Simulation of the rotational Brownian dynamics of a simple, segmentally flexible model: The elastic trumbbell

Abstract

The rotational dynamics of a segmentally flexible model, the elastic trumbbell, has been studied using a Brownian dynamics simulation technique. The model is composed of three beads jointed by two bonds. A potential that is quadratic in the bending angle describes the partial flexibility of the model. The correlation analysis of the simulated trajectories gives rotational correlation functions, of which we have preferentially studied those of the second Legendre polynomial of the reorientation angle of the bond and end-to-end vectors. The relaxation times derived from these correlation functions are compared with those predicted by other treatments of the rotational dynamics of segmentally flexible macromolecules.