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Topics in Core-Collapse Supernova Theory: The Formation of Black Holes and the Transport of Neutrinos
Get PDFCore-Collapse Supernovae are one of the most complex astrophysical systems in the universe. They deeply entwine aspects of physics and astrophysics that are rarely side by side in nature. To accurately model core-collapse supernovae one must self-consistently combine general relativity, nuclear physics, neutrino physics, and magneto-hydrodynamics in a symmetry-free computational environment. This is a challenging task, as each one of these aspects on its own is an area of great study. We take an open approach in an effort to encourage collaboration in the core-collapse supernovae community.
In this thesis, we develop a new open-source general-relativistic spherically-symmetric Eulerian hydrodynamics code for studying stellar collapse, protoneutron star formation, and evolution until black hole formation. GR1D includes support for finite temperature equations of state and an efficient and qualitatively accurate treatment of neutrino leakage. GR1D implements spherically-symmetric rotation, allowing for the study of slowly rotating stellar collapse. GR1D is available at http://www.stellarcollapse.org
We use GR1D to perform an extensive study of black hole formation in failing core-collapse supernovae. Over 100 presupernova models from various sources are used in over 700 total simulations. We systematically explore the dependence of black hole formation on the input physics: initial zero-age main sequence (ZAMS) mass and metallicity, nuclear equation of state, rotation, and stellar mass loss rates. Assuming the core-collapse supernova mechanism fails and a black hole forms, we find that the outcome, for a given equation of state, can be estimated, to first order, by a single parameter, the compactness of the stellar core at bounce. By comparing the protoneutron star structure at the onset of gravitational instability with solutions of the Tolman-Oppenheimer-Volkof equations, we find that thermal pressure support in the outer protoneutron star core is responsible for raising the maximum protoneutron star mass by up to 25% above the cold neutron star value. By artificially increasing neutrino heating, we find the critical neutrino heating efficiency required for exploding a given progenitor structure and connect these findings with ZAMS conditions. This establishes, albeit approximately, for the first time based on actual collapse simulations, the mapping between ZAMS parameters and the outcome of core collapse.
We also use GR1D to study proposed progenitors of long-duration gamma-ray bursts. We find that many of the proposed progenitors have core structures similar to garden-variety core-collapse supernovae. These are not expected to form black holes, a key ingredient of the collapsar model of long-duration gamma-ray bursts. The small fraction of proposed progenitors that are compact enough to form black holes have fast rotating iron cores, making them prone to a magneto-rotational explosion and the formation of a protomagnetar rather than a black hole.
Finally, we present preliminary work on a fully general-relativistic neutrino transport code and neutrino-interaction library. Following along with the trends explored in our black hole formation study, we look at the dependence of the neutrino observables on the bounce compactness. We find clear relationships that will allow us to extract details of the core structure from the next galactic supernova. Following the open approach of GR1D, the neutrino transport code will be made open-source upon completion. The open-source neutrino-interaction library, NuLib, is already available at http://www.nulib.org.</p
Pheromones in Free-Living and Parasitic Nematodes
Get PDFNematodes are among the most diverse phyla of animals, occupying almost every ecological niche available. Their ubiquity has led to a number of problems for civilization, including the loss of crops and the spread of neglected tropical diseases. Because they are responsible for a broad range of agricultural and human diseases, many pheromone-mediated nematode behaviors have been described but very few pheromones have been identified.
We report, via high-performance liquid chromatography electrospray ionization mass spectrometry, the discovery that many free-living and parasitic nematodes secrete small-molecule pheromones called ascarosides. These pheromones, called ascarosides, were first found to play a role in sex attraction and induction into a stress-resistant diapausal life stage in the free-living organism, Caenorhabditis elegans. We have performed a double-blind purification of the female sex pheromone in the sour paste nematode Panagrellus redivivus and report that the female sex pheromone is composed of at least two ascarosides. We have also found that both free-living and parasitic nematodes respond to different concentrations of ascarosides through attraction or repulsion, demonstrating cross-species communication. These results suggest that ascarosides could be a universal nematode cue, similar to the role of N-Acyl homoserine lactones in bacteria quorum sensing.
