ASU Electronic Theses and Dissertations
This collection includes most of the ASU Theses and Dissertations from 2011 to present. ASU Theses and Dissertations are available in downloadable PDF format; however, a small percentage of items are under embargo. Information about the dissertations/theses includes degree information, committee members, an abstract, supporting data or media.
In addition to the electronic theses found in the ASU Digital Repository, ASU Theses and Dissertations can be found in the ASU Library Catalog.
Dissertations and Theses granted by Arizona State University are archived and made available through a joint effort of the ASU Graduate College and the ASU Libraries. For more information or questions about this collection contact or visit the Digital Repository ETD Library Guide or contact the ASU Graduate College at gradformat@asu.edu.
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- Creators: Alford, Terry
- Creators: Ghirlanda, Giovanna
Description
Cyanovirin-N (CV-N) is a naturally occurring lectin originally isolated from the cyanobacteria Nostoc ellipsosporum. This 11 kDa lectin is 101 amino acids long with two binding sites, one at each end of the protein. CV-N specifically binds to terminal Manα1-2Manα motifs on the branched, high mannose Man9 and Man8 glycosylations found on enveloped viruses including Ebola, Influenza, and HIV. wt-CVN has micromolar binding to soluble Manα1-2Manα and also inhibits HIV entry at low nanomolar concentrations. CV-N's high affinity and specificity for Manα1-2Manα makes it an excellent lectin to study for its glycan-specific properties. The long-term aim of this project is to make a variety of mutant CV-Ns to specifically bind other glycan targets. Such a set of lectins may be used as screening reagents to identify biomarkers and other glycan motifs of interest. As proof of concept, a T7 phage display library was constructed using P51G-m4-CVN genes mutated at positions 41, 44, 52, 53, 56, 74, and 76 in binding Domain B. Five CV-N mutants were selected from the library and expressed in BL21(DE3) E. coli. Two of the mutants, SSDGLQQ-P51Gm4-CVN and AAGRLSK-P51Gm4-CVN, were sufficiently stable for characterization and were examined by CD, Tm, ELISA, and glycan array. Both proteins have CD minima at approximately 213 nm, indicating largely β-sheet structure, and have Tm values greater than 40°C. ELISA against gp120 and RNase B demonstrate both proteins' ability to bind high mannose glycans. To more specifically determine the binding specificity of each protein, AAGRLSK-P51Gm4-CVN, SSDGLQQ-P51Gm4-CVN, wt-CVN, and P51G-m4-CVN were sent to the Consortium for Functional Glycomics (CFG) for glycan array analysis. AAGRLSK-P51Gm4-CVN, wt-CVN, and P51G-m4-CVN, have identical specificities for high mannose glycans containing terminal Manα1-2Manα. SSDGLQQ-P51Gm4-CVN binds to terminal GlcNAcα1-4Gal motifs and a subgroup of high mannose glycans bound by P51G-m4-CVN. SSDGLQQ-wt-CVN was produced to restore anti-HIV activity and has a high nanomolar EC50 value compared to wt-CVN's low nanomolar activity. Overall, these experiments show that CV-N Domain B can be mutated and retain specificity identical to wt-CVN or acquire new glycan specificities. This first generation information can be used to produce glycan-specific lectins for a variety of applications.
ContributorsRuben, Melissa (Author) / Ghirlanda, Giovanna (Thesis advisor) / Allen, James (Committee member) / Wachter, Rebekka (Committee member) / Arizona State University (Publisher)
Created2013
Description
The overall goal of this research project was to assess the feasibility of investigating the effects of microgravity on mineralization systems in unit gravity environments. If possible to perform these studies in unit gravity earth environments, such as earth, such systems can offer markedly less costly and more concerted research efforts to study these vitally important systems. Expected outcomes from easily accessible test environments and more tractable studies include the development of more advanced and adaptive material systems, including biological systems, particularly as humans ponder human exploration in deep space. The specific focus of the research was the design and development of a prototypical experimental test system that could preliminarily meet the challenging design specifications required of such test systems. Guided by a more unified theoretical foundation and building upon concept design and development heuristics, assessment of the feasibility of two experimental test systems was explored. Test System I was a rotating wall reactor experimental system that closely followed the specifications of a similar test system, Synthecon, designed by NASA contractors and thus closely mimicked microgravity conditions of the space shuttle and station. The latter includes terminal velocity conditions experienced by both innate material systems, as well as, biological systems, including living tissue and humans but has the ability to extend to include those material test systems associated with mineralization processes. Test System II is comprised of a unique vertical column design that offered more easily controlled fluid mechanical test conditions over a much wider flow regime that was necessary to achieving terminal velocities under free convection-less conditions that are important in mineralization processes. Preliminary results indicate that Test System II offers distinct advantages in studying microgravity effects in test systems operating in unit gravity environments and particularly when investigating mineralization and related processes. Verification of the Test System II was performed on validating microgravity effects on calcite mineralization processes reported earlier others. There studies were conducted on calcite mineralization in fixed-wing, reduced gravity aircraft, known as the `vomit comet' where reduced gravity conditions are include for very short (~20second) time periods. Preliminary results indicate that test systems, such as test system II, can be devised to assess microgravity conditions in unit gravity environments, such as earth. Furthermore, the preliminary data obtained on calcite formation suggest that strictly physicochemical mechanisms may be the dominant factors that control adaptation in materials processes, a theory first proposed by Liu et al. Thus the result of this study may also help shine a light on the problem of early osteoporosis in astronauts and long term interest in deep space exploration.
