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Aksimentiev, Aleksei Clegg, Robert M. Aksimentiev, Aleksei Tajkhorshid, Emad Stack, John D. Wells, David 2012-09-18T21:15:26Z 2012-09-18T21:15:26Z 2012-08 2012-09-18T21:15:26Z 2012-08 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. Item withdrawn by Mark Zulauf (zulauf@illinois.edu) on 2012-06-28T20:05:17Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 1 Wells_David.pdf: 29472011 bytes, checksum: 422cea3ea7fc1825e05bba8da05cfbf3 (MD5) Made available in DSpace on 2012-09-18T21:15:26Z (GMT). No. of bitstreams: 2 Wells_David.pdf: 29472011 bytes, checksum: 422cea3ea7fc1825e05bba8da05cfbf3 (MD5) license.txt: 4061 bytes, checksum: 5350352919e1b525a91c4187624b1d99 (MD5) http://hdl.handle.net/2142/34407 en Copyright 2012 David Wells molecular dynamics simulation Grid-Steered Molecular Dynamics (g-smd) Deoxyribonucleic acid (dna) graphene microtubule Nanoscale control in biological and synthetic systems Physics 1244 Physics 0240 University of Illinois at Urbana-Champaign Dissertation Ph.D. PHD:Physics -UIUC 10KS0240PHD