Solitons in a double pendulums chain model, and DNA roto-torsional dynamics

Details Solitons in a double pendulums chain model, and DNA roto-torsional dynamics Solitons in a double pendulums chain model, and DNA roto-torsional dynamics

2006-04-21

arxiv.org/abs/q-bio/0604027v2

J. Nonlin. Math. Phys. 14 (2007), 128-146

Biology

Quantitative Biology

Biomolecules

Scientific paper

It was first suggested by Englander et al to model the nonlinear dynamics of DNA relevant to the transcription process in terms of a chain of coupled pendulums. In a related paper [q-bio.BM/0604014] we argued for the advantages of an extension of this approach based on considering a chain of double pendulums with certain characteristics. Here we study a simplified model of this kind, focusing on its general features and nonlinear travelling wave excitations; in particular, we show that some of the degrees of freedom are actually slaved to others, allowing for an effective reduction of the relevant equations.

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