%0 Journal Article
%T Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential
%A G. Gaeta
%J Quantitative Biology
%D 2006
%I arXiv
%R 10.2991/jnmp.2007.14.1.6
%X The Yakushevich (Y) model provides a very simple pictures of DNA torsion dynamics, yet yields remarkably correct predictions on certain physical characteristics of the dynamics. In the standard Y model, the interaction between bases of a pair is modelled by a harmonic potential, which becomes anharmonic when described in terms of the rotation angles; here we substitute to this different types of improved potentials, providing a more physical description of the H-bond mediated interactions between the bases. We focus in particular on soliton solutions; the Y model predicts the correct size of the nonlinear excitations supposed to model the ``transcription bubbles'', and this is essentially unchanged with the improved potential. Other features of soliton dynamics, in particular curvature of soliton field configurations and the Peierls-Nabarro barrier, are instead significantly changed.
%U http://arxiv.org/abs/q-bio/0604004v1