UMD Theses and Dissertations
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Item The Effects of Liquid Alkane Fuel Structure on Catalyst-Enhanced Combustion(2018) Dube, Grant; Oran, Elaine S; Lee, Ivan C; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The U.S. Army is developing micro-combustors for use in soldier-portable power generation systems. Many of the challenges associated with micro-combustion can be potentially overcome using a catalyst, but the effects of the catalyst on ignition under the low temperature, atmospheric conditions seen in the field are not well understood. To better understand catalytic ignition phenomena under these conditions, a Catalytic Ignition and Emissions Tester (CIET) was developed and used to investigate the effects of liquid alkane fuel structure during catalyst enhanced ignition. Various mixtures of n-octane and iso-octane, as well as single component n-dodecane and n-hexadecane, were chosen as simple, surrogate test fuels to represent gasoline, jet fuel, and diesel, respectively. Fuel reactivity was shown to decrease with increased branching for all metrics tested while the effects of chain length were less definitive. The global apparent activation energies of all fuels tested were found to be in the range of 41-61 kJ/mol with 95% confidence, significantly lower than those previously reported for non-catalytic hydrocarbon combustion (>100 kJ/mol).Item STRUCTURAL AND FUNCTIONAL STUDIES OF CYCLIC K48-LINKED DIUBIQUITIN(2016) Sundar, Adithya; Fushman, David; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)K48-linked di-ubiquitin exists in a dynamic equilibrium between open and closed states. The structure of K48-Ub2 in the closed conformation features a hydrophobic interface formed between the two Ub domains. The same hydrophobic residues at the interface are involved in binding to ubiquitin-associated (UBA) domains. Cyclization of K48-Ub2 should limit the range of conformations available for such interactions. Interestingly, cyclic K48-linked Ub2 (cycUb2) has been found in vivo and can be isolated in vitro to study its structure and dynamics. In this study, a crystal structure of cycUb2 was obtained, and the dynamics of cycUb2 were characterized by solution NMR. The crystal structure of cycUb2, which is in agreement with solution NMR data, is closed with the hydrophobic patches of each Ub domain buried at the interface. Despite its structural constraints, cycUb2 was still able to interact with UBA domains, albeit with lower affinity.Item THE UNCERTAINTY OF SPACEBORNE OBSERVATION OF VEGETATION STRUCTURE IN THE TAIGA-TUNDRA ECOTONE: A CASE STUDY IN NORTHERN SIBERIA(2015) Montesano, Paul; Dubayah, Ralph; Geography; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The ability to characterize vegetation structure in the taiga-tundra ecotone (TTE) at fine spatial scales is critical given its heterogeneity and the central role of its patterns on ecological processes in the high northern latitudes and global change scenarios. This research focuses on quantifying the uncertainty of TTE forest structure observations from remote sensing at fine spatial scales. I first quantify the uncertainty of forest biomass estimates from current airborne and spaceborne active remote sensing systems and a planned spaceborne LiDAR (ICESat-2) across sparse forest gradients. At plot-scales, current spaceborne models of biomass either explain less than a third of model variation or have biomass estimate uncertainties ranging from 50-100%. Simulations of returns from the planned ICESat-2 for a similar gradient show the uncertainty of near-term estimates vary according to the ground length along which returns are collected. The 50m length optimized the resolution of forest structure, for which there is a trade-off between horizontal precision of the measurement and vertical structure detail. At this scale biomass error ranges from 20-50%, which precludes identifying actual differences in aboveground live biomass density at 10 Mg•ha-1 intervals. These broad plot-scale uncertainties in structure from current and planned sensors provided the basis for examining a data integration technique with multiple sensors to measure the structure of sparse TTE forests. Spaceborne estimates of canopy height used complementary surface elevation measurements from passive optical and LiDAR to provide a means for directly measuring TTE forest height from spaceborne sensors. This spaceborne approach to estimating forest height was deployed to assess the spaceborne potential for examining the patterns of TTE forest structure explained with a conceptual biogeographic model linking TTE patterns and its dynamics. A patch-based analysis was used to scale estimates of TTE forest structure from multiple sensors and provided a means to simultaneously examine the horizontal and vertical structure of groups of TTE trees. The uncertainty of forest patch height estimates provides focus for improving spaceborne depictions of TTE structure patterns associated with recent change that may explain the variability of this change and the vulnerability of TTE forest structure.Item THE INTERPLAY OF SUBSTRATE, PROTEIN AND ITS COFACTOR IN CONTROLLING THE CATALYTIC PROPERTIES OF HUMAN IODOTYROSINE DEIODINASE(2014) Hu, Jimin; Rokita, Steven E; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Human