Most cited papers (RSCI)

321. Golovkin M.V., Nechipurenko D.Y., Il’icheva I.A., Panchenko L.A., Polozov R.V., Grokhovsky S.L., Nechipurenko Y.D.
     [RETRACTED PAPER] Calculational methods for electrophoretic cleavage pattern analysis of DNA
     Computer Research and Modeling, 2009, v. 1, no. 3, pp. 287-295

     The article was retracted on May 3, 2022 at the request of the authors due to the fact that the data included in the article were published in the article by Nechipurenko Y.D., Golovkin M.V., Nechipurenko D.Yu., Ilyicheva I.A., Panchenko L. .A., Polozov R.V., Grokhovsky S.L. Kharakternye osobennosti rasshchepleniya DNK ul'trazvukom [Characteristic features of DNA cleavage by ultrasound]. Journal of Structural Chemistry, 2009, volume 50, number 5, pages 1045-1052 (in Russian).

     Views (last year): 3. Citations: 1 (RSCI).
322. Shuvalova E.V.
     Quantum and classical approaches to a biological problem of particle transition through non-stationary barriers
     Computer Research and Modeling, 2009, v. 1, no. 3, pp. 337-351

     The most part of biological tasks coincide with temperature areas, where quantum and classical effects are equivalent, or the classical one is dominating. The extent of influence of quantum or classical effect was considered in the work in application to one of the most significant problems of biological activity: particle transition through non-stationary barriers. It is interesting that the results obtained using different approaches, quantum and classical, are the same. It seems that the particle dynamics is characterized by non-coherent relaxation with rate of diffusion.

     Keywords: biological activity of the molecules, particle transition through barriers.
     Citations: 1 (RSCI).
323. Borisov A.V., Trifonov A.Y., Shapovalov A.V.
     Semiclassical solutions localized in a neighborhood of a circle for the Gross–Pitaevskii equation
     Computer Research and Modeling, 2009, v. 1, no. 4, pp. 359-365

     Non-collapsing soliton-like wave functions are shown to exist in semiclassical approximation for the Bose-Einstein condensate model based on the Gross–Pitaevskii equation with attractive nonlinearity and external field of magnetic trap of special form.

     Keywords: Gross–Pitaevskii equation, Bose–Einstein condensate, magneto-optical trap.
     Citations: 1 (RSCI).
324. Shirkov P.D., Zubanov A.M.
     Two-stage single ROW methods with complex coefficients for autonomous systems of ODE
     Computer Research and Modeling, 2010, v. 2, no. 1, pp. 19-32

     The basic subset of two-stage Rosenbrock schemes with complex coefficients for numerical solution of autonomous systems of ordinary differential equations (ODE) has been considered. Numerical realization of such schemes requires one LU-decomposition, two computations of right side function and one computation of Jacoby matrix of the system per one step. The full theoretical investigation of accuracy and stability of such schemes have been done. New A-stable methods of the 3-rd order of accuracy with different properties have been constructed. There are high order L-decremented schemes as well as schemes with simple estimation of the main term of truncation error which is necessary for automatic evaluation of time step. Testing of new methods has been performed.

     Keywords: stiff systems, schemes with complex coefficients, A-stability.
     Citations: 1 (RSCI).
325. Glyakina A.V., Galzitskaya O.V., Balabaev N.K.
     Investigation of the mechanical properties of immunoglobulinbinding domains of proteins L and G using the molecular dynamics simulations
     Computer Research and Modeling, 2010, v. 2, no. 1, pp. 73-81

     Mechanical unfolding of two identical in structure but differ in their amino acid sequences immunoglobulinbinding domains of proteins L and G under the action of external forces have been investigating  using the method of molecular dynamics with explicit model of solvent. Mechanical characteristics of these proteins have been calculated. It has been shown that in the way of the mechanical unfolding of both proteins appear intermediate states. Calculations revealed three significantly different ways of mechanical unfolding of proteins L and G.

     Citations: 1 (RSCI).
326. Romanovsky M.Y., Vidov P.V., Pyrkin V.A.
     Is a tick an elementary jump in a random walks scheme on the stock market?
     Computer Research and Modeling, 2010, v. 2, no. 2, pp. 219-223

     In this paper average times between elementary jumps of stock returns on the Russian market were experimentally studied. Considering the scaling of the probability density function of stock returns on different time intervals it is shown that an elementary jump in the random walks scheme for financial instrument returns is a unit price change (tick) that corresponds to a single deal on the stock market.

     Keywords: random walks, return fluctuations, Levy distribution.
     Views (last year): 3. Citations: 1 (RSCI).
327. Yurkin A.V.
     Ray trajectories, binomial coefficients of a new type, and the binary system
     Computer Research and Modeling, 2010, v. 2, no. 4, pp. 359-397

     The paper describes a new algorithm of construction of the nonlinear arithmetic triangle on the basis of numerical simulation and the binary system. It demonstrates that the numbers that fill the nonlinear arithmetic triangle may be binomial coefficients of a new type. An analogy has been drawn with the binomial coefficients calculated with the use of the Pascal triangle. The paper provides a geometrical interpretation of binomials of different types in considering the branching systems of rays.

     Keywords: nonlinear arithmetic triangle, binary system, binomial coefficients, branching systems of rays, lasers.
     Views (last year): 5. Citations: 1 (RSCI).
328. Usenko V.A., Lobanov A.I.
     Flow relaxation method in solving quasilinear parabolic equations
     Computer Research and Modeling, 2011, v. 3, no. 1, pp. 47-53

     This article proposes a numeric method of solution of quasilinear parabolic equations, based on the flux approximation, describes the implementation of the method on a rectangular grid and presents numerical results. Unlike methods used in common practice, this method uses an approximation of flows in non-dilated template. For each iteration of the Newton method it is possible to solve a linear problem using the method of upper relaxation (SOR). Compared with the methods of flux sweeping, the considered method has greater potential for use in modern parallel computing system.

     Keywords: parabolic quasilinear equation, red-black ordering, difference scheme, qasilinearization, SOR.
     Views (last year): 1. Citations: 1 (RSCI).
329. Borisov A.V., Trifonov A.Y., Shapovalov A.V.
     Convection effect on two-dimensional dynamics in the nonlocal reaction-diffusion model
     Computer Research and Modeling, 2011, v. 3, no. 1, pp. 55-61

     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.

     Keywords: reaction-diffusion, convection, nonlocal competition losses, Fisher–Kolmogorov–Petrovsky–Piscounov equation.
     Views (last year): 3. Citations: 1 (RSCI).
330. Popinako A.V.
     Molecular modeling and dynamics of serotonin 5-HT3 receptor and ligands
     Computer Research and Modeling, 2011, v. 3, no. 3, pp. 329-334

     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.

     Keywords: membrane receptors, ligands, molecular dynamics.
     Citations: 1 (RSCI).

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