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.
Displaying 1 - 10 of 85
Description
The principle of Darwinian evolution has been applied in the laboratory to nucleic acid molecules since 1990, and led to the emergence of in vitro evolution technique. The methodology of in vitro evolution surveys a large number of different molecules simultaneously for a pre-defined chemical property, and enrich for molecules with the particular property. DNA and RNA sequences with versatile functions have been identified by in vitro selection experiments, but many basic questions remain to be answered about how these molecules achieve their functions. This dissertation first focuses on addressing a fundamental question regarding the molecular recognition properties of in vitro selected DNA sequences, namely whether negatively charged DNA sequences can be evolved to bind alkaline proteins with high specificity. We showed that DNA binders could be made, through carefully designed stringent in vitro selection, to discriminate different alkaline proteins. The focus of this dissertation is then shifted to in vitro evolution of an artificial genetic polymer called threose nucleic acid (TNA). TNA has been considered a potential RNA progenitor during early evolution of life on Earth. However, further experimental evidence to support TNA as a primordial genetic material is lacking. In this dissertation we demonstrated the capacity of TNA to form stable tertiary structure with specific ligand binding property, which suggests a possible role of TNA as a pre-RNA genetic polymer. Additionally, we discussed the challenges in in vitro evolution for TNA enzymes and developed the necessary methodology for future TNA enzyme evolution.
ContributorsYu, Hanyang (Author) / Chaput, John C (Thesis advisor) / Chen, Julian (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
The ribosome is a ribozyme and central to the biosynthesis of proteins in all organisms. It has a strong bias against non-alpha-L-amino acids, such as alpha-D-amino acids and beta-amino acids. Additionally, the ribosome is only able to incorporate one amino acid in response to one codon. It has been demonstrated that reengineering of the peptidyltransferase center (PTC) of the ribosome enabled the incorporation of both alpha-D-amino acids and beta-amino acids into full length protein. Described in Chapter 2 are five modified ribosomes having modifications in the peptidyltrasnferase center in the 23S rRNA. These modified ribosomes successfully incorporated five different beta-amino acids (2.1 - 2.5) into E. coli dihydrofolate reductase (DHFR). The second project (Chapter 3) focused on the study of the modified ribosomes facilitating the incorporation of the dipeptide glycylphenylalanine (3.25) and fluorescent dipeptidomimetic 3.26 into DHFR. These ribosomes also had modifications in the peptidyltransferase center in the 23S rRNA of the 50S ribosomal subunit. The modified DHFRs having beta-amino acids 2.3 and 2.5, dipeptide glycylphenylalanine (3.25) and dipeptidomimetic 3.26 were successfully characterized by the MALDI-MS analysis of the peptide fragments produced by "in-gel" trypsin digestion of the modified proteins. The fluorescent spectra of the dipeptidomimetic 3.26 and modified DHFR having fluorescent dipeptidomimetic 3.26 were also measured. The type I and II DNA topoisomerases have been firmly established as effective molecular targets for many antitumor drugs. A "classical" topoisomerase I or II poison acts by misaligning the free hydroxyl group of the sugar moiety of DNA and preventing the reverse transesterfication reaction to religate DNA. There have been only two classes of compounds, saintopin and topopyrones, reported as dual topoisomerase I and II poisons. Chapter 4 describes the synthesis and biological evaluation of topopyrones. Compound 4.10, employed at 20 µM, was as efficient as 0.5 uM camptothecin, a potent topoisomerase I poison, in stabilizing the covalent binary complex (~30%). When compared with a known topoisomerase II poison, etoposide (at 0.5 uM), topopyorone 4.10 produced similar levels of stabilized DNA-enzyme binary complex (~34%) at 5 uM concentration.
