Most viewed papers

391. Krasnikov G.Ya., Zaitsev N.A., Matyushkin I.V., Korobov S.V.
     The peculiarities of cellular automata visualization in nanoelectronics
     Computer Research and Modeling, 2012, v. 4, no. 4, pp. 735-756

     The general formalization of visualization models in cellular automata (CA) scope is presented, their classification is examined. It also describes possible approaches to the sound scales generation. We consider special cases of visualization manners for CA of various dimensions. By a simple 3D CA example the features of nanoscale systems imaging are indicated.

     Keywords: cellular automata, visualization, nanotechnology, modeling, multimedia.
     Views (last year): 3. Citations: 3 (RSCI).
392. Plusnina T.Yu., Voronova E.N., Goltzev V.N., Pogosyan S.I., Yakovleva O.V., Riznichenko G.Yu., Rubin A.B.
     Reduced model of photosystem II and its use to evaluate the photosynthetic apparatus characteristics according to the fluorescence induction curves
     Computer Research and Modeling, 2012, v. 4, no. 4, pp. 943-958

     The approach for the analysis of some large-scale biological systems, on the base of quasiequilibrium stages is proposed. The approach allows us to reduce the detailed large-scaled models and obtain the simplified model with an analytical solution. This makes it possible to reproduce the experimental curves with a good accuracy. This approach has been applied to a detailed model of the primary processes of photosynthesis in the reaction center of photosystem II. The resulting simplified model of photosystem II describes the experimental fluorescence induction curves for higher and lower plants, obtained under different light intensities. Derived relationships between variables and parameters of detailed and simplified models, allow us to use parameters of simplified model to describe the dynamics of various states of photosystem II detailed model.

     Keywords: photosystem II, fluorescence induction curves, model reduction.
     Views (last year): 3. Citations: 2 (RSCI).
393. Risnik D.V., Levich A.P., Bulgakov N.G., Bikbulatov E.S., Bikbulatova E.M., Ershov Y.V., Konuhov I.V., Korneva L.G., Lazareva V.I., Litvinov A.S., Maksimov V.N., Mamihin S.V., Osipov V.A., Otyukova N.G., Poddubnii S.A., Pirina I.L., Sokolova E.A., Stepanova I.E., Fursova P.V., Celmovich O.L.
     Searching for connections between biological and physico-chemical characteristics of Rybinsk reservoir ecosystem. Part 1. Criteria of connection nonrandomness
     Computer Research and Modeling, 2013, v. 5, no. 1, pp. 83-105

     Based on contents of phytoplankton pigments, fluorescence samples and some physico-chemical characteristics of the Rybinsk reservoir waters, searching for connections between biological and physicalchemical characteristics is working out. The standard methods of statistical analysis (correlation, regression), methods of description of connection between qualitative classes of characteristics, based on deviation of the studied characteristics distribution from independent distribution, are studied. A method of searching for boundaries of quality classes by criterion of maximum connection coefficient is offered.

     Keywords: fluorescence, phytoplankton, pigments, chlorophyll, Yule coefficient, Pearson coefficient, searching for connection, Rybinsk reservoir.
     Views (last year): 3. Citations: 6 (RSCI).
394. Kuznetsov V.L., Rudkovskiy A.S.
     Model of 3D electromagnetic field with 2D periodic structures interaction
     Computer Research and Modeling, 2013, v. 5, no. 2, pp. 213-224

     An application of the invariant imbedding method to describe the interaction of 3D electromagnetic field with 2D photonic crystal of finite thickness, formed by a dielectric circular cylinder or square bars, is considered in this paper. Matrix coefficients of transmission and reflection for waves at different angles of incidence were calculated taking into account different types of polarization and non-coplanar diffraction.

     Keywords: Invariant embedding method, Photonic crystal, Non-coplanar diffraction.
     Views (last year): 3.
395. Zolotyh T.A., Kosilov A.T., Ozherelyev V.V.
     Simulation of copper nanocrystal plastic deformation at uniaxial tension
     Computer Research and Modeling, 2013, v. 5, no. 2, pp. 225-230

     Computer simulation of plastic deformation of FCC copper nanocrystal in the process of uniaxial tension in a direction [001] is performed by methods of molecular dynamics and a static relaxation. It is shown that thermoelastic martensite transformation is responsible for plastic deformation, FCC lattice is reconstructed into HCP lattice. Orientation relationship of contacting phases is identified.

