Most cited papers (RSCI)

21. Bratsun D.A.
    Effect of subcritical excitation of oscillations in stochastic systems with time delay. Part I. Regulation of gene expression
    Computer Research and Modeling, 2011, v. 3, no. 4, pp. 421-438

    We study excitation of oscillations in the stochastic gene systems with time-delayed feedback loop during transcription. The oscillations arise due to interaction noise and time delay even when deterministic counterpart of the system exhibits stationary behaviour. This effect becomes important when degree-of-freedom of a system is not high, and role of fluctuations becomes principal. The analytical solution of master-equation is obtained. The results of numerical simulations are presented.

    Keywords: time-delay, stochastic systems, oscillations, gene regulation.
    Views (last year): 6. Citations: 12 (RSCI).
22. Vorontsov K.V., Potapenko A.A.
    Regularization, robustness and sparsity of probabilistic topic models
    Computer Research and Modeling, 2012, v. 4, no. 4, pp. 693-706

    We propose a generalized probabilistic topic model of text corpora which can incorporate heuristics of Bayesian regularization, sampling, frequent parameters update, and robustness in any combinations. Wellknown models PLSA, LDA, CVB0, SWB, and many others can be considered as special cases of the proposed broad family of models. We propose the robust PLSA model and show that it is more sparse and performs better that regularized models like LDA.

    Keywords: text analysis, topic modeling, probabilistic latent semantic analysis, EM-algorithm, latent Dirichlet allocation, Gibbs sampling, Bayesian regularization, perplexity, robusteness.
    Views (last year): 25. Citations: 12 (RSCI).
23. Trifonov S.V., Kholodov Y.A.
    Study and optimization of wireless sensor network based on ZigBee protocol
    Computer Research and Modeling, 2012, v. 4, no. 4, pp. 855-869

    Algorithms of wireless sensor networks operation based on modified ZigBee/IEEE 802.15.4 protocol stack and problems of energy saving with simultaneous decrease of network latency are studied. Theoretical computations are given. Roles distribution and routers schedule assignment algorithms are described. Both results of experiments carried out with real devices and results of simulations with ns-2 (open-source network simulator) are given and analyzed.

    Keywords: sensor network, wireless network, ZigBee, IEEE 802.15.4, discrete-event simulation, optimal schedule.
    Views (last year): 5. Citations: 12 (RSCI).
24. Bratsun D.A., Zakharov A.P., Pismen L.M.
    Multiscale mathematical modeling occurrence and growth of a tumour in an epithelial tissue
    Computer Research and Modeling, 2014, v. 6, no. 4, pp. 585-604

    In this paper we propose a mathematical model of cancer tumour occurrence in a quasi twodimensional epithelial tissue. Basic model of the epithelium growth describes the appearance of intensive movement and growth of tissue when it is damaged. The model includes the effects of division of cells and intercalation. It is assumed that the movement of cells is caused by the wave of mitogen-activated protein kinase (MAPK), which in turn activated by the chemo-mechanical signal propagating along tissue due to its local damage. In this paper it is assumed that cancer cells arise from local failure of spatial synchronization of circadian rhythms. The study of the evolutionary dynamics of the model could determine the chemo-physical properties of a tumour, and spatial relationship between the occurrence of cancer cells and development of the entire tissue parameters coordinating its evolution through the exchange of chemical and mechanical signals.

    Keywords: mathematical modeling, cancer growth, circadian rhythms, gene regulation, synchronization, complex systems.
    Views (last year): 10. Citations: 12 (RSCI).
25. Parovik R.I.
    Mathematical modeling of oscillator hereditarity
    Computer Research and Modeling, 2015, v. 7, no. 5, pp. 1001-1021

    The paper considers hereditarity oscillator which is characterized by oscillation equation with derivatives of fractional order $\beta$ and $\gamma$, which are defined in terms of Gerasimova-Caputo. Using Laplace transform were obtained analytical solutions and the Green’s function, which are determined through special functions of Mittag-Leffler and Wright generalized function. It is proved that for fixed values of $\beta = 2$ and $\gamma = 1$, the solution found becomes the classical solution for a harmonic oscillator. According to the obtained solutions were built calculated curves and the phase trajectories hereditarity oscillatory process. It was found that in the case of an external periodic influence on hereditarity oscillator may occur effects inherent in classical nonlinear oscillators.

    Keywords: hereditarity, fractal oscillator, generalized function Wright, phase trajectories, resonance.
    Views (last year): 4. Citations: 12 (RSCI).
26. Karavaev A.S., Kopysov S.P.
    The method of unstructured hexahedral mesh generation from volumetric data
    Computer Research and Modeling, 2013, v. 5, no. 1, pp. 11-24

    The method of conversion of surface representation to the voxel data is developed. Voxel data based algorithm of hexahedral mesh generation is proposed.

