Theses and Dissertations
This collection includes both ASU Theses and Dissertations, submitted by graduate students, and the Barrett, Honors College theses submitted by undergraduate students.
Displaying 1 - 10 of 86
Description
Reductive dechlorination by members of the bacterial genus Dehalococcoides is a common and cost-effective avenue for in situ bioremediation of sites contaminated with the chlorinated solvents, trichloroethene (TCE) and perchloroethene (PCE). The overarching goal of my research was to address some of the challenges associated with bioremediation timeframes by improving the rates of reductive dechlorination and the growth of Dehalococcoides in mixed communities. Biostimulation of contaminated sites or microcosms with electron donor fails to consistently promote dechlorination of PCE/TCE beyond cis-dichloroethene (cis-DCE), even when the presence of Dehalococcoides is confirmed. Supported by data from microcosm experiments, I showed that the stalling at cis-DCE is due a H2 competition in which components of the soil or sediment serve as electron acceptors for competing microorganisms. However, once competition was minimized by providing selective enrichment techniques, I illustrated how to obtain both fast rates and high-density Dehalococcoides using three distinct enrichment cultures. Having achieved a heightened awareness of the fierce competition for electron donor, I then identified bicarbonate (HCO3-) as a potential H2 sink for reductive dechlorination. HCO3- is the natural buffer in groundwater but also the electron acceptor for hydrogenotrophic methanogens and homoacetogens, two microbial groups commonly encountered with Dehalococcoides. By testing a range of concentrations in batch experiments, I showed that methanogens are favored at low HCO3 and homoacetogens at high HCO3-. The high HCO3- concentrations increased the H2 demand which negatively affected the rates and extent of dechlorination. By applying the gained knowledge on microbial community management, I ran the first successful continuous stirred-tank reactor (CSTR) at a 3-d hydraulic retention time for cultivation of dechlorinating cultures. I demonstrated that using carefully selected conditions in a CSTR, cultivation of Dehalococcoides at short retention times is feasible, resulting in robust cultures capable of fast dechlorination. Lastly, I provide a systematic insight into the effect of high ammonia on communities involved in dechlorination of chloroethenes. This work documents the potential use of landfill leachate as a substrate for dechlorination and an increased tolerance of Dehalococcoides to high ammonia concentrations (2 g L-1 NH4+-N) without loss of the ability to dechlorinate TCE to ethene.
ContributorsDelgado, Anca Georgiana (Author) / Krajmalnik-Brown, Rosa (Thesis advisor) / Cadillo-Quiroz, Hinsby (Committee member) / Halden, Rolf U. (Committee member) / Rittmann, Bruce E. (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2013
Description
There is a pervasive need in the defense industry for conformal, low-profile, efficient and broadband (HF-UHF) antennas. Broadband capabilities enable shared aperture multi-function radiators, while conformal antenna profiles minimize physical damage in army applications, reduce drag and weight penalties in airborne applications and reduce the visual and RF signatures of the communication node. This dissertation is concerned with a new class of antennas called Magneto-Dielectric wire antennas (MDWA) that provide an ideal solution to this ever-present and growing need. Magneto-dielectric structures (μr>1;εr>1) can partially guide electromagnetic waves and radiate them by leaking off the structure or by scattering from any discontinuities, much like a metal antenna of the same shape. They are attractive alternatives to conventional whip and blade antennas because they can be placed conformal to a metallic ground plane without any performance penalty. A two pronged approach is taken to analyze MDWAs. In the first, antenna circuit models are derived for the prototypical dipole and loop elements that include the effects of realistic dispersive magneto-dielectric materials of construction. A material selection law results, showing that: (a) The maximum attainable efficiency is determined by a single magnetic material parameter that we term the hesitivity: Closely related to Snoek's product, it measures the maximum magnetic conductivity of the material. (b) The maximum bandwidth is obtained by placing the highest amount of μ" loss in the frequency range of operation. As a result, high radiation efficiency antennas can be obtained not only from the conventional low loss (low μ") materials but also with highly lossy materials (tan(δm)>>1). The second approach used to analyze MDWAs is through solving the Green function problem of the infinite magneto-dielectric cylinder fed by a current loop. This solution sheds light on the leaky and guided waves supported by the magneto-dielectric structure and leads to useful design rules connecting the permeability of the material to the cross sectional area of the antenna in relation to the desired frequency of operation. The Green function problem of the permeable prolate spheroidal antenna is also solved as a good approximation to a finite cylinder.
