DNA electrophoresis in confined, periodic geometries: A new lakes-straits model

Emergent slow dynamics of collapsed polymers flowing through porous media

Using hydrodynamic simulations, we study the single polymers flowing through model porous media (close-packed colloidal crystal). In good solvent or high flow rates, the polymer transport is similar to gel electrophoresis, with size-dependent sieving for L_{c}/L≲1 and size-independent biased reptation for L_{c}/L≳1 (L_{c} is the polymer contour length and L is the diameter of colloids forming the porous media). Importantly, in bad solvent and low flow rates, the polymers show an extra window of size-dependent velocity for 1≲L_{c}/L≲2, where the polymer transport is controlled by a globule-stretch transition at pore throats, and the transport velocity is much slower than reptation.

Free-energy cost of localizing a single monomer of a confined polymer

We describe a simple Monte Carlo simulation method to calculate the free-energy cost of localizing a single monomer of a polymer confined to a cavity. The localization position is chosen to be on the inside surface of the confining cavity. The method is applied to a freely jointed hard-sphere polymer chain confined to cavities of spherical and cubic geometries. In the latter case, we consider localization at a corner and at the center of a face of the confining cube. We consider cases of end-monomer localization both with and without tethering of the other end monomer to a point on the surface. We also examine localization of monomers at arbitrary positions along the contour of the polymer. We characterize the dependence of the free energy on the cavity size and shape, the localization position, and the polymer length. The quantitative trends can be understood using standard scaling arguments and use of a simple theoretical model. The results are relevant to those theories of polymer translocation that focus on the importance of the free-energy barrier as the translocation process requires an initial localization of a monomer to the position of a nanopore.