Most viewed papers

341. Aristov V.V., Ilyin O.V.
     Description of the rapid invasion processes by means of the kinetic model
     Computer Research and Modeling, 2014, v. 6, no. 5, pp. 829-838

     Recently many investigations have been devoted to theoretical models in new areas concerning description of different biological, sociological and historical processes. In the present paper we investigate the nazi Germany invasion in Poland, France and USSR from the kinetic theory point of view. We model this process with the Cauchy boundary problem for the two-element kinetic equations with spatial uniform initial conditions. The solution of the problem is given in the form of the traveling wave and the propagation velocity of a frontline depends on the quotient between initial forces concentrations. Moreover it is obtained that the general solution of the model can be obtained in terms of the quadratures and elementary functions. Finally it is shown that the frontline velocities are complied with the historical data.

     Keywords: kinetic theory, models of aggression.
     Views (last year): 4. Citations: 1 (RSCI).
342. Varshavsky L.E.
     Control theory methods for creating market structures
     Computer Research and Modeling, 2014, v. 6, no. 5, pp. 839-859

     Control theory methods for creating market structures are discussed for two cases: when market participants are pursuing aims 1) of maximal growth and 2) of maximum economic efficiency of their firms. For the first case method based on variable structure systems principles is developed. For the second case dynamic game approach is proposed based on computation of Nash–Cournot and Stackelberg strategies with the help of Z-transform.

     Keywords: market structures, oligopolistic markets, variable structure systems, dynamical games, optimal strategies.
     Views (last year): 4. Citations: 4 (RSCI).
343. Ozerov I.V., Osipov A.N.
     Kinetic model of DNA double-strand break repair in primary human fibroblasts exposed to low-LET irradiation with various dose rates
     Computer Research and Modeling, 2015, v. 7, no. 1, pp. 159-176

     Here we demonstrate the results of kinetic modeilng of DNA double-strand breaks induction and repair and phosphorilated histone H2AX ($\gamma$-H2AX) and Rad51 foci formation in primary human fibroblasts exposed to low-LET ionizing radiation (IR). The model describes two major paths of DNA double-strand breaks repair: non-homologous end joining (NHEJ) and homologous recombination (HR) and considers interactions between DNA and several repair proteins (DNA-PKcs, ATM, Ku70/80, XRCC1, XRCC4, Rad51, RPA, etc.) using mass action equations and Michaelis–Menten kinetics. Experimental data on DNA rejoining kinetics and $\gamma$-H2AX and Rad51 foci formation in vicinity of double strand breaks in primary human fibroblasts exposed to low-LET IR with various dose rates and exposure times was utilized for training and statistical validation of the model.

     Keywords: DNA double-strand breaks, DNA repair, kinetic modeling, low-LET ionizing radiation, dose rate.
     Views (last year): 4. Citations: 3 (RSCI).
344. Zenkov A.V.
     Deviation from Benford’s law and identification of author peculiarities in texts
     Computer Research and Modeling, 2015, v. 7, no. 1, pp. 197-201

     The distribution of the first significant digit in numerals of connected texts is considered. Benford's law is found to hold approximately for them. Deviations from Benford's law are statistically significant author peculiarities that allow, under certain conditions, to distinguish between parts of the text with a different authorship.

     Keywords: Benford’s law, Statistical hypothesis testing, Mann–Whitney U-test.
     Views (last year): 4. Citations: 6 (RSCI).
345. Levchenko E.A., Trifonov A.Y., Shapovalov A.V.
     Semiclassical approximation for the nonlocal multidimensional Fisher–Kolmogorov–Petrovskii–Piskunov equation
     Computer Research and Modeling, 2015, v. 7, no. 2, pp. 205-219

     Semiclassical asymptotic solutions with accuracy $O(D^{N/2})$, $N\geqslant3$ are constructed for the multidimensional Fisher–Kolmogorov–Petrovskii–Piskunov equation in the class of trajectory-concentrated functions. Using the symmetry operators a countable set of asymptotic solutions with accuracy $O(D^{3/2})$ is obtained. Asymptotic solutions of two-dimensional Fisher–Kolmogorov–Petrovskii–Piskunov equation are found in explicit
     form.

     Keywords: nonlocal Fisher–Kolmogorov–Petrovskii–Piskunov equation, asymptotic solution, Einstein— Ehrenfest system.
     Views (last year): 4.
346. Kolobov A.V., Kuznetsov M.B.
     Mathematical modeling of low invasive tumor growth with account of inactivation of vascular endothelial growth factor by antiangiogenic drug
     Computer Research and Modeling, 2015, v. 7, no. 2, pp. 361-374

     A mathematical model of tumor growth in tissue taking into account angiogenesis and antiangiogenic therapy is developed. In the model the convective flows in tissue are considered as well as individual motility of tumor cells. It is considered that a cell starts to migrate if the nutrient concentration falls lower than the critical level and returns into proliferation in the region with high nutrient concentration. Malignant cells in the state of metabolic stress produce vascular endothelial growth factor (VEGF), stimulating tumor angiogenesis, which increases the nutrient supply. In this work an antiangiogenic drug which bounds irreversibly to VEGF, converting it to inactive form, is modeled. Numerical analysis of influence of antiangiogenic drug concentration and efficiency on tumor rate of growth and structure is performed. It is shown that antiangiogenic therapy can decrease the growth of low-invasive tumor, but is not able to stop it completely.

