Результаты поиска по 'solitons':
Найдено статей: 14
  1. Grinevich A.A., Ryasik A.A., Yakushevich L.V.
    Motion of DNA open states influenced by random force
    Computer Research and Modeling, 2015, v. 7, no. 6, pp. 1295-1307

    It is known that in the native state the DNA molecule always contains some amount of locally unwound regions, often called the open states of DNA. It is believed that these states play an important role in DNA-protein recognition and that the study of the open states dynamics may shed further light on the mechanisms of regulation of transcription and replication. In this paper we consider the effect of the thermostat on the movement of the open states in the artificial sequence consisting of four homogeneous regions. We construct the energetic profile of the sequence and investigate the trajectories of the movement of the open states under the action of a random force.

    Keywords: DNA open states, solitons, random force.
    Views (last year): 3.
  2. Lakhno V.D., Fialko N.S.
    Mechanism of soliton stopping in a molecular chain without dispersion
    Computer Research and Modeling, 2009, v. 1, no. 1, pp. 93-99

    It is shown by computer simulation that moving soliton-like solution exists in a molecular chain without dispersion. The speed of the solitary wave decreases with time. This decrease can be explained physically due to excitation of sites by moving wave. Maximum wave track length is estimated.

    Keywords: soliton, oscillations, wave propagation.
    Views (last year): 2. Citations: 1 (RSCI).
  3. Grinevich A.A., Ryasik A.A., Yakushevich L.V.
    The dynamics of polynucleotide chain consisting of two different homogeneous sequences, divided by interface
    Computer Research and Modeling, 2013, v. 5, no. 2, pp. 241-253

    To research dynamics of inhomogeneous polynucleotide DNA chain the Y-model with no dissipation term was used. Basing on this model using numerical methods calculations were carried out, which have shown the behaviour of nonlinear conformational excitation (kink), spreading along the inhomogeneous polynucleotide chain, consisting of two different homogeneous nucleotide sequences. As numerical analysis shows there are three ways of behaviour of the nonlinear kink excitation spreading along the DNA chain. After reaching the interface between two homogeneous sequences consisting of different types of bases kink can a) reflect, b) pass the interface with acceleration (increase its velocity), c) pass the interface with deceleration (decrease its velocity).

    Keywords: solitons, DNA, Y-model, sine-Gordon equation, numerical methods.
    Views (last year): 1. Citations: 3 (RSCI).
  4. Tsyganov M.A., Biktashev V.N.
    Soliton and half-soliton interaction of solitary waves in excitable media with non-linear cross-diffusion
    Computer Research and Modeling, 2009, v. 1, no. 1, pp. 109-115

    We have studied properties of non-linear waves in a mathematical model of a predator – prey system with taxis. We demonstrate that, for systems with negative and positive taxis there typically exists a large region in the parameter space, where the waves demonstrate quasi-soliton interaction; colliding waves can penetrate through each other, and waves can also reflect from impermeable boundaries. In this paper, we use numerical simulations to demonstrate also a new wave phenomenon — a half-soliton interaction of waves, when of two colliding waves, one annihilates and the other continues to propagate. We show that this effect depends on the «ages» or, equivalently, «widths» of the colliding waves.

    Keywords: soliton, wave propagation, predator-prey system, cross-diffusion.
    Views (last year): 3.
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