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Title page for ETD etd-11282007-144800


Type of Document Dissertation
Author Payne, Christina Marie
Author's Email Address christina.payne@vanderbilt.edu
URN etd-11282007-144800
Title Molecular dynamics simulation of a nanoscale device for fast sequencing of DNA.
Degree PhD
Department Chemical Engineering
Advisory Committee
Advisor Name Title
Peter T. Cummings Committee Chair
Clare McCabe Committee Member
G. Kane Jennings Committee Member
Jens Meiler Committee Member
M. Douglas LeVan Committee Member
Keywords
  • genomic sequencing
  • molecular dynamics
  • LAMMPS
  • Electrophoresis
  • Nnanotechnology
  • electrode charge dynamics
  • Nucleotide sequence -- Instruments -- Design and construction
  • Molecular dynamics -- Simulation methods
  • DNA
  • translocation
  • Ultramicroelectrodes -- Design and construction
Date of Defense 2007-11-12
Availability unrestricted
Abstract
We report a molecular-simulation based modeling of transport and orientation properties of single-stranded DNA molecules in a nanoscale channel as a part of a larger nanoscale device designed for rapid DNA sequencing. The proposed novel nanotechnology concept modeled in these simulations offers the possibility of unprecedented rapidity in the detection of DNA sequences. The proposed device consists of a detection gate, created by two metal nano-electrodes separated by approximately two to five nanometers, placed between two nonconductive plates. The DNA molecules in aqueous solution contained between the plates will be driven by an electric field through the detection gate. Individual base pairs within the DNA sequence are to be determined experimentally by examining the variations in the tunneling conductance as the DNA passes through the gate. We are conducting large-scale molecular dynamics simulations to study the transport and orientation of the DNA segment as it passes through the nanogate. Molecular dynamics is used to determine feasible and ideal gate widths, optimal applied electric field magnitude, and strand length effects. Results from these molecular dynamics simulations are presented and compared to bulk simulation results. Additionally, we present compelling evidence of the applicability of a recently developed model for the interaction between metal nanostructures and charged species, electrode charge dynamics (ECD), over the commonly applied such model, based on the universal force field (UFF).
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