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.

Twist solitons in macromolecules: from DNA to polyethylene

CADONI, MARIANO;
2009

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.
DNA models; solitons
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11584/23171
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