ContributorsMaini, Rumit (Author) / Hecht, Sidney M. (Thesis advisor) / Gould, Ian (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
The biological and chemical diversity of protein structure and function can be greatly expanded by position-specific incorporation of non-natural amino acids bearing a variety of functional groups. Non-cognate amino acids can be incorporated into proteins at specific sites by using orthogonal aminoacyl-tRNA synthetase/tRNA pairs in conjunction with nonsense, rare, or 4-bp codons. There has been considerable progress in developing new types of amino acids, in identifying novel methods of tRNA aminoacylation, and in expanding the genetic code to direct their position. Chemical aminoacylation of tRNAs is accomplished by acylation and ligation of a dinucleotide (pdCpA) to the 3'-terminus of truncated tRNA. This strategy allows the incorporation of a wide range of natural and unnatural amino acids into pre-determined sites, thereby facilitating the study of structure-function relationships in proteins and allowing the investigation of their biological, biochemical and biophysical properties. Described in Chapter 1 is the current methodology for synthesizing aminoacylated suppressor tRNAs. Aminoacylated suppressor tRNACUAs are typically prepared by linking pre-aminoacylated dinucleotides (aminoacyl-pdCpAs) to 74 nucleotide (nt) truncated tRNAs (tRNA-COH) via a T4 RNA ligase mediated reaction. Alternatively, there is another route outlined in Chapter 1 that utilizes a different pre-aminoacylated dinucleotide, AppA. This dinucleotide has been shown to be a suitable substrate for T4 RNA ligase mediated coupling with abbreviated tRNA-COHs for production of 76 nt aminoacyl-tRNACUAs. The synthesized suppressor tRNAs have been shown to participate in protein synthesis in vitro, in an S30 (E. coli) coupled transcription-translation system in which there is a UAG codon in the mRNA at the position corresponding to Val10. Chapter 2 describes the synthesis of two non-proteinogenic amino acids, L-thiothreonine and L-allo-thiothreonine, and their incorporation into predetermined positions of a catalytically competent dihydrofolate reductase (DHFR) analogue lacking cysteine. Here, the elaborated proteins were site-specifically derivitized with a fluorophore at the thiothreonine residue. The synthesis and incorporation of phosphorotyrosine derivatives into DHFR is illustrated in Chapter 3. Three different phosphorylated tyrosine derivatives were prepared: bis-nitrobenzylphosphoro-L-tyrosine, nitrobenzylphosphoro-L-tyrosine, and phosphoro-L-tyrosine. Their ability to participate in a protein synthesis system was also evaluated.
ContributorsNangreave, Ryan Christopher (Author) / Hecht, Sidney M. (Thesis advisor) / Yan, Hao (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2013
Description
Solution conformations and dynamics of proteins and protein-DNA complexes are often difficult to predict from their crystal structures. The crystal structure only shows a snapshot of the different conformations these biological molecules can have in solution. Multiple different conformations can exist in solution and potentially have more importance in the biological activity. DNA sliding clamps are a family of proteins with known crystal structures. These clamps encircle the DNA and enable other proteins to interact more efficiently with the DNA. Eukaryotic PCNA and prokaryotic β clamp are two of these clamps, some of the most stable homo-oligomers known. However, their solution stability and conformational equilibrium have not been investigated in depth before. Presented here are the studies involving two sliding clamps: yeast PCNA and bacterial β clamp. These studies show that the β clamp has a very different solution stability than PCNA. These conclusions were reached through various different fluorescence-based experiments, including fluorescence correlation spectroscopy (FCS), Förster resonance energy transfer (FRET), single molecule fluorescence, and various time resolved fluorescence techniques. Interpretations of these, and all other, fluorescence-based experiments are often affected by the properties of the fluorophores employed. Often the fluorescence properties of these fluorophores are influenced by their microenvironments. Fluorophores are known to sometimes interact with biological molecules, and this can have pronounced effects on the rotational mobility and photophysical properties of the dye. Misunderstanding the effect of these photophysical and rotational properties can lead to a misinterpretation of the obtained data. In this thesis, photophysical behaviors of various organic dyes were studied in the presence of deoxymononucleotides to examine more closely how interactions between fluorophores and DNA bases can affect fluorescent properties. Furthermore, the properties of cyanine dyes when bound to DNA and the effect of restricted rotation on FRET are presented in this thesis. This thesis involves studying fluorophore photophysics in various microenvironments and then expanding into the solution stability and dynamics of the DNA sliding clamps.
ContributorsRanjit, Suman (Author) / Levitus, Marcia (Thesis advisor) / Lindsay, Stuart (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
Photovoltaic (PV) module nameplates typically provide the module's electrical characteristics at standard test conditions (STC). The STC conditions are: irradiance of 1000 W/m2, cell temperature of 25oC and sunlight spectrum at air mass 1.5. However, modules in the field experience a wide range of environmental conditions which affect their electrical characteristics and render the nameplate data insufficient in determining a module's overall, actual field performance. To make sound technical and financial decisions, designers and investors need additional performance data to determine the energy produced by modules operating under various field conditions. The angle of incidence (AOI) of sunlight on PV modules is one of the major parameters which dictate the amount of light reaching the solar cells. The experiment was carried out at the Arizona State University- Photovoltaic Reliability Laboratory (ASU-PRL). The data obtained was processed in accordance with the IEC 61853-2 model to obtain relative optical response of the modules (response which does not include the cosine effect). The results were then compared with theoretical models for air-glass interface and also with the empirical model developed by Sandia National Laboratories. The results showed that all modules with glass as the superstrate had identical optical response and were in agreement with both the IEC 61853-2 model and other theoretical and empirical models. The performance degradation of module over years of exposure in the field is dependent upon factors such as environmental conditions, system configuration, etc. Analyzing the degradation of power and other related performance parameters over time will provide vital information regarding possible degradation rates and mechanisms of the modules. An extensive study was conducted by previous ASU-PRL students on approximately 1700 modules which have over 13 years of hot- dry climatic field condition. An analysis of the results obtained in previous ASU-PRL studies show that the major degradation in crystalline silicon modules having glass/polymer construction is encapsulant discoloration (causing short circuit current drop) and solder bond degradation (causing fill factor drop due to series resistance increase). The power degradation for crystalline silicon modules having glass/glass construction was primarily attributed to encapsulant delamination (causing open-circuit voltage drop).
