Single-chain conformation and dynamics in connected chambers: Theory and simulation of translocation and threading

Confinement in a series of small chambers connected by narrow pores may be viewed as a model system for translocation in the absence of an applied force, as well as for more general instances of spatially heterogeneous confinement relevant to biological and materials applications. Brownian dynamics simulations are performed for single chains equilibrated in this system, and a theoretical treatment is developed. Short chains undergo translocation between chambers, while long chains thread several chambers and diffuse more rapidly. Measures of chain size and mobility are analyzed and compared.