Soliton-like excitation in a nonlinear model of DNA dynamics with viscosity

DOI10.3934/MBE.2008.5.205MaRDI QIDQ960589zbMATH OpenOpenAlexWikidataFDO

Authors C. B. Tabi, Alidou Mohamadou, Timoléon C. Kofané

Publication date 28 December 2008

Published in Mathematical Biosciences and Engineering (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://doi.org/10.3934/mbe.2008.5.205

zbMATH Keywords

bubble solitondensity energyDNA dynamicsGinzburg-Landau equationJacobian elliptic functions

Mathematics Subject Classification ID

Elliptic functions and integrals (33E05) Soliton equations (35Q51) KdV equations (Korteweg-de Vries equations) (35Q53) Dynamical systems in fluid mechanics, oceanography and meteorology (37N10) Dynamical systems in biology (37N25) Solitary waves for incompressible inviscid fluids (76B25) Protein sequences, DNA sequences (92D20)

Review text

The study of solitary wave solutions is of prime significance for nonlinear physical systems. The Peyrard-Bishop model for DNA dynamics is generalized specifically to include the difference among bases pairs and viscosity. The small amplitude dynamics of the model is studied analytically and reduced to a discrete complex Ginzburg-Landau (DCGL) equation. Exact solutions of the obtained wave equation are obtained by the mean of the extended Jacobian elliptic function approach. These amplitude solutions are made of bubble solitons. The propagation of a soliton-like excitation in a DNA is then investigated through numerical integration of the motion equations. We show that discreteness can drastically change the soliton shape. The impact of viscosity as well as elasticity on DNA dynamic is also presented. The profile of solitary wave structures as well as the energy which is initially evenly distributed over the lattice are displayed for some fixed parameters.

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• The Impact of Viscosity on the DNA Dynamics
• Solitons in the Peyrard–Bishop model of DNA and the Renormalization Group method
• Base pairs opening and bubble transport in damped DNA dynamics with transport memory effects
• DNA-RNA transcription as an impact of viscosity
• Comprehensive error sensitivity analysis of nonlinear dynamics in DNA denaturation using the PB-DNA model

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