Simulating the Capture and Translocation of a Polymer by a Nanopore with a Full External Field Profile

Speaker: Sarah Vollmer

Affiliation: UOIT

The passage of a polymer across a membrane through a constricting, nanoscale passage-way is central to many biological processes. Given this biomedical relevance as well as new nanotechnologies such as sequencing DNA using nanopores, the translocation process has been studied in detail both experimentally and through computer simulations. In the majority of the simulation work, the polymer is assumed to be in a relaxed, equilibrium condition at the start of translocation. This research project tests this assumption by simulating the capture of the polymer by the nanopore as well as the translocation process itself. The configuration of the polymer, described by the radius of gyration, is measured at various stages of the capture- translocation process. We find that due to the effects of the field outside of the pore, the polymer is never found in an equilibrium state and is instead either compressed or elongated. These results are shown to depend on the drift-diffusion balance and affect the scaling of the translocation time with polymer length. This work presents a new simulation methodology that has the potential to bring simulation and experimental studies of translocation into closer agreement.