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
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Item Intercellular transport of RNA can limit heritable epigenetic changes(2021) Shugarts, Nathan Maxwell; Jose, Antony M; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)RNAs in circulation carry sequence-specific regulatory information between cells in animal, plant, and host-pathogen systems. The accumulation of specific RNA species in circulation during human disease states therefore implicates such RNAs in disease-related gene regulation. However, mechanisms of RNA secretion, accumulation and import into cells are not well understood and yet are directly taken advantage of in the delivery of recently approved RNA-based therapeutics. In the tractable animal Caenorhabditis elegans, double-stranded RNA (dsRNA) can be delivered into circulation, accumulate within the germline and reach progeny, raising the potential for intergenerational effects from endogenous RNAs released into parental circulation. Here we provide evidence for spatial, temporal, and substrate specificity in the transport of dsRNA in C. elegans from parental circulation to progeny. Temporary loss of dsRNA transport resulted in the persistent accumulation of mRNA from a germline gene. The expression of this gene varied among siblings and even between gonad arms within one animal. Perturbing RNA regulation of the gene created new epigenetic states that lasted for many generations. Thus, one role for the transport of dsRNA into the C. elegans germline in every generation is to limit heritable changes in gene expression. We speculate that transport of extracellular RNA into germ cells in other systems could similarly buffer against heritable change across generations.Item TRACKING TRANSPORT OF ‘CHEMICAL COCKTAILS’ OF TRACE METALS USING SENSORS IN URBAN STREAMS(2020) Morel, Carol; Kaushal, Sujay; Geology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Understanding transport mechanisms and temporal patterns in metals concentrations and fluxes in urban streams are important for developing best management practices and restoration strategies to improve water quality. In some cases, in situ sensors can be used to estimate unknown concentrations and fluxes of trace metals or to interpolate between sampling events. Continuous sensor data from the United States Geological Survey were analyzed to determine statistically significant relationships between lead, copper, zinc, cadmium and mercury with turbidity, specific conductance, dissolved oxygen, and discharge for the Hickey Run, Watts Branch, and Rock Creek watersheds in the Washington, D.C. region. At Rock Creek, there were significant negative linear relationships between Hg and Pb and specific conductance (p<0.05). Watershed monitoring approaches using continuous sensor data have the potential to characterize the frequency, magnitude, and composition of pulses in concentrations and loads of trace metals, which could improve management and restoration of urban streams.Item Spatial and Temporal Variability in Suspended Sediment Characteristics in the Surface Layer of the Upper Chesapeake Bay(2020) Barletta, Stephanie Marie; Sanford, Lawrence P; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Periodic high discharge events flush suspended sediments from the Susquehanna River and Conowingo Dam reservoir into the upper Chesapeake Bay, which extends from the mouth of the Susquehanna River to the Bay Bridge near Annapolis, MD. Sediment characteristics in the surface layer of the upper Bay and changes in these characteristics with varying river discharge and distance downstream are not well known. In order to develop an integrated understanding of surface layer sediment dynamics, several in-situ data sets were examined at the Bay head and downstream along the Bay’s center channel, providing data on the spatial and temporal variability of suspended particle characteristics including concentration, settling speed, bulk density, and size. It was found that particles are entirely disaggregated at the Dam, later aggregating to a limited extent down Bay, and that downstream characteristics are more weakly linked to Susquehanna flow at lower flows and longer distances.Item Fully Anisotropic Solution of the Three Dimensional Boltzmann Transport Equation(2016) VanGessel, Francis; Chung, Peter W.; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The development of accurate modeling techniques for nanoscale thermal transport is an active area of research. Modern day nanoscale devices have length scales of tens of nanometers and are prone to overheating, which reduces device performance and lifetime. Therefore, accurate temperature profiles are needed to predict the reliability of nanoscale devices. The majority of models that appear in the literature obtain temperature profiles through the solution of the Boltzmann transport equation (BTE). These models often make simplifying assumptions about the nature of the quantized energy carriers (phonons). Additionally, most previous work has focused on simulation of planar two dimensional structures. This thesis presents a method which captures the full anisotropy of the Brillouin zone within a three dimensional solution to the BTE. The anisotropy of the Brillouin zone is captured by solving the BTE for all vibrational modes allowed by the Born Von-Karman boundary conditions.Item Microturbulent transport of non-Maxwellian alpha particles(2015) Wilkie, George John; Dorland, William; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)A burning Deuterium-Tritium plasma is one which depends upon fusion-produced alpha particles for self-heating. Whether a plasma can reach a burning state requires knowledge of the transport of alpha particles, and turbulence is one such source of transport. The alpha particle distribution in collisional equilibrium forms a non-Maxwellian tail which spans orders of magnitude in energy, and it is this tail that is responsible for heating the plasma. Newly-born high-energy alpha particles are not expected to respond to turbulence as strongly as alpha particles that have slowed down to the bulk plasma temperature. This dissertation presents a low-collisionality derivation of gyrokinetics relevant for alpha particles and describes the