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: Si, Jennie
- Creators: Fromme, Petra
Description
Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been determined to date, often due to difficulties associated with the growth of sufficiently large and well-ordered crystals. This work has been focused on showing the first proof of concept for using membrane protein nanocrystals and microcrystals for high-resolution structure determination. Upon determining that crystals of the membrane protein Photosystem I, which is the largest and most complex membrane protein crystallized to date, exist with only a hundred unit cells with sizes of less than 200 nm on an edge, work was done to develop a technique that could exploit the growth of the Photosystem I nanocrystals and microcrystals. Femtosecond X-ray protein nanocrystallography was developed for use at the first high-energy X-ray free electron laser, the LCLS at SLAC National Accelerator Laboratory, in which a liquid jet would bring fully hydrated Photosystem I nanocrystals into the interaction region of the pulsed X-ray source. Diffraction patterns were recorded from millions of individual PSI nanocrystals and data from thousands of different, randomly oriented crystallites were integrated using Monte Carlo integration of the peak intensities. The short pulses ( 70 fs) provided by the LCLS allowed the possibility to collect the diffraction data before the onset of radiation damage, exploiting the diffract-before-destroy principle. At the initial experiments at the AMO beamline using 6.9- Å wavelength, Bragg peaks were recorded to 8.5- Å resolution, and an electron-density map was determined that did not show any effects of X-ray-induced radiation damage. Recently, femtosecond X-ray protein nanocrystallography experiments were done at the CXI beamline of the LCLS using 1.3- Å wavelength, and Bragg reflections were recorded to 3- Å resolution; the data are currently being processed. Many additional techniques still need to be developed to explore the femtosecond nanocrystallography technique for experimental phasing and time-resolved X-ray crystallography experiments. The first proof-of-principle results for the femtosecond nanocrystallography technique indicate the incredible potential of the technique to offer a new route to the structure determination of membrane proteins.
ContributorsHunter, Mark (Author) / Fromme, Petra (Thesis advisor) / Wolf, George (Committee member) / Levitus, Marcia (Committee member) / Arizona State University (Publisher)
Created2011
Description
With the increasing focus on developing environmentally benign electronic packages, lead-free solder alloys have received a great deal of attention. Mishandling of packages, during manufacture, assembly, or by the user may cause failure of solder joint. A fundamental understanding of the behavior of lead-free solders under mechanical shock conditions is lacking. Reliable experimental and numerical analysis of lead-free solder joints in the intermediate strain rate regime need to be investigated. This dissertation mainly focuses on exploring the mechanical shock behavior of lead-free tin-rich solder alloys via multiscale modeling and numerical simulations. First, the macroscopic stress/strain behaviors of three bulk lead-free tin-rich solders were tested over a range of strain rates from 0.001/s to 30/s. Finite element analysis was conducted to determine appropriate specimen geometry that could reach a homogeneous stress/strain field and a relatively high strain rate. A novel self-consistent true stress correction method is developed to compensate the inaccuracy caused by the triaxial stress state at the post-necking stage. Then the material property of micron-scale intermetallic was examined by micro-compression test. The accuracy of this measure is systematically validated by finite element analysis, and empirical adjustments are provided. Moreover, the interfacial property of the solder/intermetallic interface is investigated, and a continuum traction-separation law of this interface is developed from an atomistic-based cohesive element method. The macroscopic stress/strain relation and microstructural properties are combined together to form a multiscale material behavior via a stochastic approach for both solder and intermetallic. As a result, solder is modeled by porous plasticity with random voids, and intermetallic is characterized as brittle material with random vulnerable region. Thereafter, the porous plasticity fracture of the solders and the brittle fracture of the intermetallics are coupled together in one finite element model. Finally, this study yields a multiscale model to understand and predict the mechanical shock behavior of lead-free tin-rich solder joints. Different fracture patterns are observed for various strain rates and/or intermetallic thicknesses. The predictions have a good agreement with the theory and experiments.