ContributorsVasantha Janakeeraman, Suryanarayana (Author) / Tamizhmani, Govindasamy (Thesis advisor) / Rogers, Bradley (Committee member) / Macia, Narciso (Committee member) / Arizona State University (Publisher)
Created2013
Description
The object of this study was a 26 year old residential Photovoltaic (PV) monocrystalline silicon (c-Si) power plant, called Solar One, built by developer John F. Long in Phoenix, Arizona (a hot-dry field condition). The task for Arizona State University Photovoltaic Reliability Laboratory (ASU-PRL) graduate students was to evaluate the power plant through visual inspection, electrical performance, and infrared thermography. The purpose of this evaluation was to measure and understand the extent of degradation to the system along with the identification of the failure modes in this hot-dry climatic condition. This 4000 module bipolar system was originally installed with a 200 kW DC output of PV array (17 degree fixed tilt) and an AC output of 175 kVA. The system was shown to degrade approximately at a rate of 2.3% per year with no apparent potential induced degradation (PID) effect. The power plant is made of two arrays, the north array and the south array. Due to a limited time frame to execute this large project, this work was performed by two masters students (Jonathan Belmont and Kolapo Olakonu) and the test results are presented in two masters theses. This thesis presents the results obtained on the north array and the other thesis presents the results obtained on the south array. The resulting study showed that PV module design, array configuration, vandalism, installation methods and Arizona environmental conditions have had an effect on this system's longevity and reliability. Ultimately, encapsulation browning, higher series resistance (potentially due to solder bond fatigue) and non-cell interconnect ribbon breakages outside the modules were determined to be the primary causes for the power loss.
ContributorsBelmont, Jonathan (Author) / Tamizhmani, Govindasamy (Thesis advisor) / Henderson, Mark (Committee member) / Rogers, Bradley (Committee member) / Arizona State University (Publisher)
Created2013
Description
Single molecule DNA Sequencing technology has been a hot research topic in the recent decades because it holds the promise to sequence a human genome in a fast and affordable way, which will eventually make personalized medicine possible. Single molecule differentiation and DNA translocation control are the two main challenges in all single molecule DNA sequencing methods. In this thesis, I will first introduce DNA sequencing technology development and its application, and then explain the performance and limitation of prior art in detail. Following that, I will show a single molecule DNA base differentiation result obtained in recognition tunneling experiments. Furthermore, I will explain the assembly of a nanofluidic platform for single strand DNA translocation, which holds the promised to be integrated into a single molecule DNA sequencing instrument for DNA translocation control. Taken together, my dissertation research demonstrated the potential of using recognition tunneling techniques to serve as a general readout system for single molecule DNA sequencing application.
ContributorsLiu, Hao (Author) / Lindsay, Stuart M (Committee member) / Yan, Hao (Committee member) / Levitus, Marcia (Committee member) / Arizona State University (Publisher)
Created2013
Description
Potential induced degradation (PID) due to high system voltages is one of the major degradation mechanisms in photovoltaic (PV) modules, adversely affecting their performance due to the combined effects of the following factors: system voltage, superstrate/glass surface conductivity, encapsulant conductivity, silicon nitride anti-reflection coating property and interface property (glass/encapsulant; encapsulant/cell; encapsulant/backsheet). Previous studies carried out at ASU's Photovoltaic Reliability Laboratory (ASU-PRL) showed that only negative voltage bias (positive grounded systems) adversely affects the performance of commonly available crystalline silicon modules. In previous studies, the surface conductivity of the glass surface was obtained using either conductive carbon layer extending from the glass surface to the frame or humidity inside an environmental chamber. This thesis investigates the influence of glass surface conductivity disruption on PV modules. In this study, conductive carbon was applied only on the module's glass surface without extending to the frame and the surface conductivity was disrupted (no carbon layer) at 2cm distance from the periphery of frame inner edges. This study was carried out under dry heat at two different temperatures (60 °C and 85 °C) and three different negative bias voltages (-300V, -400V, and -600V). To replicate closeness to the field conditions, half of the selected modules were pre-stressed under damp heat for 1000 hours (DH 1000) and the remaining half under 200 hours of thermal cycling (TC 200). When the surface continuity was disrupted by maintaining a 2 cm gap from the frame to the edge of the conductive layer, as demonstrated in this study, the degradation was found to be absent or negligibly small even after 35 hours of negative bias at elevated temperatures. This preliminary study appears to indicate that the modules could become immune to PID losses if the continuity of the glass surface conductivity is disrupted at the inside boundary of the frame. The surface conductivity of the glass, due to water layer formation in a humid condition, close to the frame could be disrupted just by applying a water repelling (hydrophobic) but high transmittance surface coating (such as Teflon) or modifying the frame/glass edges with water repellent properties.
