Rouse Model with Internal Friction:  A Coarse Grained Framework for Single Biopolymer Dynamics

Abstract

Recent work has highlighted an intimate link between the internal friction of single biopolymers and dynamics on an underlying energy landscape of conformational change. Here, we examine the coarse-grained dynamics of flexible biopolymers by incorporating local internal friction sources into the successful Rouse model of polymer dynamics. Our main result is a closed-form expression of the frequency response function of a Rouse chain with and without internal friction. We find that the regimes in which internal friction and solvent friction dominate are characterized by single-mode dumbbell (| J (ω → ∞)| ∼ ω -1 ) and Rouse-like behavior (| J (ω → ∞)| ∼ ω -1/2 ), respectively. A real-space analysis shows these behaviors are due to a frequency-dependent length of chain that can respond to perturbations. By distinguishing dissipation due to internal conformational change with that from the solvent, the RIF model provides a simple and generic basis for probing the structure and dynamics of single biomolecules in stretching experiments.