upgrades made to the GS2 flux-tube code to handle general non-Maxwellian energy distributions. With the ability to run self-consistent simulations with a population of alpha particles, we can examine certain assumptions commonly made about alpha particles in the context of microturbulence. It is found that microturbulence can compete with collisional slowing-down, altering the distribution further. One assumption that holds well in electrostatic turbulence is the trace approximation, which is built upon to develop a model for efficiently calculating the coupled radial-energy turbulent transport of a non-Maxwellian species. A new code was written for this purpose and corrections to the global alpha particle heating profile due to microturbulence in an ITER-like scenario are presented along with sensitivity studies.Item In Situ Growth and Doping Studies of Topological Insulator Bismuth Selenide(2015) Hellerstedt, John Thery; Fuhrer, Michael; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The past decade has borne witness to the rapid development of a new field of theoretical and experimental condensed matter physics commonly referred to as "topological insulators". In a (experimentalist's) single sentence a topological insulator can be thought of as material that behaves like an empty metal box: the i-dimensional material (i = 2,3) is insulating, but conducting states exist at the (i-1)-dimensional boundaries. These edge or surface states possess non-trivial properties that have generated interest and excitement for their potential utility in solving practical problems in spin electronics as well as the creation of condensed matter systems for realizing and testing new physics. The most extensively studied materials systems with these properties suffer a major drawback in that the interior of the metal box is not "empty" (insulating) but instead filled with metal. The goal of this work has been to understand why the box is full instead of empty, and explore a particular pathway to making it empty. To address these outstanding questions in the literature pertaining to the persistent n-doping of topological insulator Bi2Se3, a custom apparatus was developed for combined epitaxial thin film growth with simultaneous, in situ measurement of transport characteristics (resistivity, Hall carrier density and mobility). Bi2Se3 films are found to be n-doped before exposure to ambient conditions and this doping appears to be interfacial in origin. This work and methodology was extended to study the efficacy of an amorphous MoO3 capping layer. MoO3 acts as an electron acceptor, p-doping the Bi2Se3 up to a |∆n| = 1x10^13 cm−2 change in carrier density. Complimentary X-ray photoemission spectroscopy (XPS) on bulk crystals showed that this was enough to put the Fermi level into the topological regime. Thin films were too highly n-doped initially to reach the topological regime, but the same magnitude change in doping was observed via the Hall effect. Finally, a Bi2Se3 film with a 100 nm capping layer of MoO3 was vented to ambient, and found to retain a stable doping for days of ambient exposure, demonstrating the effectiveness of MoO3 for passivation.Item Theory of graphene transport properties(2013) Li, Qiuzi; Das Sarma, Sankar; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Graphene is of great fundamental interest and has potential applications in disruptive novel technologies. In order to study the novel phenomena in graphene, it is essential to understand its electron transport properties and in particular the main factors limiting its transport mobility. In this dissertation, we study the transport properties of graphene in the presence of electron-hole puddles induced by charged impurities which are invariably present in the graphene environment. We calculate the graphene conductivity by taking into account the non-mean-field two-component nature of transport in the highly inhomogeneous density and potential landscape, where activated transport across the potential fluctuations in the puddle regimes coexists with regular metallic diffusive transport. Our theoretical calculation explains the non-monotonic feature of the temperature dependent transport, which is experimentally generically observed in low mobility graphene samples. Our theory also predicts the existence of an intriguing "disorder by order" phenomenon in graphene transport where higher-quality (and thus more ordered) samples, while having higher mobility at high carrier density, will manifest more strongly insulating (and thus effectively more disordered) behavior as the carrier density is lowered compared with lower quality samples (with higher disorder), which exhibit an approximate resistivity saturation phenomenon at low carrier density near the Dirac point. This predicted behavior, simulating a metal-insulator transition, arises from the suppression of Coulomb disorder induced inhomogeneous puddles near the charge neutrality point in high quality graphene samples. We then study carrier transport through graphene on SrTiO3 substrates by considering the relative contributions of Coulomb and resonant impurity scattering to graphene resistivity. We establish that the nonuniversal high-density behavior of &sigma(n) in different graphene samples on various substrates arises from the competition among different scattering mechanisms, and it is entirely possible for graphene transport to be dominated by qualitatively different scattering mechanisms at high and low carrier densities. Finally, we calculate the graphene conductivity as a function of carrier density, taking into account possible correlations in the spatial distribution of the Coulomb impurity disorder in the environment. We find that the conductivity could increase with increasing impurity density if there is sufficient inter-impurity correlation present in the system.Item FUNCTIONAL INSIGHTS INTO HRG-1-MEDIATED HEME TRANSPORT(2012) Yuan, Xiaojing; Hamza, Iqbal; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Heme is an essential cofactor involved in various biological processes including oxygen transport, xenobiotic detoxification, oxidative metabolism, gas sensing, circadian rhythm, signal transduction, microRNA processing and thyroid hormone synthesis. Heme is also an essential nutrient for