Matching Items (180)
Description
A synbody is a newly developed protein binding peptide which can be rapidly produced by chemical methods. The advantages of the synbody producing process make it a potential human proteome binding reagent. Most of the synbodies are designed to bind to specific proteins. The peptides incorporated in a synbody are discovered with peptide microarray technology. Nevertheless, the targets for unknown synbodies can also be discovered by searching through a protein mixture. The first part of this thesis mainly focuses on the process of target searching, which was performed with immunoprecipitation assays and mass spectrometry analysis. Proteins are pulled down from the cell lysate by certain synbodies, and then these proteins are identified using mass spectrometry. After excluding non-specific bindings, the interaction between a synbody and its real target(s) can be verified with affinity measurements. As a specific example, the binding between 1-4-KCap synbody and actin was discovered. This result proved the feasibility of the mass spectrometry based method and also suggested that a high throughput synbody discovery platform for the human proteome could be developed. Besides the application of synbody development, the peptide microarray technology can also be used for immunosignatures. The composition of all types of antibodies existing in one's blood is related to an individual's health condition. A method, called immunosignaturing, has been developed for early disease diagnosis based on this principle. CIM10K microarray slides work as a platform for blood antibody detection in immunosignaturing. During the analysis of an immunosignature, the data from these slides needs to be validated by using landing light peptides. The second part of this thesis focuses on the validation of the data. A biotinylated peptide was used as a landing light on the new CIM10K slides. The data was collected in several rounds of tests and indicated that the variation among landing lights was significantly reduced by using the newly prepared biotinylated peptide compared with old peptide mixture. Several suggestions for further landing light improvement are proposed based on the results.
ContributorsSun, Minyao (Author) / Johnston, Stephen Albert (Thesis advisor) / Diehnelt, Chris Wayne (Committee member) / Stafford, Phillip (Committee member) / Arizona State University (Publisher)
Created2011
Description
Ge1-ySny alloys represent a new class of photonic materials for integrated optoelectronics on Si. In this work, the electrical and optical properties of Ge1-ySny alloy films grown on Si, with concentrations in the range 0 ≤ y ≤ 0.04, are studied via a variety of methods. The first microelectronic devices from GeSn films were fabricated using newly developed CMOS-compatible protocols, and the devices were characterized with respect to their electrical properties and optical response. The detectors were found to have a detection range that extends into the near-IR, and the detection edge is found to shift to longer wavelengths with increasing Sn content, mainly due to the compositional dependence of the direct band gap E0. With only 2 % Sn, all of the telecommunication bands are covered by a single detector. Room temperature photoluminescence was observed from GeSn films with Sn content up to 4 %. The peak wavelength of the emission was found to shift to lower energies with increasing Sn content, corresponding to the decrease in the direct band gap E0 of the material. An additional peak in the spectrum was assigned to the indirect band gap. The separation between the direct and indirect peaks was found to decrease with increasing Sn concentration, as expected. Electroluminescence was also observed from Ge/Si and Ge0.98Sn0.02 photodiodes under forward bias, and the luminescence spectra were found to match well with the observed photoluminescence spectra. A theoretical expression was developed for the luminescence due to the direct band gap and fit to the data.
ContributorsMathews, Jay (Author) / Menéndez, Jose (Thesis advisor) / Kouvetakis, John (Thesis advisor) / Drucker, Jeffery (Committee member) / Chizmeshya, Andrew (Committee member) / Ponce, Fernando (Committee member) / Arizona State University (Publisher)
Created2011
Description
A novel concept for integration of flame-assisted fuel cells (FFC) with a gas turbine is analyzed in this paper. Six different fuels (CH4, C3H8, JP-4, JP-5, JP-10(L), and H2) are investigated for the analytical model of the FFC integrated gas turbine hybrid system. As equivalence ratio increases, the efficiency of the hybrid system increases initially then decreases because the decreasing flow rate of air begins to outweigh the increasing hydrogen concentration. This occurs at an equivalence ratio of 2 for CH4. The thermodynamic cycle is analyzed using a temperature entropy diagram and a pressure volume diagram. These thermodynamic diagrams show as equivalence ratio increases, the power generated by the turbine in the hybrid setup decreases. Thermodynamic analysis was performed to verify that energy is conserved and the total chemical energy going into the system was equal to the heat rejected by the system plus the power generated by the system. Of the six fuels, the hybrid system performs best with H2 as the fuel. The electrical efficiency with H2 is predicted to be 27%, CH4 is 24%, C3H8 is 22%, JP-4 is 21%, JP-5 is 20%, and JP-10(L) is 20%. When H2 fuel is used, the overall integrated system is predicted to be 24.5% more efficient than the standard gas turbine system. The integrated system is predicted to be 23.0% more efficient with CH4, 21.9% more efficient with C3H8, 22.7% more efficient with JP-4, 21.3% more efficient with JP-5, and 20.8% more efficient with JP-10(L). The sensitivity of the model is investigated using various fuel utilizations. When CH4 fuel is used, the integrated system is predicted to be 22.7% more efficient with a fuel utilization efficiency of 90% compared to that of 30%.
