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

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dc.contributor.advisorKiang, Ching-Hwa
dc.contributor.committeeMemberDeem, Michael W.
dc.contributor.committeeMemberNordlander, Peter J.
dc.creatorFrey, Eric
dc.date.accessioned2013-06-05T14:54:10Z
dc.date.accessioned2013-06-05T14:54:22Z
dc.date.available2013-06-05T14:54:10Z
dc.date.available2013-06-05T14:54:22Z
dc.date.created2012-12
dc.date.issued2013-06-05
dc.date.submittedDecember 2012
dc.date.updated2013-06-05T14:54:22Z
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.
dc.format.mimetypeapplication/pdf
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>.
dc.identifier.slug123456789/ETD-2012-12-210
dc.identifier.urihttps://hdl.handle.net/1911/71276
dc.language.isoeng
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.
dc.subjectCrooks fluctuation theorem
dc.subjectDNA
dc.subjectSingle molecule
dc.subjectPoly(da)
dc.subjectJarzynski equality
dc.subjectFree energy landscape
dc.titleExperimental Free Energy Landscape Reconstruction of DNA Unstacking Using Crooks Fluctuation Theorem
dc.typeThesis
dc.type.materialText
thesis.degree.departmentPhysics and Astronomy
thesis.degree.disciplineNatural Sciences
thesis.degree.grantorRice University
thesis.degree.levelMasters
thesis.degree.nameMaster of Science
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