Rotational Brownian dynamics of semiflexible broken rods

Abstract

Using the Brownian dynamics simulation technique, we study the rotational dynamics of a semiflexible broken rod. We employ a suitable bead model with stiff springs between beads and strong forces opposing to bending, except at the joint where flexibility is variable. We consider mostly broken rods with equal arms. From the simulated Brownian trajectories we obtain the correlation function for the second order Legendre polynomial of the reorientational angle of the end-to-end vector and of the arm vector. These correlation functions are closely related to fluorescence anisotropy decay and electric birefringence decay, respectively. In the first case, the relaxation time for a completely flexible rod agrees with the Harvey-Wegener theory, and in the second, the longest relaxation time agrees well with that obtained from the rigid-body treatment over the whole range of flexibility. Furthermore, we discuss the relative importance of flexibility in both types of decay. Finally, we present results for a case with unequal arms, confirming the validity of the Harvey-Wegener theory and the rigid-body treatment.