Nanoscale control in biological and synthetic systems

The ability to control a system is at the heart of experimental science. Modern experimental methods have pushed the length scale at which control is possible down to the nanometer level. Indeed, methods for manipulating single molecules have in some ways outstripped the ability to observe the systems under study. The “computational microscope” of the molecular dynamics (MD) simulation method provides insight into the behavior of systems at the atomic level, enabling the visualization of systems far beyond the limits of any experimental method. Moreover, MD facilitates experimentation with a virtually unlimited level of control. In this dissertation, I describe my efforts to enhance the ability to control MD simulations, and to use MD simulations to illuminate experimental systems. I have implemented and subsequently enhanced a flexible and powerful method for applying force in MD simulations, and have used this method to investigate microtubules and DNA translocation through the biological nanopore α-hemolysin. I have also employed MD simulations to explore methods for enhancing experimental control over the translocation of DNA through synthetic nanopores.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Physics

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2012

Author dc:creator

• Wells, David

Contributors dc:contributor

• Aksimentiev, Aleksei
• Clegg, Robert M.
• Tajkhorshid, Emad
• Stack, John D.

• molecular dynamics
• simulation
• Grid-Steered Molecular Dynamics (g-smd)
• Deoxyribonucleic acid (dna)
• graphene
• microtubule

Statement dc:rights

• Copyright 2012 David Wells

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/34407

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/34407