Most cited papers (RSCI)

231. Mokin A.Y.
     On spectral properties of a nonselfadjoint difference operator
     Computer Research and Modeling, 2010, v. 2, no. 2, pp. 143-150

     The eigenvalue problem for a nonselfadjoint difference operator with nonconstant coefficient is considered. The main peculiarity of the problem is that its solution satisfies a two-point nonlocal boundary condition. Multiplicity of eigenvalues is discussed and a region where all eigenvalues reside is defined taking into account a very generic assumption about the nonconstant coefficient.

     Keywords: eigenvalue problem, nonselfadjoint difference operator.
     Views (last year): 1. Citations: 2 (RSCI).
232. Asylbaev N.A.
     Mathematical modeling of steppe fires
     Computer Research and Modeling, 2010, v. 2, no. 4, pp. 377-384

     We consider the two-dimensional mathematical model of wildfire. Numerical solution algorithm based on the method of large particles was developed for this model.

     Keywords: modeling, steppe fires.
     Views (last year): 3. Citations: 2 (RSCI).
233. Potapov I.S., Volkov E.I.
     Dynamics analysis of coupled synthetic genetic repressilators
     Computer Research and Modeling, 2010, v. 2, no. 4, pp. 403-418

     We have investigated dynamics of synthetic genetic oscillators — repressilators — coupled through autoinducer diffusion. The model of the system with phase-repulsive coupling structure is under consideration. We have examined emergence of periodic regimes, stable inhomogeneous steady states depending on the main systems’ parameters: coupling strength and maximal transcription rate. It has been shown that autoinducer production module added to the isolated repressilator cause the limit cycle to disappear through infinite period bifurcation for sufficiently large transcription rate. We have found hysteresis of limit cycle and stable steady state the size of which is determined by ratio between mRNA and protein lifetimes. Two coupled oscillators system demonstrates stable anti-phase oscillations which can become a chaotic regime through invariant torus emergence or via Feigenbaum scenario.

     Keywords: oscillator, genetic circuit, autoinducer, bifurcation analysis.
     Views (last year): 2. Citations: 2 (RSCI).
234. Nechipurenko Y.D., Nechipurenko D.Y., Il’icheva I.A., Golovkin M.V., Panchenko L.A., Polozov R.V., Grokhovsky S.L.
     DNA conformational dynamics: approach to the physical mapping of genome
     Computer Research and Modeling, 2010, v. 2, no. 4, pp. 419-428

     Recently we have developed a new method for studying DNA based on ultrasound - induced cleavage of DNA sugar-phosphate backbone. Relative cleavage rates of the phosphodiester bonds in all 16 dinucleotides have been determined. The increased amount of data sampling (of more than 20 000 nucleotides) made it also possible to obtain cleavage rates in all 256 possible tetranucleotides. These values quantitatively characterize sequence effects on conformational dynamics of DNA sugar phosphate backbone. Same type of DNA heterogeneity have been discovered and studied using its chemical cleavage induced by various chemical agents and DNAse I. The presence of essential heterogeneity in structural properties of DNA might be a key for physical mapping of the genomes, i.e. determining the structural profiles being responsible for DNA recognition by gene expression regulation machinery.

     Keywords: ultrasonic cleavage of DNA, sequence effects on DNA structure, DNA flexibility, d(CpG) dinucleotide.
     Views (last year): 2. Citations: 2 (RSCI).
235. Novikov O.A., Rovenska O.G.
     Approximation of the periodical functions of hight smoothness by the right-angled
     linear methods
     Computer Research and Modeling, 2011, v. 3, no. 3, pp. 255-264

     We obtain asymptotic equalities for upper bounds of the deviations of the right-angled de la Vallee Poussin sums taken over classes of periodical functions of two variables of high smoothness. These equalities guarantee the solvability of the Kolmogorov–Nikol’skii problem for the right-angled de la Vallee Poussin sums on the specified classes of functions.

