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Title:Biomolecular transport at and through two-dimensional materials
Author(s):Shankla, Manish
Director of Research:Aksimentiev, Aleksei
Doctoral Committee Chair(s):Aksimentiev, Aleksei
Doctoral Committee Member(s):Leburton, Jean-Pierre; Shukla, Diwakar; Pogorelov, Taras
Department / Program:School of Molecular & Cell Bio
Discipline:Biophysics & Computnl Biology
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):Two-dimensional (2D) materials, Graphene, Nanopore Sequencing, DNA Sequencing, Desalination, Molecular Dynamics, MoS2
Abstract:Two-dimensional (2D) materials have transformed single molecule nanoscale manipulation and molecular detection. Graphene is one such 2D material whose single-atom thickness and high in-plane electrical conductivity enables potential nanopore sensing applications for controllable nanofluidics and nanopore sensing applications conducive towards biomolecule sequencing. A nanopore sequencer operates by recording the ionic current as a single-stranded DNA molecule is electrophoretically driven through a nanopore; ionic current blockades unique to each nucleotide provide a key to the sequence readout. 2D materials provide the ultimate resolution by isolating one or two nucleotides in the nanopore at a given instance. A major challenge limiting the applications of nanopores for sequencing is the stochastic transport of DNA through the nanopore contributing to noise in the readout. Experiments have tested DNA transport though graphene nanopores however the strong hydrophobic interactions between DNA and graphene limit DNA capture and transport. To increase throughput, exper- iments tested geometric modifications and chemical functionalization of the nanopore as well as altering the solvent conditions to control the passage of DNA through the nanopore with varying degrees of success. To optimize and test the design of nanopores in 2D materials, an atomistic description of these processes is extremely valuable. Here, several modalities of controlling DNA and ion transport through graphene nanopores are compre- hensively investigated using all-atom molecular dynamics simulations. The first modality is an application of local electric potentials on the surface of free-standing graphene membranes to limit the transport speed of DNA. Charge on the graphene membrane was discovered to limit DNA transport as well as effect the conformation of adsorbed DNA on the surface of graphene. Similar potentials applied on the surface of graphene-silica-graphene hetrostructures were found to modulate the ion selectivity and induce ionic current rectification useful to serve as elements of a nanofluidic circuit. The second modality focuses on a con- trolled method of DNA delivery to the nanopore by harnessing the strong physioadsorption of DNA onto graphene and defects naturally present on the surface of graphene to guide the lateral transport of DNA to the nanopore opening. The defect guided delivery method may be potentially be used for precise delivery, concentration and storage of scarce biomolecular species and on-demand chemical reactions. Transport of DNA through the 2D material MoS2 in a specialized viscosity gradient was also investigated to determine the nature of molecular transport in unique solvent conditions. Lipid transport diffusion on graphene and the osmotic permeability and selectivity of the biological nanopore OmpF were characterized in conjunction with experiments. Results presented in this dissertation provide key insights into the design of solid-state nanopore based DNA sequencing devices.
Issue Date:2019-11-21
Type:Text
URI:http://hdl.handle.net/2142/106450
Rights Information:Copyright 2019 Manish Shankla
Date Available in IDEALS:2020-03-02
Date Deposited:2019-12


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