Electronic Thesis and Dissertation Repository

Thesis Format

Monograph

Degree

Master of Science

Program

Applied Mathematics

Supervisor

Denniston Colin

Abstract

Single chain translocation has been eagerly studied for more than two decades due to its importance in biological processes and also, providing a better understanding of polymer dynamics. Polymer translocation can be divided into three stages of reaching the pore, entering the pore and passing through it. We study the delivery of the chain from the bulk to the entrance, which is called the capture process, for a single chain driven by hydrodynamic flow. Our molecular dynamics-lattice Boltzmann simulations show that the converging flow around the nanopore not only facilitates the process of finding the pore but also deforms the chain in a way that the insertion happens mostly by one of the ends. We explain why single-file capture happens most often despite the formation of folded shapes or hairpins.

Summary for Lay Audience

One of the fundamental processes involved in the survival and functioning of cells is the ability of the cell to exchange matter with its environment. This exchange consists of the motion of different molecules into or out of the cell through very narrow pores, namely nanopores. An important group of molecules taking part in this process are polymers, long chain-like molecules which look like spaghetti noodles. In the present work, we investigate the effect of fluid flow on polymer capture, the process of finding the entrance of a nanopore, using computer programs. We observed that the non-uniform fluid flow approaching the nanopore stretches the polymer chain which can result in the unravelling of folded shapes (hairpins) and promoting single-file capture.

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