ContributorsRupiper, Lauren Nicole (Author) / Milcarek, Ryan (Thesis director) / Wang, Liping (Committee member) / Mechanical and Aerospace Engineering Program (Contributor) / School for Engineering of Matter,Transport & Enrgy (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Immunosignaturing is a new immunodiagnostic technology that uses random-sequence peptide microarrays to profile the humoral immune response. Though the peptides have little sequence homology to any known protein, binding of serum antibodies may be detected, and the pattern correlated to disease states. The aim of my dissertation is to analyze the factors affecting the binding patterns using monoclonal antibodies and determine how much information may be extracted from the sequences. Specifically, I examined the effects of antibody concentration, competition, peptide density, and antibody valence. Peptide binding could be detected at the low concentrations relevant to immunosignaturing, and a monoclonal's signature could even be detected in the presences of 100 fold excess naive IgG. I also found that peptide density was important, but this effect was not due to bivalent binding. Next, I examined in more detail how a polyreactive antibody binds to the random sequence peptides compared to protein sequence derived peptides, and found that it bound to many peptides from both sets, but with low apparent affinity. An in depth look at how the peptide physicochemical properties and sequence complexity revealed that there were some correlations with properties, but they were generally small and varied greatly between antibodies. However, on a limited diversity but larger peptide library, I found that sequence complexity was important for antibody binding. The redundancy on that library did enable the identification of specific sub-sequences recognized by an antibody. The current immunosignaturing platform has little repetition of sub-sequences, so I evaluated several methods to infer antibody epitopes. I found two methods that had modest prediction accuracy, and I developed a software application called GuiTope to facilitate the epitope prediction analysis. None of the methods had sufficient accuracy to identify an unknown antigen from a database. In conclusion, the characteristics of the immunosignaturing platform observed through monoclonal antibody experiments demonstrate its promise as a new diagnostic technology. However, a major limitation is the difficulty in connecting the signature back to the original antigen, though larger peptide libraries could facilitate these predictions.
ContributorsHalperin, Rebecca (Author) / Johnston, Stephen A. (Thesis advisor) / Bordner, Andrew (Committee member) / Taylor, Thomas (Committee member) / Stafford, Phillip (Committee member) / Arizona State University (Publisher)
Created2011
Description
As existing solar cell technologies come closer to their theoretical efficiency, new concepts that overcome the Shockley-Queisser limit and exceed 50% efficiency need to be explored. New materials systems are often investigated to achieve this, but the use of existing solar cell materials in advanced concept approaches is compelling for multiple theoretical and practical reasons. In order to include advanced concept approaches into existing materials, nanostructures are used as they alter the physical properties of these materials. To explore advanced nanostructured concepts with existing materials such as III-V alloys, silicon and/or silicon/germanium and associated alloys, fundamental aspects of using these materials in advanced concept nanostructured solar cells must be understood. Chief among these is the determination and predication of optimum electronic band structures, including effects such as strain on the band structure, and the material's opto-electronic properties. Nanostructures have a large impact on band structure and electronic properties through quantum confinement. An additional large effect is the change in band structure due to elastic strain caused by lattice mismatch between the barrier and nanostructured (usually self-assembled QDs) materials. To develop a material model for advanced concept solar cells, the band structure is calculated for single as well as vertical array of quantum dots with the realistic effects such as strain, associated with the epitaxial growth of these materials. The results show significant effect of strain in band structure. More importantly, the band diagram of a vertical array of QDs with different spacer layer thickness show significant change in band offsets, especially for heavy and light hole valence bands when the spacer layer thickness is reduced. These results, ultimately, have significance to develop a material model for advance concept solar cells that use the QD nanostructures as absorbing medium. The band structure calculations serve as the basis for multiple other calculations. Chief among these is that the model allows the design of a practical QD advanced concept solar cell, which meets key design criteria such as a negligible valence band offset between the QD/barrier materials and close to optimum band gaps, resulting in the predication of optimum material combinations.