     Keywords: mathematical modeling, tumor, VEGF, antiangiogenic therapy.
     Views (last year): 4. Citations: 1 (RSCI).
347. Khoruzhnikov S.E., Grudinin V.A., Sadov O.L., Shevel A.Y., Kairkanov A.B.
     Preliminary study of big data transfer over computer network
     Computer Research and Modeling, 2015, v. 7, no. 3, pp. 421-427

     The transfer of Big Data over computer network is important and unavoidable operation in the past, now and in any feasible future. There are a number of methods to transfer the data over computer global network (Internet) with a range of tools. In this paper the transfer of one piece of Big Data from one point in the Internet to another point in Internet in general over long range distance: many thousands kilometers. Several free of charge systems to transfer the Big Data are analyzed here. The most important architecture features are emphasized and suggested idea to add SDN Openflow protocol technique for fine tuning the data transfer over several parallel data links.

     Keywords: data, Linux, transfer, SDN, Openflow, network.
     Views (last year): 4.
348. Cheremisina E.N., Senner A.E.
     The use of GIS INTEGRO in searching tasks for oil and gas deposits
     Computer Research and Modeling, 2015, v. 7, no. 3, pp. 439-444

     GIS INTEGRO is the geo-information software system forming the basis for the integrated interpretation of geophysical data in researching a deep structure of Earth. GIS INTEGRO combines a variety of computational and analytical applications for the solution of geological and geophysical problems. It includes various interfaces that allow you to change the form of representation of data (raster, vector, regular and irregular network of observations), the conversion unit of map projections, application blocks, including block integrated data analysis and decision prognostic and diagnostic tasks.

     The methodological approach is based on integration and integrated analysis of geophysical data on regional profiles, geophysical potential fields and additional geological information on the study area. Analytical support includes packages transformations, filtering, statistical processing, calculation, finding of lineaments, solving direct and inverse tasks, integration of geographic information.

     Technology and software and analytical support was tested in solving problems tectonic zoning in scale 1:200000, 1:1000000 in Yakutia, Kazakhstan, Rostov region, studying the deep structure of regional profiles 1:S, 1-SC, 2-SAT, 3-SAT and 2-DV, oil and gas forecast in the regions of Eastern Siberia, Brazil.

     The article describes two possible approaches of parallel calculations for data processing 2D or 3D nets in the field of geophysical research. As an example presented realization in the environment of GRID of the application software ZondGeoStat (statistical sensing), which create 3D net model on the basis of data 2d net. The experience has demonstrated the high efficiency of the use of environment of GRID during realization of calculations in field of geophysical researches.

     Keywords: parallel calculations, GRID, geophysical research, data processing, 3D net model, GIS INTEGRO, ZondGeoStat.
     Views (last year): 4.
349. Bogdanov A.V., Gankevich I.G., Gayduchok V.Yu., Yuzhanin N.V.
     Running applications on a hybrid cluster
     Computer Research and Modeling, 2015, v. 7, no. 3, pp. 475-483

     A hybrid cluster implies the use of computational devices with radically different architectures. Usually, these are conventional CPU architecture (e.g. x86_64) and GPU architecture (e. g. NVIDIA CUDA). Creating and exploiting such a cluster requires some experience: in order to harness all computational power of the described system and get substantial speedup for computational tasks many factors should be taken into account. These factors consist of hardware characteristics (e.g. network infrastructure, a type of data storage, GPU architecture) as well as software stack (e.g. MPI implementation, GPGPU libraries). So, in order to run scientific applications GPU capabilities, software features, task size and other factors should be considered.

     This report discusses opportunities and problems of hybrid computations. Some statistics from tests programs and applications runs will be demonstrated. The main focus of interest is open source applications (e. g. OpenFOAM) that support GPGPU (with some parts rewritten to use GPGPU directly or by replacing libraries).

     There are several approaches to organize heterogeneous computations for different GPU architectures out of which CUDA library and OpenCL framework are compared. CUDA library is becoming quite typical for hybrid systems with NVIDIA cards, but OpenCL offers portability opportunities which can be a determinant factor when choosing framework for development. We also put emphasis on multi-GPU systems that are often used to build hybrid clusters. Calculations were performed on a hybrid cluster of SPbU computing center.

     Keywords: GPGPU, HPC, computational clusters, OpenFOAM, LINPACK, ViennaCL, CUDA, OpenCL.
     Views (last year): 4.
350. Minkin A.S., Knizhnik A.A., Potapkin B.V.
     OpenCL realization of some many-body potentials
     Computer Research and Modeling, 2015, v. 7, no. 3, pp. 549-558

     Modeling of carbon nanostructures by means of classical molecular dynamics requires a lot of computations. One of the ways to improve the performance of basic algorithms is to transform them for running on SIMD-type computing systems such as systems with dedicated GPU. In this work we describe the development of algorithms for computation of many-body interaction based on Tersoff and embedded-atom potentials by means of OpenCL technology. OpenCL standard provides universality and portability of the algorithms and can be successfully used for development of the software for heterogeneous computing systems. The performance of algorithms is evaluated on CPU and GPU hardware platforms. It is shown that concurrent memory writes is effective for Tersoff bond order potential. The same approach for embedded-atom potential is shown to be slower than algorithm without concurrent memory access. Performance evaluation shows a significant GPU acceleration of energy-force evaluation algorithms for many-body potentials in comparison to the corresponding serial implementations.

     Keywords: GPGPU, OpenCL, many-body potentials, Tersoff potential, embedded-atom potential, atomic operations.
     Views (last year): 4. Citations: 1 (RSCI).

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