Conformation and dynamics of model polymer in connected chamber-pore system

Abstract

Single polymer chains under spatially heterogeneous confinement are investigated through simulation of a chain in an infinite linear series of chambers and pores. Conformational properties studied include the number of occupied chambers and the radius of gyration along the chamber axis, both of which vary with chain length and chamber size according to simple scaling predictions. The probability distribution of chain spatial extent along the chamber axis is characterized by distinct peaks and troughs corresponding to favored and disfavored chain sizes. The large scale dynamics is characterized by the center-of-mass diffusion constant along the chamber axis, which exhibits an exponential dependence on chamber size with dramatically slower diffusion in larger chambers. Stepping time distributions change as the chamber size increases or chain length decreases from a symmetric form to a Poisson distribution. The evolution of the dynamics is suggestive of a substantial barrier, independent of chain length, that controls the large-scale motion for short-enough chains in large-enough chambers. Other known signatures of anomalous, nondiffusive dynamics are also observed. The onset of barrier-controlled or anomalous dynamics is conjectured to be the result of chains occupying only a small number of chambers simultaneously.