K. Klenin et al., A BROWNIAN DYNAMICS PROGRAM FOR THE SIMULATION OF LINEAR AND CIRCULARDNA AND OTHER WORMLIKE CHAIN POLYELECTROLYTES, Biophysical journal, 74(2), 1998, pp. 780-788
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.