DNA Free Energy Landscapes and RNA Nano-Self-Assembly Using Atomic Force Microscopy

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dc.contributor.advisorKiang, Ching-Hwaen_US
dc.contributor.committeeMemberDeem, Michael W.en_US
dc.contributor.committeeMemberAjayan, Pulickel M.en_US
dc.creatorFrey, Eric Williamen_US
dc.date.accessioned2014-08-26T19:23:32Zen_US
dc.date.available2014-08-26T19:23:32Zen_US
dc.date.created2014-05en_US
dc.date.issued2014-03-26en_US
dc.date.submittedMay 2014en_US
dc.date.updated2014-08-26T19:23:32Zen_US
dc.description.abstractThere is an important conceptual lesson which has long been appreciated by those who work in biophysics and related interdisciplinary fields. While the extraordinary behavior of biological matter is governed by its detailed atomic structure and random fluctuations, and is therefore difficult to predict, it can nevertheless be understood within simplified frameworks. Such frameworks model the system as consisting of only one or a few components, and model the behavior of the system as the occupation of a single state out of a small number of states available. The emerging widespread application of nanotechnology, such as atomic force microscopy (AFM), has expanded this understanding in eye-opening new levels of detail by enabling nano-scale control, measurement, and visualization of biological molecules. This thesis describes two independent projects, both of which illuminate this understanding using AFM, but which do so from very different perspectives. The organization of this thesis is as follows. Chapter 1 begins with an experimental background and introduction to AFM, and then describes our setup in both single-molecule manipulation and imaging modes. In Chapter 2, we describe the first project, the motivation for which is to extend methods for the experimental determination of the free energy landscape of a molecule. This chapter relies on the analysis of single-molecule manipulation data. Chapter 3 describes the second project, the motivation for which is to create RNA-based nano-structures suitable for future applications in living mammalian cells. This chapter relies mainly on imaging. Chapters 2 and 3 can thus be read and understood separately.en_US
dc.format.mimetypeapplication/pdfen_US
dc.identifier.citationFrey, Eric William. "DNA Free Energy Landscapes and RNA Nano-Self-Assembly Using Atomic Force Microscopy." (2014) Diss., Rice University. <a href="https://hdl.handle.net/1911/76719">https://hdl.handle.net/1911/76719</a>.en_US
dc.identifier.urihttps://hdl.handle.net/1911/76719en_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.subjectFree energy landscapeen_US
dc.subjectCrooks fluctuation theoremen_US
dc.subjectSingle molecule manipulationen_US
dc.subjectJarzynski equalityen_US
dc.subjectEquilibriumen_US
dc.subjectNonequilibriumen_US
dc.subjectPoly(da)en_US
dc.subjectAtomic force microscopyen_US
dc.subjectSelf-assemblyen_US
dc.subjectRNAen_US
dc.subjectNanostructureen_US
dc.titleDNA Free Energy Landscapes and RNA Nano-Self-Assembly Using Atomic Force Microscopyen_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.levelDoctoralen_US
thesis.degree.nameDoctor of Philosophyen_US
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