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 100
Description
Recently, the use of zinc oxide (ZnO) nanowires as an interphase in composite materials has been demonstrated to increase the interfacial shear strength between carbon fiber and an epoxy matrix. In this research work, the strong adhesion between ZnO and carbon fiber is investigated to elucidate the interactions at the interface that result in high interfacial strength. First, molecular dynamics (MD) simulations are performed to calculate the adhesive energy between bare carbon and ZnO. Since the carbon fiber surface has oxygen functional groups, these were modeled and MD simulations showed the preference of ketones to strongly interact with ZnO, however, this was not observed in the case of hydroxyls and carboxylic acid. It was also found that the ketone molecules ability to change orientation facilitated the interactions with the ZnO surface. Experimentally, the atomic force microscope (AFM) was used to measure the adhesive energy between ZnO and carbon through a liftoff test by employing highly oriented pyrolytic graphite (HOPG) substrate and a ZnO covered AFM tip. Oxygen functionalization of the HOPG surface shows the increase of adhesive energy. Additionally, the surface of ZnO was modified to hold a negative charge, which demonstrated an increase in the adhesive energy. This increase in adhesion resulted from increased induction forces given the relatively high polarizability of HOPG and the preservation of the charge on ZnO surface. It was found that the additional negative charge can be preserved on the ZnO surface because there is an energy barrier since carbon and ZnO form a Schottky contact. Other materials with the same ionic properties of ZnO but with higher polarizability also demonstrated good adhesion to carbon. This result substantiates that their induced interaction can be facilitated not only by the polarizability of carbon but by any of the materials at the interface. The versatility to modify the magnitude of the induced interaction between carbon and an ionic material provides a new route to create interfaces with controlled interfacial strength.
ContributorsGalan Vera, Magdian Ulises (Author) / Sodano, Henry A (Thesis advisor) / Jiang, Hanqing (Committee member) / Solanki, Kiran (Committee member) / Oswald, Jay (Committee member) / Speyer, Gil (Committee member) / Arizona State University (Publisher)
Created2013
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
"Sensor Decade" has been labeled on the first decade of the 21st century. Similar to the revolution of micro-computer in 1980s, sensor R&D; developed rapidly during the past 20 years. Hard workings were mainly made to minimize the size of devices with optimal the performance. Efforts to develop the small size devices are mainly concentrated around Micro-electro-mechanical-system (MEMS) technology. MEMS accelerometers are widely published and used in consumer electronics, such as smart phones, gaming consoles, anti-shake camera and vibration detectors. This study represents liquid-state low frequency micro-accelerometer based on molecular electronic transducer (MET), in which inertial mass is not the only but also the conversion of mechanical movement to electric current signal is the main utilization of the ionic liquid. With silicon-based planar micro-fabrication, the device uses a sub-micron liter electrolyte droplet sealed in oil as the sensing body and a MET electrode arrangement which is the anode-cathode-cathode-anode (ACCA) in parallel as the read-out sensing part. In order to sensing the movement of ionic liquid, an imposed electric potential was applied between the anode and the cathode. The electrode reaction, I_3^-+2e^___3I^-, occurs around the cathode which is reverse at the anodes. Obviously, the current magnitude varies with the concentration of ionic liquid, which will be effected by the movement of liquid droplet as the inertial mass. With such structure, the promising performance of the MET device design is to achieve 10.8 V/G (G=9.81 m/s^2) sensitivity at 20 Hz with the bandwidth from 1 Hz to 50 Hz, and a low noise floor of 100 ug/sqrt(Hz) at 20 Hz.
ContributorsLiang, Mengbing (Author) / Yu, Hongyu (Thesis advisor) / Jiang, Hanqing (Committee member) / Kozicki, Micheal (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
Woven fabric composite materials are widely used in the construction of aircraft engine fan containment systems, mostly due to their high strength to weight ratios and ease of implementation. The development of a predictive model for fan blade containment would provide great benefit to engine manufactures in shortened development cycle time, less risk in certification and fewer dollars lost to redesign/recertification cycles. A mechanistic user-defined material model subroutine has been developed at Arizona State University (ASU) that captures the behavioral response of these fabrics, namely Kevlar® 49, under ballistic loading. Previously developed finite element models used to validate the consistency of this material model neglected the effects of the physical constraints imposed on the test setup during ballistic testing performed at NASA Glenn Research Center (NASA GRC). Part of this research was to explore the effects of these boundary conditions on the results of the numerical simulations. These effects were found to be negligible in most instances. Other material models for woven fabrics are available in the LS-DYNA finite element code. One of these models, MAT234: MAT_VISCOELASTIC_LOOSE_FABRIC (Ivanov & Tabiei, 2004) was studied and implemented in the finite element simulations of ballistic testing associated with the FAA ASU research. The results from these models are compared to results obtained from the ASU UMAT as part of this research. The results indicate an underestimation in the energy absorption characteristics of the Kevlar 49 fabric containment systems. More investigation needs to be performed in the implementation of MAT234 for Kevlar 49 fabric. Static penetrator testing of Kevlar® 49 fabric was performed at ASU in conjunction with this research. These experiments are designed to mimic the type of loading experienced during fan blade out events. The resulting experimental strains were measured using a non-contact optical strain measurement system (ARAMIS).