ContributorsFei, Huiyang (Author) / Jiang, Hanqing (Thesis advisor) / Chawla, Nikhilesh (Thesis advisor) / Tasooji, Amaneh (Committee member) / Mobasher, Barzin (Committee member) / Rajan, Subramaniam D. (Committee member) / Arizona State University (Publisher)
Created2011
Description
Molybdenum (Mo) is a key trace nutrient for biological assimilation of nitrogen, either as nitrogen gas (N2) or nitrate (NO3-). Although Mo is the most abundant metal in seawater (105 nM), its concentration is low (<5 nM) in most freshwaters today, and it was scarce in the ocean before 600 million years ago. The use of Mo for nitrogen assimilation can be understood in terms of the changing Mo availability through time; for instance, the higher Mo content of eukaryotic vs. prokaryotic nitrate reductase may have stalled proliferation of eukaryotes in low-Mo Proterozoic oceans. Field and laboratory experiments were performed to study Mo requirements for NO3- assimilation and N2 fixation, respectively. Molybdenum-nitrate addition experiments at Castle Lake, California revealed interannual and depth variability in plankton community response, perhaps resulting from differences in species composition and/or ammonium availability. Furthermore, lake sediments were elevated in Mo compared to soils and bedrock in the watershed. Box modeling suggested that the largest source of Mo to the lake was particulate matter from the watershed. Month-long laboratory experiments with heterocystous cyanobacteria (HC) showed that <1 nM Mo led to low N2 fixation rates, while 10 nM Mo was sufficient for optimal rates. At 1500 nM Mo, freshwater HC hyperaccumulated Mo intercellularly, whereas coastal HC did not. These differences in storage capacity were likely due to the presence in freshwater HC of the small molybdate-binding protein, Mop, and its absence in coastal and marine cyanobacterial species. Expression of the mop gene was regulated by Mo availability in the freshwater HC species Nostoc sp. PCC 7120. Under low Mo (<1 nM) conditions, mop gene expression was up-regulated compared to higher Mo (150 and 3000 nM) treatments, but the subunit composition of the Mop protein changed, suggesting that Mop does not bind Mo in the same manner at <1 nM Mo that it can at higher Mo concentrations. These findings support a role for Mop as a Mo storage protein in HC and suggest that freshwater HC control Mo cellular homeostasis at the post-translational level. Mop's widespread distribution in prokaryotes lends support to the theory that it may be an ancient protein inherited from low-Mo Precambrian oceans.
ContributorsGlass, Jennifer (Author) / Anbar, Ariel D (Thesis advisor) / Shock, Everett L (Committee member) / Jones, Anne K (Committee member) / Hartnett, Hilairy E (Committee member) / Elser, James J (Committee member) / Fromme, Petra (Committee member) / Arizona State University (Publisher)
Created2011
Biological and immunological characterization of plant-produced HIV-1 Gag/dgp41 virus-like particles
Description
Anti-retroviral drugs and AIDS prevention programs have helped to decrease the rate of new HIV-1 infections in some communities, however, a prophylactic vaccine is still needed to control the epidemic world-wide. Despite over two decades of research, a vaccine against HIV-1 remains elusive, although recent clinical trials have shown promising results. Recent successes have focused on highly conserved, mucosally-targeted antigens within HIV-1 such as the membrane proximal external region (MPER) of the envelope protein, gp41. MPER has been shown to play critical roles in the viral mucosal transmission, though this peptide is not immunogenic on its own. Gag is a structural protein configuring the enveloped virus particles, and has been suggested to constitute a target of the cellular immunity potentially controlling the viral load. It was hypothesized that HIV-1 enveloped virus-like particles (VLPs) consisting of Gag and a deconstructed form of gp41 comprising the MPER, transmembrane, and cytoplasmic domains (dgp41) could be expressed in plants. Plant-optimized HIV-1 genes were constructed and expressed in Nicotiana benthamiana by stable transformation, or transiently using a tobacco mosaic virus-based expression system or a combination of both. Results of biophysical, biochemical and electron microscopy characterization demonstrated that plant cells could support not only the formation of HIV-1 Gag VLPs, but also the accumulation of VLPs that incorporated dgp41. These particles were purified and utilized in mice immunization experiments. Prime-boost strategies combining systemic and mucosal priming with systemic boosting using two different vaccine candidates (VLPs and CTB-MPR - a fusion of MPER and the B-subunit of cholera toxin) were administered to BALB/c mice. Serum antibody responses against both the Gag and gp41 antigens could be elicited in mice systemically primed with VLPs and these responses could be recalled following systemic boosting with VLPs. In addition, mucosal priming with VLPs allowed for a robust boosting response against Gag and gp41 when boosted with either candidate. Functional assays of these antibodies are in progress to test the antibodies' effectiveness in neutralizing and preventing mucosal transmission of HIV-1. This immunogenicity of plant-based Gag/dgp41 VLPs represents an important milestone on the road towards a broadly-efficacious and inexpensive subunit vaccine against HIV-1.
