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 164
Description
The concept of vaccination dates back further than Edward Jenner's first vaccine using cowpox pustules to confer immunity against smallpox in 1796. Nevertheless, it was Jenner's success that gave vaccines their name and made vaccinia virus (VACV) of particular interest. More than 200 years later there is still the need to understand vaccination from vaccine design to prediction of vaccine efficacy using mathematical models. Post-exposure vaccination with VACV has been suggested to be effective if administered within four days of smallpox exposure although this has not been definitively studied in humans. The first and second chapters analyze post-exposure prophylaxis of VACV in an animal model using v50ΔB13RMγ, a recombinant VACV expressing murine interferon gamma (IFN-γ) also known as type II IFN. While untreated animals infected with wild type VACV die by 10 days post-infection (dpi), animals treated with v50ΔB13RMγ 1 dpi had decreased morbidity and 100% survival. Despite these differences, the viral load was similar in both groups suggesting that v50ΔB13RMγ acts as an immunoregulator rather than as an antiviral. One of the main characteristics of VACV is its resistance to type I IFN, an effect primarily mediated by the E3L protein, which has a Z-DNA binding domain and a double-stranded RNA (dsRNA) binding domain. In the third chapter a VACV that independently expresses both domains of E3L was engineered and compared to wild type in cells in culture. The dual expression virus was unable to replicate in the JC murine cell line where both domains are needed together for replication. Moreover, phosphorylation of the dsRNA dependent protein kinase (PKR) was observed at late times post-infection which indicates that both domains need to be linked together in order to block the IFN response. Because smallpox has already been eradicated, the utility of mathematical modeling as a tool for predicting disease spread and vaccine efficacy was explored in the last chapter using dengue as a disease model. Current modeling approaches were reviewed and the 2000-2001 dengue outbreak in a Peruvian region was analyzed. This last section highlights the importance of interdisciplinary collaboration and how it benefits research on infectious diseases.
ContributorsHolechek, Susan A (Author) / Jacobs, Bertram L (Thesis advisor) / Castillo-Chavez, Carlos (Committee member) / Frasch, Wayne (Committee member) / Hogue, Brenda (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2011
Description
Radiation-induced gain degradation in bipolar devices is considered to be the primary threat to linear bipolar circuits operating in the space environment. The damage is primarily caused by charged particles trapped in the Earth's magnetosphere, the solar wind, and cosmic rays. This constant radiation exposure leads to early end-of-life expectancies for many electronic parts. Exposure to ionizing radiation increases the density of oxide and interfacial defects in bipolar oxides leading to an increase in base current in bipolar junction transistors. Radiation-induced excess base current is the primary cause of current gain degradation. Analysis of base current response can enable the measurement of defects generated by radiation exposure. In addition to radiation, the space environment is also characterized by extreme temperature fluctuations. Temperature, like radiation, also has a very strong impact on base current. Thus, a technique for separating the effects of radiation from thermal effects is necessary in order to accurately measure radiation-induced damage in space. This thesis focuses on the extraction of radiation damage in lateral PNP bipolar junction transistors and the space environment. It also describes the measurement techniques used and provides a quantitative analysis methodology for separating radiation and thermal effects on the bipolar base current.
ContributorsCampola, Michael J (Author) / Barnaby, Hugh J (Thesis advisor) / Holbert, Keith E. (Committee member) / Vasileska, Dragica (Committee member) / Arizona State University (Publisher)
Created2011
Description
HIV/AIDS is the sixth leading cause of death worldwide and the leading cause of death among women of reproductive age living in low-income countries. Clinicians in industrialized nations monitor the efficacy of antiretroviral drugs and HIV disease progression with the HIV-1 viral load assay, which measures the copy number of HIV-1 RNA in blood. However, viral load assays are not widely available in sub-Saharan Africa and cost between 50-$139 USD per test on average where available. To address this problem, a mixed-methods approach was undertaken to design a novel and inexpensive viral load diagnostic for HIV-1 and to evaluate barriers to its adoption in a developing country. The assay was produced based on loop-mediated isothermal amplification (LAMP). Blood samples from twenty-one individuals were spiked with varying concentrations of HIV-1 RNA to evaluate the sensitivity and specificity of LAMP. Under isothermal conditions, LAMP was performed with an initial reverse-transcription step (RT-LAMP) and primers designed for HIV-1 subtype C. Each reaction generated up to a few billion copies of target DNA within an hour. Presence of target was detected through naked-eye observation of a fluorescent indicator and verified by DNA gel electrophoresis and real-time fluorescence. The assay successfully detected the presence of HIV in samples with a broad range of HIV RNA concentration, from over 120,000 copies/reaction to 120 copies/reaction. In order to better understand barriers to adoption of LAMP in developing countries, a feasibility study was undertaken in Tanzania, a low-income country facing significant problems in healthcare. Medical professionals in Northern Tanzania were surveyed for feedback regarding perspectives of current HIV assays, patient treatment strategies, availability of treatment, treatment priorities, HIV transmission, and barriers to adoption of the HIV-1 LAMP assay. The majority of medical providers surveyed indicated that the proposed LAMP assay is too expensive for their patient populations. Significant gender differences were observed in response to some survey questions. Female medical providers were more likely to cite stigma as a source problem of the HIV epidemic than male medical providers while males were more likely to cite lack of education as a source problem than female medical providers.
