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GPU-accelerated hybrid systems for high-performance computing in bio-informatics
Computer Research and Modeling, 2010, v. 2, no. 2, pp. 163-167Views (last year): 2. Citations: 6 (RSCI).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.
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Analysis of stochastically forced equilibria and noise-induced transitions in nonlinear discrete systems
Computer Research and Modeling, 2013, v. 5, no. 4, pp. 559-571Views (last year): 1. Citations: 2 (RSCI).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.
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Analysis of noise-induced destruction of coexistence regimes in «prey–predator» population model
Computer Research and Modeling, 2016, v. 8, no. 4, pp. 647-660Views (last year): 14. Citations: 4 (RSCI).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.
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On the construction and properties of WENO schemes order five, seven, nine, eleven and thirteen. Part 2. Numerical examples
Computer Research and Modeling, 2016, v. 8, no. 6, pp. 885-910Views (last year): 13.WENO schemes (weighted, essentially non oscillating) are currently having a wide range of applications as approximate high order schemes for discontinuous solutions of partial differential equations. These schemes are used for direct numerical simulation (DNS) and large eddy simmulation in the gas dynamic problems, problems for DNS in MHD and even neutron kinetics. This work is dedicated to clarify some characteristics of WENO schemes and numerical simulation of specific tasks. Results of the simulations can be used to clarify the field of application of these schemes. The first part of the work contained proofs of the approximation properties, stability and convergence of WENO5, WENO7, WENO9, WENO11 and WENO13 schemes. In the second part of the work the modified wave number analysis is conducted that allows to conclude the dispersion and dissipative properties of schemes. Further, a numerical simulation of a number of specific problems for hyperbolic equations is conducted, namely for advection equations (one-dimensional and two-dimensional), Hopf equation, Burgers equation (with low dissipation) and equations of non viscous gas dynamics (onedimensional and two-dimensional). For each problem that is implying a smooth solution, the practical calculation of the order of approximation via Runge method is performed. The influence of a time step on nonlinear properties of the schemes is analyzed experimentally in all problems and cross checked with the first part of the paper. In particular, the advection equations of a discontinuous function and Hopf equations show that the failure of the recommendations from the first part of the paper leads first to an increase in total variation of the solution and then the approximation is decreased by the non-linear dissipative mechanics of the schemes. Dissipation of randomly distributed initial conditions in a periodic domain for one-dimensional Burgers equation is conducted and a comparison with the spectral method is performed. It is concluded that the WENO7–WENO13 schemes are suitable for direct numerical simulation of turbulence. At the end we demonstrate the possibility of the schemes to be used in solution of initial-boundary value problems for equations of non viscous gas dynamics: Rayleigh–Taylor instability and the reflection of the shock wave from a wedge with the formation a complex configuration of shock waves and discontinuities.
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Analysis of the possibility of investigation of hydrodynamic responses and landing dynamics of space module impacting water with FlowVision CFD software
Computer Research and Modeling, 2017, v. 9, no. 1, pp. 47-55Views (last year): 10.The results of verification carried out for investigations of hydrodynamic effect on reentry conicalsegmental space vehicle are presented in the paper. The program complex Flow Vision is used for this analysis. The purpose of the study is verification of using Flow Vision program complex for problem solving mentioned above on the base of comparison between calculated and experimental data, obtained on the Apollo landing models and new development reentry spacecraft of manned transporting spaceship designed by RSC Energia. The comparison was carried out through the data of pressure values on spacecraft model surfaces during its water landing and inertia center motion parameters.
The results of study show good agreement between experimental and calculated data of force effects on vehicle construction during water landing and its motion parameters in the water medium. Computer simulation sufficiently well reproduces influence of initial velocities & water entry angles variations on water landing process.
Using of computer simulation provides simultaneous acquisition of all data information needed for investigation of water landing peculiarities during construction design, notably, hydrodynamic effects for structural strength calculations, parameters and dynamics of center mass motion and vehicle revolution around center mass for estimation water landing conditions, as well as vehicle stability after landing.
Obtained results confirm suitability of using Flow Vision program complex for water landing vehicle investigations and investigations of influence of different landing regimes through wide initial condition change range, that permits considerably decrease extent of expensive experimental tests and realize landing conditions which are sufficiently complicated for realizing in model physical experiments.
