Matching Items (52)
Description
ABSTRACT Peptide microarrays may prove to be a powerful tool for proteomics research and clinical diagnosis applications. Fodor et al. and Maurer et al. have shown proof-of-concept methods of light- and electrochemically-directed peptide microarray fabrication on glass and semiconductor microchips respectively. In this work, peptide microarray fabrication based on the abovementioned techniques were optimized. In addition, MALDI mass spectrometry based peptide synthesis characterization on semiconductor microchips was developed and novel applications of a CombiMatrix (CBMX) platform for electrochemically controlled synthesis were explored. We have investigated performance of 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) derivatives as photo-labile protecting group. Specifically, influence of substituents on 4 and 5 positions of phenyl ring of NPPOC group on the rate of photolysis and the yield of the amine was investigated. The results indicated that substituents capable of forming a π-network with the nitro group enhanced the rate of photolysis and yield. Once such properly substituted NPPOC groups were used, the rate of photolysis/yield depended on the nature of protected amino group indicating that a different chemical step during the photo-cleavage process became the rate limiting step. We also focused on electrochemically-directed parallel synthesis of high-density peptide microarrays using the CBMX technology referred to above which uses electrochemically generated acids to perform patterned chemistry. Several issues related to peptide synthesis on the CBMX platform were studied and optimized, with emphasis placed on the reactions of electro-generated acids during the deprotection step of peptide synthesis. We have developed a MALDI mass spectrometry based method to determine the chemical composition of microarray synthesis, directly on the feature. This method utilizes non-diffusional chemical cleavage from the surface, thereby making the chemical characterization of high-density microarray features simple, accurate, and amenable to high-throughput. CBMX Corp. has developed a microarray reader which is based on electro-chemical detection of redox chemical species. Several parameters of the instrument were studied and optimized and novel redox applications of peptide microarrays on CBMX platform were also investigated using the instrument. These include (i) a search of metal binding catalytic peptides to reduce overpotential associated with water oxidation reaction and (ii) an immobilization of peptide microarrays using electro-polymerized polypyrrole.
ContributorsKumar, Pallav (Author) / Woodbury, Neal (Thesis advisor) / Allen, James (Committee member) / Johnston, Stephen (Committee member) / Arizona State University (Publisher)
Created2013
Description
Rapid processing and reduced end-of-range diffusion effects demonstrate that susceptor-assisted microwave annealing is an efficient processing alternative for electrically activating dopants and removing ion-implantation damage in ion-implanted semiconductors. Sheet resistance and Hall measurements provide evidence of electrical activation. Raman spectroscopy and ion channeling analysis monitor the extent of ion implantation damage and recrystallization. The presence of damage and defects in ion implanted silicon, and the reduction of the defects as a result of annealing, is observed by Rutherford backscattering spectrometry, moreover, the boron implanted silicon is further investigated by cross-section transmission electron microscopy. When annealing B+ implanted silicon, the dissolution of small extended defects and growth of large extended defects result in reduced crystalline quality that hinders the electrical activation process. Compared to B+ implanted silicon, phosphorus implanted samples experience more effective activation and achieve better crystalline quality. Comparison of end-of-range dopants diffusion resulting from microwave annealing and rapid thermal annealing (RTA) is done using secondary ion mass spectroscopy. Results from microwave annealed P+ implanted samples show that almost no diffusion occurs during time periods required for complete dopant activation and silicon recrystallization. The relative contributions to heating of the sample, by a SiC susceptor, and by Si self-heating in the microwave anneal, were also investigated. At first 20s, the main contributor to the sample's temperature rise is Si self-heating by microwave absorption.