Because ascarosides are nonvolatile, they can only mediate close-range communication. Nematodes have a well-characterized capacity for long-range chemoattraction to a range of volatile cues. However, no studies have been done towards characterizing natural volatile cues derived from nematodes. Here I describe the discovery of volatile cues are produced by male-female species in the genus Caenorhabditis, but are lacking in the hermaphroditic species C. elegans, C. briggsae, and C. sp11. These volatile cues attract males (and sometimes females) from other Caenorhabditis species, demonstrating a cross-species gonochoristic cue.</p
Fundamental Studies of Early Transition Metal-Ligand Multiple Bonds: Structure, Electronics, and Catalysis
Get PDFTwo major topics are covered: the first section is focused on the structure, electronics, stoichiometric reactivity and catalysis of nonmetallocene early transition metal complexes that often contain metal-ligand multiple bonds (Chapters 2-4); the second section is dedicated to the development of hydrazide(2-) ligands for group 5 elements, which were heretofore unexplored as ligands for group 5 (Chapters 5-6).
A series of tantalum imido and amido complexes supported by a pyridine linked bis(phenolate) (ONO) ligand has been synthesized. Characterization of these complexes via X ray crystallography reveals both Cs and C2 binding modes of the bis(phenolate)pyridine ligand. DFT calculations and molecular orbital analyses of the complexes have revealed that the preference for Cs symmetric ligand binding is a result of Ta-O π bonding: in cases where Ta-O π bonding is overridden by stronger Ta N π bonding, C2 symmetric ligand binding is preferred because this is the lowest energy geometric conformation.
Titanium and zirconium complexes supported by a related pyridine bis(anilide) ligand (NNN = pyridine 2,6 bis(N-mesitylanilide)) have been synthesized. The ligand geometry of these complexes is dictated solely by chelate ring strain rather than metal-ligand π-bonding. These complexes were tested as propylene polymerization precatalysts, with most complexes giving low to moderate activities (10^2-10^4 g/mol*h) for the formation of polypropylene.
(ONO)TiX2 complexes are highly active precatalysts for the intermolecular hydroamination of internal alkynes with primary arylamines and some alkylamines. (ONO)TiBn2 also cyclotrimerizes dimethylacetylene. During the cyclotrimerization reaction the Ti(IV) precatalyst is reduced to Ti(II), which is the active species for catalysis. The mechanism of formation of TiII has been investigated and an (ONO)Ti(II) species has been trapped by ethylene and crystallographically characterized.
Hydrazide complexes (dme)TaCl3(NNPh2) and (dme)NbCl3(NNPh2) (dme = 1,2 dimethoxyethane) were synthesized. Unlike the corresponding imido derivatives, (dme)TaCl3(NNPh2) is dark blue due to an LMCT that has been lowered in energy as a result of an Nα-Nβ antibonding interaction that raises the HOMO. Reaction of (dme)TaCl3(NNPh2) with a variety of neutral, mono and dianionic ligands generates the corresponding ligated complexes retaining the k-1 bound [TaNNPh2] moiety.
Furthermore, a series of colorful terminal hydrazide complexes of the type (dme)MCl3(NNR2) (M = Nb, Ta; R = alkyl or aryl) or (MeCN)WCl4(NNR2) have been synthesized. Perturbing the electronic environment of the β nitrogen significantly impacts the lowest-energy charge transition in these complexes, and in the W complexes leads to metal based reduction. The photophysics of these complexes highlights the importance of the difference in reduction potential between metal centers, and could lead to differences in ligand- and/or metal-based redox chemistry in early transition metal hydrazidos, especially in the context of N2 fixation.
Finally, the hydroxy-bridged dimer [(COD)IrOH]2 (COD = 1,5-cyclooctadiene) cleanly C-H activates indene and cyclopentadiene to form (COD)Ir(η3-indenyl) and (COD)Ir(η5-C5H5), respectively. The kinetics of the formation of (COD)Ir(η3-indenyl) has been investigated, and the mechanism involves coordination of indene to the dimeric [(COD)IrOH]2 followed by rate determining C-H activation from the dimer-indene unit.</p
Fields, Forces, and Flows: What Laboratory Experiments Reveal About the Dynamics of Arched Plasma Structures
Get PDFMagnetic flux tubes and, more generally, magnetic field structures that link a plasma volume to its boundary are prominent features in plasma systems of significant interest, such as the solar atmosphere and the interiors of magnetic fusion devices.
