Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential

Details Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential

2006-04-04

arxiv.org/abs/q-bio/0604004v1

J. Nonlin. Math. Phys. 14 (2007), 57-81

Biology

Quantitative Biology

Biomolecules

Scientific paper

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.

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