  Experiments using nanofluidic devices have proven effective in characterizing
the physical properties of polymers confined to small cavities. Two recent
studies using such methods examined the organization and dynamics of two DNA
molecules in box-like cavities with strong confinement in one direction and
with square and elliptical cross sections in the lateral plane. Motivated by
these experiments, we employ Monte Carlo and Brownian dynamics simulations to
study the physical behaviour of two polymers confined to small cavities with
shapes comparable to those used in the experiments. We quantify the effects of
varying the following polymer properties and confinement dimensions on the
organization and dynamics of the polymers: the polymer width, the polymer
contour length ratio, the cavity cross-sectional area, and the degree of cavity
elongation for cavities with rectangular and elliptical cross sections. We find
that the tendency for polymers to segregate is enhanced by increasing polymer
width. For sufficiently small cavities, increasing cavity elongation promotes
segregation and localization of identical polymers to opposite sides of the
cavity along its long axis. A free-energy barrier controls the rate of polymers
swapping positions, and the observed dynamics are roughly in accord with
predictions of a simple theoretical model. Increasing the contour length
difference between polymers significantly affects their organization in the
cavity. In the case of a large linear polymer co-trapped with a small ring
polymer in an elliptical cavity, the small polymer tends to lie near the
lateral confining walls, and especially at the cavity poles for highly
elongated ellipses.

Soft Condensed Matter