ContributorsTatapudi, Sai Ravi Vasista (Author) / Tamizhmani, Govindasamy (Thesis advisor) / Srinivasan, Devarajan (Committee member) / Rogers, Bradley (Committee member) / Arizona State University (Publisher)
Created2012
Description
ABSTRACT As the use of photovoltaic (PV) modules in large power plants continues to increase globally, more studies on degradation, reliability, failure modes, and mechanisms of field aged modules are needed to predict module life expectancy based on accelerated lifetime testing of PV modules. In this work, a 26+ year old PV power plant in Phoenix, Arizona has been evaluated for performance, reliability, and durability. The PV power plant, called Solar One, is owned and operated by John F. Long's homeowners association. It is a 200 kWdc, standard test conditions (STC) rated power plant comprised of 4000 PV modules or frameless laminates, in 100 panel groups (rated at 175 kWac). The power plant is made of two center-tapped bipolar arrays, the north array and the south array. Due to a limited time frame to execute this large project, this work was performed by two masters students (Jonathan Belmont and Kolapo Olakonu) and the test results are presented in two masters theses. This thesis presents the results obtained on the south array and the other thesis presents the results obtained on the north array. Each of these two arrays is made of four sub arrays, the east sub arrays (positive and negative polarities) and the west sub arrays (positive and negative polarities), making up eight sub arrays. The evaluation and analyses of the power plant included in this thesis consists of: visual inspection, electrical performance measurements, and infrared thermography. A possible presence of potential induced degradation (PID) due to potential difference between ground and strings was also investigated. Some installation practices were also studied and found to contribute to the power loss observed in this investigation. The power output measured in 2011 for all eight sub arrays at STC is approximately 76 kWdc and represents a power loss of 62% (from 200 kW to 76 kW) over 26+ years. The 2011 measured power output for the four south sub arrays at STC is 39 kWdc and represents a power loss of 61% (from 100 kW to 39 kW) over 26+ years. Encapsulation browning and non-cell interconnect ribbon breakages were determined to be the primary causes for the power loss.
ContributorsOlakonu, Kolapo (Author) / Tamizhmani, Govindasamy (Thesis advisor) / Srinivasan, Devarajan (Committee member) / Rogers, Bradley (Committee member) / Arizona State University (Publisher)
Created2012
Description
The F1Fo ATP synthase is required for energy conversion in almost all living organisms. The F1 complex is a molecular motor that uses ATP hydrolysis to drive rotation of the γ–subunit. It has not been previously possible to resolve the speed and position of the γ–subunit of the F1–ATPase as it rotates during a power stroke. The single molecule experiments presented here measured light scattered from 45X91 nm gold nanorods attached to the γ–subunit that provide an unprecedented 5 μs resolution of rotational position as a function of time. The product of velocity and drag, which were both measured directly, resulted in an average torque of 63±8 pN nm for the Escherichia coli F1-ATPase that was determined to be independent of the load. The rotational velocity had an initial (I) acceleration phase 15° from the end of the catalytic dwell, a slow (S) acceleration phase during ATP binding/ADP release (15°–60°), and a fast (F) acceleration phase (60°–90°) containing an interim deceleration (ID) phase (75°–82°). High ADP concentrations decreased the velocity of the S phase proportional to 'ADP-release' dwells, and the F phase proportional to the free energy derived from the [ADP][Pi]/[ATP] chemical equilibrium. The decreased affinity for ITP increased ITP-binding dwells by 10%, but decreased velocity by 40% during the S phase. This is the first direct evidence that nucleotide binding contributes to F1–ATPase torque. Mutations that affect specific phases of rotation were identified, some in regions of F1 previously considered not to contribute to rotation. Mutations βD372V and γK9I increased the F phase velocity, and γK9I increased the depth of the ID phase. The conversion between S and F phases was specifically affected by γQ269L. While βT273D, βD305E, and αR283Q decreased the velocity of all phases, decreases in velocity due to βD302T, γR268L and γT82A were confined to the I and S phases. The correlations between the structural locations of these mutations and the phases of rotation they affect provide new insight into the molecular basis for F1–ATPase γ-subunit rotation.
ContributorsMartin, James (Author) / Frasch, Wayne D (Thesis advisor) / Chandler, Douglas (Committee member) / Gaxiola, Roberto (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2012