ContributorsSalamone, Damien Thomas (Author) / Jacobs, Bertram L (Thesis advisor) / Marsiglia, Flavio (Committee member) / Stout, Valerie (Committee member) / Johnson, Crista (Committee member) / Arizona State University (Publisher)
Created2011
Description
There will always be a need for high current/voltage transistors. A transistor that has the ability to be both or either of these things is the silicon metal-silicon field effect transistor (MESFET). An additional perk that silicon MESFET transistors have is the ability to be integrated into the standard silicon on insulator (SOI) complementary metal oxide semiconductor (CMOS) process flow. This makes a silicon MESFET transistor a very valuable device for use in any standard CMOS circuit that may usually need a separate integrated circuit (IC) in order to switch power on or from a high current/voltage because it allows this function to be performed with a single chip thereby cutting costs. The ability for the MESFET to cost effectively satisfy the needs of this any many other high current/voltage device application markets is what drives the study of MESFET optimization. Silicon MESFETs that are integrated into standard SOI CMOS processes often receive dopings during fabrication that would not ideally be there in a process made exclusively for MESFETs. Since these remnants of SOI CMOS processing effect the operation of a MESFET device, their effect can be seen in the current-voltage characteristics of a measured MESFET device. Device simulations are done and compared to measured silicon MESFET data in order to deduce the cause and effect of many of these SOI CMOS remnants. MESFET devices can be made in both fully depleted (FD) and partially depleted (PD) SOI CMOS technologies. Device simulations are used to do a comparison of FD and PD MESFETs in order to show the advantages and disadvantages of MESFETs fabricated in different technologies. It is shown that PD MESFET have the highest current per area capability. Since the PD MESFET is shown to have the highest current capability, a layout optimization method to further increase the current per area capability of the PD silicon MESFET is presented, derived, and proven to a first order.
ContributorsSochacki, John (Author) / Thornton, Trevor J (Thesis advisor) / Schroder, Dieter (Committee member) / Vasileska, Dragica (Committee member) / Goryll, Michael (Committee member) / Arizona State University (Publisher)
Created2011
Description
In very small electronic devices the alternate capture and emission of carriers at an individual defect site located at the interface of Si:SiO2 of a MOSFET generates discrete switching in the device conductance referred to as a random telegraph signal (RTS) or random telegraph noise (RTN). In this research work, the integration of random defects positioned across the channel at the Si:SiO2 interface from source end to the drain end in the presence of different random dopant distributions are used to conduct Ensemble Monte-Carlo ( EMC ) based numerical simulation of key device performance metrics for 45 nm gate length MOSFET device. The two main performance parameters that affect RTS based reliability measurements are percentage change in threshold voltage and percentage change in drain current fluctuation in the saturation region. It has been observed as a result of the simulation that changes in both and values moderately decrease as the defect position is gradually moved from source end to the drain end of the channel. Precise analytical device physics based model needs to be developed to explain and assess the EMC simulation based higher VT fluctuations as experienced for trap positions at the source side. A new analytical model has been developed that simultaneously takes account of dopant number variations in the channel and depletion region underneath and carrier mobility fluctuations resulting from fluctuations in surface potential barriers. Comparisons of this new analytical model along with existing analytical models are shown to correlate with 3D EMC simulation based model for assessment of VT fluctuations percentage induced by a single interface trap. With scaling of devices beyond 32 nm node, halo doping at the source and drain are routinely incorporated to combat the threshold voltage roll-off that takes place with effective channel length reduction. As a final study on this regard, 3D EMC simulation method based computations of threshold voltage fluctuations have been performed for varying source and drain halo pocket length to illustrate the threshold voltage fluctuations related reliability problems that have been aggravated by trap positions near the source at the interface compared to conventional 45 nm MOSFET.