     Keywords: (ψ, β)-derivative, the right-angled de la Vallee Poussin sums, Kolmogorov–Nikol'skiy problem.
     Citations: 2 (RSCI).
236. Zhmurov A.A., Barsegov V.A., Trifonov S.V., Kholodov Y.A., Kholodov A.S.
     Efficient Pseudorandom number generators for biomolecular simulations on graphics processors
     Computer Research and Modeling, 2011, v. 3, no. 3, pp. 287-308

     Langevin Dynamics, Monte Carlo, and all-atom Molecular Dynamics simulations in implicit solvent require a reliable source of pseudorandom numbers generated at each step of calculation. We present the two main approaches for implementation of pseudorandom number generators on a GPU. In the first approach, inherent in CPU-based calculations, one PRNG produces a stream of pseudorandom numbers in each thread of execution, whereas the second approach builds on the ability of different threads to communicate, thus, sharing random seeds across the entire device. We exemplify the use of these approaches through the development of Ran2, Hybrid Taus, and Lagged Fibonacci algorithms. As an application-based test of randomness, we carry out LD simulations of N independent harmonic oscillators coupled to a stochastic thermostat. This model allows us to assess statistical quality of pseudorandom numbers. We also profile performance of these generators in terms of the computational time, memory usage, and the speedup factor (CPU/GPU time).

     Keywords: GPU, pseudorandom numbers, PRNG, biomolecules.
     Views (last year): 11. Citations: 2 (RSCI).
237. Yakushevich L.V.
     Biomechanics of DNA: rotational oscillations of bases
     Computer Research and Modeling, 2011, v. 3, no. 3, pp. 319-328

     In this paper we study the rotational oscillations of the nitrous bases forming a central pair in a short DNA fragment consisting of three base pairs. A simple mechanical analog of the fragment where the bases are imitated by pendulums and the interactions between pendulums — by springs, has been constructed. We derived Lagrangian of the model system and the nonlinear equations of motions. We found solutions in the homogeneous case when the fragment considered consists of identical base pairs: Adenine-Thymine (AT- pair) or Guanine-Cytosine (GC-pair). The trajectories of the model system in the configuration space were also constructed.

     Keywords: DNA, modeling, rotational oscillations of bases.
     Views (last year): 3. Citations: 2 (RSCI).
238. Gorshenin A.K.
     On application of the asymptotic tests for estimating the number of mixture distribution components
     Computer Research and Modeling, 2012, v. 4, no. 1, pp. 45-53

     The paper demonstrates the efficiency of asymptotically most powerful test of statistical hypotheses about the number of mixture components in the adding and splitting component models. Test data are the samples from different finite normal mixtures. The results are compared for various significance levels and weights.

     Keywords: finite mixture of normal distributions, asymptotically most powerful test.
     Views (last year): 1. Citations: 2 (RSCI).
239. Budak V.P., Zheltov V.S., Kalakutsky T.K.
     Local estimations of Monte Carlo method with the object spectral representation in the solution of global illumination
     Computer Research and Modeling, 2012, v. 4, no. 1, pp. 75-84

     The article deals with the local and double local estimation of the Monte Carlo method for solving the equation of global illumination. The local estimation allows calculating the illumination at any point at the approximation of diffuse reflection, whereas the double local estimation allows calculating directly the luminance at a given point in a given direction. The article presents the mathematical basis of local estimations and the basic stages of the software implementation. The representation of three-dimensional objects in the basis of spherical functions and the possibility of using them in the local estimations are also considered.

     Keywords: global illumination, Monte Carlo, local estimation, double local estimation.
     Citations: 2 (RSCI).
240. Dyachenko E.N., Dueck J.G.
     Modeling of sedimentation and filtration layer formation by discrete element method
     Computer Research and Modeling, 2012, v. 4, no. 1, pp. 105-120

     The numerical model of sedimentation and suspension filtration is proposed in this paper. The model is based on dynamic variant of discrete element method. This model represents the particles behavior on microand meso-scales: pores, arches, flocks formation. In addition, the proposed model qualitatively reproduces macro phenomenon: sedimentation of particle layer, slow shrinkage of the layer, sealing of the layer under its own weight of the particles and the external applied force.

     Keywords: sedimentation layer formation, filtration cake consolidation, discrete element method.
     Views (last year): 1. Citations: 2 (RSCI).

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