Development of bead-spring polymer models using the constant extension ensemble

Abstract

We have examined a new method for generating coarse-grained models of polymers. The resulting models consist of bead-spring chains with the spring force law taken from the force-extension behavior in the constant extension ensemble. This method, called the polymer ensemble transformation method, is applied to the freely jointed chain. The resulting model illustrates why current bead-spring chain models are insufficient in describing polymer behavior at high discretization. Applying the method to the freely jointed chain with unequal rod lengths showed the effect of varying flexibility in the chain. The method was also used to generate a bead-spring model of F-actin, which shows how the method is not restricted to one molecular model and can even be applied to experimental data. The current limitations of the method are discussed, including the need for approximate bending potentials to model the worm-like chain with a bead-spring chain. We discuss practical issues such as using the bead-spring models in Brownian dynamics simulations and develop a simple spring force law that can accurately represent a freely jointed chain with only a few rods per spring. Because of the functional form of this new force law, existing computer simulations can be easily modified.