ContributorsZhao, Zhao (Author) / Alford, Terry Lynn (Thesis advisor) / Theodore, David (Committee member) / Krause, Stephen (Committee member) / Arizona State University (Publisher)
Created2013
Description
Microwave (MW), thermal, and ultraviolet (UV) annealing were used to explore the response of Ag structures on a Ge-Se chalcogenide glass (ChG) thin film as flexible radiation sensors, and Te-Ti chalcogenide thin films as a material for diffusion barriers in microelectronics devices and processing of metallized Cu. Flexible resistive radiation sensors consisting of Ag electrodes on a Ge20Se80 ChG thin film and polyethylene naphthalate substrate were exposed to UV radiation. The sensors were mounted on PVC tubes of varying radii to induce bending strains and annealed under ambient conditions up to 150 oC. Initial sensor resistance was measured to be ~1012 Ω; after exposure to UV radiation, the resistance was ~104 Ω. Bending strain and low temperature annealing had no significant effect on the resistance of the sensors. Samples of Cu on Te-Ti thin films were annealed in vacuum for up to 30 minutes and were stable up to 500 oC as revealed using Rutherford backscattering spectrometry (RBS) and four-point-probe analysis. X-ray diffractometry (XRD) indicates Cu grain growth up to 500 oC and phase instability of the Te-Ti barrier at 600 oC. MW processing was performed in a 2.45-GHz microwave cavity on Cu/Te-Ti films for up to 30 seconds to induce oxide growth. Using a calibrated pyrometer above the sample, the temperature of the MW process was measured to be below a maximum of 186 oC. Four-point-probe analysis shows an increase in resistance with an increase in MW time. XRD indicates growth of CuO on the sample surface. RBS suggests oxidation throughout the Te-Ti film. Additional samples were exposed to 907 J/cm2 UV radiation in order to ensure other possible electromagnetically induced mechanisms were not active. There were no changes observed using XRD, RBS or four point probing.
ContributorsRoos, Benjamin, 1990- (Author) / Alford, Terry L. (Thesis advisor) / Theodore, David (Committee member) / Kozicki, Michael (Committee member) / Arizona State University (Publisher)
Created2013
Description
Semiconductor manufacturing economics necessitate the development of innovative device measurement techniques for quick assessment of products. Several novel electrical measurement techniques will be proposed for screening silicon device parameters. The studied parameters range from oxide reliability, and carrier lifetime in MOS capacitors to the power MOSFET reverse recovery.
It will be shown that positive charge trapping is a dominant process when thick oxides are stressed through the ramped voltage test (RVT). Exploiting the physics behind positive charge generation/trapping at high electric fields, a fast I-V measurement technique is proposed that can be used to effectively distinguish the ultra-thick oxides' intrinsic quality at low electric fields.
Next, two novel techniques will be presented for studying the carrier lifetime in MOS Capacitor devices. It will be shown that the deep-level transient spectroscopy (DLTS) can be applied to MOS test structures as a swift mean for screening the generation lifetime. Recombination lifetime will also be addressed by introducing the optically-excited MOS technique as a promising tool.
The last part of this work is devoted to the reverse recovery behavior of the body diode of power MOSFETs. The correct interpretation of the LDMOS reverse recovery is challenging and requires special attention. A simple approach will be presented to extract meaningful lifetime values from the reverse recovery of LDMOS body-diodes exploiting their gate voltage and the magnitude of the reverse bias.
It will be shown that positive charge trapping is a dominant process when thick oxides are stressed through the ramped voltage test (RVT). Exploiting the physics behind positive charge generation/trapping at high electric fields, a fast I-V measurement technique is proposed that can be used to effectively distinguish the ultra-thick oxides' intrinsic quality at low electric fields.
Next, two novel techniques will be presented for studying the carrier lifetime in MOS Capacitor devices. It will be shown that the deep-level transient spectroscopy (DLTS) can be applied to MOS test structures as a swift mean for screening the generation lifetime. Recombination lifetime will also be addressed by introducing the optically-excited MOS technique as a promising tool.
The last part of this work is devoted to the reverse recovery behavior of the body diode of power MOSFETs. The correct interpretation of the LDMOS reverse recovery is challenging and requires special attention. A simple approach will be presented to extract meaningful lifetime values from the reverse recovery of LDMOS body-diodes exploiting their gate voltage and the magnitude of the reverse bias.
