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Title:Transport properties of synthetic nanopores
Author(s):Cruz, Eduardo
Director of Research:Schulten, Klaus J.
Doctoral Committee Chair(s):Schulten, Klaus J.
Doctoral Committee Member(s):Aksimentiev, Aleksei; Aluru, Narayana R.; Timp, Gregory L.
Department / Program:School of Molecular & Cell Bio
Discipline:Biophysics & Computnl Biology
Degree Granting Institution:University of Illinois at Urbana-Champaign
Subject(s):synthetic nanopore
molecular dynamics simulations
ionic rectification
water contact angle
amorphous silica
polyethylene terephthalate
Abstract:In recent years, advances in nanotechnology have allowed researchers to manufacture pores in synthetic membranes with subnanometer precision, so-called synthetic nanopores. Immersed in aqueous solution, these nanopores can be deployed to study the translocation of charged molecules and ions, a process of main importance in biology. However, researchers run into problems to build and control such small devices. Surface properties, thermal fluctuations and the discreteness of matter dominate at the nanoscale, producing phenomena not observed in the microscale. Indeed, little is known about the molecular level dynamics inside nanopores or the mechanism by which molecules and ions interact with nanopore walls. Molecular dynamics simulations can provide detailed atomistic images involving nanopores and physiological solutions. The work presented in this thesis uses molecular dynamics simulations to study synthetic nanopores made with two different materials: silica and polyethylene terephthalate. For simulated silica nanopores, the lack of suitable force fields to represent the interactions of the silica with other molecules in solution is a mayor problem. To address this problem, a novel silica force field was developed, which accurately reproduces the hydrophobicity of realistic amorphous silica surfaces. Such force field was employed to study the ionic conduction through silica nanopores. The simulations revealed that the atomic topography of the silica nanopore plays a major role in ionic conduction, producing phenomena such as ionic rectification. For polymeric polyethylene terephthalate nanopores, this thesis presents a protocol to assemble atomic models of polymeric bulk materials, which are then used to sculpt polymer nanopore models that reproduce the key features of experimental devices, namely a conical geometry and a negative surface charge density. The polymeric nanopore models were used to study on a novel phenomenon reported in nanopores, so called nanoprecipitation oscillations. The simulations unveiled the atomic detail mechanism of the nanoprecipitation phenomenon.
Issue Date:2010-05-14
Rights Information:Copyright 2010 Eduardo Cruz
Date Available in IDEALS:2010-05-14
Date Deposited:2010-05

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