In order to study the fundamental physics of these systems, experiments were conducted in the laboratory using a magnetized plasma gun to produce individual arched, plasma-filled magnetic flux tubes. More complex plasma topologies were also explored. The absence of confining walls allowed plasmas to evolve freely — which they did, very dynamically, over the course of several microseconds. The experiment setup featured excellent reproducibility, extensive diagnostic accessibility, and several tunable parameters. In particular, a plasma "color coding" technique and magnetic measurements provided new and interesting results.
The single arches or "loops" of plasma exhibited sustained axial collimation, even during a dramatic evolution from a small, semicircular arch into a kinked structure up to seven times larger. The loops' magnetic structure was verified as consistent with that of a flux tube, and their evolution was found to be in quantitative agreement with two interrelated magnetohydrodynamic (MHD) theories: a simplified hoop force model for the axis expansion and a recently proposed MHD flow model for the collimation. More complex plasma structures were found to be similarly dominated by the effects of the magnetic field, exhibiting behavior that was highly repeatable but varied significantly from one magnetic structure to the next.
These findings suggest that MHD-driven flows are an important mechanism for the transport of plasma in arched flux tubes and other magnetic plasma structures. Because MHD has no inherent length scale, the forces driving the evolution of these experiments are expected to similarly affect other systems with low plasma beta and a high Lundquist number.</p
Establishing a Genetic and Exogenous Toolbox for Studying Multiple Stages of Vertebrate Development in vivo
Get PDFUnderstanding of cell behavior during vertebrate development and repair has been greatly facilitated by advances in biological imaging. Importantly, more powerful tools to generate contrast within the tissue make in vivo analyses of these processes in time and space more tractable. Here, I present my efforts to develop and refine an imaging toolbox to study in vivo cell shape, dynamics, structure, and behavior in the zebrafish vertebrate model system. Mosaic analysis and targeted photoconversion illuminate fine morphological details as cells migrate during gastrulation, revealing cell connections that span several cell diameters across the embryo. These intercellular bridges link cells between lineage boundaries and allow cells to share membrane components on a developmentally relevant time scale. The PhOTO zebrafish transgenic lines combine the strengths of sparse and global cell labeling to monitor cell dynamics and morphology at any stage in the lifetime of the zebrafish. I demonstrate targeted and instantaneous sparse cell tracking in the context of global cell behavior in the embryo, and I also isolate a subset of slowly dividing cells populating a regenerating adult tail fin. Combining fluorescence and endogenous second harmonic generation (SHG) imaging as a tool to study early muscle structure and organization within whole zebrafish muscle compartments uncovers the source of vernier-patterned signal in highly ordered myosin arrays. Instead of being physical distortions in muscle sarcomeres, these patterns may result from an optical artifact of SHG imaging, since comparable signal is not visible in both the SHG and fluorescence channels. To complement the aforementioned genetic labeling and endogenous contrast tools, barium titanate SHG nanoprobes — exogenous and nontoxic SHG-capable nanomaterial tags — are refined for cell labeling in the zebrafish. Silane functionalization acts as a platform for further surface modifications, including: multistep chemical additions, non-reactive surface coating modifications, and antibody linkages for cell targeting applications. The power of each of these tools lies in their compatibility with one another: combining the fluorescence and SHG contrast approaches described here may enable high-resolution imaging at a variety of developmental stages to appreciate the multifaceted cell behaviors governing vertebrate developmental programs more completely
Compressed Sensing Receivers: Theory, Design, and Performance Limits
Get PDFThe past 50 years have seen tremendous developments in electronics due to the rise and rapid development of IC-fabrication technology [1]. In addition to the production of cheap and abundant computing resources, another area of rapid advancement has been wireless technologies. While the central focus of wireless research has been mobile communication, an area of increasing importance concerns the development of sensing/spectral applications over bandwidths exceeding multiple GHz. Such systems have many applications ranging from scientific to military. Although some solutions exist, their large size, weight, and power make more-efficient solutions desirable.
