Transport properties of synthetic nanopores

Cruz, Eduardo

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https://hdl.handle.net/2142/15530 Copy

Description

Title

Transport properties of synthetic nanopores

Author(s)

Cruz, Eduardo

Issue Date

2010-05-14T20:44:22Z

Director of Research (if dissertation) or Advisor (if thesis)

Schulten, Klaus J.

Doctoral Committee Chair(s)

Schulten, Klaus J.

Committee Member(s)

• Aksimentiev, Aleksei
• Aluru, Narayana R.
• Timp, Gregory L.

Department of Study

School of Molecular & Cell Bio

Discipline

Biophysics & Computnl Biology

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• synthetic nanopore
• molecular dynamics simulations
• ionic rectification
• nanoprecipitation
• 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.

Graduation Semester

2010-05

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http://hdl.handle.net/2142/15530

Copyright and License Information

Copyright 2010 Eduardo Cruz

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