A composite model for DNA torsion dynamics

Abstract

DNA torsion dynamics is essential in the transcription process; a simple model for it, in reasonable agreement with experimental observations, has been proposed by Yakushevich (Y) and developed by several authors; in this, the DNA subunits made of a nucleoside and the attached nitrogen bases are described by a single degree of freedom. In this paper we propose and investigate, both analytically and numerically, a ``composite'' version of the Y model, in which the nucleoside and the base are described by separate degrees of freedom. The model proposed here contains as a particular case the Y model and shares with it many features and results, but represents an improvement from both the conceptual and the phenomenological point of view. It provides a more realistic description of DNA and possibly a justification for the use of models which consider the DNA chain as uniform. It shows that the existence of solitons is a generic feature of the underlying nonlinear dynamics and is to a large extent independent of the detailed modelling of DNA. The model we consider supports solitonic solutions, qualitatively and quantitatively very similar to the Y solitons, in a fully realistic range of all the physical parameters characterizing the DNA.

29 pages

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Cited by in corpus (17)

• Physics of base-pairing dynamics in DNA
• Heat conductivity of DNA double helix
• Soliton-like base pair opening in a helicoidal DNA: An analogy with helimagnet and cholesterics
• Nonlinear molecular excitations in a completely inhomogeneous DNA chain
• Perturbed soliton-like molecular excitations in a deformed DNA chain
• Theoretical and Experimental Investigations of DNA Open States
• Simple Combined Model for Nonlinear Excitations in DNA
• Solitons in a double pendulums chain model, and DNA roto-torsional dynamics
• Propagation of twist solitons in real DNA chains
• Twist solitons in complex macromolecules: from DNA to polyethylene
• A symmetry breaking mechanism for selecting the speed of relativistic solitons
• Anharmonic stacking in supercoiled DNA
• Sine-Gordon solitons, auxiliary fields, and singular limit of a double pendulums chain
• Coupled Schrödinger equations as a model of interchain excitation transport in the DNA
• Self-organised criticality in base-pair breathing in DNA with a defect
• On the Pseudo-Schrödinger Equation approximation of the Transfer-Integral operator for 1-dimensional DNA models
• Logarithmic Stability for Coefficients Inverse Problem of Coupled Wave Equations