Towards more realistic dynamical models for DNA secondary structure

Details Towards more realistic dynamical models for DNA secondary structure Towards more realistic dynamical models for DNA secondary structure

2005-12-14

arxiv.org/abs/physics/0512123v1

Chemical Physics Letters 419 (2006) 434

Physics

Biological Physics

accepted for publication in Chemical Physics Letters

Scientific paper

10.1016/j.cplett.2005.12.009

We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate perpendicular to the sequence axis. We show, through molecular dynamics simulations, that the model has the correct behaviour at the denaturation transition.

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