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 75
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
Manufacture of building materials requires significant energy, and as demand for these materials continues to increase, the energy requirement will as well. Offsetting this energy use will require increased focus on sustainable building materials. Further, the energy used in building, particularly in heating and air conditioning, accounts for 40 percent of a buildings energy use. Increasing the efficiency of building materials will reduce energy usage over the life time of the building. Current methods for maintaining the interior environment can be highly inefficient depending on the building materials selected. Materials such as concrete have low thermal efficiency and have a low heat capacity meaning it provides little insulation. Use of phase change materials (PCM) provides the opportunity to increase environmental efficiency of buildings by using the inherent latent heat storage as well as the increased heat capacity. Incorporating PCM into concrete via lightweight aggregates (LWA) by direct addition is seen as a viable option for increasing the thermal storage capabilities of concrete, thereby increasing building energy efficiency. As PCM change phase from solid to liquid, heat is absorbed from the surroundings, decreasing the demand on the air conditioning systems on a hot day or vice versa on a cold day. Further these materials provide an additional insulating capacity above the value of plain concrete. When the temperature drops outside the PCM turns back into a solid and releases the energy stored from the day. PCM is a hydrophobic material and causes reductions in compressive strength when incorporated directly into concrete, as shown in previous studies. A proposed method for mitigating this detrimental effect, while still incorporating PCM into concrete is to encapsulate the PCM in aggregate. This technique would, in theory, allow for the use of phase change materials directly in concrete, increasing the thermal efficiency of buildings, while negating the negative effect on compressive strength of the material.
ContributorsSharma, Breeann (Author) / Neithalath, Narayanan (Thesis advisor) / Mobasher, Barzin (Committee member) / Rajan, Subramaniam D. (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
The main objective of this study is to investigate the mechanical behaviour of cementitious based composites subjected dynamic tensile loading, with effects of strain rate, temperature, addition of short fibres etc. Fabric pullout model and tension stiffening model based on finite difference model, previously developed at Arizona State University were used to help study the bonding mechanism between fibre and matrix, and the phenomenon of tension stiffening due to the addition of fibres and textiles. Uniaxial tension tests were conducted on strain-hardening cement-based composites (SHCC), textile reinforced concrete (TRC) with and without addition of short fibres, at the strain rates ranging from 25 s-1 to 100 s-1. Historical data on quasi-static tests of same materials were used to demonstrate the effects including increases in average tensile strength, strain capacity, work-to-fracture due to high strain rate. Polyvinyl alcohol (PVA), glass, polypropylene were employed as reinforcements of concrete. A state-of-the-art phantom v7 high speed camera was setup to record the video at frame rate of 10,000 fps. Random speckle pattern of texture style was made on the surface of specimens for image analysis. An optical non-contacting deformation measurement technique referred to as digital image correlation (DIC) method was used to conduct the image analysis by means of tracking the displacement field through comparison between the reference image and deformed images. DIC successfully obtained full-filed strain distribution, strain versus time responses, demonstrated the bonding mechanism from perspective of strain field, and corrected the stress-strain responses.
ContributorsYao, Yiming (Author) / Barzin, Mobasher (Thesis advisor) / Rajan, Subramaniam D. (Committee member) / Neithalath, Narayanan (Committee member) / Arizona State University (Publisher)
Created2013
Description
Properties of random porous material such as pervious concrete are strongly dependant on its pore structure features. This research deals with the development of an understanding of the relationship between the material structure and the mechanical and functional properties of pervious concretes. The fracture response of pervious concrete specimens proportioned for different porosities, as a function of the pore structure features and fiber volume fraction, is studied. Stereological and morphological methods are used to extract the relevant pore structure features of pervious concretes from planar images. A two-parameter fracture model is used to obtain the fracture toughness (KIC) and critical crack tip opening displacement (CTODc) from load-crack mouth opening displacement (CMOD) data of notched beams under three-point bending. The experimental results show that KIC is primarily dependent on the porosity of pervious concretes. For a similar porosity, an increase in pore size results in a reduction in KIC. At similar pore sizes, the effect of fibers on the post-peak response is more prominent in mixtures with a higher porosity, as shown by the residual load capacity, stress-crack extension relationships, and GR curves. These effects are explained using the mean free spacing of pores and pore-to-pore tortuosity in these systems. A sensitivity analysis is employed to quantify the influence of material design parameters on KIC. This research has also focused on studying the relationship between permeability and tortuosity as it pertains to porosity and pore size of pervious concretes. Various ideal geometric shapes were also constructed that had varying pore sizes and porosities. The pervious concretes also had differing pore sizes and porosities. The permeabilities were determined using three different methods; Stokes solver, Lattice Boltzmann method and the Katz-Thompson equation. These values were then compared to the tortuosity values determined using a Matlab code that uses a pore connectivity algorithm. The tortuosity was also determined from the inverse of the conductivity determined from a numerical analysis that was necessary for using the Katz-Thompson equation. These tortuosity values were then compared to the permeabilities. The pervious concretes and ideal geometric shapes showed consistent similarities betbetween their tortuosities and permeabilities.
ContributorsRehder, Benjamin (Author) / Neithalath, Narayanana (Thesis advisor) / Mobasher, Barzin (Committee member) / Rajan, Subramaniam D. (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
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
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