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.
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- Creators: Yan, Hao
- Creators: Kavazanjian, Edward
- Creators: Mobasher, Barzin
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 alkali activation of aluminosilicate materials as binder systems derived from industrial byproducts have been extensively studied due to the advantages they offer in terms enhanced material properties, while increasing sustainability by the reuse of industrial waste and byproducts and reducing the adverse impacts of OPC production. Fly ash and ground granulated blast furnace slag are commonly used for their content of soluble silica and aluminate species that can undergo dissolution, polymerization with the alkali, condensation on particle surfaces and solidification. The following topics are the focus of this thesis: (i) the use of microwave assisted thermal processing, in addition to heat-curing as a means of alkali activation and (ii) the relative effects of alkali cations (K or Na) in the activator (powder activators) on the mechanical properties and chemical structure of these systems. Unsuitable curing conditions instigate carbonation, which in turn lowers the pH of the system causing significant reductions in the rate of fly ash activation and mechanical strength development. This study explores the effects of sealing the samples during the curing process, which effectively traps the free water in the system, and allows for increased aluminosilicate activation. The use of microwave-curing in lieu of thermal-curing is also studied in order to reduce energy consumption and for its ability to provide fast volumetric heating. Potassium-based powder activators dry blended into the slag binder system is shown to be effective in obtaining very high compressive strengths under moist curing conditions (greater than 70 MPa), whereas sodium-based powder activation is much weaker (around 25 MPa). Compressive strength decreases when fly ash is introduced into the system. Isothermal calorimetry is used to evaluate the early hydration process, and to understand the reaction kinetics of the alkali powder activated systems. A qualitative evidence of the alkali-hydroxide concentration of the paste pore solution through the use of electrical conductivity measurements is also presented, with the results indicating the ion concentration of alkali is more prevalent in the pore solution of potassium-based systems. The use of advanced spectroscopic and thermal analysis techniques to distinguish the influence of studied parameters is also discussed.
ContributorsChowdhury, Ussala (Author) / Neithalath, Narayanan (Thesis advisor) / Rajan, Subramanium D. (Committee member) / Mobasher, Barzin (Committee member) / Arizona State University (Publisher)
Created2013
Description
In a laboratory setting, the soil volume change behavior is best represented by using various testing standards on undisturbed or remolded samples. Whenever possible, it is most precise to use undisturbed samples to assess the volume change behavior but in the absence of undisturbed specimens, remodeled samples can be used. If that is the case, the soil is compacted to in-situ density and water content (or matric suction), which should best represent the expansive profile in question. It is standard practice to subject the specimen to a wetting process at a particular net normal stress. Even though currently accepted laboratory testing standard procedures provide insight on how the profile conditions changes with time, these procedures do not assess the long term effects on the soil due to climatic changes. In this experimental study, an assessment and quantification of the effect of multiple wetting/drying cycles on the volume change behavior of two different naturally occurring soils was performed. The changes in wetting and drying cycles were extreme when comparing the swings in matric suction. During the drying cycle, the expansive soil was subjected to extreme conditions, which decreased the moisture content less than the shrinkage limit. Nevertheless, both soils were remolded at five different compacted conditions and loaded to five different net normal stresses. Each sample was subjected to six wetting and drying cycles. During the assessment, it was evident from the results that the swell/collapse strain is highly non-linear at low stress levels. The strain-net normal stress relationship cannot be defined by one single function without transforming the data. Therefore, the dataset needs to be fitted to a bi-modal logarithmic function or to a logarithmic transformation of net normal stress in order to use a third order polynomial fit. It was also determined that the moisture content changes with time are best fit by non-linear functions. For the drying cycle, the radial strain was determined to have a constant rate of change with respect to the axial strain. However, for the wetting cycle, there was not enough radial strain data to develop correlations and therefore, an assumption was made based on 55 different test measurements/observations, for the wetting cycles. In general, it was observed that after each subsequent cycle, higher swelling was exhibited for lower net normal stress values; while higher collapse potential was observed for higher net normal stress values, once the net normal stress was less than/greater than a threshold net normal stress value. Furthermore, the swelling pressure underwent a reduction in all cases. Particularly, the Anthem soil exhibited a reduction in swelling pressure by at least 20 percent after the first wetting/drying cycle; while Colorado soil exhibited a reduction of 50 percent. After about the fourth cycle, the swelling pressure seemed to stabilized to an equilibrium value at which a reduction of 46 percent was observed for the Anthem soil and 68 percent reduction for the Colorado soil. The impact of the initial compacted conditions on heave characteristics was studied. Results indicated that materials compacted at higher densities exhibited greater swell potential. When comparing specimens compacted at the same density but at different moisture content (matric suction), it was observed that specimens compacted at higher suction would exhibit higher swelling potential, when subjected to the same net normal stress. The least amount of swelling strain was observed on specimens compacted at the lowest dry density and the lowest matric suction (higher water content). The results from the laboratory testing were used to develop ultimate heave profiles for both soils. This analysis showed that even though the swell pressure for each soil decreased with cycles, the amount of heave would increase or decrease depending upon the initial compaction condition. When the specimen was compacted at 110% of optimum moisture content and 90% of maximum dry density, it resulted in an ultimate heave reduction of 92 percent for Anthem and 685 percent for Colorado soil. On the other hand, when the soils were compacted at 90% optimum moisture content and 100% of the maximum dry density, Anthem specimens heave 78% more and Colorado specimens heave was reduced by 69%. Based on the results obtained, it is evident that the current methods to estimate heave and swelling pressure do not consider the effect of wetting/drying cycles; and seem to fail capturing the free swell potential of the soil. Recommendations for improvement current methods of practice are provided.
