The dynamics of polynucleotide chain consisting of two different homogeneous sequences, divided by interface

Grinevich A.A., Ryasik A.A., Yakushevich L.V.
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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
Citation in English: 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, vol. 5, no. 2, pp. 241-253
Citation in English: 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, vol. 5, no. 2, pp. 241-253
DOI: 10.20537/2076-7633-2013-5-2-241-253
URL: http://crm-en.ics.org.ru/journal/article/2017/
Creative Commons License This work is licensed under a Creative Commons Attribution-NoDerivs 3.0 Unported License.
According to Crossref, this article is cited by:
  • Andrei Anatolevich Grinevich, Artem Andreevich Ryasik, L. V. Yakushevich. Motion of DNA open states influenced by random force. // Computer Research and Modeling. — 2015. — V. 7, no. 6. — P. 1295. DOI: 10.20537/2076-7633-2015-7-6-1295-1307
  • L. A. Krasnobaeva, L. V. Yakushevich. Rotational dynamics of bases in the gene coding interferon alpha 17 (IFNA17). // Journal of Bioinformatics and Computational Biology. — 2015. — V. 13, no. 01. — P. 1540002. DOI: 10.1142/S0219720015400028
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