Twist solitons in complex macromolecules: from DNA to polyethylene

DOI10.1016/J.IJNONLINMEC.2008.03.010MaRDI QIDQ620330zbMATH OpenOpenAlexFDO

Authors Mariano Cadoni, Roberto De Leo, Sergio Demelio, Giuseppe Gaeta

Publication date 19 January 2011

Published in International Journal of Non-Linear Mechanics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0710.4475

zbMATH Keywords

DNAnon-linear dynamicspolyethilenesolitons

Mathematics Subject Classification ID

PDEs in connection with biology, chemistry and other natural sciences (35Q92) Dynamical systems in biology (37N25) Protein sequences, DNA sequences (92D20)

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.

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• Parametric resonance in DNA
• Dynamics of conformational switchings of bistable quasi-one-dimensional macromolecules with nonlinear longitudinal stretching present
• Propagation of twist solitons in fully inhomogeneous DNA chains
• Solitary waves in helicoidal models of DNA dynamics
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• Extended class of exact twistons and crystalline polyethylene
• Speed selection for coupled wave equations
• Theory of the deformation of aligned polyethylene
• Numerical analysis of solitons profiles in a composite model for DNA torsion dynamics
• A minimal model of DNA dynamics in interaction with RNA-polymerase

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