ContributorsRosenbalm, Daniel Curtis (Author) / Zapata, Claudia E (Thesis advisor) / Houston, Sandra L. (Committee member) / Kavazanjian, Edward (Committee member) / Witczak, Mathew W (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 effect of earthquake-induced liquefaction on the local void ratio distribution of cohesionless soil is evaluated using x-ray computed tomography (CT) and an advanced image processing software package. Intact, relatively undisturbed specimens of cohesionless soil were recovered before and after liquefaction by freezing and coring soil deposits created by pluviation and by sedimentation through water. Pluviated soil deposits were liquefied in the small geotechnical centrifuge at the University of California at Davis shared-use National Science Foundation (NSF)-supported Network for Earthquake Engineering Simulation (NEES) facility. A soil deposit created by sedimentation through water was liquefied on a small shake table in the Arizona State University geotechnical laboratory. Initial centrifuge tests employed Ottawa 20-30 sand but this material proved to be too coarse to liquefy in the centrifuge. Therefore, subsequent centrifuge tests employed Ottawa F60 sand. The shake table test employed Ottawa 20-30 sand. Recovered cores were stabilized by impregnation with optical grade epoxy and sent to the University of Texas at Austin NSF-supported facility at the University of Texas at Austin for high-resolution CT scanning of geologic media. The local void ratio distribution of a CT-scanned core of Ottawa 20-30 sand evaluated using Avizo® Fire, a commercially available advanced program for image analysis, was compared to the local void ratio distribution established on the same core by analysis of optical images to demonstrate that analysis of the CT scans gave similar results to optical methods. CT scans were subsequently conducted on liquefied and not-liquefied specimens of Ottawa 20-30 sand and Ottawa F60 sand. The resolution of F60 specimens was inadequate to establish the local void ratio distribution. Results of the analysis of the Ottawa 20-30 specimens recovered from the model built for the shake table test showed that liquefaction can substantially influence the variability in local void ratio, increasing the degree of non-homogeneity in the specimen.
ContributorsGutierrez, Angel (Author) / Kavazanjian, Edward (Thesis advisor) / Houston, Sandra (Committee member) / Zapata, Claudia (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
Buildings consume a large portion of the world's energy, but with the integration of phase change materials (PCMs) in building elements this energy cost can be greatly reduced. The addition of PCMs into building elements, however, becomes a challenge to model and analyze how the material actually affects the energy flow and temperatures in the system. This research work presents a comprehensive computer program used to model and analyze PCM embedded wall systems. The use of the finite element method (FEM) provides the tool to analyze the energy flow of these systems. Finite element analysis (FEA) can model the transient analysis of a typical climate cycle along with nonlinear problems, which the addition of PCM causes. The use of phase change materials is also a costly material expense. The initial expense of using PCMs can be compensated by the reduction in energy costs it can provide. Optimization is the tool used to determine the optimal point between adding PCM into a wall and the amount of energy savings that layer will provide. The integration of these two tools into a computer program allows for models to be efficiently created, analyzed and optimized. The program was then used to understand the benefits between two different wall models, a wall with a single layer of PCM or a wall with two different PCM layers. The effect of the PCMs on the inside wall temperature along with the energy flow across the wall are computed. The numerical results show that a multi-layer PCM wall was more energy efficient and cost effective than the single PCM layer wall. A structural analysis was then performed on the optimized designs using ABAQUS v. 6.10 to ensure the structural integrity of the wall was not affected by adding PCM layer(s).
ContributorsStockwell, Amie (Author) / Rajan, Subramaniam D. (Thesis advisor) / Neithalath, Narayanan (Thesis advisor) / Mobasher, Barzin (Committee member) / Arizona State University (Publisher)
Created2013