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Volume 15   Issue 1   Year 2020
Investigation of DNA Breather Dynamics in A Model with Non-Local Inter-Site Interaction

Geraskin E.I.1, Lakhno V.D.2, Chetverikov A.P.1, Shigaev A.S.2

1Saratov National Research State University n.a. N.G. Chernyshevsky, Saratov, Russia
2Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia

Abstract. A variant of the Peyrard-Bishop-Dauxois model is proposed, which takes account of the partially delocalized nature of DNA stacking interactions. It is shown that the nonlocal nature of the inter-site potential can lead to an increase in the local cooperativity of the base pairs' opening an increasing in the number of simultaneously opening adjacent nucleotide pairs during the denaturation bubble's nucleation. The process of the formation and propagation of mobile breathers excited by the initial displacements of a number of nucleotide pairs has been studied. It is revealed that taking account of the non-local coupling in the Peyrard-Bishop-Dauxois model, while maintaining the remaining parameters of the model, leads to a decrease in the speed of the mobile breather and an increase in the probability of nucleation of the denaturation bubble.

Key words: DNA, mobile breather, stacking interactions, denaturation bubble, nucleation, Peyrard-Bishop-Dauxois model.

 

Table of Contents Original Article
Math. Biol. Bioinf.
2020;15(1):93-105
doi: 10.17537/2020.15.93
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 

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