iodotyrosine deiodinase (hIYD) belongs to nitro-FMN reductase superfamily and is responsible for recycling iodine from the I-Tyr (monoiodotyrosine) and I2-Tyr (diiodotyrosine) formed as byproducts of thyroid hormone synthesis. Heterologous expression of hIYD lacking its membrane domain in E. coli provided large quantities of highly pure hIYD that allowed for its physical and biochemical studies. Its kinetic parameters, binding constants and crystal structure were characterized. Substrate was able to induced dramatic effects on FMN coordination in hIYD, including the zwitterionic region of I-Tyr interacts with the N3 and O4 of the FMN, the OH of Thr239 moved close to N5 of FMN (from 4.8 Å to 3.1Å) and allowed the formation of a hydrogen bond. The aromatic ring of I-Tyr additionally stacks above the FMN. Accumulation of the neutral semiquinone was observed during the reduction of hIYD in the presence of substrate analogue 3-fluoro-L-tyrosine (F-Tyr). In the absence of ligand, only the oxidized and two-electron reduced forms of FMN were observed. Among all of the interactions to FMN in hIYD, H-bonding at the N5 FMN was identified as most important to control the redox of flavin. Mutagenesis of Thr239 to Ala removed this H-bonding as confirmed by the crystal structure of hIYDT239A*F-Tyr. As a result, no semiquinone was detected during the titration of hIYDT239A in the presence of F-Tyr. The deiodination activity of T239A was also dramatically decreased (10-fold). The zwitterion region of the substrate was found critical for binding to enzyme. Modifications of the zwitterion region resulted in at least a 500-fold increase in KD. The catalytic activity was unlikely determined by the zwitterion region since all of the modified substrates exhibited similar initial rates as the native substrate under conditions in which their concentration equaled their KD. The pH dependence of hIYD binding indicated that the phenolic group of I2-Tyr is also critical for binding and the hIYD prefers binding to the phenolate form of substrate. All the results presented in this thesis support the current proposed catalytic mechanism of IYD involving a stepwise electron transfer process.Item COMPUTATIONAL METHODS IN PROTEIN STRUCTURE, EVOLUTION AND NETWORKS.(2013) Cao, Chen; Moult, John; Molecular and Cell Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The advent of new sequencing technology has resulted in the accumulation of a large amount of information on human DNA variation. In order to make sense of these data in the context of biology and medicine, new methods are needed both for analysis and for integration with other resources. In this work: 1) I studied the distribution pattern of human DNA variants across populations using data from the 1000 genomes project and investigated several evolutionary biology questions from the perspective of population genomics. I found population level support for trends previously observed between species, including selection against deleterious variants, and lower frequency of variants in highly expressed genes and highly connected genes. I was also able to show that the correlation between synonymous and non-synonymous variant levels is a consequence of both mutation prevalence variation across the genome and shared selection pressure. 2) I performed a systematic evaluation of the effectiveness of GWAS (Genome Wide Association Studies) for finding potential drug targets and discovered the method is very ineffective for this purpose. I proposed two reasons to explain this finding, selection against variants in drug targets and the relatively short length of drug target genes. I discovered that GWAS genes and drug targets are closely associated in the biological network, and on that basis, developed a machine learning algorithm to leverage the GWAS results for the identification of potential drug targets, making use of biological network information. As a result, I identified some potential drug repurposing opportunities. 3) I developed a method to increase the number of protein structure models available for interpreting the impact of human non-synonymous variants, important for not only the understanding the mechanisms of genetic disease but also in the study of human protein evolution. The method enables the impact of approximately 40% more missense variants to be reliably modeled. In summary, these three projects demonstrate that value of computational methods in addressing a wide range of problems in protein structure, evolution, and networks.Item Analyze Municipal Annexations: Case Studies in Frederick and Caroline Counties of Maryland, 1990-2010(2012) Pomeroy, Jennifer Yongmei; Geores, Martha E; Geography; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Municipal annexations play an important role in converting undeveloped land to development, influencing landscape change. However, the existing literature does not explore the links between annexation and development. An additional inadequacy is the failure to consider environment/landscape aspect of annexation. Therefore, this dissertation proposes a new theoretical framework that is drawn upon political ecology and structuration theory to examine annexation phenomenon processes: environmental/landscape sensitivity and its causal social structures. Frederick and