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 93
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
An embedded HVDC system is a dc link with at least two ends being physically connected within a single synchronous ac network. The thesis reviews previous works on embedded HVDC, proposes a dynamic embedded HVDC model by PSCAD program, and compares the transient stability performance among AC, DC and embedded HVDC. The test results indicate that by installing the embedded HVDC, AC network transient stability performance has been largely improved. Therefore the thesis designs a novel frequency control topology for embedded HVDC. According to the dynamic performance test results, when the embedded HVDC system equipped with a frequency control, the system transient stability will be improved further.
ContributorsYu, Jicheng (Author) / Karady, George G. (Thesis advisor) / Hui, Yu (Committee member) / Holbert, Keith E. (Committee member) / Arizona State University (Publisher)
Created2013
Description
Recent trends in the electric power industry have led to more attention to optimal operation of power transformers. In a deregulated environment, optimal operation means minimizing the maintenance and extending the life of this critical and costly equipment for the purpose of maximizing profits. Optimal utilization of a transformer can be achieved through the use of dynamic loading. A benefit of dynamic loading is that it allows better utilization of the transformer capacity, thus increasing the flexibility and reliability of the power system. This document presents the progress on a software application which can estimate the maximum time-varying loading capability of transformers. This information can be used to load devices closer to their limits without exceeding the manufacturer specified operating limits. The maximally efficient dynamic loading of transformers requires a model that can accurately predict both top-oil temperatures (TOTs) and hottest-spot temperatures (HSTs). In the previous work, two kinds of thermal TOT and HST models have been studied and used in the application: the IEEE TOT/HST models and the ASU TOT/HST models. And, several metrics have been applied to evaluate the model acceptability and determine the most appropriate models for using in the dynamic loading calculations. In this work, an investigation to improve the existing transformer thermal models performance is presented. Some factors that may affect the model performance such as improper fan status and the error caused by the poor performance of IEEE models are discussed. Additional methods to determine the reliability of transformer thermal models using metrics such as time constant and the model parameters are also provided. A new production grade application for real-time dynamic loading operating purpose is introduced. This application is developed by using an existing planning application, TTeMP, as a start point, which is designed for the dispatchers and load specialists. To overcome the limitations of TTeMP, the new application can perform dynamic loading under emergency conditions, such as loss-of transformer loading. It also has the capability to determine the emergency rating of the transformers for a real-time estimation.
ContributorsZhang, Ming (Author) / Tylavsky, Daniel J (Thesis advisor) / Ayyanar, Raja (Committee member) / Holbert, Keith E. (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
Underground cables have been widely used in big cities. This is because underground cables offer the benefits of reducing visual impact and the disturbance caused by bad weather (wind, ice, snow, and the lightning strikes). Additionally, when placing power lines underground, the maintenance costs can also be reduced as a result. The underground cable rating calculation is the most critical part of designing the cable construction and cable installation. In this thesis, three contributions regarding the cable ampacity study have been made. First, an analytical method for rating of underground cables has been presented. Second, this research also develops the steady state and transient ratings for Salt River Project (SRP) 69 kV underground system using the commercial software CYMCAP for several typical substations. Third, to find an alternative way to predict the cable ratings, three regression models have been built. The residual plot and mean square error for the three methods have been analyzed. The conclusion is dawn that the nonlinear regression model provides the sufficient accuracy of the cable rating prediction for SRP's typical installation.
ContributorsWang, Tong (Author) / Tylavsky, Daniel (Thesis advisor) / Karady, George G. (Committee member) / Holbert, Keith E. (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
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
A fully automated logic design methodology for radiation hardened by design (RHBD) high speed logic using fine grained triple modular redundancy (TMR) is presented. The hardening techniques used in the cell library are described and evaluated, with a focus on both layout techniques that mitigate total ionizing dose (TID) and latchup issues and flip-flop designs that mitigate single event transient (SET) and single event upset (SEU) issues. The base TMR self-correcting master-slave flip-flop is described and compared to more traditional hardening techniques. Additional refinements are presented, including testability features that disable the self-correction to allow detection of manufacturing defects. The circuit approach is validated for hardness using both heavy ion and proton broad beam testing. For synthesis and auto place and route, the methodology and circuits leverage commercial logic design automation tools. These tools are glued together with custom CAD tools designed to enable easy conversion of standard single redundant hardware description language (HDL) files into hardened TMR circuitry. The flow allows hardening of any synthesizable logic at clock frequencies comparable to unhardened designs and supports standard low-power techniques, e.g. clock gating and supply voltage scaling.
ContributorsHindman, Nathan (Author) / Clark, Lawrence T (Thesis advisor) / Holbert, Keith E. (Committee member) / Barnaby, Hugh (Committee member) / Allee, David (Committee member) / Arizona State University (Publisher)
Created2012
Description
The dissolution of metal layers such as silver into chalcogenide glass layers such as germanium selenide changes the resistivity of the metal and chalcogenide films by a great extent. It is known that the incorporation of the metal can be achieved by ultra violet light exposure or thermal processes. In this work, the use of metal dissolution by exposure to gamma radiation has been explored for radiation sensor applications. Test structures were designed and a process flow was developed for prototype sensor fabrication. The test structures were designed such that sensitivity to radiation could be studied. The focus is on the effect of gamma rays as well as ultra violet light on silver dissolution in germanium selenide (Ge30Se70) chalcogenide glass. Ultra violet radiation testing was used prior to gamma exposure to assess the basic mechanism. The test structures were electrically characterized prior to and post irradiation to assess resistance change due to metal dissolution. A change in resistance was observed post irradiation and was found to be dependent on the radiation dose. The structures were also characterized using atomic force microscopy and roughness measurements were made prior to and post irradiation. A change in roughness of the silver films on Ge30Se70 was observed following exposure. This indicated the loss of continuity of the film which causes the increase in silver film resistance following irradiation. Recovery of initial resistance in the structures was also observed after the radiation stress was removed. This recovery was explained with photo-stimulated deposition of silver from the chalcogenide at room temperature confirmed with the re-appearance of silver dendrites on the chalcogenide surface. The results demonstrate that it is possible to use the metal dissolution effect in radiation sensing applications.
ContributorsChandran, Ankitha (Author) / Kozicki, Michael N (Thesis advisor) / Holbert, Keith E. (Committee member) / Barnaby, Hugh (Committee member) / Arizona State University (Publisher)
Created2012