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 97
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
Photosynthesis, one of the most important processes in nature, has provided an energy basis for nearly all life on Earth, as well as the fossil fuels we use today to power modern society. This research aims to mimic the photosynthetic process of converting incident solar energy into chemical potential energy in the form of a fuel via systems capable of carrying out photo-induced electron transfer to drive the production of hydrogen from water. Herein is detailed progress in using photo-induced stepwise electron transfer to drive the oxidation of water and reduction of protons to hydrogen. In the design, use of more blue absorbing porphyrin dyes to generate high-potential intermediates for oxidizing water and more red absorbing phthalocyanine dyes for forming the low potential charge needed for the production of hydrogen have been utilized. For investigating water oxidation at the photoanode, high potential porphyrins such as, bis-pyridyl porphyrins and pentafluorophenyl porphyrins have been synthesized and experiments have aimed at the co-immobilization of this dye with an IrO2-nH2O catalyst on TiO2. To drive the cathodic reaction of the water splitting photoelectrochemical cell, utilization of silicon octabutoxy-phthalocyanines have been explored, as they offer good absorption in the red to near infrared, coupled with low potential photo-excited states. Axially and peripherally substituted phthalocyanines bearing carboxylic anchoring groups for the immobilization on semiconductors such as TiO2 has been investigated. Ultimately, this work should culminate in a photoelectrochemical cell capable of splitting water to oxygen and hydrogen with the only energy input from light. A series of perylene dyes bearing multiple semi-conducting metal oxide anchoring groups have been synthesized and studied. Results have shown interfacial electron transfer between these perylenes and TiO2 nanoparticles encapsulated within reverse micelles and naked nanoparticles. The binding process was followed by monitoring the hypsochromic shift of the dye absorption spectra over time. Photoinduced electron transfer from the singlet excited state of the perylenes to the TiO2 conduction band is indicated by emission quenching of the TiO2-bound form of the dyes and confirmed by transient absorption measurements of the radical cation of the dyes and free carriers (injected electrons) in the TiO2.
ContributorsBergkamp, Jesse J (Author) / Moore, Ana L (Thesis advisor) / Mariño-Ochoa, Ernesto (Thesis advisor) / Gust, Devens J (Committee member) / Gould, Ian (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
A new theoretical model was developed utilizing energy conservation methods in order to determine the fully-atomized cross-sectional Sauter mean diameters of pressure-swirl atomizers. A detailed boundary-layer assessment led to the development of a new viscous dissipation model for droplets in the spray. Integral momentum methods were also used to determine the complete velocity history of the droplets and entrained gas in the spray. The model was extensively validated through comparison with experiment and it was found that the model could predict the correct droplet size with high accuracy for a wide range of operating conditions. Based on detailed analysis, it was found that the energy model has a tendency to overestimate the droplet diameters for very low injection velocities, Weber numbers, and cone angles. A full parametric study was also performed in order to unveil some underlying behavior of pressure-swirl atomizers. It was found that at high injection velocities, the kinetic energy in the spray is significantly larger than the surface tension energy, therefore, efforts into improving atomization quality by changing the liquid's surface tension may not be the most productive. From the parametric studies it was also shown how the Sauter mean diameter and entrained velocities vary with increasing ambient gas density. Overall, the present energy model has the potential to provide quick and reasonably accurate solutions for a wide range of operating conditions enabling the user to determine how different injection parameters affect the spray quality.
ContributorsMoradi, Ali (Author) / Lee, Taewoo (Thesis advisor) / Herrmann, Marcus (Committee member) / Huang, Huei-Ping (Committee member) / Arizona State University (Publisher)
Created2013
Description
As the genetic information storage vehicle, deoxyribonucleic acid (DNA) molecules are essential to all known living organisms and many viruses. It is amazing that such a large amount of information about how life develops can be stored in these tiny molecules. Countless scientists, especially some biologists, are trying to decipher the genetic information stored in these captivating molecules. Meanwhile, another group of researchers, nanotechnologists in particular, have discovered that the unique and concise structural features of DNA together with its information coding ability can be utilized for nano-construction efforts. This idea culminated in the birth of the field of DNA nanotechnology which is the main topic of this dissertation. The ability of rationally designed DNA strands to self-assemble into arbitrary nanostructures without external direction is the basis of this field. A series of novel design principles for DNA nanotechnology are presented here, from topological DNA nanostructures to complex and curved DNA nanostructures, from pure DNA nanostructures to hybrid RNA/DNA nanostructures. As one of the most important and pioneering fields in controlling the assembly of materials (both DNA and other materials) at the nanoscale, DNA nanotechnology is developing at a dramatic speed and as more and more construction approaches are invented, exciting advances will emerge in ways that we may or may not predict.