ContributorsKessans, Sarah (Author) / Mor, Tsafrir S (Thesis advisor) / Matoba, Nobuyuki (Committee member) / Mason, Hugh (Committee member) / Hogue, Brenda (Committee member) / Fromme, Petra (Committee member) / Arizona State University (Publisher)
Created2011
Description
The cyanobacterium Synechocystis sp. PCC 6803 performs oxygenic photosynthesis. Light energy conversion in photosynthesis takes place in photosystem I (PSI) and photosystem II (PSII) that contain chlorophyll, which absorbs light energy that is utilized as a driving force for photosynthesis. However, excess light energy may lead to formation of reactive oxygen species that cause damage to photosynthetic complexes, which subsequently need repair or replacement. To gain insight in the degradation/biogenesis dynamics of the photosystems, the lifetimes of photosynthetic proteins and chlorophyll were determined by a combined stable-isotope (15N) and mass spectrometry method. The lifetimes of PSII and PSI proteins ranged from 1-33 and 30-75 hours, respectively. Interestingly, chlorophyll had longer lifetimes than the chlorophyll-binding proteins in these photosystems. Therefore, photosynthetic proteins turn over and are replaced independently from each other, and chlorophyll is recycled from the damaged chlorophyll-binding proteins. In Synechocystis, there are five small Cab-like proteins (SCPs: ScpA-E) that share chlorophyll a/b-binding motifs with LHC proteins in plants. SCPs appear to transiently bind chlorophyll and to regulate chlorophyll biosynthesis. In this study, the association of ScpB, ScpC, and ScpD with damaged and repaired PSII was demonstrated. Moreover, in a mutant lacking SCPs, most PSII protein lifetimes were unaffected but the lifetime of chlorophyll was decreased, and one of the nascent PSII complexes was missing. SCPs appear to bind PSII chlorophyll while PSII is repaired, and SCPs stabilize nascent PSII complexes. Furthermore, aminolevulinic acid biosynthesis, an early step of chlorophyll biosynthesis, was impaired in the absence of SCPs, so that the amount of chlorophyll in the cells was reduced. Finally, a deletion mutation was introduced into the sll1906 gene, encoding a member of the putative bacteriochlorophyll delivery (BCD) protein family. The Sll1906 sequence contains possible chlorophyll-binding sites, and its homolog in purple bacteria functions in proper assembly of light-harvesting complexes. However, the sll1906 deletion did not affect chlorophyll degradation/biosynthesis and photosystem assembly. Other (parallel) pathways may exist that may fully compensate for the lack of Sll1906. This study has highlighted the dynamics of photosynthetic complexes in their biogenesis and turnover and the coordination between synthesis of chlorophyll and photosynthetic proteins.
ContributorsYao, Cheng I Daniel (Author) / Vermaas, Wim (Thesis advisor) / Fromme, Petra (Committee member) / Roberson, Robert (Committee member) / Webber, Andrew (Committee member) / Arizona State University (Publisher)
Created2011
Description
Increasing demand for high strength powder metallurgy (PM) steels has resulted in the development of dual phase PM steels. In this work, the effects of thermal aging on the microstructure and mechanical behavior of dual phase precipitation hardened powder metallurgy (PM) stainless steels of varying ferrite-martensite content were examined. Quantitative analyses of the inherent porosity and phase fractions were conducted on the steels and no significant differences were noted with respect to aging temperature. Tensile strength, yield strength, and elongation to fracture all increased with increasing aging temperature reaching maxima at 538oC in most cases. Increased strength and decreased ductility were observed in steels of higher martensite content. Nanoindentation of the individual microconstituents was employed to obtain a fundamental understanding of the strengthening contributions. Both the ferrite and martensite hardness values increased with aging temperature and exhibited similar maxima to the bulk tensile properties. Due to the complex non-uniform stresses and strains associated with conventional nanoindentation, micropillar compression has become an attractive method to probe local mechanical behavior while limiting strain gradients and contributions from surrounding features. In this study, micropillars of ferrite and martensite were fabricated by focused ion beam (FIB) milling of dual phase precipitation hardened powder metallurgy (PM) stainless steels. Compression testing was conducted using a nanoindenter equipped with a flat punch indenter. The stress-strain curves of the individual microconstituents were calculated from the load-displacement curves less the extraneous displacements of the system. Using a rule of mixtures approach in conjunction with porosity corrections, the mechanical properties of ferrite and martensite were combined for comparison to tensile tests of the bulk material, and reasonable agreement was found for the ultimate tensile strength. Micropillar compression experiments of both as sintered and thermally aged material allowed for investigation of the effect of thermal aging.
