Characterization of nanopores with internal cavities for DNA manipulation using Langevin dynamics simulations

Abstract

A novel nanopore geometry is proposed, in which a larger internal cavity is located inside a traditional nanopore. Polymer translocation through this geometry is studied using coarse-grained Langevin dynamics. The most striking result is that translocation time through the system is found to be minimal for polymers of medium length: both longer and shorter chains take longer to translocate. The length at which this occurs is named the critical length. This phenomenon arises as a balance between the driving electric force field and the entropic barrier that must be overcome in order for the polymer to exit the internal cavity. More detailed characterization of the system over a range of simulation parameters elucidate the physical mechanisms important to this mechanism. Using these results, a simplified free energy model is constructed and is solved analytically to predict the critical chain length as a function of applied field strength and cavity size. Good agreement is recovered between this theoretical model and numerical measurements over a range of parameters, and bounds of applicability are discussed. Applications of this new nanopore design are discussed.