Twist solitons in complex macromolecules: from DNA to polyethylene
arXiv:0710.4475 · doi:10.1016/j.ijnonlinmec.2008.03.010
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.
New version substantially longer, with new applications to Polyethylene. To appear in "International Journal of Non-Linear Mechanics"
References in corpus (15)
- Single-molecule experiments in biological physics: methods and applications
- Helicoidal model for DNA opening
- Statistical Mechanics of Torque Induced Denaturation of DNA
- On the nonlinear dynamics of topological solitons in DNA
- Theoretical study of collective modes in DNA at ambient temperature
- A composite model for DNA torsion dynamics
- Weierstrass's criterion and compact solitary waves
- Discrete breathers in polyethylene chain
- Solitons in the Yakushevich model of DNA beyond the contact approximation
- Exact Topological Twistons in Crystalline Polyethylene
- Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential
- Solitons in a double pendulums chain model, and DNA roto-torsional dynamics
- Vector Nonlinear Klein-Gordon Lattices: General Derivation of Small Amplitude Envelope Soliton Solutions
- A symmetry breaking mechanism for selecting the speed of relativistic solitons
- Sine-Gordon solitons, auxiliary fields, and singular limit of a double pendulums chain