ContributorsSebastian, Tom (Author) / Diaz, Rodolfo E (Thesis advisor) / Pan, George (Committee member) / Aberle, James T., 1961- (Committee member) / Kozicki, Michael (Committee member) / Arizona State University (Publisher)
Created2013
Description
Microwave (MW), thermal, and ultraviolet (UV) annealing were used to explore the response of Ag structures on a Ge-Se chalcogenide glass (ChG) thin film as flexible radiation sensors, and Te-Ti chalcogenide thin films as a material for diffusion barriers in microelectronics devices and processing of metallized Cu. Flexible resistive radiation sensors consisting of Ag electrodes on a Ge20Se80 ChG thin film and polyethylene naphthalate substrate were exposed to UV radiation. The sensors were mounted on PVC tubes of varying radii to induce bending strains and annealed under ambient conditions up to 150 oC. Initial sensor resistance was measured to be ~1012 Ω; after exposure to UV radiation, the resistance was ~104 Ω. Bending strain and low temperature annealing had no significant effect on the resistance of the sensors. Samples of Cu on Te-Ti thin films were annealed in vacuum for up to 30 minutes and were stable up to 500 oC as revealed using Rutherford backscattering spectrometry (RBS) and four-point-probe analysis. X-ray diffractometry (XRD) indicates Cu grain growth up to 500 oC and phase instability of the Te-Ti barrier at 600 oC. MW processing was performed in a 2.45-GHz microwave cavity on Cu/Te-Ti films for up to 30 seconds to induce oxide growth. Using a calibrated pyrometer above the sample, the temperature of the MW process was measured to be below a maximum of 186 oC. Four-point-probe analysis shows an increase in resistance with an increase in MW time. XRD indicates growth of CuO on the sample surface. RBS suggests oxidation throughout the Te-Ti film. Additional samples were exposed to 907 J/cm2 UV radiation in order to ensure other possible electromagnetically induced mechanisms were not active. There were no changes observed using XRD, RBS or four point probing.
ContributorsRoos, Benjamin, 1990- (Author) / Alford, Terry L. (Thesis advisor) / Theodore, David (Committee member) / Kozicki, Michael (Committee member) / Arizona State University (Publisher)
Created2013
Description
Microbial mat communities that inhabit hot springs in Yellowstone National Park have been studied for their biodiversity, energetics and evolutionary history, yet little is know about how these communities cope with nutrient limitation. In the present study the changes in assimilatory gene expression levels for nitrogen (nrgA), phosphorus (phoA), and iron (yusV) were measured under various nutrient enrichment experiments. While results for nrgA and phoA were inconclusive, results for yusV showed an increase in expression with the addition of N and Fe. This is the first data that shows the impact of nutrients on siderophore uptake regulation in hot spring microbes.