ContributorsSeyedmadani, Kimia (Author) / Pizziconi, Vincent (Thesis advisor) / Towe, Bruce (Committee member) / Alford, Terry (Committee member) / Arizona State University (Publisher)
Created2013
Description
As crystalline silicon solar cells continue to get thinner, the recombination of carriers at the surfaces of the cell plays an ever-important role in controlling the cell efficiency. One tool to minimize surface recombination is field effect passivation from the charges present in the thin films applied on the cell surfaces. The focus of this work is to understand the properties of charges present in the SiNx films and then to develop a mechanism to manipulate the polarity of charges to either negative or positive based on the end-application. Specific silicon-nitrogen dangling bonds (·Si-N), known as K center defects, are the primary charge trapping defects present in the SiNx films. A custom built corona charging tool was used to externally inject positive or negative charges in the SiNx film. Detailed Capacitance-Voltage (C-V) measurements taken on corona charged SiNx samples confirmed the presence of a net positive or negative charge density, as high as +/- 8 x 1012 cm-2, present in the SiNx film. High-energy (~ 4.9 eV) UV radiation was used to control and neutralize the charges in the SiNx films. Electron-Spin-Resonance (ESR) technique was used to detect and quantify the density of neutral K0 defects that are paramagnetically active. The density of the neutral K0 defects increased after UV treatment and decreased after high temperature annealing and charging treatments. Etch-back C-V measurements on SiNx films showed that the K centers are spread throughout the bulk of the SiNx film and not just near the SiNx-Si interface. It was also shown that the negative injected charges in the SiNx film were stable and present even after 1 year under indoor room-temperature conditions. Lastly, a stack of SiO2/SiNx dielectric layers applicable to standard commercial solar cells was developed using a low temperature (< 400 °C) PECVD process. Excellent surface passivation on FZ and CZ Si substrates for both n- and p-type samples was achieved by manipulating and controlling the charge in SiNx films.
ContributorsSharma, Vivek (Author) / Bowden, Stuart (Thesis advisor) / Schroder, Dieter (Committee member) / Honsberg, Christiana (Committee member) / Roedel, Ronald (Committee member) / Alford, Terry (Committee member) / Arizona State University (Publisher)
Created2013
Description
Microwave dielectrics are widely used to make resonators and filters in telecommunication systems. The production of thin films with high dielectric constant and low loss could potentially enable a marked reduction in the size of devices and systems. However, studies of these materials in thin film form are very sparse. In this research, experiments were carried out on practical high-performance dielectrics including ZrTiO4-ZnNb2O6 (ZTZN) and Ba(Co,Zn)1/3Nb2/3O3 (BCZN) with high dielectric constant and low loss tangent. Thin films were deposited by laser ablation on various substrates, with a systematical study of growth conditions like substrate temperature, oxygen pressure and annealing to optimize the film quality, and the compositional, microstructural, optical and electric properties were characterized. The deposited ZTZN films were randomly oriented polycrystalline on Si substrate and textured on MgO substrate with a tetragonal lattice change at elevated temperature. The BCZN films deposited on MgO substrate showed superior film quality relative to that on other substrates, which grow epitaxially with an orientation of (001) // MgO (001) and (100) // MgO (100) when substrate temperature was above 500 oC. In-situ annealing at growth temperature in 200 mTorr oxygen pressure was found to enhance the quality of the films, reducing the peak width of the X-ray Diffraction (XRD) rocking curve to 0.53o and the χmin of channeling Rutherford Backscattering Spectrometry (RBS) to 8.8% when grown at 800oC. Atomic Force Microscopy (AFM) was used to study the topography and found a monotonic decrease in the surface roughness when the growth temperature increased. Optical absorption and transmission measurements were used to determine the energy bandgap and the refractive index respectively. A low-frequency dielectric constant of 34 was measured using a planar interdigital measurement structure. The resistivity of the film is ~3×1010 ohm·cm at room temperature and has an activation energy of thermal activated current of 0.66 eV.