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The present article sets out the scientific approach of Dmitry Sergeevich Chernavskii to the modelling of economic processes. It recounts the history of works of Dmitry Sergeyevich on the economic front, its milestones and achievements. One of the most important advances in the economic analysis was the prediction by a team of scientists headed by D. S. Chernavskii, the major crises that have occurred in our country over the last 20 years, namely, the default of 1998, the crisis of industrial production in the second half of the 2000s, the 2008 crisis and the ensuing recession. As an example, the dynamic analysis of the global macroeconomic processes shows the model of functioning of the dollar as the world currency. On this particular example shows the possibility of seigniorage due to the issue of the dollar and the calculated “window of opportunity” that allows you to issue dollars as the global currency, without prejudice to its own economy.
A model for the development of a closed society (without external economic relations) in the one-product approach is considered as an example of dynamic analysis of the economy of a separate state. The model is based on the principles of market economy, i.e. the dynamics of prices is determined by the balance of supply and demand. It is shown that in the general case, the state of market equilibrium is not unique. Several steady states with different levels of production and consumption are possible. Effect of addressed emission of money in underproductive state is considered. It is shown that, depending on its size it can lead to the transition to a highly productive condition, and just cause inflation without transition. The relationship of these results with the “Keynesian” and “monetarist” approaches is discussed.
Keywords: the economy, crises, dynamic analysis, dollar, seigniorage, mathematical model, emission, inflation, the digital economy.Views (last year): 5. Citations: 2 (RSCI). -
Modeling the physical processes of a powerful nuclear explosion on an asteroid
Computer Research and Modeling, 2019, v. 11, no. 5, pp. 861-877As part of the paper, a physical and theoretical analysis of the impact processes of various factors of a highaltitude and high-energy nuclear explosion on the asteroid in extra-atmospheric conditions of open space is done. It is shown that, in accordance with the energy and permeability of the plasma of explosion products, X-ray and gamma-neutron radiation, a layered structure with a different energy density depending on angular coordinates is formed on the surface of the asteroid. The temporal patterns of the energy transformation for each layer is clarified and the roles of various photo- and collision processes are determined. The effect of a high-speed plasma flow is erosive in nature, and the plasma pulse is transmitted to the asteroid. The paper presents that in a thin layer of x-ray absorption, the asteroid substance is heated to high temperatures and as a result of its expansion, a recoil impulse is formed, which is not decisive due to the small mass of the expanding high-temperature plasma. Calculations shows that the main impulse received by an asteroid is associated with the entrainment of a heated layer of a substance formed by a neutron flux (7.5 E 1014 g E cm/s). It is shown that an asteroid with a radius of ~100 m acquires a velocity of . 100 cm/s. The calculations were performed taking into account the explosion energy spent on the destruction of the amorphous structure of the asteroid material (~1 eV/atom = 3.8 E 1010 erg/g) and ionization in the region of the high-temperature layer. Based on a similar analysis, an approximation is obtained for estimating the average size of fragments in the event of the possible destruction of the asteroid by shock waves generated inside it under the influence of pressure impulses. A physical experiment was conducted in laboratory conditions, simulating the fragmentation of a stone asteroid and confirming the validity of the obtained dependence on the selected values of certain parameters. As a result of numerical studies of the effects of the explosion, carried out at different distances from the surface of the asteroid, it is shown that taking into account the real geometry of the spallation layer gives the optimal height for the formation of the maximum asteroid momentum by a factor of 1.5 greater than similar estimates according to the simplified model. A two-stage concept of the impact of nuclear explosions on an asteroid using radar guidance tools is proposed. The paper analyzes the possible impact of the emerging ionization interference on the radar tracking of the movement of large fragments of the asteroid in the space-time evolution of all elements of the studied dynamic system.
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Numerical study of the interaction of a shock wave with moving rotating bodies with a complex shape
Computer Research and Modeling, 2021, v. 13, no. 3, pp. 513-540The work is devoted to the development of a computational algorithm of the Cartesian grid method for studying the interaction of a shock wave with moving bodies with a piecewise linear boundary. The interest in such problems is connected with direct numerical simulation of two-phase media flows. The effect of the particle shape can be important in the problem of dust layer dispersion behind a passing shock wave. Experimental data on the coefficient of aerodynamic drag of non-spherical particles are practically absent.
Mathematical model is based on the two-dimensional Euler equations, which are solved in a region with varying boundaries. The defining system of equations is integrated using an explicit scheme and the Cartesian grid method. The computational algorithm at the time integration step includes: determining the step value, calculating the dynamics of the body movement (determining the force and moment acting on the body; determining the linear and angular velocities of the body; calculating the new coordinates of the body), calculating the gas parameters. At each time step, all cells are divided into two classes – external (inside the body or intersected by its boundaries) and internal (completely filled with gas). The solution of the Euler equations is constructed only in the internal ones. The main difficulty is the calculation of the numerical flux through the edges common to the internal and external cells intersected by the moving boundaries of the bodies. To calculate this flux, we use a two-wave approximation for solving the Riemann problem and the Steger-Warming scheme. A detailed description of the numerical algorithm is presented.
