Modes simulations of DNA denaturation dynamics

We present a model of DNA for use in computer simulations; This model is si mple enough to allow long-time large-scale dynamics simulations, while, on the other hand, it is sophisticated enough to describe both double stranded and single stranded DNA and the transition between the two. We employed ou r simple model in the simulation of denaturation of double stranded DNA hel ices using Langevin dynamics. These are the first simulations of its kind o f DNA denaturation. We have studied the melting behavior for several short double-stranded sequences of different composition. Duplexes of different l engths were considered, and also base pair mismatches were included in the study. Results are in good agreement with experimental data. (C) 2001 Ameri can Institute of Physics.