Multistep brownian dynamics: Application to short wormlike chains

Brownian dynamics simulations of short wormlike chains are carried out using the method of Ermak and McCammon [(1978) J. Chem. Phys. 69, 1352–1360]. Following Hagerman and Zimm [(1981) Biopolymers 20, 1481–1502], the wormlike chain is modeled as a string of beads. In each simulation, the dynamic evolution of an ensemble of 100 randomly generated chains is calculated for a period of from 3 to 200 ns. Two different “experiments,” fluorescence depolarization and dynamic light scattering, were performed in these simulations. Since we are primarily interested in the bending motions and not the torsional motions in this work, we have placed the transition moments along the local symmetry axis of the wormlike chain in the fluorescence depolarization “experiment.” As predicted by the Barkley and Zimm theory [(1979) J. Chem. Phys. 70, 2991–3008], a considerable amount of rapid bending motion was detected by fluorescence depolarization, though not as much as predicted by theory. We conclude that these differences are primarily due to differences between the model used in the theory and the simulations. The light‐scattering experiment was found to be insensitive to internal motion in the low scattering angle limit.