ContributorsFein, Jonathan (Author) / Rajan, Subramaniam D. (Thesis advisor) / Mobasher, Barzin (Committee member) / Jiang, Hanqing (Committee member) / Arizona State University (Publisher)
Created2012
Description
Dealloying induced stress corrosion cracking is particularly relevant in energy conversion systems (both nuclear and fossil fuel) as many failures in alloys such as austenitic stainless steel and nickel-based systems result directly from dealloying. This study provides evidence of the role of unstable dynamic fracture processes in dealloying induced stress-corrosion cracking of face-centered cubic alloys. Corrosion of such alloys often results in the formation of a brittle nanoporous layer which we hypothesize serves to nucleate a crack that owing to dynamic effects penetrates into the un-dealloyed parent phase alloy. Thus, since there is essentially a purely mechanical component of cracking, stress corrosion crack propagation rates can be significantly larger than that predicted from electrochemical parameters. The main objective of this work is to examine and test this hypothesis under conditions relevant to stress corrosion cracking. Silver-gold alloys serve as a model system for this study since hydrogen effects can be neglected on a thermodynamic basis, which allows us to focus on a single cracking mechanism. In order to study various aspects of this problem, the dynamic fracture properties of monolithic nanoporous gold (NPG) were examined in air and under electrochemical conditions relevant to stress corrosion cracking. The detailed processes associated with the crack injection phenomenon were also examined by forming dealloyed nanoporous layers of prescribed properties on un-dealloyed parent phase structures and measuring crack penetration distances. Dynamic fracture in monolithic NPG and in crack injection experiments was examined using high-speed (106 frames s-1) digital photography. The tunable set of experimental parameters included the NPG length scale (20-40 nm), thickness of the dealloyed layer (10-3000 nm) and the electrochemical potential (0.5-1.5 V). The results of crack injection experiments were characterized using the dual-beam focused ion beam/scanning electron microscopy. Together these tools allow us to very accurately examine the detailed structure and composition of dealloyed grain boundaries and compare crack injection distances to the depth of dealloying. The results of this work should provide a basis for new mathematical modeling of dealloying induced stress corrosion cracking while providing a sound physical basis for the design of new alloys that may not be susceptible to this form of cracking. Additionally, the obtained results should be of broad interest to researchers interested in the fracture properties of nano-structured materials. The findings will open up new avenues of research apart from any implications the study may have for stress corrosion cracking.
ContributorsSun, Shaofeng (Author) / Sieradzki, Karl (Thesis advisor) / Jiang, Hanqing (Committee member) / Peralta, Pedro (Committee member) / Arizona State University (Publisher)
Created2012
Description
The focus of this investigation is on the optimum placement of a limited number of dampers, fewer than the number of blades, on a bladed disk to induce the smallest amplitude of blade response. The optimization process considers the presence of random mistuning, i.e. small involuntary variations in blade stiffness properties resulting, say, from manufacturing variability. Designed variations of these properties, known as intentional mistuning, is considered as an option to reduce blade response and the pattern of two blade types (A and B blades) is then part of the optimization in addition to the location of dampers on the disk. First, this study focuses on the formulation and validation of dedicated algorithms for the selection of the damper locations and the intentional mistuning pattern. Failure of one or several of the dampers could lead to a sharp rise in blade response and this issue is addressed by including, in the optimization, the possibility of damper failure to yield a fail-safe solution. The high efficiency and accuracy of the optimization algorithms is assessed in comparison with computationally very demanding exhaustive search results. Second, the developed optimization algorithms are applied to nonlinear dampers (underplatform friction dampers), as well as to blade-blade dampers, both linear and nonlinear. Further, the optimization of blade-only and blade-blade linear dampers is extended to include uncertainty or variability in the damper properties induced by manufacturing or wear. It is found that the optimum achieved without considering such uncertainty is robust with respect to it. Finally, the potential benefits of using two different types of friction dampers differing in their masses (A and B types), on a bladed disk are considered. Both A/B pattern and the damper masses are optimized to obtain the largest benefit compared to using identical dampers of optimized masses on every blade. Four situations are considered: tuned disks, disks with random mistuning of blade stiffness, and, disks with random mistuning of both blade stiffness and damper normal forces with and without damper variability induced by manufacturing and wear. In all cases, the benefit of intentional mistuning of friction dampers is small, of the order of a few percent.
ContributorsMurthy, Raghavendra Narasimha (Author) / Mignolet, Marc P (Thesis advisor) / Rajan, Subramaniam D. (Committee member) / Lentz, Jeff (Committee member) / Chattopadhyay, Aditi (Committee member) / Jiang, Hanqing (Committee member) / Arizona State University (Publisher)
Created2012