ContributorsAshraf, Nabil Shovon (Author) / Vasileska, Dragica (Thesis advisor) / Schroder, Dieter (Committee member) / Goodnick, Stephen (Committee member) / Goryll, Michael (Committee member) / Arizona State University (Publisher)
Created2011
Description
The past two decades have been monumental in the advancement of microchips designed for a diverse range of medical applications and bio-analysis. Owing to the remarkable progress in micro-fabrication technology, complex chemical and electro-mechanical features can now be integrated into chip-scale devices for use in biosensing and physiological measurements. Some of these devices have made enormous contributions in the study of complex biochemical processes occurring at the molecular and cellular levels while others overcame the challenges of replicating various functions of human organs as implant systems. This thesis presents test data and analysis of two such systems. First, an ISFET based pH sensor is characterized for its performance in a continuous pH monitoring application. Many of the basic properties of ISFETs including I-V characteristics, pH sensitivity and more importantly, its long term drift behavior have been investigated. A new theory based on frequent switching of electric field across the gate oxide to decrease the rate of current drift has been successfully implemented with the help of an automated data acquisition and switching system. The system was further tested for a range of duty cycles in order to accurately determine the minimum length of time required to fully reset the drift. Second, a microfluidic based vestibular implant system was tested for its underlying characteristics as a light sensor. A computer controlled tilt platform was then implemented to further test its sensitivity to inclinations and thus it‟s more important role as a tilt sensor. The sensor operates through means of optoelectronics and relies on the signals generated from photodiode arrays as a result of light being incident on them. ISFET results show a significant drop in the overall drift and good linear characteristics. The drift was seen to reset at less than an hour. The photodiodes show ideal I-V comparison between photoconductive and photovoltaic modes of operation with maximum responsivity at 400nm and a shunt resistance of 394 MΩ. Additionally, post-processing of the tilt sensor to incorporate the sensing fluids is outlined. Based on several test and fabrication results, a possible method of sealing the open cavity of the chip using a UV curable epoxy has been discussed.
ContributorsMamun, Samiha (Author) / Christen, Jennifer Blain (Thesis advisor) / Goryll, Michael (Committee member) / Yu, Hongyu (Committee member) / Arizona State University (Publisher)
Created2011
Description
Rhodoferax antarcticus strain ANT.BR, a purple nonsulfur bacterium isolated from a microbial mat in Ross Island, Antarctica, is the first described anoxygenic phototrophic bacterium that is adapted to cold habitats and is the first beta-proteobacterium to undergo complete genome sequencing. R. antarcticus has unique absorption spectra and there are no obvious intracytoplasmic membranes in cells grown phototrophically, even under low light intensity. Analysis of the finished genome sequence reveals a single chromosome (3,809,266 bp) and a large plasmid (198,615 bp) that together harbor 4,262 putative genes. The genome contains two types of Rubiscos, Form IAq and Form II, which are known to exhibit quite different kinetic properties in other bacteria. The presence of multiple Rubisco forms could give R. antarcticus high metabolic flexibility in diverse environments. Annotation of the complete genome sequence along with previous experimental results predict the presence of structural genes for three types of light-harvesting (LH) complexes, LH I (B875), LH II (B800/850), and LH III (B800/820). There is evidence that expression of genes for the LH II complex might be inhibited when R. antarcticus is under low temperature and/or low light intensity. These interesting condition-dependent light-harvesting apparatuses and the control of their expression are very valuable for the further understanding of photosynthesis in cold environments. Finally, R. antarcticus exhibits a highly motile lifestyle. The genome content and organization of all putative polar flagella genes are characterized and discussed.
ContributorsZhao, Tingting, M.S (Author) / Touchman, Jeffrey (Thesis advisor) / Rosenberg, Michael (Committee member) / Redding, Kevin (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2011
Description
The oceans play an essential role in global biogeochemical cycles and in regulating climate. The biological carbon pump, the photosynthetic fixation of carbon dioxide by phytoplankton and subsequent sequestration of organic carbon into deep water, combined with the physical carbon pump, make the oceans the only long-term net sink for anthropogenic carbon dioxide. A full understanding of the workings of the biological carbon pump requires a knowledge of the role of different taxonomic groups of phytoplankton (protists and cyanobacteria) to organic carbon export. However, this has been difficult due to the degraded nature of particles sinking into particle traps, the main tools employed by oceanographers to collect sinking particulate matter in the ocean. In this study DNA-based molecular methods, including denaturing gradient gel electrophoresis, cloning and sequencing, and taxon-specific quantitative PCR, allowed for the first time for the identification of which protists and cyanobacteria contributed to the material collected by the traps in relation to their presence in the euphotic zone. I conducted this study at two time-series stations in the subtropical North Atlantic Ocean, one north of the Canary Islands, and one located south of Bermuda. The Bermuda study allowed me to investigate seasonal and interannual changes in the contribution of the plankton community to particle flux. I could also show that small unarmored taxa, including representatives of prasinophytes and cyanobacteria, constituted a significant fraction of sequences recovered from sediment trap material. Prasinophyte sequences alone could account for up to 13% of the clone library sequences of trap material during bloom periods. These observations contradict a long-standing paradigm in biological oceanography that only large taxa with mineral shells are capable of sinking while smaller, unarmored cells are recycled in the euphotic zone through the microbial loop. Climate change and a subsequent warming of the surface ocean may lead to a shift in the protist community toward smaller cell size in the future, but in light of these findings these changes may not necessarily lead to a reduction in the strength of the biological carbon pump.
