Most viewed papers

461. Komarov A.S.
     Models of plant succession and soil dynamics at climate changes
     Computer Research and Modeling, 2009, v. 1, no. 4, pp. 405-413

     Main theoretical considerations of dynamical changes of forest vegetation are discussed. It is shown that vegetation dynamics (succession) and soil dynamics are linked, and common dynamics is a result of biological turnover of nutrition elements. Main modelling approaches are examined and unsolved problems are formulated. An example of computer experiment on comparison of forest growth at stationary and global warming scenario is considered.

     Keywords: succession, soil dynamics.
     Views (last year): 2. Citations: 9 (RSCI).
462. Mamonov P.A., Krasilnikov P.M., Knox P.P., Rubin A.B.
     Modelling of conformational change within photosynthetic reaction center of Rb. sphaeroides bacteria
     Computer Research and Modeling, 2009, v. 1, no. 4, pp. 437-448

     A possible conformational change, which accompanies electron tranport in Rb. sphaeroides photosynthetic reaction center (RC), was studied using quantum-chemical approach. A kinetic model which takes into account two conformational states of RC is proposed. The model quantitatively describes experimental temperature dependencies of recombination reaction rate P⁺Q_A^- → PQ_A. Quantum-chemical modeling of primary quinone (Q_A) binding site permits one to propose a minor shift of Q_A as a conformational change of interest. The shift is accompanied by break of a hydrogen bond between 4–C=O group of Q_A and histidine M²¹⁹, and formation of a new hydrogen bond between Q_A and hydroxyl group of threonine M²²². Characteristics of this conformational change were obtained from quantum-chemical calculations and match parameters of kinetic model in qualitative fashion.

     Keywords: Rhodobacter sphaeroides, photosynthetic reaction center, conformational change, reaction of recombination.
     Views (last year): 2.
463. Fialko N.S.
     Mixed algorithm for modeling of charge transfer in DNA on long time intervals
     Computer Research and Modeling, 2010, v. 2, no. 1, pp. 63-72

     Charge transfer in DNA is simulated by a discrete Holstein model «quantum particle + classical site chain + interaction». Thermostat temperature is taken into account as stochastic force, which acts on classical sites (Langevin equation). Thus dynamics of charge migration along the chain is described by ODE system with stochastic right-hand side. To integrate the system numerically, algorithms of order 1 or 2 are usually applied. We developed «mixed» algorithm having 4th order of accuracy for fast «quantum» variables (note that in quantum subsystem the condition «sum of probabilities of charge being on site is time-constant» must be held), and 2nd order for slow classical variables, which are affecting by stochastic force. The algorithm allows us to calculate trajectories on longer time intervals as compared to standard algorithms. Model calculations of polaron disruption in homogeneous chain caused by temperature fluctuations are given as an example.

     Keywords: DNA, Holstein model, Langevin equation, integration algorithm for ODE with stochastic right-hand side.
     Views (last year): 2. Citations: 2 (RSCI).
464. Kondratyev M.S., Kabanov A.V., Komarov V.M.
     Modeling of helix formation in peptides containing aspartic and glutamic residues
     Computer Research and Modeling, 2010, v. 2, no. 1, pp. 83-90

     In present work we used the methods of molecular dynamics simulations and quantum chemistry to study the concept, according to which aspartic and glutamic residues play a key role in initiation of helix formation in oligopeptides. It has been shown, that the first turn of the alpha-helix can be organized from various amino acid sequences with Asp and Glu residues on the N-terminus. Thermodynamic properties of such a process were analyzed. The obtained results do not interfere with known experimental and statistical data and they substantially elaborate present views on the processes of early peptide folding stages.

     Keywords: alpha-helix, amino acids, molecular dynamics simulation, quantum chemistry, H-bonding.
     Views (last year): 2. Citations: 4 (RSCI).
465. Sobolev O.V., Lunina N.L., Lunin V.Yu.
     The use of cluster analysis methods for the study of a set of feasible solutions of the phase problem in biological crystallography
     Computer Research and Modeling, 2010, v. 2, no. 1, pp. 91-101

     X-ray diffraction experiment allows determining of magnitudes of complex coefficients in the decomposition of the studied electron density distribution into Fourier series. The determination of the lost in the experiment phase values poses the central problem of the method, namely the phase problem. Some methods for solving of the phase problem result in a set of feasible solutions. Cluster analysis method may be used to investigate the composition of this set and to extract one or several typical solutions. An essential feature of the approach is the estimation of the closeness of two solutions by the map correlation between two aligned Fourier syntheses calculated with the use of phase sets under comparison. An interactive computer program ClanGR was designed to perform this analysis.

     Keywords: biological crystallography, phase problem, cluster analysis.
     Views (last year): 2.
466. Rezaev R.O., Trifonov A.Y., Shapovalov A.V.
     The Einstein−Ehrenfest system of (0, M)-type and asymptotical solutions of the multidimensional nonlinear Fokker−Planck−Kolmogorov equation
     Computer Research and Modeling, 2010, v. 2, no. 2, pp. 151-160

     Semiclassical approximation formalism is developed for the multidimensional Fokker–Planck–Kolmogorov equation with non-local and nonlinear drift vector with respect to a small diffusion coefficient D, D→0, in the class of trajectory concentrated functions. The Einstein−Ehrenfest system of (0, M)-type is obtained. A family of semiclassical solutions localized around a point driven by the Einstein−Ehrenfest system accurate to O(D^(M+1)/2) is found.

     Keywords: nonlinear Fokker−Planck−Kolmogorov equation, semiclassical asymptotics, WKB-Maslov method, Einstein−Ehrenfest system.
     Views (last year): 2.
467. Dzhoraev A.R.
     GPU-accelerated hybrid systems for high-performance computing in bio-informatics
     Computer Research and Modeling, 2010, v. 2, no. 2, pp. 163-167

     Modern GPUs are massively-parallel processors, offering substantial amount of computational power in energy-efficient package. We discuss the benefits of utilizing this computing power for modeling problems in bio-informatics, such as molecular dynamics, quantum chemistry and sequence analysis.

     Keywords: GPU, bioinformatics, molecular dynamics, quantum chemistry, sequence analysis.
     Views (last year): 2. Citations: 6 (RSCI).
468. Samarin V.V.
     Mathematical modeling of dinuclear systems in low energy nuclear reactions
     Computer Research and Modeling, 2010, v. 2, no. 4, pp. 385-392

     Numerical methods of obtaining collective and one-particle states were used for the quantum description of two-nuclear systems behavior at the initial stage of near-barrier heavy nuclei fusion. The collective exited states in such systems represent concordant oscillations of surfaces of spherical nuclei. The one-particle states of the external neutrons are similar to the states of valence electrons of diatomic molecules.

     Keywords: two-nuclei systems, methods of Schrödinger equation solving.
     Views (last year): 2.
469. 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).
470. 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).

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