A BROWNIAN DYNAMICS PROGRAM FOR THE SIMULATION OF LINEAR AND CIRCULARDNA AND OTHER WORMLIKE CHAIN POLYELECTROLYTES

For the interpretation of solution structural and dynamic data of line ar and circular DNA molecules in the kb range, and for the prediction of the effect of local structural changes on the global conformation o f such DNAs, we have developed an efficient and easy way to set up a p rogram based on a second-order explicit Brownian dynamics algorithm. T he DNA is modeled by a chain of rigid segments interacting through har monic spring potentials for bending, torsion, and stretching. The elec trostatics are handled using precalculated energy tables for the inter actions between DNA segments as a function of relative orientation and distance. Hydrodynamic interactions are treated using the Rotne-Prage r tenser. While maintaining acceptable precision, the simulation can b e accelerated by recalculating this tensor only once in a certain numb er of steps.