ContributorsElhami Khorasani, Arash (Author) / Alford, Terry L. (Thesis advisor) / Goryll, Michael (Committee member) / Theodore, David (Committee member) / Arizona State University (Publisher)
Created2015
Description
The healthcare system in this country is currently unacceptable. New technologies may contribute to reducing cost and improving outcomes. Early diagnosis and treatment represents the least risky option for addressing this issue. Such a technology needs to be inexpensive, highly sensitive, highly specific, and amenable to adoption in a clinic. This thesis explores an immunodiagnostic technology based on highly scalable, non-natural sequence peptide microarrays designed to profile the humoral immune response and address the healthcare problem. The primary aim of this thesis is to explore the ability of these arrays to map continuous (linear) epitopes. I discovered that using a technique termed subsequence analysis where epitopes could be decisively mapped to an eliciting protein with high success rate. This led to the discovery of novel linear epitopes from Plasmodium falciparum (Malaria) and Treponema palladium (Syphilis), as well as validation of previously discovered epitopes in Dengue and monoclonal antibodies. Next, I developed and tested a classification scheme based on Support Vector Machines for development of a Dengue Fever diagnostic, achieving higher sensitivity and specificity than current FDA approved techniques. The software underlying this method is available for download under the BSD license. Following this, I developed a kinetic model for immunosignatures and tested it against existing data driven by previously unexplained phenomena. This model provides a framework and informs ways to optimize the platform for maximum stability and efficiency. I also explored the role of sequence composition in explaining an immunosignature binding profile, determining a strong role for charged residues that seems to have some predictive ability for disease. Finally, I developed a database, software and indexing strategy based on Apache Lucene for searching motif patterns (regular expressions) in large biological databases. These projects as a whole have advanced knowledge of how to approach high throughput immunodiagnostics and provide an example of how technology can be fused with biology in order to affect scientific and health outcomes.
ContributorsRicher, Joshua Amos (Author) / Johnston, Stephen A. (Thesis advisor) / Woodbury, Neal (Committee member) / Stafford, Phillip (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Arizona State University (Publisher)
Created2014
Description
This thesis discusses the use of low temperature microwave anneal as an alternative technique to recrystallize materials damaged or amorphized due to implantation techniques. The work focuses on the annealing of high-Z doped Si wafers that are incapable of attaining high temperatures required for recrystallizing the damaged implanted layers by microwave absorption The increasing necessity for quicker and more efficient processing techniques motivates study of the use of a single frequency applicator microwave cavity along with a Fe2O3 infused SiC-alumina susceptor/applicator as an alternative post implantation process. Arsenic implanted Si samples of different dopant concentrations and implantation energies were studied pre and post microwave annealing. A set of as-implanted Si samples were also used to assess the effect of inactive dopants against presence of electrically active dopants on the recrystallization mechanisms. The extent of damage repair and Si recrystallization of the damage caused by arsenic and Si implantation of Si is determined by cross-section transmission electron microscopy and Raman spectroscopy. Dopant activation is evaluated for the As implanted Si by sheet resistance measurements. For the same, secondary ion mass spectroscopy analysis is used to compare the extent of diffusion that results from such microwave annealing with that experienced when using conventional rapid thermal annealing (RTA). Results show that compared to susceptor assisted microwave annealing, RTA caused undesired dopant diffusion. The SiC-alumina susceptor plays a predominant role in supplying heat to the Si substrate, and acts as an assistor that helps a high-Z dopant like arsenic to absorb the microwave energy using a microwave loss mechanism which is a combination of ionic and dipole losses. Comparisons of annealing of the samples were done with and without the use of the susceptor, and confirm the role played by the susceptor, since the samples donot recrystallize when the surface heating mechanism provided by the susceptor is not incorporated. Variable frequency microwave annealing was also performed over the as-implanted Si samples for durations and temperatures higher than the single frequency microwave anneal, but only partial recrystallization of the damaged layer was achieved.
ContributorsVemuri, Rajitha (Author) / Alford, Terry L. (Thesis advisor) / Theodore, David (Committee member) / Krause, Stephen (Committee member) / Arizona State University (Publisher)
Created2011
Description
Nucleosomes are the basic repetitive unit of eukaryotic chromatin and are responsible for packing DNA inside the nucleus of the cell. They consist of a complex of eight histone proteins (two copies of four proteins H2A, H2B, H3 and H4) around which 147 base pairs of DNA are wrapped in ~1.67 superhelical turns. Although the nucleosomes are stable protein-DNA complexes, they undergo spontaneous conformational changes that occur in an asynchronous fashion. This conformational dynamics, defined by the "site-exposure" model, involves the DNA unwrapping from the protein core and exposing itself transiently before wrapping back. Physiologically, this allows regulatory proteins to bind to their target DNA sites during cellular processes like replication, DNA repair and transcription. Traditional biochemical assays have stablished the equilibrium constants for the accessibility to various sites along the length of the nucleosomal DNA, from its end to the middle of the dyad axis. Using fluorescence correlation spectroscopy (FCS), we have established the position dependent rewrapping rates for nucleosomes. We have also used Monte Carlo simulation methods to analyze the applicability of FRET fluctuation spectroscopy towards conformational dynamics, specifically motivated by nucleosome dynamics. Another important conformational change that is involved in cellular processes is the disassembly of nucleosome into its constituent particles. The exact pathway adopted by nucleosomes is still not clear. We used dual color fluorescence correlation spectroscopy to study the intermediates during nucleosome disassembly induced by changing ionic strength. Studying the nature of nucleosome conformational change and the kinetics is very important in understanding gene expression. The results from this thesis give a quantitative description to the basic unit of the chromatin.