ContributorsStewart, Jennifer (Author) / Chawla, Nikhilesh (Thesis advisor) / Jiang, Hanqing (Committee member) / Krause, Stephen (Committee member) / Arizona State University (Publisher)
Created2011
Description
ATP synthase is a large multimeric protein complex responsible for generating the energy molecule adenosine triphosphate (ATP) in most organisms. The catalysis involves the rotation of a ring of c-subunits, which is driven by the transmembrane electrochemical gradient. This dissertation reports how the eukaryotic c-subunit from spinach chloroplast ATP synthase has successfully been expressed in Escherichia coli and purified in mg quantities by incorporating a unique combination of methods. Expression was accomplished using a codon optimized gene for the c-subunit, and it was expressed as an attachment to the larger, more soluble, native maltose binding protein (MBP-c1). The fusion protein MBP-c1 was purified on an affinity column, and the c1 subunit was subsequently severed by protease cleavage in the presence of detergent. Final purification of the monomeric c1 subunit was accomplished using reversed phase column chromatography with ethanol as an eluent. Circular dichroism spectroscopy data showed clear evidence that the purified c-subunit is folded with the native alpha-helical secondary structure. Recent experiments appear to indicate that this monomeric recombinant c-subunit forms an oligomeric ring that is similar to its native tetradecameric form when reconstituted in liposomes. The F-type ATP synthase c-subunit stoichiometry is currently known to vary from 8 to 15 subunits among different organisms. This has a direct influence on the metabolic requirements of the corresponding organism because each c-subunit binds and transports one H+ across the membrane as the ring makes a complete rotation. The c-ring rotation drives rotation of the gamma-subunit, which in turn drives the synthesis of 3 ATP for every complete rotation. The availability of a recombinantly produced c-ring will lead to new experiments which can be designed to investigate the possible factors that determine the variable c-ring stoichiometry and structure.
ContributorsLawrence, Robert Michael (Author) / Fromme, Petra (Thesis advisor) / Chen, Julian J.L. (Committee member) / Woodbury, Neal W. (Committee member) / Arizona State University (Publisher)
Created2011
Description
There is increasing interest in the medical and behavioral health communities towards developing effective strategies for the treatment of chronic diseases. Among these lie adaptive interventions, which consider adjusting treatment dosages over time based on participant response. Control engineering offers a broad-based solution framework for optimizing the effectiveness of such interventions. In this thesis, an approach is proposed to develop dynamical models and subsequently, hybrid model predictive control schemes for assigning optimal dosages of naltrexone, an opioid antagonist, as treatment for a chronic pain condition known as fibromyalgia. System identification techniques are employed to model the dynamics from the daily diary reports completed by participants of a blind naltrexone intervention trial. These self-reports include assessments of outcomes of interest (e.g., general pain symptoms, sleep quality) and additional external variables (disturbances) that affect these outcomes (e.g., stress, anxiety, and mood). Using prediction-error methods, a multi-input model describing the effect of drug, placebo and other disturbances on outcomes of interest is developed. This discrete time model is approximated by a continuous second order model with zero, which was found to be adequate to capture the dynamics of this intervention. Data from 40 participants in two clinical trials were analyzed and participants were classified as responders and non-responders based on the models obtained from system identification. The dynamical models can be used by a model predictive controller for automated dosage selection of naltrexone using feedback/feedforward control actions in the presence of external disturbances. The clinical requirement for categorical (i.e., discrete-valued) drug dosage levels creates a need for hybrid model predictive control (HMPC). The controller features a multiple degree-of-freedom formulation that enables the user to adjust the speed of setpoint tracking, measured disturbance rejection and unmeasured disturbance rejection independently in the closed loop system. The nominal and robust performance of the proposed control scheme is examined via simulation using system identification models from a representative participant in the naltrexone intervention trial. The controller evaluation described in this thesis gives credibility to the promise and applicability of control engineering principles for optimizing adaptive interventions.
