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Date of Award

9-2013

Document Type

Campus Access

Degree Name

Doctor of Philosophy (PhD)

Degree Program

Physics

First Advisor

Murugappan Muthukumar

Second Advisor

Adrian Parsegian

Third Advisor

Narayanan Menon

Subject Categories

Biophysics | Physics

Abstract

Over recent decades, the structure and movement of a linear, flexible polyelectrolyte is a phenomenon of fundamental interest, both in experiment and theory. The investigation of the phenomenon guides approaches to fundamental biological sciences and polymer sciences. Computer simulations offer us the opportunity to treat macromolecules as entity and build structural models. This dissertation effectively modeled the polyelectrolyte with a coarse-grained model. We applied Langevin dynamics to the modeled system with a flexible polyelectrolyte chain and counterions. The globule-coil transition of the polyelectrolyte chain was induced by changing the solvent quality or by tensions on the ends of the polyelectrolyte. With Langevin dynamics simulations, we demonstrated that the counterion condensation was changed corresponding to changes of solvent quality or stretching forces. In accordance with the theory of polymer translocation, simulations in this dissertation uncovered the nonuniversal features of polymer translocation through a short solid state nanopore. Based on these studies, we presented the dependence of the polymer translocation events and the polymer translocation time on the applied voltage and the sequence of the polymer chain. We also modeled a system of template DNA, MspA pore and phi29 DNA polymerase with coarse-grained models and applied Langevin dynamics to the simulation. This simulation investigated and uncovered how the phi29 DNA polymerase controlled the DNA sequencing under the applied external voltage. Polymer dynamics of the template DNA during the replicative activity of phi29 DNA polymerase were also investigated.

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