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The use of cluster analysis methods for the study of a set of feasible solutions of the phase problem in biological crystallography
Computer Research and Modeling, 2010, v. 2, no. 1, pp. 91-101Views (last year): 2.X-ray diffraction experiment allows determining of magnitudes of complex coefficients in the decomposition of the studied electron density distribution into Fourier series. The determination of the lost in the experiment phase values poses the central problem of the method, namely the phase problem. Some methods for solving of the phase problem result in a set of feasible solutions. Cluster analysis method may be used to investigate the composition of this set and to extract one or several typical solutions. An essential feature of the approach is the estimation of the closeness of two solutions by the map correlation between two aligned Fourier syntheses calculated with the use of phase sets under comparison. An interactive computer program ClanGR was designed to perform this analysis.
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Molecular modeling and dynamics of serotonin 5-HT3 receptor and ligands
Computer Research and Modeling, 2011, v. 3, no. 3, pp. 329-334Citations: 1 (RSCI).The problem of ligand binding to certain receptor proteins is of central importance in cellular signaling, but it is still unresolved at a molecular level. In order to enhance our understanding of the molecular mechanisms we used a biophysical approach to study a serotonin-gated ion channel. The molecular model of 5-HT3 receptor extracellular domain was created using computer-based homology modeling. The docking method was used for building complexes of the 5-HT3 receptor and ligands. Some different activities were investigated by the method of molecular dynamics.
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Modeling of spatialtemporal migration for closely related species
Computer Research and Modeling, 2011, v. 3, no. 4, pp. 477-488We consider a model of populations that are closely related and share a common areal. System of nonlinear parabolic equations is formulated that incorporates nonlinear diffusion and migration flows induced by nonuniform densities of population and carrying capacity. We employ the method of lines and study the impact of migration on scenarios of local competition and coexistence of species. Conditions on system parameters are determined when a nontrivial family of steady states is formed.
Keywords: dynamics of populations, nonlinear parabolic equations.Views (last year): 6. Citations: 9 (RSCI). -
Investigation of water injection influence on hydrocyclone separation performance
Computer Research and Modeling, 2012, v. 4, no. 4, pp. 803-810In this paper particularities of the swirling turbulent flow of monodisperse suspension in the hydrocyclone with injector are investigated on the base of the numerical simulation. The 2D axisymmetric approximation of Reynolds Stresses Model and model of mixture is used to describe the swirling turbulent flow field of suspension and particles parameters in the hydrocyclone. Special attention is paid to the clarification of mechanisms of injection influence on the reorganization of hydrodynamic field and finally on classification mechanisms. It is shown that tangential injection method stronger effects separation curve compared to the radial one.
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Comparative analysis of optimization methods for electrical energy losses interval evaluation problem
Computer Research and Modeling, 2013, v. 5, no. 2, pp. 231-239Views (last year): 2. Citations: 1 (RSCI).This article is dedicated to a comparison analysis of optimization methods, in order to perform an interval estimation of electrical energy technical losses in distribution networks of voltage 6–20 kV. The issue of interval evaluation is represented as a multi-dimensional conditional minimization/maximization problem with implicit target function. A number of numerical optimization methods of first and zero orders is observed, with the aim of determining the most suitable for the problem of interest. The desired algorithm is BOBYQA, in which the target function is replaced with its quadratic approximation in some trusted region.
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Model method of vertical chlorophyll concentration reconstruction from satellite data
Computer Research and Modeling, 2013, v. 5, no. 3, pp. 473-482Views (last year): 5. Citations: 2 (RSCI).A model, describing the influence of external factors on temporal evolution of phytoplankton distribution in a horizontally-homogenous water layer, is presented. This model is based upon the reactiondiffusion equation and takes into account the main factors of influence: mineral nutrients, insolation and temperature. The mineral nutrients and insolation act oppositely on spatial phytoplankton distribution. The results of numerical modeling are presented and the prospect of applying this model to reconstruction of phytoplankton distribution from sea-surface satellite data is discussed. The model was used to estimate the chlorophyll content of the Peter the Great Bay (Sea of Japan).
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Comparative analysis of Darcy and Brinkman models at studying of transient conjugate natural convection in a porous cylindrical cavity
Computer Research and Modeling, 2013, v. 5, no. 4, pp. 623-634Views (last year): 1. Citations: 4 (RSCI).Comparative analysis of two models of porous medium (Dacry and Brinkman) on an example of mathematical simulation of transient natural convection in a porous vertical cylindrical cavity with heat-conducting shell of finite thickness in conditions of convective cooling from an environment has been carried out. The boundary-value problem of mathematical physics formulated in dimensionless variables such as stream function, vorticity and temperature has been solved by implicit finite difference method. The presented verification results validate used numerical approach and also confirm that the solution is not dependent on the mesh size. Features of the conjugate heat transfer problems with considered models of porous medium have been determined.
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Credit risk assessment on the basis of multidimensional analysis
Computer Research and Modeling, 2013, v. 5, no. 5, pp. 893-901Views (last year): 7. Citations: 19 (RSCI).The article is devoted to description the author's method of multidimensional analysis for generate an predictive assessment of organizations’ credit risk, based on the credit history information, which taking into account value and period of credit. An example of credit risk assessment is given.
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Analysis of stochastic attractors for time-delayed quadratic discrete model of population dynamics
Computer Research and Modeling, 2015, v. 7, no. 1, pp. 145-157Views (last year): 3. Citations: 1 (RSCI).We consider a time-delayed quadratic discrete model of population dynamics under the influence of random perturbations. Analysis of stochastic attractors of the model is performed using the methods of direct numerical simulation and the stochastic sensitivity function technique. A deformation of the probability distribution of random states around the stable equilibria and cycles is studied parametrically. The phenomenon of noise-induced transitions in the zone of discrete cycles is demonstrated.
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Pareto optimal analysis of global warming prevention by geoengineering methods
Computer Research and Modeling, 2015, v. 7, no. 5, pp. 1097-1108Views (last year): 1. Citations: 3 (RSCI).The study is based on a three-dimensional hydrodynamic global climate coupled model, including ocean model with real depths and continents configuration, sea ice evolution model and energy and moisture balance atmosphere model. Aerosol concentration from the year 2010 to 2100 is calculated as a controlling parameter to stabilize mean year surface air temperature. It is shown that by this way it is impossible to achieve the space and seasonal uniform approximation to the existing climate, although it is possible significantly reduce the greenhouse warming effect. Climate will be colder at 0.1–0.2 degrees in the low and mid-latitudes and at high latitudes it will be warmer at 0.2–1.2 degrees. The Pareto frontier is investigated and visualized for two parameters — atmospheric temperature mean square deviation for the winter and summer seasons. The Pareto optimal amount of sulfur emissions would be between 23.5 and 26.5 TgS/year.
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