Transport properties of synthetic nanopores

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.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biophysics & Computnl Biology

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2010

Author dc:creator

• Cruz, Eduardo

Contributors dc:contributor

• Schulten, Klaus J.
• Aksimentiev, Aleksei
• Aluru, Narayana R.
• Timp, Gregory L.

• synthetic nanopore
• molecular dynamics simulations
• ionic rectification
• nanoprecipitation
• water contact angle
• amorphous silica
• polyethylene terephthalate

Statement dc:rights

• Copyright 2010 Eduardo Cruz

Language dc:language

en

Handle dc:identifier

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

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/15530