Keywords

Translocation, semiflexible polymer, nanopore, brownian dynamics simulation, langevin dynamics, polymer sequencing, md simulation, biophysics, soft matter physics

Abstract

The transport of a biomolecule through a nanopore occurs in many biological functions such as, DNA or RNA transport across nuclear pores and the translocation of proteins across the eukaryotic endoplasmic reticulum. In addition to the biological processes, it has potential applications in technology such as, drug delivery, gene therapy, and single molecule sensing. The DNA translocation through a synthetic nanopore device is considered as the basis for cheap and fast sequencing technology. Motivated by the experimental advances, many theoretical models have been developed. In this thesis, we explore the dynamics of driven translocation of a semiflexible polymer through a nanopore in two dimensions (2D) using Langevin dynamics (LD) simulation. By carrying out extensive simulation as a function of different parameters such as, driving force, length and rigidity of the chain, viscosity of the solvent, and diameter of the nanopore, we provide a detailed description of the translocation process. Our studies are relevant for fundamental understanding of the translocation process which is essential for making accurate nano-pore based devices.

Notes

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Graduation Date

2015

Semester

Fall

Advisor

Bhattacharya, Aniket

Degree

Doctor of Philosophy (Ph.D.)

College

College of Sciences

Department

Physics

Degree Program

Physics

Format

application/pdf

Identifier

CFE0005915

URL

http://purl.fcla.edu/fcla/etd/CFE0005915

Language

English

Release Date

12-15-2016

Length of Campus-only Access

1 year

Access Status

Doctoral Dissertation (Open Access)

Subjects

Dissertations, Academic -- Sciences; Sciences -- Dissertations, Academic

Restricted to the UCF community until 12-15-2016; it will then be open access.

Included in

Physics Commons

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