Transport properties of rigid and flexible macromolecules by brownian dynamics simulation

Abstract

The method of Ermak and McCammon [Ermak, D. L. & McCammon, J. A. (1978) J. Chem. Phys. 69, 1352–1360] is used to simulate the Brownian dynamics of a system of identical, interacting beads. In the present study, we use the method to obtain transport coefficients for a variety of rigid and flexible structures modeled as arrays of spherical subunits. Constraints are enforced using the SHAKE algorithm or a modification, SHAKE‐HI, that is described for the first time. In SHAKE‐HI, hydrodynamic interactions between subunits are taken into account when the constraints are enforced. Use of SHAKE‐HI yields transport coefficients that are in perfect agreement with those obtained by other methods. The primary advantage of the present method is its generality. We also propose that multistep Brownian dynamics may be important in simulating actual experiments (such as fluorescence depolarization) on well‐defined model systems that possess an arbitrary degree of internal flexibility.