ContributorsThorne, Michele (Author) / Elser, James J (Thesis advisor) / Touchman, Jeffrey (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2012
Description
The prevalence of antibiotic resistant bacterial pathogens has increased since the introduction of penicillin in the 1940s. Insufficient development of novel antibacterial agents is leaving us with a failing arsenal of therapies to combat these pathogenic organisms. We have identified a clay mineral mixture (designated CB) that exhibits in vitro antibacterial activity against a broad spectrum of bacterial pathogens, yet the antibacterial mechanism of action remains unknown. Antibacterial susceptibility testing of four different clay samples collected from the same source revealed that these natural clays had markedly different antibacterial activity. X-ray diffraction analyses of these minerals revealed minor mineralogical differences across the samples; however, ICP analyses demonstrated that the concentrations of many elements, Fe, Co, Cu, Ni, and Zn in particular, vary greatly across the four clay mixture leachates. Supplementation of a non-antibacterial leachate containing lower concentrations of Fe, Co, Ni, Cu, and Zn to final ion concentrations and a pH equivalent to that of the antibacterial leachate resulted in antibacterial activity against E. coli and MRSA, confirming the role of these ions in the in vitro antibacterial clay mixture leachates. The prevailing hypothesis is that metal ions participate in redox cycling and produce ROS, leading to oxidative damage to macromolecules and resulting in cellular death. However, E. coli cells showed no increase in DNA or protein oxidative lesions and a slight increase in lipid peroxidation following exposure to CB-L. Supplementation of CB-L with ROS scavengers eliminated oxidative damage in E. coli, but did not rescue the cells from killing, indicating that in vitro killing is due to direct metal toxicity and not to indirect oxidative damage. Finally, we ion-exchanged non-antibacterial clays with Fe, Co, Cu, and Zn and established antibacterial activity in these samples. Treatment of MRSA skin infections with both natural and ion-exchanged clays significantly decreased the bacterial load after 7 days of treatment. We conclude that 1) in vitro clay-mediated killing is due to toxicity associated directly with released metal ions and not to indirect oxidative damage and 2) that in vivo killing is due to the physical properties of the clays rather than metal ion toxicity.
ContributorsOtto, Caitin Carol (Author) / Haydel, Shelley (Thesis advisor) / Stout, Valerie (Committee member) / Roberson, Robby (Committee member) / Sandrin, Todd (Committee member) / Rege, Kaushal (Committee member) / Arizona State University (Publisher)
Created2014
Description
The design and development of analog/mixed-signal (AMS) integrated circuits (ICs) is becoming increasingly expensive, complex, and lengthy. Rapid prototyping and emulation of analog ICs will be significant in the design and testing of complex analog systems. A new approach, Programmable ANalog Device Array (PANDA) that maps any AMS design problem to a transistor-level programmable hardware, is proposed. This approach enables fast system level validation and a reduction in post-Silicon bugs, minimizing design risk and cost. The unique features of the approach include 1) transistor-level programmability that emulates each transistor behavior in an analog design, achieving very fine granularity of reconfiguration; 2) programmable switches that are treated as a design component during analog transistor emulating, and optimized with the reconfiguration matrix; 3) compensation of AC performance degradation through boosting the bias current. Based on these principles, a digitally controlled PANDA platform is designed at 45nm node that can map AMS modules across 22nm to 90nm technology nodes. A systematic emulation approach to map any analog transistor to 45nm PANDA cell is proposed, which achieves transistor level matching accuracy of less than 5% for ID and less than 10% for Rout and Gm. Circuit level analog metrics of a voltage-controlled oscillator (VCO) emulated by PANDA, match to those of the original designs in 22nm and 90nm nodes with less than a 5% error. Several other 90nm and 22nm analog blocks are successfully emulated by the 45nm PANDA platform, including a folded-cascode operational amplifier and a sample-and-hold module (S/H). Further capabilities of PANDA are demonstrated by the first full-chip silicon of PANDA which is implemented on 65nm process This system consists of a 24×25 cell array, reconfigurable interconnect and configuration memory. The voltage and current reference circuits, op amps and a VCO with a phase interpolation circuit are emulated by PANDA.