ContributorsHan, Dongran (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Ros, Anexandra (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2012
Description
The heat transfer enhancements available from expanding the cross-section of a boiling microchannel are explored analytically and experimentally. Evaluation of the literature on critical heat flux in flow boiling and associated pressure drop behavior is presented with predictive critical heat flux (CHF) and pressure drop correlations. An optimum channel configuration allowing maximum CHF while reducing pressure drop is sought. A perturbation of the channel diameter is employed to examine CHF and pressure drop relationships from the literature with the aim of identifying those adequately general and suitable for use in a scenario with an expanding channel. Several CHF criteria are identified which predict an optimizable channel expansion, though many do not. Pressure drop relationships admit improvement with expansion, and no optimum presents itself. The relevant physical phenomena surrounding flow boiling pressure drop are considered, and a balance of dimensionless numbers is presented that may be of qualitative use. The design, fabrication, inspection, and experimental evaluation of four copper microchannel arrays of different channel expansion rates with R-134a refrigerant is presented. Optimum rates of expansion which maximize the critical heat flux are considered at multiple flow rates, and experimental results are presented demonstrating optima. The effect of expansion on the boiling number is considered, and experiments demonstrate that expansion produces a notable increase in the boiling number in the region explored, though no optima are observed. Significant decrease in the pressure drop across the evaporator is observed with the expanding channels, and no optima appear. Discussion of the significance of this finding is presented, along with possible avenues for future work.
ContributorsMiner, Mark (Author) / Phelan, Patrick E (Thesis advisor) / Baer, Steven (Committee member) / Chamberlin, Ralph (Committee member) / Chen, Kangping (Committee member) / Herrmann, Marcus (Committee member) / Arizona State University (Publisher)
Created2013
Description
The numerical climate models have provided scientists, policy makers and the general public, crucial information for climate projections since mid-20th century. An international effort to compare and validate the simulations of all major climate models is organized by the Coupled Model Intercomparison Project (CMIP), which has gone through several phases since 1995 with CMIP5 being the state of the art. In parallel, an organized effort to consolidate all observational data in the past century culminates in the creation of several "reanalysis" datasets that are considered the closest representation of the true observation. This study compared the climate variability and trend in the climate model simulations and observations on the timescales ranging from interannual to centennial. The analysis focused on the dynamic climate quantity of zonal-mean zonal wind and global atmospheric angular momentum (AAM), and incorporated multiple datasets from reanalysis and the most recent CMIP3 and CMIP5 archives. For the observation, the validation of AAM by the length-of-day (LOD) and the intercomparison of AAM revealed a good agreement among reanalyses on the interannual and the decadal-to-interdecadal timescales, respectively. But the most significant discrepancies among them are in the long-term mean and long-term trend. For the simulations, the CMIP5 models produced a significantly smaller bias and a narrower ensemble spread of the climatology and trend in the 20th century for AAM compared to CMIP3, while CMIP3 and CMIP5 simulations consistently produced a positive trend for the 20th and 21st century. Both CMIP3 and CMIP5 models produced a wide range of the magnitudes of decadal and interdecadal variability of wind component of AAM (MR) compared to observation. The ensemble means of CMIP3 and CMIP5 are not statistically distinguishable for either the 20th- or 21st-century runs. The in-house atmospheric general circulation model (AGCM) simulations forced by the sea surface temperature (SST) taken from the CMIP5 simulations as lower boundary conditions were carried out. The zonal wind and MR in the CMIP5 simulations are well simulated in the AGCM simulations. This confirmed SST as an important mediator in regulating the global atmospheric changes due to GHG effect.
ContributorsPaek, Houk (Author) / Huang, Huei-Ping (Thesis advisor) / Adrian, Ronald (Committee member) / Wang, Zhihua (Committee member) / Anderson, James (Committee member) / Herrmann, Marcus (Committee member) / Arizona State University (Publisher)
Created2013
Description
A clean and sustainable alternative to fossil fuels is solar energy. For efficient use of solar energy to be realized, artificial systems that can effectively capture and convert sunlight into a usable form of energy have to be developed. In natural photosynthesis, antenna chlorophylls and carotenoids capture sunlight and transfer the resulting excitation energy to the photosynthetic reaction center (PRC). Small reorganization energy, λ and well-balanced electronic coupling between donors and acceptors in the PRC favor formation of a highly efficient charge-separated (CS) state. By covalently linking electron/energy donors to acceptors, organic molecular dyads and triads that mimic natural photosynthesis were synthesized and studied. Peripherally linked free base phthalocyanine (Pc)-fullerene (C60) and a zinc (Zn) phthalocyanine-C60 dyads were synthesized. Photoexcitation of the Pc moiety resulted in singlet-singlet energy transfer to the attached C60, followed by electron transfer. The lifetime of the CS state was 94 ps. Linking C60 axially to silicon (Si) Pc, a lifetime of the CS state of 4.5 ns was realized. The exceptionally long-lived CS state of the SiPc-C60 dyad qualifies it for applications in solar energy conversion devices. A secondary electron donor was linked to the dyad to obtain a carotenoid (Car)-SiPc-C60 triad and ferrocene (Fc)-SiPc-C60 triad. Excitation of the SiPc moiety resulted in fast electron transfer from the Car or Fc secondary electron donors to the C60. The lifetime of the CS state was 17 ps and 1.2 ps in Car-SiPc-C60 and Fc-SiPc-C60, respectively. In Chapter 3, an efficient synthetic route that yielded regioselective oxidative porphyrin dimerization is presented. Using Cu2+ as the oxidant, meso-β doubly-connected fused porphyrin dimers were obtained in very high yields. Removal of the copper from the macrocycle affords a free base porphyrin dimer. This allows for exchange of metals and provides a route to a wider range of metallporphyrin dimers. In Chapter 4, the development of an efficient and an expedient route to bacteriopurpurin synthesis is discussed. Meso-10,20- diformylation of porphyrin was achieved and one-pot porphyrin diacrylate synthesis and cyclization to afford bacteriopurpurin was realized. The bacteriopurpurin had a reduction potential of - 0.85 V vs SCE and λmax, 845 nm.
