Matching Items (237)
Description
Type Ia supernovae are important, but mysterious cosmological tools. Their standard brightnesses have enabled cosmologists to measure extreme distances and to discover dark energy. However, the nature of their progenitor mechanisms remains elusive, with many competing models offering only partial clues to their origins. Here, type Ia supernova delay times are explored using analytical models. Combined with a new observation technique, this model places new constraints on the characteristic time delay between the formation of stars and the first type Ia supernovae. This derived delay time (500 million years) implies low-mass companions for single degenerate progenitor scenarios. In the latter portions of this dissertation, two progenitor mechanisms are simulated in detail; white dwarf collisions and mergers. From the first of these simulations, it is evident that white dwarf collisions offer a viable and unique pathway to producing type Ia supernovae. Many of the combinations of masses simulated produce sufficient quantities of 56Ni (up to 0.51 solar masses) to masquerade as normal type Ia supernovae. Other combinations of masses produce 56Ni yields that span the entire range of supernova brightnesses, from the very dim and underluminous, with 0.14 solar masses, to the over-bright and superluminous, with up to 1.71 solar masses. The 56Ni yield in the collision simulations depends non-linearly on total system mass, mass ratio, and impact parameter. Using the same numerical tools as in the collisions examination, white dwarf mergers are studied in detail. Nearly all of the simulations produce merger remnants consisting of a cold, degenerate core surrounded by a hot accretion disk. The properties of these disks have strong implications for various viscosity treatments that have attempted to pin down the accretion times. Some mass combinations produce super-Chandrasekhar cores on shorter time scales than viscosity driven accretion. A handful of simulations also exhibit helium detonations on the surface of the primary that bear a resemblance to helium novae. Finally, some of the preliminary groundwork that has been laid for constructing a new numerical tool is discussed. This new tool advances the merger simulations further than any research group has done before, and has the potential to answer some of the lingering questions that the merger study has uncovered. The results of thermal diffusion tests using this tool have a remarkable correspondence to analytical predictions.
ContributorsRaskin, Cody (Author) / Scannapieco, Evan (Thesis advisor) / Rhoads, James (Committee member) / Young, Patrick (Committee member) / Mcnamara, Allen (Committee member) / Timmes, Francis (Committee member) / Arizona State University (Publisher)
Created2011
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
Telomerase ribonucleoprotein is a unique reverse transcriptase that adds telomeric DNA repeats to chromosome ends. Telomerase RNA (TER) is extremely divergent in size, sequence and has to date only been identified in vertebrate, yeast, ciliate and plant species. Herein, the identification and characterization of TERs from an evolutionarily distinct group, filamentous fungi, is presented. Based on phylogenetic analysis of 69 TER sequences and mutagenesis analysis of in vitro reconstituted Neurospora telomerase, we discovered a conserved functional core in filamentous fungal TERs sharing homologous structural features with vertebrate TERs. This core contains the template-pseudoknot and P6/P6.1 domains, essential for enzymatic activity, which retain function in trans. The in vitro reconstituted Neurospora telomerase is highly processive, synthesizing canonical TTAGGG repeats. Similar to Schizosaccharomycetes pombe, filamentous fungal TERs utilize the spliceosomal splicing machinery for 3' processing. Neurospora telomerase, while associating with the Est1 protein in vivo, does not bind homologous Ku or Sm proteins found in both budding and fission yeast telomerase holoenzyme, suggesting a unique biogenesis pathway. The development of Neurospora as a model organism to study telomeres and telomerase may shed light upon the evolution of the canonical TTAGGG telomeric repeat and telomerase processivity within fungal species.
ContributorsQi, Xiaodong (Author) / Chen, Julian (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Chaput, John (Committee member) / Arizona State University (Publisher)
Created2011
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
Galaxies with strong Lyman-alpha (Lya) emission line (also called Lya galaxies or emitters) offer an unique probe of the epoch of reionization - one of the important phases when most of the neutral hydrogen in the universe was ionized. In addition, Lya galaxies at high redshifts are a powerful tool to study low-mass galaxy formation. Since current observations suggest that the reionization is complete by redshift z~ 6, it is therefore necessary to discover galaxies at z > 6, to use their luminosity function (LF) as a probe of reionization. I found five z = 7.7 candidate Lya galaxies with line fluxes > 7x10-18 erg/s/cm/2 , from three different deep near-infrared (IR) narrowband (NB) imaging surveys in a volume > 4x104Mpc3. From the spectroscopic followup of four candidate galaxies, and with the current spectroscopic sensitivity, the detection of only the brightest candidate galaxy can be ruled out at 5 sigma level. Moreover, these observations successfully demonstrate that the sensitivity necessary for both, the NB imaging as well as the spectroscopic followup of z~ 8 Lya galaxies can be reached with the current instrumentation. While future, more sensitive spectroscopic observations are necessary, the observed Lya LF at z = 7.7 is consistent with z = 6.6 LF, suggesting that the intergalactic medium (IGM) is relatively ionized even at z = 7.7, with neutral fraction xHI≤ 30%. On the theoretical front, while several models of Lya emitters have been developed, the physical nature of Lya emitters is not yet completely known. Moreover, multi-parameter models and their complexities necessitates a simpler model. I have developed a simple, single-parameter model to populate dark mater halos with Lya emitters. The central tenet of this model, different from many of the earlier models, is that the star-formation rate (SFR), and hence the Lya luminosity, is proportional to the mass accretion rate rather than the total halo mass. This simple model is successful in reproducing many observable including LFs, stellar masses, SFRs, and clustering of Lya emitters from z~ 3 to z~ 7. Finally, using this model, I find that the mass accretion, and hence the star-formation in > 30% of Lya emitters at z~ 3 occur through major mergers, and this fraction increases to ~ 50% at z~7.
