Configuration biased Monte Carlo and Brownian dynamics simulations of semiflexible polymers in extensional flows

Configuration Biased Monte Carlo (CBMC) and Non-Equilibrium Brownian Dynamics (NEED) simulations are used to understand the dynamics of semi-flexible macromolecules undergoing extensional flow. The mathematical model utilizes a discretized version of the Kratky-Porod wormlike (or persistent) chain as the building block, and using kinetic theory, generalized to include flow. In steady, potential flows, the solution of the Fokker-Planck equation exists and is used in the generation of trial and acceptance moves in the CBMC scheme. For the NEED, the Fokker-Planck equation is converted to a Stochastic Differential Equation (SDE) from which the simulation algorithm is obtained: Various conformational quantities are monitored, under both steady-state and transient conditions, with the primary independent variable being the flexibility parameter beta, the bending constant of the chain. It is found that the model is able to describe qualitatively many of the experimentally observed effects in such systems. In particular, we find that there is a direct link between the molecular flexibility and its birefringence response in an elongational flow field. We are able to draw conclusions by considering the behavior of molecular-conformational quantities such as the radius of gyration and the moment of inertia.