ContributorsDahal, Som Nath (Author) / Honsberg, Christiana (Thesis advisor) / Goodnick, Stephen (Committee member) / Roedel, Ronald (Committee member) / Ponce, Fernando (Committee member) / Arizona State University (Publisher)
Created2011
Description
Raman scattering from Ge-Si core-shell nanowires is investigated theoretically and experimentally. A theoretical model that makes it possible to extract quantitative strain information from the measured Raman spectra is presented for the first time. Geometrical and elastic simplifications are introduced to keep the model analytical, which facilitates comparison with experimental results. In particular, the nanowires are assumed to be cylindrical, and their elastic constants isotropic. The simple analytical model is subsequently validated by performing numerical calculations using realistic nanowire geometries and cubic, anisotropic elastic constants. The comparison confirms that the analytic model is an excellent approximation that greatly facilitates quantitative Raman work, with expected errors in the strain determination that do not exceed 10%. Experimental Raman spectra of a variety of core-shell nanowires are presented, and the strain in the nanowires is assessed using the models described above. It is found that all structures present a significant degree of strain relaxation relative to ideal, fully strained Ge-Si core-shell structures. The analytical models are modified to quantify this strain relaxation.
ContributorsSingh, Rachna (Author) / Menéndez, Jose (Thesis advisor) / Drucker, Jeffery (Committee member) / Ponce, Fernando (Committee member) / Tsen, Kong-Thon (Committee member) / Bennett, Peter (Committee member) / Arizona State University (Publisher)
Created2011
Description
ABSTRACT Group III-nitride semiconductor materials have been commercially used in fabrication of light-emitting diodes (LEDs) and laser diodes (LDs) covering the spectral range from UV to visible and infrared, and exhibit unique properties suitable for modern optoelectronic applications. Great advances have recently happened in the research and development in high-power and high-efficiency blue-green-white LEDs, blue LDs and other optoelectronic applications. However, there are still many unsolved challenges with these materials. In this dissertation, several issues concerning structural, electronic and optical properties of III-nitrides have been investigated using a combination of transmission electron microscopy (TEM), electron holography (EH) and cathodoluminescence (CL) techniques. First, a trend of indium chemical inhomogeneity has been found as the indium composition increases for the InGaN epitaxial layers grown by hydride vapor phase epitaxy. Second, different mechanisms contributing to the strain relaxation have been studied for non-polar InGaN epitaxial layers grown on zinc oxide (ZnO) substrate. Third, various structural morphologies of non-polar InGaN epitaxial layers grown on free-standing GaN substrate have been investigated. Fourth, the effect of the growth temperature on the performance of GaN lattice-matched InAlN electron blocking layers has been studied. Finally, the electronic and optical properties of GaN nanowires containing a AlN/GaN superlattice structure have been investigated showing relatively small internal electric field and superlattice- and defect-related emissions along the nanowires.
ContributorsSun, Kewei (Author) / Ponce, Fernando (Thesis advisor) / Smith, David (Committee member) / Treacy, Michael (Committee member) / Drucker, Jeffery (Committee member) / Schmidt, Kevin (Committee member) / Arizona State University (Publisher)
Created2011
Raman spectroscopy characterization of anharmonicity and alloying effects in semiconductor materials
Description
The chemical sensitivity and spatial resolution of Raman spectroscopy, combined with the sensitivity of modern systems that can easily detect single atomic layers, have made this technique a preferred choice for the strain characterization of complex systems such as nanoscale complementary metal-oxide-semiconductor - CMOS - devices. A disadvantage of Raman spectroscopy, however, is that the shifts associated with strain are not related to the geometrical deformations in any obvious way, so that careful calibrations are needed to determine the anharmonic coefficients (p, q and r) that relate strain to Raman shifts. A new set of measurements of the Raman shift in strained Ge films grown on relaxed SiGe buffer layers deposited on Si substrates is presented, and thereby, a new consistent set of values for the parameters p and q for Ge has been proposed. In this dissertation the study of the vibrational properties of Ge1-xSnx alloys has also been reported. The temperature dependence of the Raman spectrum of Ge-rich Ge1-x Snx and Ge1-x-ySi xSny alloys has been determined in the 10 K - 450 K range. The Raman line shift and width changes as a function of temperature are found to be virtually identical to those observed in bulk Ge. This result shows that the anharmonic decay process responsible for the temperature dependence is extremely robust against the alloy perturbation.
