Collision of a field-driven polymer with a finite-sized obstacle: A Brownian dynamics simulation

We study the problem of a field-driven polymer chain of N monomers of size a colliding with a finite-sized obstacle of radius R in the presence of thermal noise. We show that there are two different mechanisms for chain release from the obstacle: "unhooking" and "rolling off". The unhooking mechanism is characterized by strong stretching of the chains at release and an unhooking time which scales with chain length. In contrast, the "rolling-off" mechanism does not impose strong stretching on the chain conformation and is dependent not upon the size of the chain, but rather upon the size of the obstacle. Thus, macroscopic mobility in an array of small, widely spaced posts provides an opportunity to separate chains according to their size, while chain mobility in an array of large circular obstacles provides information on the size of the obstacles. While important at small time scales, diffusion does not contribute significantly to the release kinetics from circular obstacles of any size R when the dimensionless field strength, defined as beta = E lambda a/(k(B)T) where lambda is charge density and E is field strength, is beta N > a/R.