ContributorsDeśapāṇḍe, Sunīla (Author) / Rivera, Daniel E. (Thesis advisor) / Si, Jennie (Committee member) / Tsakalis, Konstantinos (Committee member) / Arizona State University (Publisher)
Created2011
Description
Due to restructuring and open access to the transmission system, modern electric power systems are being operated closer to their operational limits. Additionally, the secure operational limits of modern power systems have become increasingly difficult to evaluate as the scale of the network and the number of transactions between utilities increase. To account for these challenges associated with the rapid expansion of electric power systems, dynamic equivalents have been widely applied for the purpose of reducing the computational effort of simulation-based transient security assessment. Dynamic equivalents are commonly developed using a coherency-based approach in which a retained area and an external area are first demarcated. Then the coherent generators in the external area are aggregated and replaced by equivalenced models, followed by network reduction and load aggregation. In this process, an improperly defined retained area can result in detrimental impacts on the effectiveness of the equivalents in preserving the dynamic characteristics of the original unreduced system. In this dissertation, a comprehensive approach has been proposed to determine an appropriate retained area boundary by including the critical generators in the external area that are tightly coupled with the initial retained area. Further-more, a systematic approach has also been investigated to efficiently predict the variation in generator slow coherency behavior when the system operating condition is subject to change. Based on this determination, the critical generators in the external area that are tightly coherent with the generators in the initial retained area are retained, resulting in a new retained area boundary. Finally, a novel hybrid dynamic equivalent, consisting of both a coherency-based equivalent and an artificial neural network (ANN)-based equivalent, has been proposed and analyzed. The ANN-based equivalent complements the coherency-based equivalent at all the retained area boundary buses, and it is designed to compensate for the discrepancy between the full system and the conventional coherency-based equivalent. The approaches developed have been validated on a large portion of the Western Electricity Coordinating Council (WECC) system and on a test case including a significant portion of the eastern interconnection.
ContributorsMa, Feng (Author) / Vittal, Vijay (Thesis advisor) / Tylavsky, Daniel (Committee member) / Heydt, Gerald (Committee member) / Si, Jennie (Committee member) / Ayyanar, Raja (Committee member) / Arizona State University (Publisher)
Created2011
Description
Proportional-Integral-Derivative (PID) controllers are a versatile category of controllers that are commonly used in the industry as control systems due to the ease of their implementation and low cost. One problem that continues to intrigue control designers is the matter of finding a good combination of the three parameters - P, I and D of these controllers so that system stability and optimum performance is achieved. Also, a certain amount of robustness to the process is expected from the PID controllers. In the past, many different methods for tuning PID parameters have been developed. Some notable techniques are the Ziegler-Nichols, Cohen-Coon, Astrom methods etc. For all these techniques, a simple limitation remained with the fact that for a particular system, there can be only one set of tuned parameters; i.e. there are no degrees of freedom involved to readjust the parameters for a given system to achieve, for instance, higher bandwidth. Another limitation in most cases is where a controller is designed in continuous time then converted into discrete-time for computer implementation. The drawback of this method is that some robustness due to phase and gain margin is lost in the process. In this work a method of tuning PID controllers using a loop-shaping approach has been developed where the bandwidth of the system can be chosen within an acceptable range. The loop-shaping is done against a Glover-McFarlane type ℋ∞ controller which is widely accepted as a robust control design method. The numerical computations are carried out entirely in discrete-time so there is no loss of robustness due to conversion and approximations near Nyquist frequencies. Some extra degrees of freedom owing to choice of bandwidth and capability of choosing loop-shapes are also involved and are discussed in detail. Finally, comparisons of this method against existing techniques for tuning PID controllers both in continuous and in discrete-time are shown. The results tell us that our design performs well for loop-shapes that are achievable through a PID controller.
ContributorsShafique, Md. Ashfaque Bin (Author) / Tsakalis, Konstantinos S. (Thesis advisor) / Rodriguez, Armando A. (Committee member) / Si, Jennie (Committee member) / Arizona State University (Publisher)
Created2011