ContributorsBagchi, Sampriti (Author) / Menéndez, Jose (Thesis advisor) / Treacy, Michael (Committee member) / Ponce, Fernando (Committee member) / Tsen, Kong-Thon (Committee member) / Rez, Peter (Committee member) / Arizona State University (Publisher)
Created2011
Description
African Swine Fever (ASF), endemic in many African countries, is now spreading to other continents. Though ASF is capable of incurring serious economic losses in affected countries, no vaccine exists to provide immunity to animals. Disease control relies largely on rapid diagnosis and the implementation of movement restrictions and strict eradication programs. Developing a scalable, accurate and low cost diagnostic for ASF will be of great help for the current situation. CIM's 10K random peptide microarray is a new high-throughput platform that allows systematic investigations of immune responses associated with disease and shows promise as a diagnostic tool. In this study, this new technology was applied to characterize the immune responses of ASF virus (ASFV) infections and immunizations. Six sets of sera from ASFV antigen immunized pigs, 6 sera from infected pigs and 20 sera samples from unexposed pigs were tested and analyzed statistically. Results show that both ASFV antigen immunized pigs and ASFV viral infected pigs can be distinguished from unexposed pigs. Since it appears that immune responses to other viral infections are also distinguishable on this platform, it holds the potential of being useful in developing a new ASF diagnostic. The ability of this platform to identify specific ASFV antibody epitopes was also explored. A subtle motif was found to be shared among a set of peptides displaying the highest reactivity for an antigen specific antibody. However, this motif does not seem to match with any antibody epitopes predicted by a linear antibody epitope prediction.
ContributorsXiao, Liang (Author) / Sykes, Kathryn (Thesis advisor) / Zhao, Zhan-Gong (Committee member) / Stafford, Phillip (Committee member) / Arizona State University (Publisher)
Created2011
Description
This thesis describes the fabrication of several new classes of Ge1-x-ySixSny materials with the required compositions and crystal quality to engineer the band gaps above and below that of elemental Ge (0.8 eV) in the near IR. The work initially focused on Ge1-x-ySixSny (1-5% Sn, 4-20% Si) materials grown on Ge(100) via gas-source epitaxy of Ge4H10, Si4H10 and SnD4. Both intrinsic and doped layers were produced with defect-free microstructure and viable thickness, allowing the fabrication of high-performance photodetectors. These exhibited low ideality factors, state-of-the-art dark current densities and adjustable absorption edges between 0.87 and 1.03 eV, indicating that the band gaps span a significant range above that of Ge. Next Sn-rich Ge1-x-ySixSny alloys (2-4% Si and 4-10% Sn) were fabricated directly on Si and were found to show significant optical emission using photoluminescence measurements, indicating that the alloys have direct band gaps below that of pure Ge in the range of 0.7-0.55 eV. A series of Sn-rich Ge1-x-ySixSny analogues (y>x) with fixed 3-4% Si content and progressively increasing Sn content in the 4-10% range were then grown on Ge buffered Si platforms for the purpose of improving the material's crystal quality. The films in this case exhibited lower defect densities than those grown on Si, allowing a meaningful study of both the direct and indirect gaps. The results show that the separation of the direct and indirect edges can be made smaller than in Ge even for non-negligible 3-4% Si content, confirming that with a suitable choice of Sn compositions the ternary Ge1-x-ySixSny reproduces all features of the electronic structure of binary Ge1-ySny, including the sought-after indirect-to-direct gap cross over. The above synthesis of optical quality Ge1-x-ySixSny on virtual Ge was made possible by the development of high quality Ge-on-Si buffers via chemical vapor deposition of Ge4H10. The resultant films exhibited structural and electrical properties significantly improved relative to state-of-the-art results obtained using conventional approaches. It was found that pure Ge4H10 facilitates the control of residual doping and enables p-i-n devices whose dark currents are not entirely determined by defects and whose zero-bias collection efficiencies are higher than those obtained from samples fabricated using alternative Ge-on-Si approaches.
ContributorsXu, Chi (Author) / Kouvetakis, John (Thesis advisor) / Menéndez, Jose (Thesis advisor) / Chizmeshya, Andrew (Committee member) / Drucker, Jeffrey (Committee member) / Ponce, Fernando (Committee member) / Arizona State University (Publisher)
Created2013