Twist solitons in complex macromolecules: from DNA to polyethylene

TL;DR

This paper explores twist solitons in complex macromolecules like DNA and polyethylene, introducing a composite model that better fits experimental data and reveals mechanisms for soliton speed selection and hierarchical dynamics.

Contribution

It presents a new composite model for DNA torsion dynamics that improves data fit and uncovers mechanisms applicable to general macromolecules such as polyethylene.

Findings

Composite model fits experimental DNA data better.

Mechanism for soliton speed selection via physical parameters.

Hierarchical separation of degrees of freedom in macromolecules.

Abstract

DNA torsion dynamics is essential in the transcription process; simple models for it have been proposed by several authors, in particular Yakushevich (Y model). These are strongly related to models of DNA separation dynamics such as the one first proposed by Peyrard and Bishop (and developed by Dauxois, Barbi, Cocco and Monasson among others), but support topological solitons. We recently developed a ``composite'' version of the Y model, in which the sugar-phosphate group and the base are described by separate degrees of freedom. This at the same time fits experimental data better than the simple Y model, and shows dynamical phenomena, which are of interest beyond DNA dynamics. Of particular relevance are the mechanism for selecting the speed of solitons by tuning the physical parameters of the non linear medium and the hierarchal separation of the relevant degrees of freedom in ``master'' and ``slave''. These mechanisms apply not only do DNA, but also to more general macromolecules, as we show concretely by considering polyethylene.