BIOMOLECULAR DYNAMICS OF DNA - STATISTICAL-MECHANICS AND DYNAMICAL MODELS

There is a growing feeling that biomolecular structure is not sufficie nt to determine biological activity which is also governed by large am plitude dynamics of the molecules. The transcription of DNA or its the rmal denaturation are typical examples. Traditional approaches use Isi ng models to describe the denaturation transition of DNA. They have to introduce phenomenological ''cooperativity factors'' to explain the r ather sharp ''melting'' of this quasi one-dimensional system. We prese nt models which describe the full dynamics of the melting. Using molec ular dynamics simulations and statistical analysis, we discuss the mec hanism of the denaturation, including precursor effects that can be re lated to large amplitude localized nonlinear excitations of the molecu le in which discreteness effects play a large role. We also show the m icroscopic origin of the cooperativity factors.