ContributorsAmacher, Jessica (Author) / Neuer, Susanne (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Lomas, Michael (Committee member) / Wojciechowski, Martin (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2011
Description
A primary motivation of research in photovoltaic technology is to obtain higher efficiency photovoltaic devices at reduced cost of production so that solar electricity can be cost competitive. The majority of photovoltaic technologies are based on p-n junction, with efficiency potential being much lower than the thermodynamic limits of individual technologies and thereby providing substantial scope for further improvements in efficiency. The thesis explores photovoltaic devices using new physical processes that rely on thin layers and are capable of attaining the thermodynamic limit of photovoltaic technology. Silicon heterostructure is one of the candidate technologies in which thin films induce a minority carrier collecting junction in silicon and the devices can achieve efficiency close to the thermodynamic limits of silicon technology. The thesis proposes and experimentally establishes a new theory explaining the operation of silicon heterostructure solar cells. The theory will assist in identifying the optimum properties of thin film materials for silicon heterostructure and help in design and characterization of the devices, along with aiding in developing new devices based on this technology. The efficiency potential of silicon heterostructure is constrained by the thermodynamic limit (31%) of single junction solar cell and is considerably lower than the limit of photovoltaic conversion (~ 80 %). A further improvement in photovoltaic conversion efficiency is possible by implementing a multiple quasi-fermi level system (MQFL). A MQFL allows the absorption of sub band gap photons with current being extracted at a higher band-gap, thereby allowing to overcome the efficiency limit of single junction devices. A MQFL can be realized either by thin epitaxial layers of alternating higher and lower band gap material with nearly lattice matched (quantum well) or highly lattice mismatched (quantum dot) structure. The thesis identifies the material combination for quantum well structure and calculates the absorption coefficient of a MQFl based on quantum well. GaAsSb (barrier)/InAs(dot) was identified as a candidate material for MQFL using quantum dot. The thesis explains the growth mechanism of GaAsSb and the optimization of GaAsSb and GaAs heterointerface.
ContributorsGhosha, Kuṇāla (Author) / Bowden, Stuart (Thesis advisor) / Honsberg, Christiana (Thesis advisor) / Vasileska, Dragica (Committee member) / Goodnick, Stephen (Committee member) / Arizona State University (Publisher)
Created2011
Description
Semiconductor devices are generally analyzed with relatively simple equations or with detailed computer simulations. Most text-books use these simple equations and show device diagrams that are frequently very simplified and occasionally incorrect. For example, the carrier densities near the pinch-off point in MOSFETs and JFETs and the minority carrier density in the base near the reverse-biased base-collector junction are frequently assumed to be zero or near zero. Also the channel thickness at the pinch-off point is often shown to approach zero. None of these assumptions can be correct. The research in thesis addresses these points. I simulated the carrier densities, potentials, electric fields etc. of MOSFETs, BJTs and JFETs at and near the pinch-off regions to determine exactly what happens there. I also simulated the behavior of the quasi-Fermi levels. For MOSFETs, the channel thickness expands slightly before the pinch-off point and then spreads out quickly in a triangular shape and the space-charge region under the channel actually shrinks as the potential increases from source to drain. For BJTs, with collector-base junction reverse biased, most minority carriers diffuse through the base from emitter to collector very fast, but the minority carrier concentration at the collector-base space-charge region is not zero. For JFETs, the boundaries of the space-charge region are difficult to determine, the channel does not disappear after pinch off, the shape of channel is always tapered, and the carrier concentration in the channel decreases progressively. After simulating traditional sized devices, I also simulated typical nano-scaled devices and show that they behave similarly to large devices. These simulation results provide a more complete understanding of device physics and device operation in those regions usually not addressed in semiconductor device physics books.
ContributorsYang, Xuan (Author) / Schroder, Dieter K. (Thesis advisor) / Vasileska, Dragica (Committee member) / Yu, Hongbin (Committee member) / Arizona State University (Publisher)
Created2011