ContributorsLi, You (Author) / Newman, Nathan (Thesis advisor) / Alford, Terry (Committee member) / Singh, Rakesh (Committee member) / Arizona State University (Publisher)
Created2013
Description
Spinal muscular atrophy (SMA) is a neurodegenerative disease that results in the loss of lower body muscle function. SMA is the second leading genetic cause of death in infants and arises from the loss of the Survival of Motor Neuron (SMN) protein. SMN is produced by two genes, smn1 and smn2, that are identical with the exception of a C to T conversion in exon 7 of the smn2 gene. SMA patients lacking the smn1 gene, rely on smn2 for production of SMN. Due to an alternative splicing event, smn2 primarily encodes a non-functional SMN lacking exon 7 (SMN D7) as well as a low amount of functional full-length SMN (SMN WT). SMN WT is ubiquitously expressed in all cell types, and it remains unclear how low levels of SMN WT in motor neurons lead to motor neuron degradation and SMA. SMN and its associated proteins, Gemin2-8 and Unrip, make up a large dynamic complex that functions to assemble ribonucleoproteins. The aim of this project was to characterize the interactions of the core SMN-Gemin2 complex, and to identify differences between SMN WT and SMN D7. SMN and Gemin2 proteins were expressed, purified and characterized via size exclusion chromatography. A stable N-terminal deleted Gemin2 protein (N45-G2) was characterized. The SMN WT expression system was optimized resulting in a 10-fold increase of protein expression. Lastly, the oligomeric states of SMN and SMN bound to Gemin2 were determined. SMN WT formed a mixture of oligomeric states, while SMN D7 did not. Both SMN WT and D7 bound to Gemin2 with a one-to-one ratio forming a heterodimer and several higher-order oligomeric states. The SMN WT-Gemin2 complex favored high molecular weight oligomers whereas the SMN D7-Gemin2 complex formed low molecular weight oligomers. These results indicate that the SMA mutant protein, SMN D7, was still able to associate with Gemin2, but was not able to form higher-order oligomeric complexes. The observed multiple oligomerization states of SMN and SMN bound to Gemin2 may play a crucial role in regulating one or several functions of the SMN protein. The inability of SMN D7 to form higher-order oligomers may inhibit or alter those functions leading to the SMA disease phenotype.
ContributorsNiday, Tracy (Author) / Allen, James P. (Thesis advisor) / Wachter, Rebekka (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2012
Description
Carrier lifetime is one of the few parameters which can give information about the low defect densities in today's semiconductors. In principle there is no lower limit to the defect density determined by lifetime measurements. No other technique can easily detect defect densities as low as 10-9 - 10-10 cm-3 in a simple, contactless room temperature measurement. However in practice, recombination lifetime τr measurements such as photoconductance decay (PCD) and surface photovoltage (SPV) that are widely used for characterization of bulk wafers face serious limitations when applied to thin epitaxial layers, where the layer thickness is smaller than the minority carrier diffusion length Ln. Other methods such as microwave photoconductance decay (µ-PCD), photoluminescence (PL), and frequency-dependent SPV, where the generated excess carriers are confined to the epitaxial layer width by using short excitation wavelengths, require complicated configuration and extensive surface passivation processes that make them time-consuming and not suitable for process screening purposes. Generation lifetime τg, typically measured with pulsed MOS capacitors (MOS-C) as test structures, has been shown to be an eminently suitable technique for characterization of thin epitaxial layers. It is for these reasons that the IC community, largely concerned with unipolar MOS devices, uses lifetime measurements as a "process cleanliness monitor." However when dealing with ultraclean epitaxial wafers, the classic MOS-C technique measures an effective generation lifetime τg eff which is dominated by the surface generation and hence cannot be used for screening impurity densities. I have developed a modified pulsed MOS technique for measuring generation lifetime in ultraclean thin p/p+ epitaxial layers which can be used to detect metallic impurities with densities as low as 10-10 cm-3. The widely used classic version has been shown to be unable to effectively detect such low impurity densities due to the domination of surface generation; whereas, the modified version can be used suitably as a metallic impurity density monitoring tool for such cases.
