Abstract:
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).
Citation:
A. A. Grinevich, A. A. Ryasik, L. V. Yakushevich, “The dynamics of polynucleotide chain consisting of two different homogeneous sequences, divided by interface”, Computer Research and Modeling, 5:2 (2013), 241–253
\Bibitem{GriRyaYak13}
\by A.~A.~Grinevich, A.~A.~Ryasik, L.~V.~Yakushevich
\paper The dynamics of polynucleotide chain consisting of two different homogeneous sequences, divided by interface
\jour Computer Research and Modeling
\yr 2013
\vol 5
\issue 2
\pages 241--253
\mathnet{http://mi.mathnet.ru/crm396}
\crossref{https://doi.org/10.20537/2076-7633-2013-5-2-241-253}
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https://www.mathnet.ru/eng/crm396
https://www.mathnet.ru/eng/crm/v5/i2/p241
This publication is cited in the following 4 articles:
Ludmila V. Yakushevich, Larisa A. Krasnobaeva, “Ideas and methods of nonlinear mathematics and theoretical physics in DNA science: the McLaughlin-Scott equation and its application to study the DNA open state dynamics”, Biophys Rev, 13:3 (2021), 315
L. V. Yakushevich, L. A. Krasnobaeva, “Plasmid pBR322 and nonlinear conformational distortions (kinks)”, Mat. Biolog. Bioinform., –
A. A. Grinevich, A. A. Ryasik, L. V. Yakushevich, “Dvizhenie otkrytykh sostoyanii DNK pod deistviem sluchainoi sily”, Kompyuternye issledovaniya i modelirovanie, 7:6 (2015), 1295–1307
L. A. Krasnobaeva, L. V. Yakushevich, “Rotational dynamics of bases in the gene coding interferon alpha 17 (IFNA17)”, J. Bioinform. Comput. Biol., 13:01 (2015), 1540002
Citation in format AMSBIB
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