Effects of dielectric mismatch and chain flexibility on the translocation barriers of charged macromolecules through solid state nanopores

Abstract

We investigate the impact of dielectric boundary forces on the translocation process of stiff charged macromolecules through solid-state nanopores by means of coarse grained molecular dynamics simulations. We find that the low dielectric permittivity of typical pore materials (compared to the surrounding water) is able to create a high free energy barrier of more than 10k_BT under low salt conditions for pore radii comparable to the Debye length. Interestingly the translocation barrier is significantly enhanced for flexible charged macromolecules. To achieve a comparable description of the free energy profile we introduce a new reaction coordinate that can describe in a consistent way the whole translocation process for flexible and stiff macromolecules, and investigate the barrier for idealized model systems of a rigid double-stranded DNA and a flexible single-stranded DNA.