Experimental Free Energy Landscape Reconstruction of DNA Unstacking Using Crooks Fluctuation Theorem

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dc.contributor.advisorKiang, Ching-Hwaen_US
dc.contributor.committeeMemberDeem, Michael W.en_US
dc.contributor.committeeMemberNordlander, Peter J.en_US
dc.creatorFrey, Ericen_US
dc.date.accessioned2013-06-05T14:54:10Zen_US
dc.date.accessioned2013-06-05T14:54:22Zen_US
dc.date.available2013-06-05T14:54:10Zen_US
dc.date.available2013-06-05T14:54:22Zen_US
dc.date.created2012-12en_US
dc.date.issued2013-06-05en_US
dc.date.submittedDecember 2012en_US
dc.date.updated2013-06-05T14:54:22Zen_US
dc.description.abstractNonequilibrium work theorems, such as the Jarzynski equality and the Crooks fluctuation theorem, allow one to use nonequilibrium measurements to determine equilibrium free energies. For example, it has been demonstrated that the Crooks fluctuation theorem can be used to determine RNA folding energies. We used single-molecule manipulation with an atomic force microscope to measure the work done on poly(dA) as it was stretched and relaxed. This single-stranded nucleic acid exhibits unique base-stacking transitions in its force-extension curve due to the strong interactions among A bases, as well as multiple pathways. Here we showed that free energy curves can be determined by using the Crooks fluctuation theorem. The nonequilibrium work theorem can be used to determine free energy curves even when there are multiple pathways.en_US
dc.format.mimetypeapplication/pdfen_US
dc.identifier.citationFrey, Eric. "Experimental Free Energy Landscape Reconstruction of DNA Unstacking Using Crooks Fluctuation Theorem." (2013) Master’s Thesis, Rice University. <a href="https://hdl.handle.net/1911/71276">https://hdl.handle.net/1911/71276</a>.en_US
dc.identifier.slug123456789/ETD-2012-12-210en_US
dc.identifier.urihttps://hdl.handle.net/1911/71276en_US
dc.language.isoengen_US
dc.rightsCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.subjectCrooks fluctuation theoremen_US
dc.subjectDNAen_US
dc.subjectSingle moleculeen_US
dc.subjectPoly(da)en_US
dc.subjectJarzynski equalityen_US
dc.subjectFree energy landscapeen_US
dc.titleExperimental Free Energy Landscape Reconstruction of DNA Unstacking Using Crooks Fluctuation Theoremen_US
dc.typeThesisen_US
dc.type.materialTexten_US
thesis.degree.departmentPhysics and Astronomyen_US
thesis.degree.disciplineNatural Sciencesen_US
thesis.degree.grantorRice Universityen_US
thesis.degree.levelMastersen_US
thesis.degree.nameMaster of Scienceen_US
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