Solitons in a double pendulums chain model, and DNA roto-torsional dynamics

DOI10.2991/JNMP.2007.14.1.10MaRDI QIDQ3607644zbMATHOpenAlexFDO

Authors Roberto De Leo, Giuseppe Gaeta, Mariano Cadoni

Publication date 26 February 2009

Published in Journal of Nonlinear Mathematical Physics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/q-bio/0604027

zbMATH Keywords

solitonsDNA dynamicsdouble pendulumnon-linear coupled equations

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Dynamical systems in biology (37N25) Soliton equations (35Q51)

Abstract: It was first suggested by Englander et al to model the nonlinear dynamics of DNA relevant to the transcription process in terms of a chain of coupled pendulums. In a related paper [q-bio.BM/0604014] we argued for the advantages of an extension of this approach based on considering a chain of double pendulums with certain characteristics. Here we study a simplified model of this kind, focusing on its general features and nonlinear travelling wave excitations; in particular, we show that some of the degrees of freedom are actually slaved to others, allowing for an effective reduction of the relevant equations.

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• Soliton excitations in an inhomogeneous DNA molecular chain
• Solitary waves in helicoidal models of DNA dynamics

Cites work

• scientific article; zbMATH DE number 1258146 (Why is no real title available?)
• Nonlinear DNA dynamics: Hierarchy of the models
• Nonlinear dynamics and statistical physics of DNA
• Solitons in Molecular Systems
• Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential
• Solitons in a nonlinear DNA model

Cited in

(8)

• Carleman estimate for wave equations coupled with the second order terms
• Lie symmetry analysis of a stochastic gene evolution in double-chain deoxyribonucleic acid system
• Propagation of twist solitons in fully inhomogeneous DNA chains
• Solitary waves in helicoidal models of DNA dynamics
• Nonlinear dynamics of DNA chain
• Speed selection for coupled wave equations
• Stationary solitary and kink solutions in the helicoidal Peyrard-Bishop model of DNA molecule
• Sine-Gordon solitons, auxiliary fields and singular limit of a double pendulums chain

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