ContributorsGurunathan, Kaushik (Author) / Levitus, Marcia (Thesis advisor) / Lindsay, Stuart (Committee member) / Woodbury, Neal (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2011
Description
Amorphous oxide semiconductors are promising new materials for various optoelectronic applications. In this study, improved electrical and optical properties upon thermal and microwave processing of mixed-oxide semiconductors are reported. First, arsenic-doped silicon was used as a model system to understand susceptor-assisted microwave annealing. Mixed oxide semiconductor films of indium zinc oxide (IZO) and indium gallium zinc oxide (IGZO) were deposited by room-temperature RF sputtering on flexible polymer substrates. Thermal annealing in different environments - air, vacuum and oxygen was done. Electrical and optical characterization was carried out before and after annealing. The degree of reversal in the degradation in electrical properties of the thin films upon annealing in oxygen was assessed by subjecting samples to subsequent vacuum anneals. To further increase the conductivity of the IGZO films, Ag layers of various thicknesses were embedded between two IGZO layers. Optical performance of the multilayer structures was improved by susceptor-assisted microwave annealing and furnace-annealing in oxygen environment without compromising on their electrical conductivity. The post-processing of the films in different environments was used to develop an understanding of mechanisms of carrier generation, transport and optical absorption. This study establishes IGZO as a viable transparent conductor, which can be deposited at room-temperature and processed by thermal and microwave annealing to improve electrical and optical performance for applications in flexible electronics and optoelectronics.
ContributorsGadre, Mandar (Author) / Alford, Terry L. (Thesis advisor) / Schroder, Dieter (Committee member) / Krause, Stephen (Committee member) / Theodore, David (Committee member) / Arizona State University (Publisher)
Created2011
Description
This work focuses on simulation of electrical resistivity and optical behaviors of thin films, where an Ag or Au thin layer is embedded in zinc oxide. Enhanced conductivity and transparency were earlier achieved with multilayer structured transparent conducting oxide (TCO) sandwich layer with metal (TCO/metal/TCO). Sputtering pattern of metal layer is simulated to obtain the morphology, covered area fraction, and the percolation strength. The resistivity as a function of the metal layer thickness fits the modeled trend of covered area fraction beyond the percolation threshold. This result not only presents the robustness of the simulation, but also demonstrates the influence of metal morphology in multilayer structure. Effective medium coefficients are defined from the coverage and percolation strength to obtain simulated optical transmittance which matches experimental observation. The coherence of resistivity and optical transmittance validates the simulation of the sputtered pattern and the incorporation of percolation theory in the model.
ContributorsFang, Chia-Ling (Author) / Alford, Terry L. (Thesis advisor) / Crozier, Peter (Committee member) / Theodore, David (Committee member) / Arizona State University (Publisher)
Created2012
Description
It has been well established that mitochondria play a critical role in the pathology of Friedreich's Ataxia. This disease is believed to be caused by a deficiency of frataxin, which research suggests is responsible for iron sulfur cluster assembly. This incomplete assembly of iron sulfur clusters is believed to be linked with dysfunctional complexes in the mitochondrial respiratory chain, increased oxidative stress, and potential cell death. Increased understanding of the pathophysiology of this disease has enabled the development of various therapeutic strategies aimed at restoring mitochondrial respiration. This thesis contains an analysis of the biological activity of several classes of antioxidants against oxidative stress induced by diethyl maleate in Friedreich's Ataxia lymphocytes and CEM leukemia cells. Analogues of vitamin E α-tocopherol have been shown to protect cells under oxidative stress. However, these same analogues show various levels of inhibition towards the electron transport chain complex I. Bicyclic pyridinols containing a ten carbon substituent provided favorable cytoprotection. N-hydroxy-4-pyridone compounds were observed to provide little protection. Similarly, analogues of CoQ10 in the form of pyridinol and pyrimidinol compounds also preserved cell viability at low concentrations.
ContributorsJaruvangsanti, Jennifer (Author) / Hecht, Sidney (Thesis advisor) / Woodbury, Neal (Committee member) / Skibo, Edward (Committee member) / Arizona State University (Publisher)
Created2012