Caroline counties in Maryland from 1990 to 2010 were the two case-study areas because both counties experience increased annexation activities and are representative of suburban and exurban settings at rural - urban continuum of the United States. The data used in this qualitative research were collected from multiple data sources, including key-person interviews, a review of Maryland's annexation log, annexation applications and meeting minutes, and observations at public meetings. Triangulating content analysis, discourse analysis, and social network analysis, this research finds that environmental/landscape is not considered more widely in annexation practices. Although environmental mitigation measures are considered at site level if a property has site environmental elements, the overall environmental/landscape sensitivity is low. It is also found that the economic-centered space remains dynamic in the annexation processes determining annexation approvals and low-density zoning. In addition, the triangulated analyses reveal that current social structures are not conducive to environmental-conscious landscape planning because environmentally oriented non-profit organizations and residents are injected at a later stage of annexation process and is not being fully considered in the evaluation process. Power asymmetry in current annexation structures is due to a lack of environmental voice in annexation processes. The voice of such groups needs to be institutionalized to facilitate more tenable annexation practices.Item Molecular Interactions of Ubiquitin and Polyubiquitin with Ubiquitin Binding Domains(2007-10-22) Haririnia, Aydin; Fushman, David; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Ubiquitin is a small protein that is covalently attached to proteins, either as a single ubiquitin moiety or as polyubiquitin chains. A cascade of enzymatic reactions is required for the isopeptide linkage between the C-terminus of ubiquitin and a lysine residue on a substrate protein or another ubiquitin. Attachment of ubiquitin or polyubiquitin, termed ubiquitination, mediates numerous cellular processes by acting as a versatile signal. The signal transmitted by the tag depends on the nature of the modification, which defines the specificity of the tag for different cellular machinery. This versatility is conferred by the variations in polyubiquitin tags, both in terms of length and lysine-linkage. Polyubiquitin chains can adopt a variety of different conformations based on these variations. The conformational and dynamic properties of the tag may optimize its binding to specific ubiquitin binding domains, therefore committing the target protein to distinct cellular outcomes. A combination of NMR methods are used to study the interaction of several ubiquitin binding domains with Lys48- and Lys63-linked di-ubiquitin, the simplest model of a polyubiquitin chain, to gain insights into polyubiquitin recognition. The di-ubiquitin binding interface with ubiquitin-interacting motifs (UIMs) and ubiquitin-associated domains (UBAs) are mapped. Structural models of the complexes are also presented. The results provide the first direct evidence that UIM binding involves a conformational transition in Lys48-linked di-ubiquitin, which opens the hydrophobic interface. The results also show that the UBA domain of Ede1 preferentially binds to Lys63-linked di-ubiquitin. Structural models of the UBA in complex with Lys48- and Lys63-linked di-ubiquitin are shown. Although ubiquitin is highly conserved in eukaryotes, it is promiscuous with regard to its binding partners, ranging from small molecules to UIM and UBA domains. This study examines the effects of point core leucine to serine mutations on UIM and UBA binding specificity. The results show that these mutations bestow ubiquitin with the ability to discriminate between ubiquitin-receptor proteins. Here, we solved the three-dimensional structure of the L69S Ub mutant in solution by NMR. These mutations have a profound effect on binding specificity while causing subtle changes in the protein's three-dimensional fold and reducing its stability. Modification of a specific lysine located on Ub's hydrophobic surface has been reported to inhibit proteasomal degradation and endocytosis. Here, the effects of mutation to tryptophan at this position are investigated within the context of binding to a proteasomal receptor protein, hHR23A, and an endocytic receptor protein, Ede1.Item SYNTHESIS OF POROUS FILMS FROM NANOPARTICLE AGGREGATES AND STUDY OF THEIR PROCESSING-STRUCTURE-PROPERTY RELATIONSHIPS(2005-12-09) Ogunsola, Oluwatosin Abiola; Ehrman, Sheryl H; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Porous films made from titania nanoparticle aggregates have a variety of uses in high surface area applications such as gas sensors, photocatalysts in treatment of wastewater and air pollutants, optical filters, and photovoltaic electrodes for low cost solar cells. A hybrid process based upon gas-to-particle conversion and particle precipitated chemical vapor deposition was used to synthesize porous films of titania nanoparticle aggregates. The residence time of particles in the reactor was varied and the influence on particle morphology and mechanical properties was studied. An increase in residence time resulted in an increase in primary