ContributorsElhami Khorasani, Arash (Author) / Alford, Terry (Thesis advisor) / Goryll, Michael (Committee member) / Bertoni, Mariana (Committee member) / Arizona State University (Publisher)
Created2013
Description
Ball Grid Array (BGA) using lead-free or lead-rich solder materials are widely used as Second Level Interconnects (SLI) in mounting packaged components to the printed circuit board (PCB). The reliability of these solder joints is of significant importance to the performance of microelectronics components and systems. Product design/form-factor, solder material, manufacturing process, use condition, as well as, the inherent variabilities present in the system, greatly influence product reliability. Accurate reliability analysis requires an integrated approach to concurrently account for all these factors and their synergistic effects. Such an integrated and robust methodology can be used in design and development of new and advanced microelectronics systems and can provide significant improvement in cycle-time, cost, and reliability. IMPRPK approach is based on a probabilistic methodology, focusing on three major tasks of (1) Characterization of BGA solder joints to identify failure mechanisms and obtain statistical data, (2) Finite Element analysis (FEM) to predict system response needed for life prediction, and (3) development of a probabilistic methodology to predict the reliability, as well as, the sensitivity of the system to various parameters and the variabilities. These tasks and the predictive capabilities of IMPRPK in microelectronic reliability analysis are discussed.
ContributorsFallah-Adl, Ali (Author) / Tasooji, Amaneh (Thesis advisor) / Krause, Stephen (Committee member) / Alford, Terry (Committee member) / Jiang, Hanqing (Committee member) / Mahajan, Ravi (Committee member) / Arizona State University (Publisher)
Created2013
Description
This thesis explores a wide array of topics related to the protein folding problem, ranging from the folding mechanism, ab initio structure prediction and protein design, to the mechanism of protein functional evolution, using multi-scale approaches. To investigate the role of native topology on folding mechanism, the native topology is dissected into non-local and local contacts. The number of non-local contacts and non-local contact orders are both negatively correlated with folding rates, suggesting that the non-local contacts dominate the barrier-crossing process. However, local contact orders show positive correlation with folding rates, indicating the role of a diffusive search in the denatured basin. Additionally, the folding rate distribution of E. coli and Yeast proteomes are predicted from native topology. The distribution is fitted well by a diffusion-drift population model and also directly compared with experimentally measured half life. The results indicate that proteome folding kinetics is limited by protein half life. The crucial role of local contacts in protein folding is further explored by the simulations of WW domains using Zipping and Assembly Method. The correct formation of N-terminal β-turn turns out important for the folding of WW domains. A classification model based on contact probabilities of five critical local contacts is constructed to predict the foldability of WW domains with 81% accuracy. By introducing mutations to stabilize those critical local contacts, a new protein design approach is developed to re-design the unfoldable WW domains and make them foldable. After folding, proteins exhibit inherent conformational dynamics to be functional. Using molecular dynamics simulations in conjunction with Perturbation Response Scanning, it is demonstrated that the divergence of functions can occur through the modification of conformational dynamics within existing fold for β-lactmases and GFP-like proteins: i) the modern TEM-1 lactamase shows a comparatively rigid active-site region, likely reflecting adaptation for efficient degradation of a specific substrate, while the resurrected ancient lactamases indicate enhanced active-site flexibility, which likely allows for the binding and subsequent degradation of different antibiotic molecules; ii) the chromophore and attached peptides of photocoversion-competent GFP-like protein exhibits higher flexibility than the photocoversion-incompetent one, consistent with the evolution of photocoversion capacity.