parasites and is the major dietary iron source for humans. Despite our extensive understanding of the mechanisms of heme synthesis and degradation in eukaryotes, little is known as to how heme is transported and trafficked in eukaryotes. Recently, CeHRG-1 and CeHRG-4 were identified as the first bona fide heme importers/transporters using the heme auxotroph, Caenorhabditis elegans. To gain mechanistic insights into the heme transport function of HRG-1-related proteins, we conducted a structure-function analysis of CeHRG-1 and CeHRG-4 by exploiting yeast mutants that are genetically defective in heme synthesis. Our studies reveal that HRG-1-related proteins transport heme across membranes through the coordinated actions of strategically placed amino acids that are topologically conserved in both, the worm and human proteins. To further dissect the functional elements that dictate their intracellular localization, we generated a series of chimeras by swapping the amino and carboxy terminal segments of CeHRG-1 and CeHRG-4. Our analysis in yeast and mammalian cells demonstrate that the C-terminal domains are essential for membrane localization of the protein, while the N-terminal domains are important for proper function, and plausibly multimerization of HRG-1-related proteins. Currently, there are no pharmacological means to aid in the study of the cellular and physiological roles of eukaryotic heme transporters. We, for the first time, developed and executed a high-throughput screen of 233,360 compounds, to identify potential antagonists of HRG-1-related proteins by utilizing parasite heme transporters as the primary screening bait. Subsequent study in parasites will provide novel drug candidates against helminths that infect humans, livestock, and plants, as well as against genetic disorders of heme and iron metabolism in humans. Taken together, results from our studies will significantly advance novel functional and therapeutic insights into HRG-1 mediated heme transport in health and disease.Item Catechols as Membrane Anion Transporters(2009) Berezin, Sofya; Davis, Jeffery T.; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)ABSTRACT Title of Document: CATECHOLS AS MEMBRANE ANION TRANSPORTERS Sofya Berezin, Doctor of Philosophy, 2009 Directed By: Professor, Jeffery T. Davis, Department of Chemistry and Biochemistry Synthetic anion transporters have potential as antimicrobials, extractants, sensors, etc. Anionophores may also help us understand how natural systems move ions across hydrophobic barriers. While bacterial siderophores and synthetic analogues use catecholates for Fe3+ uptake, this work reports of catechols facilitating biomembrane transport of anions. We demonstrate that simple bis-catechol III-25 is an anion transporter whose activity depends on catechol's substitution and amphiphilicity. We also describe liposomal assays and devised quantitative description that allows one to study facilitated anion transport. These assays indicate that selectivity of III-25 follows the Hofmeister bias: anions which are easier to dehydrate are made more permeable to the membrane by this bis-catechol. We believe that our description of the ion selectivity and mechanism for III-25 opens an outstanding opportunity for those interested in determining the selectivity and mechanism for other synthetic and natural biomembrane ion transporters. In the beginning of this project we investigated number of simple amides and phenols to evaluate their relative affinity and stoichiometry of interaction with Cl- anion. ESI-MS and 1H NMR analysis showed that a dimer, catechol2*Cl-, was the major complex formed when TBA+Cl- was mixed with excess catechol. Based on this finding we attached two catechols to a TREN scaffold. A hydrophobic alkyl amide groups were linked to TREN's third position. Surprisingly, this simple design led to the active analogs III-23 - III-26. A medium-length, III-25, was the most active compound, indicating that ion transport ability depends on the ability to partition into the biomembrane. Finally, we noticed that the experimentally observed weak dependence of the transport rates on the anion's hydration energy, namely, kAnion decreasing in the order ClO4- > I- > NO3- > Br- > Cl-, is also seen for some of Nature's anion transporters. Thus, anion permeation into the CFTR chloride channel shows a similar trend. We also observed a nonlinear dependence of kAnion on the concentration of bis-catechol. These findings led us to believe that self-association of III-25 provides transient pores that allow permeation without requiring complete dehydration of the inorganic anions. Future efforts will include incorporating selectivity filters into these bis-catechols to help overcome the Hofmeister bias.Item Stadspoort Amsterdam(2009) Marcelis, Ritsaart Jens; Williams, Isaac S; Schumacher, Thomas L; Architecture; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This thesis will attempt to redevelop the immediate context of Amsterdam's central train station in order to reinvigorate the station's intended purpose of serving as a gateway to the city. Implicit in this goal is the need to examine the transportation and visitor functions housed on the site and to resolve them in a more urbanistically coherent way. However, the main focus of the thesis is to investigate the history and culture of the city and to synthesize them into a built form which is clearly evocative of Amsterdam's gestalt. Since architecture inherently reflects the attitudes of the community that produced it, it is hoped that much of this synthesis may be achieved by examining the tectonic approaches used in Amsterdam's recent and distant architectural past and then reinterpreting them for the twenty-first century. A secondary focus for the thesis is to attempt to repair the rift in the city's urban fabric that was caused by locating the station at Amsterdam's waterfront, effectively splitting the city in two. Although the primary area of interest is the plaza in front of the station, this secondary focus will necessitate interventions both in the station itself and on its waterfront edge. By means of these investigations and interventions it is hoped that the site can be reinvigorated as a culturally and urbanistically significant entryway to the city.