(325c) Polymer Transport through Nanopores: Simulation Study on Role of Polymer-Pore Patterns Under an Electric Field

Single-file electrophoretic transport of charged polymers through nanopores is of tremendous current interest in view of its potential applications in DNA sequencing technology. There are three major steps for the transport: polymer capture, nucleation into the pore, and the eventual successful threading. The experimental facts on this phenomenon are very rich and the phenomenology associated with each of these three stages is yet to be fully understood. Our present work focuses on understanding the underlying principals of the translocation process, with an emphasis on the pore-polymer interactions. We use Langevin dynamics simulations to study a variety of polymer and pore designs. For a uniformly charged linear polymer, we propose a nanopore design with charge patterns along the pore length. The charge pattern introduces a free energy well in the translocation process, resulting into slower translocation. Variation in the charge pattern length reveals the existence of a critical length for which the polymer is trapped inside the well, causing a significant delay during the pore ejection stage. This trapping of the polymer is modeled using an appropriate free energy landscape and the Fokker-Planck formalism.  The predictions of this theory are in qualitative agreement with the simulation results across different pore and polymer lengths. More significantly, a linear polymer with charge patterns along its backbone passing through such a pore with charge patterns shows rich kinetic behavior during all three stages of translocation. A significant delay is introduced even in the pore entrance and threading stages, due to pattern matching. These results suggest using charge pattern matching as a potential design strategy to identify specific parts of a DNA sequence. Furthermore, we have identified criteria for endowing stochastic resonance between a polymer undergoing translocation and an externally driven oscillatory electric field. In a related study, we simulate the translocation of charged star polymers through an uncharged pore. Star polymers with different functionalities show rich translocation kinetics when passing through such a pore. The mean translocation time varies non-monotonically with the polymer functionality, suggesting the use of nanopores as a filtering and analytical technique for star polymers.