Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential

DOI10.2991/JNMP.2007.14.1.6zbMATH Open1165.35439arXivq-bio/0604004OpenAlexW3099693478MaRDI QIDQ3607640FDOQ3607640

Authors: Giuseppe Gaeta 

Publication date: 26 February 2009

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

Abstract: The Yakushevich (Y) model provides a very simple pictures of DNA torsion dynamics, yet yields remarkably correct predictions on certain physical characteristics of the dynamics. In the standard Y model, the interaction between bases of a pair is modelled by a harmonic potential, which becomes anharmonic when described in terms of the rotation angles; here we substitute to this different types of improved potentials, providing a more physical description of the H-bond mediated interactions between the bases. We focus in particular on soliton solutions; the Y model predicts the correct size of the nonlinear excitations supposed to model the ``transcription bubbles, and this is essentially unchanged with the improved potential. Other features of soliton dynamics, in particular curvature of soliton field configurations and the Peierls-Nabarro barrier, are instead significantly changed.

Full work available at URL: https://arxiv.org/abs/q-bio/0604004

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zbMATH Keywords

DNAPeierls-Nabarro barriersoliton solutionsMorse potentialintrapair potentialYakushevich model

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Oscillation, zeros of solutions, mean value theorems, etc. in context of PDEs (35B05) Soliton equations (35Q51)

Cites Work

• Title not available (Why is that?)
• Solitons in Molecular Systems
• Nonlinear dynamics and statistical physics of DNA
• Nonlinear DNA dynamics: Hierarchy of the models
• Solitons in a nonlinear DNA model

Cited In (9)

• The influence of the DNA torque on the dynamics of transcription bubbles in plasmid PTTQ18
• DNA-RNA transcription as an impact of viscosity
• Solitons in a double pendulums chain model, and DNA roto-torsional dynamics
• Conformational B-A transition in the model of DNA molecule with asymmetric double-well interaction potential of nucleotides
• Numerical analysis of solitons profiles in a composite model for DNA torsion dynamics
• Twist solitons in complex macromolecules: from DNA to polyethylene
• Stationary solitary and kink solutions in the helicoidal Peyrard-Bishop model of DNA molecule
• Dynamic of DNA's possible impact on its damage
• Discrete instability in the DNA double helix

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