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 85
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
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
Scaling of the classical planar MOSFET below 20 nm gate length is facing not only technological difficulties but also limitations imposed by short channel effects, gate and junction leakage current due to quantum tunneling, high body doping induced threshold voltage variation, and carrier mobility degradation. Non-classical multiple-gate structures such as double-gate (DG) FinFETs and surrounding gate field-effect-transistors (SGFETs) have good electrostatic integrity and are an alternative to planar MOSFETs for below 20 nm technology nodes. Circuit design with these devices need compact models for SPICE simulation. In this work physics based compact models for the common-gate symmetric DG-FinFET, independent-gate asymmetric DG-FinFET, and SGFET are developed. Despite the complex device structure and boundary conditions for the Poisson-Boltzmann equation, the core structure of the DG-FinFET and SGFET models, are maintained similar to the surface potential based compact models for planar MOSFETs such as SP and PSP. TCAD simulations show differences between the transient behavior and the capacitance-voltage characteristics of bulk and SOI FinFETs if the gate-voltage swing includes the accumulation region. This effect can be captured by a compact model of FinFETs only if it includes the contribution of both types of carriers in the Poisson-Boltzmann equation. An accurate implicit input voltage equation valid in all regions of operation is proposed for common-gate symmetric DG-FinFETs with intrinsic or lightly doped bodies. A closed-form algorithm is developed for solving the new input voltage equation including ambipolar effects. The algorithm is verified for both the surface potential and its derivatives and includes a previously published analytical approximation for surface potential as a special case when ambipolar effects can be neglected. The symmetric linearization method for common-gate symmetric DG-FinFETs is developed in a form free of the charge-sheet approximation present in its original formulation for bulk MOSFETs. The accuracy of the proposed technique is verified by comparison with exact results. An alternative and computationally efficient description of the boundary between the trigonometric and hyperbolic solutions of the Poisson-Boltzmann equation for the independent-gate asymmetric DG-FinFET is developed in terms of the Lambert W function. Efficient numerical algorithm is proposed for solving the input voltage equation. Analytical expressions for terminal charges of an independent-gate asymmetric DG-FinFET are derived. The new charge model is C-infinity continuous, valid for weak as well as for strong inversion condition of both the channels and does not involve the charge-sheet approximation. This is accomplished by developing the symmetric linearization method in a form that does not require identical boundary conditions at the two Si-SiO2 interfaces and allows for volume inversion in the DG-FinFET. Verification of the model is performed with both numerical computations and 2D TCAD simulations under a wide range of biasing conditions. The model is implemented in a standard circuit simulator through Verilog-A code. Simulation examples for both digital and analog circuits verify good model convergence and demonstrate the capabilities of new circuit topologies that can be implemented using independent-gate asymmetric DG-FinFETs.
ContributorsDessai, Gajanan (Author) / Gildenblat, Gennady (Committee member) / McAndrew, Colin (Committee member) / Cao, Yu (Committee member) / Barnaby, Hugh (Committee member) / Arizona State University (Publisher)
Created2012
Description
Test cost has become a significant portion of device cost and a bottleneck in high volume manufacturing. Increasing integration density and shrinking feature sizes increased test time/cost and reduce observability. Test engineers have to put a tremendous effort in order to maintain test cost within an acceptable budget. Unfortunately, there is not a single straightforward solution to the problem. Products that are tested have several application domains and distinct customer profiles. Some products are required to operate for long periods of time while others are required to be low cost and optimized for low cost. Multitude of constraints and goals make it impossible to find a single solution that work for all cases. Hence, test development/optimization is typically design/circuit dependent and even process specific. Therefore, test optimization cannot be performed using a single test approach, but necessitates a diversity of approaches. This works aims at addressing test cost minimization and test quality improvement at various levels. In the first chapter of the work, we investigate pre-silicon strategies, such as design for test and pre-silicon statistical simulation optimization. In the second chapter, we investigate efficient post-silicon test strategies, such as adaptive test, adaptive multi-site test, outlier analysis, and process shift detection/tracking.
