Numerical analysis of solitons profiles in a composite model for DNA to rsion dynamics

TL;DR

This paper numerically analyzes a generalized DNA model that allows independent base movement, demonstrating that solitons are a robust feature of DNA dynamics and improving the model's realism over previous approaches.

Contribution

It introduces a more realistic composite DNA model that supports solitons without unphysical parameters, extending the Yakushevich model's findings.

Findings

Solitons are a generic feature of nonlinear DNA dynamics.

The model supports realistic soliton solutions without unphysical parameters.

The model improves conceptual and phenomenological understanding of DNA behavior.

Abstract

We present the results of our numerical analysis of a "composite" model of DNA which generalizes a well-known elementary torsional model of Yakushevich by allowing bases to move independently from the backbone. The model shares with the Yakushevich model many features and results but it 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. As opposite to the Yakushevich model, where it is needed to use an unphysical value for the torsion in order to induce the correct velocity of sound, the model we consider supports solitonic solutions, qualitatively and quantitatively very similar to the Yakushevich solitons, in a fully realistic range of all the physical parameters characterizing the DNA.