ContributorsZou, Taisong (Author) / Ozkan, Sefika B (Thesis advisor) / Thorpe, Michael F (Committee member) / Woodbury, Neal W (Committee member) / Vaiana, Sara M (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2014
Interactions driving the collapse of islet amyloid polypeptide: implications for amyloid aggregation
Description
Human islet amyloid polypeptide (hIAPP), also known as amylin, is a 37-residue intrinsically disordered hormone involved in glucose regulation and gastric emptying. The aggregation of hIAPP into amyloid fibrils is believed to play a causal role in type 2 diabetes. To date, not much is known about the monomeric state of hIAPP or how it undergoes an irreversible transformation from disordered peptide to insoluble aggregate. IAPP contains a highly conserved disulfide bond that restricts hIAPP(1-8) into a short ring-like structure: N_loop. Removal or chemical reduction of N_loop not only prevents cell response upon binding to the CGRP receptor, but also alters the mass per length distribution of hIAPP fibers and the kinetics of fibril formation. The mechanism by which N_loop affects hIAPP aggregation is not yet understood, but is important for rationalizing kinetics and developing potential inhibitors. By measuring end-to-end contact formation rates, Vaiana et al. showed that N_loop induces collapsed states in IAPP monomers, implying attractive interactions between N_loop and other regions of the disordered polypeptide chain . We show that in addition to being involved in intra-protein interactions, the N_loop is involved in inter-protein interactions, which lead to the formation of extremely long and stable β-turn fibers. These non-amyloid fibers are present in the 10 μM concentration range, under the same solution conditions in which hIAPP forms amyloid fibers. We discuss the effect of peptide cyclization on both intra- and inter-protein interactions, and its possible implications for aggregation. Our findings indicate a potential role of N_loop-N_loop interactions in hIAPP aggregation, which has not previously been explored. Though our findings suggest that N_loop plays an important role in the pathway of amyloid formation, other naturally occurring IAPP variants that contain this structural feature are incapable of forming amyloids. For example, hIAPP readily forms amyloid fibrils in vitro, whereas the rat variant (rIAPP), differing by six amino acids, does not. In addition to being highly soluble, rIAPP is an effective inhibitor of hIAPP fibril formation . Both of these properties have been attributed to rIAPP's three proline residues: A25P, S28P and S29P. Single proline mutants of hIAPP have also been shown to kinetically inhibit hIAPP fibril formation. Because of their intrinsic dihedral angle preferences, prolines are expected to affect conformational ensembles of intrinsically disordered proteins. The specific effect of proline substitutions on IAPP structure and dynamics has not yet been explored, as the detection of such properties is experimentally challenging due to the low molecular weight, fast reconfiguration times, and very low solubility of IAPP peptides. High-resolution techniques able to measure tertiary contact formations are needed to address this issue. We employ a nanosecond laser spectroscopy technique to measure end-to-end contact formation rates in IAPP mutants. We explore the proline substitutions in IAPP and quantify their effects in terms of intrinsic chain stiffness. We find that the three proline mutations found in rIAPP increase chain stiffness. Interestingly, we also find that residue R18 plays an important role in rIAPP's unique chain stiffness and, together with the proline residues, is a determinant for its non-amyloidogenic properties. We discuss the implications of our findings on the role of prolines in IDPs.
ContributorsCope, Stephanie M (Author) / Vaiana, Sara M (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Ros, Robert (Committee member) / Lindsay, Stuart M (Committee member) / Ozkan, Sefika B (Committee member) / Arizona State University (Publisher)
Created2013
Description
ABSTRACT Along with the fast development of science and technology, the studied materials are becoming more complicated and smaller. All these achievements have advanced with the fast development of powerful tools currently, such as Scanning electron microscopy (SEM), Focused Ion Beam (FIB), Transmission electron microscopy (TEM), Energy dispersive X-ray spectroscopy (EDX), Electron energy loss spectroscopy (EELS) and so on. SiTiO3 thin film, which is grown on Si (100) single crystals, attracts a lot of interest in its structural and electronic properties close to its interface. Valence EELS is used to investigate the Plasmon excitations of the ultrathin SrTiO3 thin film which is sandwiched between amorphous Si and crystalline Si layers. On the other hand, theoretical simulations based on dielectric functions have been done to interpret the experimental results. Our findings demonstrate the value of valence electron energy-loss spectroscopy in detecting a local change in the effective electron mass. Recently it is reported that ZnO-LiYbO2 hybrid phosphor is an efficient UV-infrared convertor for silicon solar cell but the mechanism is still not very clear. The microstructure of Li and Yb co-doped ZnO has been studied by SEM and EDX, and our results suggest that a reaction (or diffusion) zone is very likely to exist between LiYbO2 and ZnO. Such diffusion regions may be responsible for the enhanced infrared emission in the Yb and Li co-doped ZnO. Furthermore, to help us study the diffusion zone under TEM in future, the radiation damage on synthesized LiYbO2 has been studied at first, and then the electronic structure of the synthesized LiYbO2 is compared with Yb2O3 experimentally and theoretically, by EELS and FEFF8 respectively.
ContributorsYang, Bo (Author) / Alford, Terry (Thesis advisor) / Jiang, Nan (Committee member) / Theodore, N. David (Committee member) / Arizona State University (Publisher)
Created2013