Date of Graduation

5-2013

Document Type

Dissertation

Degree Name

Doctor of Philosophy in Physics (PhD)

Degree Level

Graduate

Department

Physics

Advisor

Jiali Li

Committee Member

Michael Lieber

Second Committee Member

David McNabb

Third Committee Member

William Oliver

Fourth Committee Member

Gregory Salamo

Fifth Committee Member

Chao-Hung Tung

Keywords

Pure sciences; Biological sciences; Applied sciences; DNA analysis; Ion beams; Nanopores; Noise sources; Resistive pulse sensing; Silicon nitride; Transmission electron microscopy

Abstract

In this dissertation, the relationship between the geometry of ion-beam sculpted solid-state nanopores and their ability to analyze single DNA molecules using resistive pulse sensing is investigated. To accomplish this, the three dimensional shape of the nanopore is determined using energy filtered and tomographic transmission electron microscopy. It is shown that this information enables the prediction of the ionic current passing through a voltage biased nanopore and improves the prediction of the magnitude of current drop signals when the nanopore interacts with single DNA molecules. The dimensional stability of nanopores in solution is monitored using this information and is improved by modifying the pore's fabrication procedure. Furthermore, the correlation between noise sources present in the nanopore and the noble gas used to form the ion beam during fabrication is investigated. Finally, the polymerase chain reaction is used to verify that DNA translocates through ion-beam sculpted nanopores.

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