University of Illinois Urbana-Champaign

Nanoscale control in biological and synthetic systems

Wells, David

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Wells_David.pdf

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

Description

Title
Nanoscale control in biological and synthetic systems
Author(s)
Wells, David
Issue Date
2012-09-18T21:15:26Z
Director of Research (if dissertation) or Advisor (if thesis)
Aksimentiev, Aleksei
Doctoral Committee Chair(s)
Clegg, Robert M.
Committee Member(s)
  • Aksimentiev, Aleksei
  • Tajkhorshid, Emad
  • Stack, John D.
Department of Study
Physics
Discipline
Physics
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Date of Ingest
2012-09-18T21:15:26Z
Keyword(s)
  • molecular dynamics
  • simulation
  • Grid-Steered Molecular Dynamics (g-smd)
  • Deoxyribonucleic acid (dna)
  • graphene
  • microtubule
Abstract
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.
Graduation Semester
2012-08
Permalink
http://hdl.handle.net/2142/34407
Copyright and License Information
Copyright 2012 David Wells

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