Nonlinear dynamics and statistical physics of DNA

Abstract

DNA is not only an essential object of study for biologists—it also raises very interesting questions for physicists. This paper discuss its nonlinear dynamics, its statistical mechanics, and one of the experiments that one can now perform at the level of a single molecule and which leads to a non-equilibrium transition at the molecular scale. After a review of experimental facts about DNA, we introduce simple models of the molecule and show how they lead to nonlinear localization phenomena that could describe some of the experimental observations. In a second step we analyse the thermal denaturation of DNA, i.e. the separation of the two strands using standard statistical physics tools as well as an analysis based on the properties of a single nonlinear excitation of the model. The last part discusses the mechanical opening of the DNA double helix, performed in single molecule experiments. We show how transition state theory combined with the knowledge of the equilibrium statistical physics of the system can be used to analyse the results.