydrogen thermodesorption and permeability taking into account nonlinear sorption-desorption dynamics on the surface and reversible capture of hydrogen atoms in the bulk. Algorithms based on difference approximations. The results of computer simulation of the hydrogen flux from a structural material sample are presented.

The paper presents results of experimental, computational and analytical study of the effect of nonequilibrium chemical activation of air-fuel mixture on effectiveness of Diesel process. The generation of a high-voltage multi-streamer discharge in combustion chamber at the compression phase is considered as the method of the activation. The description of electrical discharge system, results of measurement and visualization are presented. The plasma-chemical kinetics of nonequilibrium ignition is analyzed to establish a passway for a proper reduction of chemical kinetics scheme. The results of numerical simulation of gas dynamic processes at presence of plasma-assisted combustion in a geometrical configuration close to the experimental one are described.

А discrete element model is applied to the problem of a spherical projectile penetration into a massive obstacle. According to the model both indenter and obstacle are described by a set of densely packed particles. To model the interaction between the particles the two-parameter Lennard–Jones potential is used. Computer implementation of the model has been carried out using parallelism on GPUs, which resulted in high spatial — temporal resolution. Based on the comparison of the results of numerical simulation with experimental data the binding energy has been identified as a function of the dynamic hardness of materials. It is shown that the use of this approach allows to accurately describe the penetration process in the range of projectile velocities 500–2500 m/c.

The paper is devoted to the analysis of the proximity of the population system to dangerous boundaries. An intersection of these boundaries results in the collapse of the stable coexistence of interacting populations. As a reason of such destruction one can consider random perturbations inevitably presented in any living system. This study is carried out on the example of the well-known model of interaction between predator and prey populations, taking into account both a stabilizing factor of the competition of predators for another than prey resources, and also a destabilizing saturation factor for predators. To describe the saturation of predators, we use the second type Holling trophic function. The dynamics of the system is studied as a function of the predator saturation, and the coefficient of predator competition for resources other than prey. The paper presents a parametric description of the possible dynamic regimes of the deterministic model. Here, local and global bifurcations are studied, and areas of sustainable coexistence of populations in equilibrium and the oscillation modes are described. An interesting feature of this mathematical model, firstly considered by Bazykin, is a global bifurcation of the birth of limit cycle from the separatrix loop. We study the effects of noise on the equilibrium and oscillatory regimes of coexistence of predator and prey populations. It is shown that an increase of the intensity of random disturbances can lead to significant deformations of these regimes right up to their destruction. The aim of this work is to develop a constructive probabilistic criterion for the proximity of the population stochastic system to the dangerous boundaries. The proposed approach is based on the mathematical technique of stochastic sensitivity functions, and the method of confidence domains. In the case of a stable equilibrium, this confidence domain is an ellipse. For the stable cycle, this domain is a confidence band. The size of the confidence domain is proportional to the intensity of the noise and stochastic sensitivity of the initial deterministic attractor. A geometric criterion of the exit of the population system from sustainable coexistence mode is the intersection of the confidence domain and the corresponding separatrix of the unforced deterministic model. An effectiveness of this analytical approach is confirmed by the good agreement of theoretical estimates and results of direct numerical simulations.