ContributorsArero, Jaro (Author) / Gust, Devens (Thesis advisor) / Moore, Ana (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
Solar energy is a promising alternative for addressing the world's current and future energy requirements in a sustainable way. Because solar irradiation is intermittent, it is necessary to store this energy in the form of a fuel so it can be used when required. The light-driven splitting of water into oxygen and hydrogen (a useful chemical fuel) is a fascinating theoretical and experimental challenge that is worth pursuing because the advance of the knowledge that it implies and the availability of water and sunlight. Inspired by natural photosynthesis and building on previous work from our laboratory, this dissertation focuses on the development of water-splitting dye-sensitized photoelectrochemical tandem cells (WSDSPETCs). The design, synthesis, and characterization of high-potential porphyrins and metal-free phthalocyanines with phosphonic anchoring groups are reported. Photocurrents measured for WSDSPETCs made with some of these dyes co-adsorbed with molecular or colloidal catalysts on TiO2 electrodes are reported as well. To guide in the design of new molecules we have used computational quantum chemistry extensively. Linear correlations between calculated frontier molecular orbital energies and redox potentials were built and tested at multiple levels of theory (from semi-empirical methods to density functional theory). Strong correlations (with r2 values > 0.99) with very good predictive abilities (rmsd < 50 mV) were found when using density functional theory (DFT) combined with a continuum solvent model. DFT was also used to aid in the elucidation of the mechanism of the thermal relaxation observed for the charge-separated state of a molecular triad that mimics the photo-induced proton coupled electron transfer of the tyrosine-histidine redox relay in the reaction center of Photosystem II. It was found that the inclusion of explicit solvent molecules, hydrogen bonded to specific sites within the molecular triad, was essential to explain the observed thermal relaxation. These results are relevant for both advancing the knowledge about natural photosynthesis and for the future design of new molecules for WSDSPETCs.
ContributorsMéndez-Hernández, Dalvin D (Author) / Moore, Ana L (Thesis advisor) / Mujica, Vladimiro (Thesis advisor) / Gust, Devens J. (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2014
Description
Increasing computational demands in data centers require facilities to operate at higher ambient temperatures and at higher power densities. Conventionally, data centers are cooled with electrically-driven vapor-compressor equipment. This paper proposes an alternative data center cooling architecture that is heat-driven. The source is heat produced by the computer equipment. This dissertation details experiments investigating the quantity and quality of heat that can be captured from a liquid-cooled microprocessor on a computer server blade from a data center. The experiments involve four liquid-cooling setups and associated heat-extraction, including a radical approach using mineral oil. The trials examine the feasibility of using the thermal energy from a CPU to drive a cooling process. Uniquely, the investigation establishes an interesting and useful relationship simultaneously among CPU temperatures, power, and utilization levels. In response to the system data, this project explores the heat, temperature and power effects of adding insulation, varying water flow, CPU loading, and varying the cold plate-to-CPU clamping pressure. The idea is to provide an optimal and steady range of temperatures necessary for a chiller to operate. Results indicate an increasing relationship among CPU temperature, power and utilization. Since the dissipated heat can be captured and removed from the system for reuse elsewhere, the need for electricity-consuming computer fans is eliminated. Thermocouple readings of CPU temperatures as high as 93°C and a calculated CPU thermal energy up to 67Wth show a sufficiently high temperature and thermal energy to serve as the input temperature and heat medium input to an absorption chiller. This dissertation performs a detailed analysis of the exergy of a processor and determines the maximum amount of energy utilizable for work. Exergy as a source of realizable work is separated into its two contributing constituents: thermal exergy and informational exergy. The informational exergy is that usable form of work contained within the most fundamental unit of information output by a switching device within a CPU. Exergetic thermal, informational and efficiency values are calculated and plotted for our particular CPU, showing how the datasheet standards compare with experimental values. The dissertation concludes with a discussion of the work's significance.
ContributorsHaywood, Anna (Author) / Phelan, Patrick E (Thesis advisor) / Herrmann, Marcus (Committee member) / Gupta, Sandeep (Committee member) / Trimble, Steve (Committee member) / Myhajlenko, Stefan (Committee member) / Arizona State University (Publisher)
Created2014