Date of Award

8-2015

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Bioengineering

Committee Member

Guigen Zhang, Committee Chair

Committee Member

Stephen Foulger

Committee Member

Christopher Saski

Committee Member

Bruce Gao

Committee Member

Alexey Vertegel

Abstract

Nanopores have been explored with the goal of achieving non-functionalized, sub-molecular sensors, primarily with the purpose of producing fast, low-cost DNA sequencers. Because of the nanoscale volume within the nanopore structure, it is possible to isolate individual molecular and sub-molecular analytes. Nanopore DNA sequencing has remained elusive due to high noise levels and the challenge of obtaining single-nucleotide resolution. However, the complete electrical double layer within the nanopore is a key feature of fluid-nanopore interaction and has been neglected in previous studies. By exploring interactions with the electrical double layer in various nanopore systems, we characterize the material, electrical, and solution dependent properties of this structure and develop a new sensing technique.

The overall goals of this project are development of a theoretically complete and useful model of the electrical double layer in a nanopore, development of a nanopore device capable of detecting and manipulating the electrical double layer, characterization of active nanofluidic control, and detection of molecular and double layer properties. By considering extensive numerical models along with experimental evaluation of the nanopore devices, we characterize the fluidic and sensor properties of the electrical double layer in a nanopore. The ability to interact with the electrochemical and structural properties of the fluid within a nanopore offers new avenues for molecular detection and manipulation.

We find that the energetic balance between the nanopore surface potential and the distribution of charged species within the electrical double layer is the key relationship governing the operation of this type of device. A method of active control of the ionic conductance through the nanopore was developed, with complete gating and on-state modulation. A molecular sensing technique was developed by correlating changes to the electrochemical potential of the solution to the physical properties of molecular analytes. The theoretical and practical limits of the nanopore sensor were tested by implementing a new type of nanopore DNA sequencer. High accuracy DNA sequences were produced by combining the double layer potential and ionic current channels in parallel, along with extensive application of signal theory, digital signal processing, and machine learning techniques.

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