     Keywords: martensite transformation, deformation, computer simulation, molecular dynamics, nanocrystal, uniaxial tension.
     Views (last year): 3. Citations: 1 (RSCI).
396. Kolmakova T.V.
     Research of deformation behavior of bone fragment at an axial compression, containing compact and spongy layers of different density
     Computer Research and Modeling, 2013, v. 5, no. 3, pp. 433-441

     The results of computer simulation of deformation behavior of bone fragment at axial compression, containing compact and spongy layers of different density, are presented. The result of calculations show that changing of prevailing type of deformation of compression of bone sample on deformation of bend and vice versa is possible at densities change of his spongy constituent and compact constituent

     Keywords: Computer simulation, compact bone, spongy bone, stress and strain state, deformation behavior.
     Views (last year): 3. Citations: 2 (RSCI).
397. Temlyakova E.A., Dzhelyadin T.R., Kamzolova S.G., Sorokin A.A.
     

     System to store DNA physical properties profiles with application to the promoters of Escherichia coli

     
     Computer Research and Modeling, 2013, v. 5, no. 3, pp. 443-450

     Database to store, search and retrieve DNA physical properties profiles has been developed and its use for analysis of E. coli promoters has been demonstrated. Unique feature of the database is in its ability to handle whole profile as single internal object type in a way similar to integers or character strings. To demonstrate utility of such database it was populated with data of 1227 known promoters, their nucleotide sequence, profile of electrostatic potential, transcription factor binding sites. Each promoter is also connected to all genes, whose transcription is controlled by that promoter. Content of the database is available for search via web interface. Source code of profile datatype and library to work with it from R/Bioconductor are available from the internet, dump of the database is available from authors by request.

     Keywords: E. coli, electrostatic potential of DNA, database, signal analysis.
     Views (last year): 3.
398. Zlenko D.V., Stovbun S.V.
     Liquid Heptane and Cylcohexane Properties Modeling
     Computer Research and Modeling, 2013, v. 5, no. 5, pp. 813-820

     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.

     Keywords: cyclohexane, molecular modeling, gas-like crystal, radial distribution function.
     Views (last year): 3. Citations: 2 (RSCI).
399. Nikitin I.S., Filimonov A.V., Yakushev V.L.
     Propagation of Rayleigh waves at oblique impact of the meteorite about the earth’s surface and their effects on buildings and structures
     Computer Research and Modeling, 2013, v. 5, no. 6, pp. 981-992

     In this paper the dynamic elasticity problem of the simultaneous normal and tangential impact on the half-space is solved. This problem simulates the oblique incidence of meteorite on the Earth’s surface. The surface Rayleigh wave is investigated. The resulting solution is used as an external effect on the high-rise building, located at some distance from the spot of falling for the safety and stability assessment of its structure. Numerical experiments were made based on the finite element software package STARK ES. Upper floors amplitudes of the selected object were calculated under such dynamic effects. Also a systematic comparison with the results at the foundation vibrations, relevant to  standard a 8-point earthquake accelerograms, was made.

     Keywords: Rayleigh wave, meteorite, earthquake.
     Views (last year): 3. Citations: 2 (RSCI).
400. Ivanov S.I., Matasov A.V., Menshutina N.V.
     Deformation model of polymer nanocomposites based on cellular automata
     Computer Research and Modeling, 2014, v. 6, no. 1, pp. 131-136

     This paper discusses the modeling of the deformation of polymer nanocomposites containing "hard" and "soft" inclusions, using cellular automata and parallel computing. The paper describes an algorithm based on the model, a comparison with experimental data is shown, software for the numerical experiment is described.

     Keywords: сellular automata, parallel computing, deformation, simulation.
     Views (last year): 3. Citations: 2 (RSCI).

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