Simulation Study On The Extension And Dynamics Of Semi-flexible Polymer Chains In Cylindrical Channel

We use coarse-grained bead-spring chain model to simulate the extension and dynamical behavior of semi-flexible homopolymer in cylindrical channels.The relationship between the extension,dynamics(diffusion and turnover)of polymer chain and the channel’s diameter and chain’s stiffness have been investigated.The scaling relations between the mean end-to-end distance of polymer along the channel<R‖>and the polymer length N,and the effective diameter of channel De,were investigated for flexible and semi-flexible polymer chains confined in long cylindrical channels.For the flexible polymer chain,scaling relation<R‖>～NDe-0.7 Was found in the classic de Gennes regime at lp2/b<De<Rg with the persistence length lp,the bond length b and the radius of gyration Rg of polymer.For the semi-flexible polymer,<R‖>～NDe-1 in the transition regime lp<De<xlp(x>1)and<R‖>～De-0.7 in the classic de Gennes regime at larger De>xlp were observed.The simulation results revealed that the scaling relation in the transition regime was due to the rod-like behavior of the semi-flexible polymer in the small regime lp<De<xlp.There is a critical channel size Dc below which the polymer cannot overturn in the channel.The size Dc increases with increasing the polymer stiff(kθ)but is independent of the polymer length.We find different behaviors of polymer diffusion in the cylindrical channel.The diffusion coefficient of flexible polymer increases with increasing the size of channel and become a constant at large channel size.But the diffusion coefficient of semi-flexible polymer has a peak at intermediate channel size,that is,there is an optimal channel for the fast diffusion of semi-flexible polymer.The novel phenomenon is explained from the difference of the diffusion of semi-rigid polymer chains in solution along the longitudinal and transverse directions of polymers.