Molecular dynamics simulations of electrophoresis of polyelectrolytes in nano confining cylindrical geometries

We consider molecular dynamics simulations of the electrophoretic motion of charged polymers in straight cylinders and cylinders with a periodic variation (or modulation) of the diameter. The electric field is always orientated along the axis of the cylinders, and it does not change direction. The fluid is modeled explicitly, also the co-ions, counterions, and the charged polymer monomers. In straight geometries, we observe no separation effect for a wide range of applied electric fields. In modulated geometries, the charged polymer chains can be separated only at low fields. At large fields, we observe separation effects in modulated geometries only if the applied field is a dc pulse electric field. A simple scaling theory to explain the observed behavior is presented.