The efficiency of the algorithm is demonstrated on the problem of lifting a cylinder with a base in the form of a circle, ellipse and rectangle behind a passing shock wave. A circular cylinder test was considered in many papers devoted to the immersed boundary methods development. A qualitative and quantitative analysis of the trajectory of the cylinder center mass is carried out on the basis of comparison with the results of simulations presented in eight other works. For a cylinder with a base in the form of an ellipse and a rectangle, a satisfactory agreement was obtained on the dynamics of its movement and rotation in comparison with the available few literary sources. Grid convergence of the results is investigated for the rectangle. It is shown that the relative error of mass conservation law fulfillment decreases with a linear rate.
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Hybrid grid method for external and internal gas dynamics
Computer Research and Modeling, 2023, v. 15, no. 3, pp. 543-565Based on the modeling method using a mesh system, an algorithm is implemented for solving a unsteady problem with moving bodies The algorithm takes into account the movement and rotation of bodies according to a given law of motion. The algorithm is applied to analysis the flow around an infinite composed of cylinders with an elliptical cross-section, which either move across the flow or rotate with a change in the angle of attack. To simulate the flow of bodies with a sharp edge, characteristic of the profiles of gas turbine machines, an algorithm for constructing a mesh of type C with the inclusion of a certain area behind the profile is implemented. The program for modeling the flow near the profile is implemented within the framework of models of Euler equations, Navier – Stokes equations in the approximation of a thin layer with laminar viscosity and turbulent viscosity in the framework of an algebraic viscosity model. The program has also been adapted to solve the problems of internal gas dynamics of turbomachines. For this purpose, the method of setting the boundary conditions at the entrance and exit from the calculated area from the velocity to the pressure drop, as well as at the lateral boundaries from the free flow to the periodicity, was changed. This made it possible to simulate the flow of gas in the inter-blade channels of compressors and turbines of gas turbine engines. To refine the algorithm, a series of calculations of the aerodynamic parameters of several turbine cascades in various subsonic and supersonic modes and their comparison with the experiment were carried out. Calculations of turbine grating parameters were carried out within the framework of the inviscid and viscous gas model. The calculation and experiment were compared by the distribution of gas parameters near the profile, as well as by the energy losses of the flow in the cascade. Calculations have shown the applicability and correctness of the program to solve this class of problems. To test the program on the problems of external subsonic aerodynamics, calculations of the aerodynamic characteristics of an isolated airfoil in an undisturbed flow were performed. The results obtained allow us to assert the applicability of the hybrid grid method to various classes of problems of applied gas dynamics.
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CFD-modeling of heat exchange beams with eutectic lead-bismuth alloy
Computer Research and Modeling, 2023, v. 15, no. 4, pp. 861-875Nowadays, active development of 4th generation nuclear reactors with liquid metal coolants takes place. Therefore, simulation of their elements and units in 3D modelling software are relevant. The thermal-hydraulic analysis of reactor units with liquid metal coolant is recognized as one of the most important directions of the complex of interconnected tasks on reactor unit parameters justification. The complexity of getting necessary information about operating conditions of reactor equipment with liquid-metal coolant on the base of experimental investigations requires the involvement of numerical simulation. The domestic CFD code FlowVision has been used as a research tool. FlowVision software has a certificate of the Scientific and Engineering Centre for Nuclear and Radiation Safety for the nuclear reactor safety simulations. Previously it has been proved that this simulation code had been successfully used for modelling processes in nuclear reactors with sodium coolant. Since at the moment the nuclear industry considers plants with lead-bismuth coolant as promising reactors, it is necessary to justify the FlowVision code suitability also for modeling the flow of such coolant, which is the goal of this work. The paper presents the results of lead-bismuth eutectic flow numerical simulation in the heat exchange tube bundle of NPP steam generator. The convergence studies on a grid and step have been carried out, turbulence model has been selected, hydraulic resistance coefficients of lattices have been determined and simulations with and without $k_\theta^{}$-$e_\theta^{}$ model are compared within the framework of fluid dynamics and heat exchange modeling in the heat-exchange tube bundle. According to the results of the study, it was found that the results of the calculation using the $k_\theta^{}$-$e_\theta^{}$ turbulence model are more precisely consistent with the correlations. A cross-verification with STAR-CCM+ software has been performed as an additional verification on the accuracy of the results, the results obtained are within the error limits of the correlations used for comparison.
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