    Keywords: hexahedral mesh, volumetric data, voxel, signed distance fields, dual contouring.
    Views (last year): 4. Citations: 11 (RSCI).
27. Kuz'min I.M., Tonkov L.E., Kopysov S.P.
    Algorithms and Software for Solving Coupled Fluid-Structure Interaction Problems on Hybrid HPC Platform
    Computer Research and Modeling, 2013, v. 5, no. 2, pp. 153-164

    In this paper, we propose a new software for simulation of fluid-structure interaction. The software is designed for solving coupled problems and provides an interface for synchronization synchronisation and data exchange between existing fluid and structural solvers. Algorithms of coupling solvers and mesh deformation are discussed. The software can be used on hybrid CPU/GPU platforms.

    Keywords: fluid-structure interaction, parallel computing, hybrid HPC platforms, computational mesh deformation, radial basic function.
    Views (last year): 1. Citations: 11 (RSCI).
28. Zenyuk D.A., Malinetsky G.G., Faller D.S.
    Simulation of corruption in hierarchical systems
    Computer Research and Modeling, 2014, v. 6, no. 2, pp. 321-329

    Simulation model of corruption in hierarchical systems which takes into account individual strategies of elements and collective behavior of large groups is proposed. Evolution of various characteristics like level of corruption or ratio of corrupted elements and their dependence on external parameters are discussed. The effectiveness of various anticorruptional strategies is examined by means of numeric analysis.

    Keywords: corruption, stochastic simulation, corporation management, graph theory, self-organization, social systems.
    Views (last year): 8. Citations: 11 (RSCI).
29. Baranov A.V., Korenkov V.V., Yurchenko V.V., Balashov N.A., Kutovskiy N.A., Semenov R.N., Svistunov S.Y.
    Approaches to cloud infrastructures integration
    Computer Research and Modeling, 2016, v. 8, no. 3, pp. 583-590

    One of the important direction of cloud technologies development nowadays is a creation of methods for integration of various cloud infrastructures. An actuality of such direction in academic field is caused by a frequent lack of own computing resources and a necessity to attract additional ones. This article is dedicated to existing approaches to cloud infrastructures integration with each other: federations and so called ‘cloud bursting’. A ‘federation’ in terms of OpenNebula cloud platform is built on a ‘one master zone and several slave ones’ schema. A term ‘zone’ means a separate cloud infrastructure in the federation. All zones in such kind of integration have a common database of users and the whole federation is managed via master zone only. Such approach is most suitable for a case when cloud infrastructures of geographically distributed branches of a single organization need to be integrated. But due to its high centralization it's not appropriate when one needs to join cloud infrastructures of different organizations. Moreover it's not acceptable at all in case of clouds based on different software platforms. A model of federative integration implemented in EGI Federated Cloud allows to connect clouds based on different software platforms but it requires a deployment of sufficient amount of additional services which are specific for EGI Federated Cloud only. It makes such approach is one-purpose and uncommon one. A ‘cloud bursting’ model has no limitations listed above but in case of OpenNebula platform what the Laboratory of Information Technologies of Joint Institute for Nuclear Research (LIT JINR) cloud infrastructure is based on such model was implemented for an integration with a certain set of commercial cloud resources providers. Taking into account an article authors’ experience in joining clouds of organizations they represent as well as with EGI Federation Cloud a ‘cloud bursting’ driver was developed by LIT JINR cloud team for OpenNebula-based clouds integration with each other as well as with OpenStack-based ones. The driver's architecture, technologies and protocols it relies on and an experience of its usage are described in the article.

    Keywords: cloud computing, integration, EGI Federated Cloud, OpenNebula, OpenStack, cloud bursting.
    Views (last year): 6. Citations: 11 (RSCI).
30. Korolev S.A., Maykov D.V.
    Identification of a mathematical model and research of the various modes of methanogenesis in mesophilic environments
    Computer Research and Modeling, 2012, v. 4, no. 1, pp. 131-141

    A mathematical model for the production of biogas from animal waste was developed. An algorithm for identification of model parameters was developed. The accuracy of model identification was performed. The result of simulation for batch and continuous modes of supply of substrate was shown. The optimum flow rate of the substrate for continuous operation was found.

    Keywords: methanogenesis, biogas, mathematical model, set of ordinary differential equations, identification of mathematical model, genetic algorithm.
    Views (last year): 10. Citations: 10 (RSCI).

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