Brownian dynamics simulation of rotational correlation functions for a three-body macromolecular model

Abstract

A former investigation [R. Ying and M. H. Peters, J. Chem. Phys. 9 1, 1287 (1989)] on the rotational dynamics of rigid and partially flexible macromolecules in solution by means of Brownian dynamics simulation methods is extended to a trimer or three‐body macromolecular model. We present expressions for the torque constraints in rigid and semirigid trimer systems that allows for a comprehensive simulation of the translational, rotational, and coupled translational–rotational motions of the three interacting spherical Brownian particles comprising the trimer (trumbell). The torque constraint expressions are verified by comparisons of the Brownian dynamics simulation results to exact analytical results for a rigid trimer system (Appendix). Computer simulations and analytical solutions for the rigid trimer system indicate that the inclusions of rotational motions of the model’s elements can have an appreciable effect on macromolecular dynamics. Macromolecular flexibility can also be easily introduced into the model through varying the parameters of the torque and force constraint expressions. Extensions to an N‐body macromolecular model are also outlined based on the trimer system studied here.