Computational studies of semiflexible polymer translocation in nanopore systems

Abstract

The translocation of double stranded DNA (dsDNA) through nanopore systems is a field with rich physics and many promising technological applications. Double stranded DNA is not fully flexible, and the translocation dynamics of semiflexible molecules are not very well understood. In this thesis, in a set of articles, several aspects of translocation with semiflexible polymers in various nanopore systems are explored using molecular dynamics simulations. We look at the effect of the capture process on the translocation dynamics of semiflexible chains for standard nanopores in detail. In collaboration with experiment, we use simulations to explore the dynamics of dsDNA in a nanofiltered nanopore device with potential applications in DNA sequencing technology. A secondary use for the nanofiltered nanopore device as an entropic cage for DNA is also examined. Simulations are used to obtain insight into the dynamics of molecules during the trapping phase.