ContributorsShet Tilvi, Vithal (Author) / Malhotra, Sangeeta (Thesis advisor) / Rhoads, James (Committee member) / Scannapieco, Evan (Committee member) / Young, Patrick (Committee member) / Jansen, Rolf (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
The use of synthetic cathinones or "bath salts" has risen dramatically in recent years with one of the most popular being Methylendioxypyrovalerone (MDPV). Following the temporary legislative ban on the sale and distribution of this compound , a multitude of other cathinone derivatives have been synthesized. The current study seeks to compare the abuse potential of MDPV with one of the emergent synthetic cathinones 4-methylethcathinone (4-MEC), based on their respective ability to lower current thresholds in an intracranial self-stimulation (ICSS) paradigm. Following acute administration (0.1, 0.5, 1 and 2 mg/kg i.p.) MDPV was found to significantly lower ICSS thresholds at all doses tested (F4,35=11.549, p<0.001). However, following acute administration (0.3,1,3,10,30 mg/kg i.p) 4-MEC produced no significant ICSS threshold depression (F5,135= 0.622, p = 0.684). Together these findings suggest that while MDPV may possess significant abuse potential, other synthetic cathinones such as 4-MEC may have a drastically reduced potential for abuse.
ContributorsWegner, Scott Andrew (Author) / Olive, M. Foster (Thesis director) / Presson, Clark (Committee member) / Sanabria, Federico (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Department of Psychology (Contributor)
Created2013-05
Description
In this thesis, we present the study of several physical properties of relativistic mat- ters under extreme conditions. We start by deriving the rate of the nonleptonic weak processes and the bulk viscosity in several spin-one color superconducting phases of quark matter. We also calculate the bulk viscosity in the nonlinear and anharmonic regime in the normal phase of strange quark matter. We point out several qualitative effects due to the anharmonicity, although quantitatively they appear to be relatively small. In the corresponding study, we take into account the interplay between the non- leptonic and semileptonic weak processes. The results can be important in order to relate accessible observables of compact stars to their internal composition. We also use quantum field theoretical methods to study the transport properties in monolayer graphene in a strong magnetic field. The corresponding quasi-relativistic system re- veals an anomalous quantum Hall effect, whose features are directly connected with the spontaneous flavor symmetry breaking. We study the microscopic origin of Fara- day rotation and magneto-optical transmission in graphene and show that their main features are in agreement with the experimental data.
ContributorsWang, Xinyang, Ph.D (Author) / Shovkovy, Igor (Thesis advisor) / Belitsky, Andrei (Committee member) / Easson, Damien (Committee member) / Peng, Xihong (Committee member) / Vachaspati, Tanmay (Committee member) / Arizona State University (Publisher)
Created2013
Description
Quasars, the visible phenomena associated with the active accretion phase of super- massive black holes found in the centers of galaxies, represent one of the most energetic processes in the Universe. As matter falls into the central black hole, it is accelerated and collisionally heated, and the radiation emitted can outshine the combined light of all the stars in the host galaxy. Studies of quasar host galaxies at ultraviolet to near-infrared wavelengths are fundamentally limited by the precision with which the light from the central quasar accretion can be disentangled from the light of stars in the surrounding host galaxy. In this Dissertation, I discuss direct imaging of quasar host galaxies at redshifts z ≃ 2 and z ≃ 6 using new data obtained with the Hubble Space Telescope. I describe a new method for removing the point source flux using Markov Chain Monte Carlo parameter estimation and simultaneous modeling of the point source and host galaxy. I then discuss applications of this method to understanding the physical properties of high-redshift quasar host galaxies including their structures, luminosities, sizes, and colors, and inferred stellar population properties such as age, mass, and dust content.
ContributorsMechtley, Matt R (Author) / Windhorst, Rogier A (Thesis advisor) / Butler, Nathaniel (Committee member) / Jansen, Rolf A (Committee member) / Rhoads, James (Committee member) / Scowen, Paul (Committee member) / Arizona State University (Publisher)
Created2014
Description
Numerical simulations are very helpful in understanding the physics of the formation of structure and galaxies. However, it is sometimes difficult to interpret model data with respect to observations, partly due to the difficulties and background noise inherent to observation. The goal, here, is to attempt to bridge this gap between simulation and observation by rendering the model output in image format which is then processed by tools commonly used in observational astronomy. Images are synthesized in various filters by folding the output of cosmological simulations of gasdynamics with star-formation and dark matter with the Bruzual- Charlot stellar population synthesis models. A variation of the Virgo-Gadget numerical simulation code is used with the hybrid gas and stellar formation models of Springel and Hernquist (2003). Outputs taken at various redshifts are stacked to create a synthetic view of the simulated star clusters. Source Extractor (SExtractor) is used to find groupings of stellar populations which are considered as galaxies or galaxy building blocks and photometry used to estimate the rest frame luminosities and distribution functions. With further refinements, this is expected to provide support for missions such as JWST, as well as to probe what additional physics are needed to model the data. The results show good agreement in many respects with observed properties of the galaxy luminosity function (LF) over a wide range of high redshifts. In particular, the slope (alpha) when fitted to the standard Schechter function shows excellent agreement both in value and evolution with redshift, when compared with observation. Discrepancies of other properties with observation are seen to be a result of limitations of the simulation and additional feedback mechanisms which are needed.
ContributorsMorgan, Robert (Author) / Windhorst, Rogier A (Thesis advisor) / Scannapieco, Evan (Committee member) / Rhoads, James (Committee member) / Gardner, Carl (Committee member) / Belitsky, Andrei (Committee member) / Arizona State University (Publisher)
Created2012