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Document Type

Open Access Dissertation

Degree Name

Doctor of Philosophy (PhD)

Degree Program

Chemical Engineering

Year Degree Awarded

2016

Month Degree Awarded

September

First Advisor

Murugappan Muthukumar

Subject Categories

Chemical Engineering | Condensed Matter Physics | Nanoscience and Nanotechnology | Polymer Science

Abstract

The idea of sequencing a DNA based on single-file translocation of the DNA through nanopores under the action of an electric field has received much attention over the past two decades due to the societal need for low cost and high-throughput sequencing. However, due to the high speed of translocation, interrogating individual bases with an acceptable signal to noise ratio as they traverse the pore has been a major problem. Experimental facts on this phenomenon are rich and the associated phenomenology is yet to be fully understood. This thesis focuses on understanding the underlying principles of polymer translocation, with an emphasis on pore-polymer interactions, polymer architecture, and polymer chain fluctuations. Langevin dynamics simulations are used to study a variety of polymer and pore designs. For a uniformly charged linear polymer, a nanopore with charge patterns along its length is proposed. Variation in the charge pattern length reveals the existence of a critical length at which the polymer is trapped, causing a significant delay during the pore emptying stage. This trapping is modeled using an appropriate free energy landscape and the Fokker-Planck formalism. The predictions of this theory are in qualitative agreement with the simulation results across different pore and polymer lengths. Moreover, a linear polymer with charge patterns along its backbone passing through such a charge-patterned pore shows rich kinetic behavior; a significant delay is introduced even in the pore entrance and threading stages due to pattern matching, suggesting the use of pore-polymer interactions to slow down translocation. In a related study, the translocation of charged star polymers through an uncharged pore is simulated. Star polymers with different functionalities show rich translocation kinetics while passing through such a pore. The mean translocation time varies non-monotonically with the polymer functionality, suggesting the use of nanopores as a filtering and analytical technique for star polymers.

Recent experiments have suggested the use of phi29 polymerase in conjunction with a protein pore (α-Hemolysin) in the presence of an electric field to slow down the polymer translocation speed, enabling reasonably successful base-calling. The role of polymer chain fluctuations inside the nanopore is evaluated using Langevin dynamics simulations on models of this construct. By monitoring the contributions of the conformational fluctuations of the polymer, the diffusional behavior of monomers of the chain under the speed resulting from the polymerase activity and externally imposed voltage gradients is computed. The simulations show that even if the translocation speed is slowed down considerably by using the polymerase-nanopore construct, the conformational fluctuations of ssDNA inside the pore are always present at high levels, resulting in high levels of noise in the detection signal.

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