ContributorsYilmaz, Ender (Author) / Ozev, Sule (Thesis advisor) / Bakkaloglu, Bertan (Committee member) / Cao, Yu (Committee member) / Christen, Jennifer Blain (Committee member) / Arizona State University (Publisher)
Created2012
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
Non-volatile memories (NVM) are widely used in modern electronic devices due to their non-volatility, low static power consumption and high storage density. While Flash memories are the dominant NVM technology, resistive memories such as phase change access memory (PRAM) and spin torque transfer random access memory (STT-MRAM) are gaining ground. All these technologies suffer from reliability degradation due to process variations, structural limits and material property shift. To address the reliability concerns of these NVM technologies, multi-level low cost solutions are proposed for each of them. My approach consists of first building a comprehensive error model. Next the error characteristics are exploited to develop low cost multi-level strategies to compensate for the errors. For instance, for NAND Flash memory, I first characterize errors due to threshold voltage variations as a function of the number of program/erase cycles. Next a flexible product code is designed to migrate to a stronger ECC scheme as program/erase cycles increases. An adaptive data refresh scheme is also proposed to improve memory reliability with low energy cost for applications with different data update frequencies. For PRAM, soft errors and hard errors models are built based on shifts in the resistance distributions. Next I developed a multi-level error control approach involving bit interleaving and subblock flipping at the architecture level, threshold resistance tuning at the circuit level and programming current profile tuning at the device level. This approach helped reduce the error rate significantly so that it was now sufficient to use a low cost ECC scheme to satisfy the memory reliability constraint. I also studied the reliability of a PRAM+DRAM hybrid memory system and analyzed the tradeoffs between memory performance, programming energy and lifetime. For STT-MRAM, I first developed an error model based on process variations. I developed a multi-level approach to reduce the error rates that consisted of increasing the W/L ratio of the access transistor, increasing the voltage difference across the memory cell and adjusting the current profile during write operation. This approach enabled use of a low cost BCH based ECC scheme to achieve very low block failure rates.
ContributorsYang, Chengen (Author) / Chakrabarti, Chaitali (Thesis advisor) / Cao, Yu (Committee member) / Ogras, Umit Y. (Committee member) / Bakkaloglu, Bertan (Committee member) / Arizona State University (Publisher)
Created2014
Description
With increasing demand for System on Chip (SoC) and System in Package (SiP) design in computer and communication technologies, integrated inductor which is an essential passive component has been widely used in numerous integrated circuits (ICs) such as in voltage regulators and RF circuits. In this work, soft ferromagnetic core material, amorphous Co-Zr-Ta-B, was incorporated into on-chip and in-package inductors in order to scale down inductors and improve inductors performance in both inductance density and quality factor. With two layers of 500 nm Co-Zr-Ta-B films a 3.5X increase in inductance and a 3.9X increase in quality factor over inductors without magnetic films were measured at frequencies as high as 1 GHz. By laminating technology, up to 9.1X increase in inductance and more than 5X increase in quality factor (Q) were obtained from stripline inductors incorporated with 50 nm by 10 laminated films with a peak Q at 300 MHz. It was also demonstrated that this peak Q can be pushed towards high frequency as far as 1GHz by a combination of patterning magnetic films into fine bars and laminations. The role of magnetic vias in magnetic flux and eddy current control was investigated by both simulation and experiment using different patterning techniques and by altering the magnetic via width. Finger-shaped magnetic vias were designed and integrated into on-chip RF inductors improving the frequency of peak quality factor from 400 MHz to 800 MHz without sacrificing inductance enhancement. Eddy current and magnetic flux density in different areas of magnetic vias were analyzed by HFSS 3D EM simulation. With optimized magnetic vias, high frequency response of up to 2 GHz was achieved. Furthermore, the effect of applied magnetic field on on-chip inductors was investigated for high power applications. It was observed that as applied magnetic field along the hard axis (HA) increases, inductance maintains similar value initially at low fields, but decreases at larger fields until the magnetic films become saturated. The high frequency quality factor showed an opposite trend which is correlated to the reduction of ferromagnetic resonant absorption in the magnetic film. In addition, experiments showed that this field-dependent inductance change varied with different patterned magnetic film structures, including bars/slots and fingers structures. Magnetic properties of Co-Zr-Ta-B films on standard organic package substrates including ABF and polyimide were also characterized. Effects of substrate roughness and stress were analyzed and simulated which provide strategies for integrating Co-Zr-Ta-B into package inductors and improving inductors performance. Stripline and spiral inductors with Co-Zr-Ta-B films were fabricated on both ABF and polyimide substrates. Maximum 90% inductance increase in hundreds MHz frequency range were achieved in stripline inductors which are suitable for power delivery applications. Spiral inductors with Co-Zr-Ta-B films showed 18% inductance increase with quality factor of 4 at frequency up to 3 GHz.
ContributorsWu, Hao (Author) / Yu, Hongbin (Thesis advisor) / Bakkaloglu, Bertan (Committee member) / Cao, Yu (Committee member) / Chickamenahalli, Shamala (Committee member) / Arizona State University (Publisher)
Created2013