particle diameter but did not significantly affect aggregate diameter, over the range of residence times considered in this study. The Young's modulus is shown to increase with a decrease in primary particle diameter. A study of the effect of post processing annealing on the particle morphology and mechanical properties was conducted. Increasing the annealing temperature resulted in particle growth at different temperatures and aggregate growth only at the highest temperature studied. The Young's modulus, however, shows only an influence of aggregate diameter, increasing as aggregate diameter increased. It is interesting to note that annealing did not result in a significant increase in Young's modulus or hardness until most of the surface area was lost. This suggests that annealing may not be the most effective process for strengthening films, if preservation of high surface area is desired. To better understand the effect of change in particle and aggregate diameters on Young's modulus, Monte Carlo and continuum methods were employed to explore structure-property relationships. A Monte Carlo method was used to simulate particle deposits and a finite element method was used to calculate the Young's modulus from strain energy of the deposits simulated. The results of this study indicate that a decrease in particle diameter increases the Young's modulus, especially below 15 nm. Aggregate size was not seen to have any effect on the Young's modulus, for the range of aggregate sizes considered. The results of these studies can be used to optimize the mechanical properties of titania films, made up of nanoparticle aggregates, for different desired applications.Item Construction Project Organizational Structuring(2005-04-20) Salgado, Carlos; Baecher, Gregory B; Civil Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This dissertation presents an extended research study of project organizational structuring design, using Mintzberg's design parameters of organization and Lucas' IT-enabled variables on construction building project organizations. To the design parameters of unit grouping, unit size, liaison devices, planning and control systems, decision-making system and design of positions, this dissertation study simultaneously considers virtual components, technological leveling, technological matrixing, electronic linking and communications. This study used Yin's multiple case holistic design approach for this extended research study with data from major successful building construction projects to illustrate the use of this extended view and compare its findings. Based on this extended research study, this dissertation develops a practical methodology for construction project organizational structuring design. Furthermore, this dissertation applied Robbins' measures of organization structure (complexity, formalization and centralization) for corroboration.Item General Theory of Nonuniform Fluids: From Hard Spheres to Ionic Fluids(2004-12-09) Chen, Yng-gwei; Weeks, John D.; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The exclusion effects of repulsive intermolecular potential cores are often modeled by hard sphere fluids, for which an accurate Hydrostatic Linear Response (HLR) equation was previous developed by Katsov in 2001 for computing the density response to general external fields. In this dissertation the HLR equation is combined with various thermodynamic integration pathways to investigate the solvation free energy of cavity insertion which characterizes the entropic cost of solvating molecules in a fluid. A Shifted Linear Response (SLR) equation is developed to build in the exact limits of external fields varying in very small ranges and fluids confined in narrow spaces, where the HLR fails qualitatively. The SLR is derived from an expansion truncated at linear order about a reference density, and an Insensitivity Criterion (IC) is proposed for determining an optimal reference density. The slow 1/r decay of the Coulomb potential is characteristically long-ranged, but it also becomes strong at short distances. The structure of ionic systems exhibits an intricate interplay between the short and long length scales of their molecular potentials. A strategy is proposed for separating the Coulomb interaction between general charge distributions into a short-ranged piece u0(r) and a slowly varying piece u1(r). In the strong coupling states of the ionic systems that we have studied, mimic systems with only the short-ranged part u0(r) are found to show very similar correlation functions. The slow decays of ion-ion and ion-dipole interactions give rise to unique long-wavelength constraints on ionic fluid structure. Local Molecular Field Theory (LMF), which maps an external field in the full system to a mimic system in the presence of a renormalized field, can correct the mimic correlations by embodying contributions from u1(r). The LMF has been applied to both uniform and nonuniform model ionic systems, and accurate results for bulk correlation functions, internal energy and the density distribution in a confined system are obtained. For a system of counterions confined by charged walls, the LMF and the mimic system have especially helped shed light on many phenomena that had previously lacked coherent physical interpretations and consistent approximations.