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Applications of Adaptive Umbrella Sampling in Biomolecular Simulation


Abstract Conformational changes in biomolecules often take place on longer timescales than are easily accessible with unbiased molecular dynamics simulations, necessitating the use of enhanced sampling techniques, such as adaptive umbrella sampling. In this technique, the conformational free energy is calculated in terms of a designated set of reaction coordinates. At the same time, estimates of this free energy are subtracted from the potential energy in order to remove free energy barriers and cause conformational changes to take place more rapidly. This dissertation presents applications of adaptive umbrella sampling to a variety of biomolecular systems. The first study investigated the effects of glycosylation in GalNAc2-MM1, an analog of glyco... (more)
Created Date 2011
Contributor Spiriti, Justin Matthew (Author) / Van Der Vaart, Arjan (Advisor) / Chizmeshya, Andrew (Advisor) / Matyushov, Dmitry (Committee member) / Fromme, Petra (Committee member) / Arizona State University (Publisher)
Subject Biophysics / Biochemistry / Physical Chemistry / adaptive umbrella sampling / cis peptide bond / Cy3-DNA interaction / DNA flexibility / molecular dynamics simulation / protein glycosylation
Type Doctoral Dissertation
Extent 218 pages
Language English
Copyright
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Note Ph.D. Chemistry 2011
Collaborating Institutions Graduate College / ASU Library
Additional Formats MODS / OAI Dublin Core / RIS


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Description Dissertation/Thesis