Diffusive transport through nanopores: What the size of a molecule is?

Abstract

A flexible molecule can adjust its shape to diffuse through a pore having a diameter smaller than its average dimension. The fluctuations of molecular dimensions as well as the rotations of the molecule inside the pores require special attention to the definition of the molecular size descriptors for diffusive transport in the pores. Within the framework of the previously proposed theory of the steric free energy barrier, we suggest an effective spherical model of a molecule of an arbitrary shape and define two size descriptors—the effective average radius of the molecule and its variance. The two geometric parameters effectively encode both the fluctuations of the molecule and its rotation in the pore. Once determined for a molecule, they can be used to estimate the steric free energy in a pore of arbitrary radius. The results can be applied to diffusive transport through biological nanopores as well as to size-exclusion molecular filtering.