ContributorsSuh, Jounghyuk (Author) / Bakkaloglu, Bertan (Thesis advisor) / Cao, Yu (Committee member) / Ozev, Sule (Committee member) / Kozicki, Michael (Committee member) / Arizona State University (Publisher)
Created2013
Description
Pathogenic Gram-negative bacteria employ a variety of molecular mechanisms to combat host defenses. Two-component regulatory systems (TCR systems) are the most ubiquitous signal transduction systems which regulate many genes required for virulence and survival of bacteria. In this study, I analyzed different TCR systems in two clinically-relevant Gram-negative bacteria, i.e., oral pathogen Porphyromonas gingivalis and enterobacterial Escherichia coli. P. gingivalis is a major causative agent of periodontal disease as well as systemic illnesses, like cardiovascular disease. A microarray study found that the putative PorY-PorX TCR system controls the secretion and maturation of virulence factors, as well as loci involved in the PorSS secretion system, which secretes proteinases, i.e., gingipains, responsible for periodontal disease. Proteomic analysis (SILAC) was used to improve the microarray data, reverse-transcription PCR to verify the proteomic data, and primer extension assay to determine the promoter regions of specific PorX regulated loci. I was able to characterize multiple genetic loci regulated by this TCR system, many of which play an essential role in hemagglutination and host-cell adhesion, and likely contribute to virulence in this bacterium. Enteric Gram-negative bacteria must withstand many host defenses such as digestive enzymes, low pH, and antimicrobial peptides (AMPs). The CpxR-CpxA TCR system of E. coli has been extensively characterized and shown to be required for protection against AMPs. Most recently, this TCR system has been shown to up-regulate the rfe-rff operon which encodes genes involved in the production of enterobacterial common antigen (ECA), and confers protection against a variety of AMPs. In this study, I utilized primer extension and DNase I footprinting to determine how CpxR regulates the ECA operon. My findings suggest that CpxR modulates transcription by directly binding to the rfe promoter. Multiple genetic and biochemical approaches were used to demonstrate that specific TCR systems contribute to regulation of virulence factors and resistance to host defenses in P. gingivalis and E. coli, respectively. Understanding these genetic circuits provides insight into strategies for pathogenesis and resistance to host defenses in Gram negative bacterial pathogens. Finally, these data provide compelling potential molecular targets for therapeutics to treat P. gingivalis and E. coli infections.
ContributorsLeonetti, Cori (Author) / Shi, Yixin (Thesis advisor) / Stout, Valerie (Committee member) / Nickerson, Cheryl (Committee member) / Sandrin, Todd (Committee member) / Arizona State University (Publisher)
Created2013
Description
The advent of new high throughput technology allows for increasingly detailed characterization of the immune system in healthy, disease, and age states. The immune system is composed of two main branches: the innate and adaptive immune system, though the border between these two states is appearing less distinct. The adaptive immune system is further split into two main categories: humoral and cellular immunity. The humoral immune response produces antibodies against specific targets, and these antibodies can be used to learn about disease and normal states. In this document, I use antibodies to characterize the immune system in two ways: 1. I determine the Antibody Status (AbStat) from the data collected from applying sera to an array of non-natural sequence peptides, and demonstrate that this AbStat measure can distinguish between disease, normal, and aged samples as well as produce a single AbStat number for each sample; 2. I search for antigens for use in a cancer vaccine, and this search results in several candidates as well as a new hypothesis. Antibodies provide us with a powerful tool for characterizing the immune system, and this natural tool combined with emerging technologies allows us to learn more about healthy and disease states.
ContributorsWhittemore, Kurt (Author) / Sykes, Kathryn (Thesis advisor) / Johnston, Stephen A. (Committee member) / Jacobs, Bertram (Committee member) / Stafford, Phillip (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2014
Description
There is an ever growing need for larger memories which are reliable and fast. New technologies to implement non-volatile memories which are large, fast, compact and cost-efficient are being studied extensively. One of the most promising technologies being developed is the resistive RAM (ReRAM). In ReRAM the resistance of the device varies with the voltage applied across it. Programmable metallization cells (PMC) is one of the devices belonging to this category of non-volatile memories.
In order to advance the development of these devices, there is a need to develop simulation models which replicate the behavior of these devices in circuits. In this thesis, a verilogA model for the PMC has been developed. The behavior of the model has been tested using DC and transient simulations. Experimental data obtained from testing PMC devices fabricated at Arizona State University have been compared to results obtained from simulation.
