Biomolecular dynamics of DNA: statistical mechanics and dynamical models

There is a growing feeling that biomolecular structure is not sufficient to determine biological activity which is also governed by large amplitude dynamics of the molecules. The transcription of DNA or its thermal denaturation are typical examples. Traditional approaches use Ising models to describe the denaturation transition of DNA. They have to introduce phenomenological "cooperativity factors" to explain the rather sharp "melting" of this quasi one-dimensional system. We present models which describe the full dynamics of the melting. Using molecular dynamics simulations and statistical analysis, we discuss the mechanism of the denaturation, including precursor effects that can be related to large amplitude localized nonlinear excitations of the molecule in which discreteness effects play a large role. We also show the microscopic origin of the cooperativity factors.