Theses and Dissertations from UMD
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New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a give thesis/dissertation in DRUM
More information is available at Theses and Dissertations at University of Maryland Libraries.
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Item Transmission Spectra of Rb 87 atoms near an Optical Nanofiber.(2016) Patterson, Burkley D.; Orozco, Luis A; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)We present measurements of the transmission spectra of 87Rb atoms at 780 nm in the vicinity of a nanofiber. A uniform distribution of fixed atoms around a nanofiber should produce a spectrum that is broadened towards the red due to shifts from the van der Waals potential. If the atoms are free, this also produces an attractive force that accelerates them until they collide with the fiber which depletes the steady-state density of near-surface atoms. It is for this reason that measurements of the van der Waals interaction are sparse. We confirm this by measuring the spectrum cold atoms from a magneto-optical trap around the fiber, revealing a symmetric line shape with nearly the natural linewidth of the transition. When we use an auxiliary 750 nm laser we are able to controllably desorb a steady flux of atoms from the fiber that reside near the surface (less than 50 nm) long enough to feel the van der Walls interaction and produce an asymmetric spectrum. We quantify the spectral asymmetry as a function of 750 nm laser power and find a maximum. Our model, which that takes into account the change in the density distribution, qualitatively explains the observations. In the future this can be used as a tool to more comprehensively study atom-surface interactions.Item Experimental, Computational and, Theoretical Analysis of the GroEL/GroES Catalytic Cycle(2014) Corsepius, Nicholas Crane; Lorimer, George H; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The GroEL/GroES system is among the best characterized molecular chaperonins, having been the focus of numerous studies since its discovery just over 40 years ago. There are several aspects of the chaperonin's catalytic cycle that have been thoroughly established, such as the positive intra-ring and negative inter-ring cooperativity that characterizes the binding of ATP, or the concerted domain movements within a ring that constitute the T → R allosteric transition. However, there are still several aspects of the GroEL/GroES catalytic cycle that are still not well understood, and the focus of this work is to address several of them. The results presented throughout this dissertation differ, sometimes drastically, from conventional wisdom, providing a new framework for the investigation of GroEL/GroES catalysis. The work presented here contains several new insights into the GroEL/GroES catalytic cycle. The complicated nature of the interaction between GroEL and its substrate proteins (SPs) has previously prevented quantitative analysis of the role that SP binding plays in the cycle. The problem is circumvented in this work by application of an SP surrogate that simultaneously mimics the effects of bound SP and allows for the quantification of allosteric states. Development of the system leads to the first ever quantification of the role of SP in the catalytic cycling of GroEL. In addition to cycle features that had not been previously addressed, there are several parts of the catalytic cycle that have simply been overlooked throughout the years or unduly simplified in previous analysis. The hydrolysis of ATP within a ring and the release of ADP from a ring are often characterized as concerted events. Both steps are crucial to the cycling of the GroEL/GroES system, and are thoroughly investigated in this work. Thorough examination reveals that neither step is well-characterized as a concerted process. Pre-steady state kinetic analysis demonstrates that hydrolysis of ATP occurs stochastically, each subunit hydrolyzing ATP independently and randomly. Pre-steady state kinetic analysis also reveals that ADP release is a multi-step process. Insight into the steps preceding/ accompanying ADP release are found in molecular dynamics (MD) simulations of the R → T allosteric relaxation. These simulations demonstrate the allosteric relaxation proceeds through a highly asymmetric series of states. Furthermore, the relaxation path taken by subunits can be described as exhibiting dynamic negative cooperativity. The analysis implicates the allosteric relaxation as the trigger that allows the GroEL/GroES system to effectively respond to environmental stimuli. The last topic addressed concerns the role of the GroEL/GroES2 symmetric complex and the mechanism governing its cycling. It has long been assumed that a ring must hydrolyze all seven ATP before it can discharge GroES. This assumption is challenged by new insight into the stochastic mechanism of ATP hydrolysis. The analysis presented in this paper undermines the idea of all-or-none cycling and builds a quantitative relationship between the nucleotide distribution in a complex and its propensity to dissociate.Item Similarity Classification and Retrieval in Cancer Images and Informatics(2008-04-26) Tahmoush, David Alan; Samet, Hanan; Computer Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Techniques in image similarity, classification, and retrieval of breast cancer images and informatics are presented in this thesis. Breast cancer images in the mammogram modality have a lot of non-cancerous structures that are similar to cancer, which makes them especially difficult to work with. Only the cancerous part of the image is relevant, so the techniques must learn to recognize cancer in noisy mammograms and extract features from that cancer to classify or retrieve similar images. There are also many types or classes of cancer with different characteristics over which the system must work. Mammograms come in sets of four, two images of each breast, which enables comparison of the left and right breast images to help determine relevant features and remove irrelevant features. Image feature comparisons are used to create a similarity function that works well in the high-dimensional space of image features. The similarity function is learned on an underlying clustering and then integrated to produce an agglomeration that is relevant to the images. This technique diagnoses breast cancer more accurately than commercial systems and other published results. In order to collect new data and capture the medical diagnosis used to create and improve these methods, as well as develop relevant feedback, an innovative image retrieval, diagnosis capture, and multiple image viewing tool is presented to fulfill the needs of radiologists. Additionally, retrieval and classification of prostate cancer data is improved using new high-dimensional techniques like dimensionally-limited distance functions and dimensional choice.