A basic memory cell known as the 1T 1R cell built using the PMC has also been simulated and verified. These memory cells have the potential to be building blocks of large scale memories. I believe that the verilogA model developed in this thesis will prove to be a powerful tool for researchers and circuit developers looking to develop non-volatile memories using alternative technologies.
In order to advance the development of these devices, there is a need to develop simulation models which replicate the behavior of these devices in circuits. In this thesis, a verilogA model for the PMC has been developed. The behavior of the model has been tested using DC and transient simulations. Experimental data obtained from testing PMC devices fabricated at Arizona State University have been compared to results obtained from simulation.
A basic memory cell known as the 1T 1R cell built using the PMC has also been simulated and verified. These memory cells have the potential to be building blocks of large scale memories. I believe that the verilogA model developed in this thesis will prove to be a powerful tool for researchers and circuit developers looking to develop non-volatile memories using alternative technologies.
ContributorsBharadwaj, Vineeth (Author) / Barnaby, Hugh (Thesis advisor) / Kozicki, Michael (Committee member) / Mikkola, Esko (Committee member) / Arizona State University (Publisher)
Created2014
Description
Nonvolatile memory (NVM) technologies have been an integral part of electronic systems for the past 30 years. The ideal non-volatile memory have minimal physical size, energy usage, and cost while having maximal speed, capacity, retention time, and radiation hardness. A promising candidate for next-generation memory is ion-conducting bridging RAM which is referred to as programmable metallization cell (PMC), conductive bridge RAM (CBRAM), or electrochemical metallization memory (ECM), which is likely to surpass flash memory in all the ideal memory characteristics. A comprehensive physics-based model is needed to completely understand PMC operation and assist in design optimization.
To advance the PMC modeling effort, this thesis presents a precise physical model parameterizing materials associated with both ion-rich and ion-poor layers of the PMC's solid electrolyte, so that captures the static electrical behavior of the PMC in both its low-resistance on-state (LRS) and high resistance off-state (HRS). The experimental data is measured from a chalcogenide glass PMC designed and manufactured at ASU. The static on- and off-state resistance of a PMC device composed of a layered (Ag-rich/Ag-poor) Ge30Se70 ChG film is characterized and modeled using three dimensional simulation code written in Silvaco Atlas finite element analysis software. Calibrating the model to experimental data enables the extraction of device parameters such as material bandgaps, workfunctions, density of states, carrier mobilities, dielectric constants, and affinities.
The sensitivity of our modeled PMC to the variation of its prominent achieved material parameters is examined on the HRS and LRS impedance behavior.
The obtained accurate set of material parameters for both Ag-rich and Ag-poor ChG systems and process variation verification on electrical characteristics enables greater fidelity in PMC device simulation, which significantly enhances our ability to understand the underlying physics of ChG-based resistive switching memory.
To advance the PMC modeling effort, this thesis presents a precise physical model parameterizing materials associated with both ion-rich and ion-poor layers of the PMC's solid electrolyte, so that captures the static electrical behavior of the PMC in both its low-resistance on-state (LRS) and high resistance off-state (HRS). The experimental data is measured from a chalcogenide glass PMC designed and manufactured at ASU. The static on- and off-state resistance of a PMC device composed of a layered (Ag-rich/Ag-poor) Ge30Se70 ChG film is characterized and modeled using three dimensional simulation code written in Silvaco Atlas finite element analysis software. Calibrating the model to experimental data enables the extraction of device parameters such as material bandgaps, workfunctions, density of states, carrier mobilities, dielectric constants, and affinities.
The sensitivity of our modeled PMC to the variation of its prominent achieved material parameters is examined on the HRS and LRS impedance behavior.
The obtained accurate set of material parameters for both Ag-rich and Ag-poor ChG systems and process variation verification on electrical characteristics enables greater fidelity in PMC device simulation, which significantly enhances our ability to understand the underlying physics of ChG-based resistive switching memory.
ContributorsRajabi, Saba (Author) / Barnaby, Hugh (Thesis advisor) / Kozicki, Michael (Committee member) / Vasileska, Dragica (Committee member) / Arizona State University (Publisher)
Created2014