At present, one of the principal bottlenecks in designing such systems is the power consumption of the back-end ADCs at the required digitization rate. ADCs are a dominant source of power consumption; it is also often the case that ADC block specifications are used to determine parameters for the rest of the signal chain, such as the RF front-end and the DSP-core which processes the digitized samples [2]. Historically, increases in system bandwidth have come from developing ADCs with superior performance.
In contrast to improving ADC performance, this work presents a system-level approach with the goal of minimizing the required digitization rate for observation of a given effective instantaneous bandwidth (EIBW). The approach was inspired by the field of compressed sensing [3–5]. Loosely stated, CS asserts that samples which represent random projections can be used to recover sparse and/or compressible signals with what was previously thought to be insufficient information. The primary contributions of this thesis include: the establishment of physical feasibility of CS-based receivers through implementation of the first fully-integrated high speed CS-based front-end known as the random-modulation pre-integrator (RMPI) [6–9], and the development of a principled design methodology based on a rigorous analytical and empirical feasibility study of the system.
The 8-channel RMPI was implemented in 90 nm CMOS and was validated by physical measurements of the fabricated chip. The implemented RMPI achieves an EIBW of 2 GHz, with > 54 dB of dynamic range. Most notably, the aggregate digitization rate is fs = 320 Msps, 12.5× lower than the Nyquist rate.</p
Engineering Immunity Against HIV
Get PDFAn effective vaccine against the human immunodeficiency virus (HIV)-1 has so far been elusive. Anti-viral vaccines against other viruses work by stimulating the production of neutralizing antibodies that block infection. To be useful, an anti-HIV vaccine preparation needs to elicit potent neutralizing antibody response with sufficient breadth to cover the diversity of HIV variants. Despite sustained research efforts, such an immunogen has been difficult to develop. We could overcome this difficulty by using gene therapy to directly instruct the body to produce anti-HIV broadly neutralizing antibodies (bNAbs). In this thesis, I describe a technology I developed termed the “Molecular Rheostat” for directing the simultaneous expression of anti-HIV surface and secreted immunoglobulins using mutant 2A “self-cleaving” peptides. I describe the application of this system to the programming of hematopoeitic stem cells to generate anti-HIV B cells as a strategy to “vaccinate” against HIV infection. I then pivot to consider alternatives to B-cell programming to produce antibodies against HIV. I investigate the modification of non-lymphoid hematopoietic cells to produce antibodies using retroviral vectors and describe the use of lentiviral vectors to program muscle to produce anti-HIV broadly neutralizing antibodies. In addition to presenting a novel tool for controlling the simultaneous expression of full-length and truncated proteins, the work described here furnishes a foundation for future development into potential gene-therapeutic prophylaxis against HIV
Toward the Upgrading of Hydrocarbons: Synthesis, Characterization, and Reactivity of Platinum and Palladium Complexes
Get PDFHerein, hydroxyl-dimers of platinum and palladium supported by diimine ligands have been prepared and studied. It was found that they are capable of activating allylic, benzylic, and aromatic carbon-hydrogen bonds. The kinetics of the C-H activation of cyclohexene with the platinum system and of indene with the palladium system were studied. In each case the rate-limiting step was found to be associative substitution. The catalytic dehydrogenation of cyclohexene to benzene with the palladium hydroxyl-dimer was investigated. The chemical oxidation of the η3-organometallic products synthesized via C-H activation of cyclohexene and indene with platinum and palladium, respectively, was explored. Treatment of these products with strong halogenating oxidants resulted in the liberation of halogenated substrates and bridging halide metal complexes. Uncharged platinum and palladium polypyrazoleborate complexes were synthesized and characterized. The kinetics of the degenerative ligand exchange of DMSO with palladium methyl DMSO complexes ligated with a polypyrazoleborate or a diimine ligand were studied and it was found that the associative substitution mechanism through which the diimine ligated complexes proceeds was unavailable to the polypyrazoleborate palladium complex. In the polypyrazoleborate system ligand exchange proceeded through a dissociative mechanism. The C-H activation substrate scope of the platinum and palladium hydroxyl-dimers was further explored. The diimine platinum hydroxyl-dimer was found to activate an allylic C-H bond in cyclopentene and form an η3-cyclopentenyl complex when heated with acid and dilute stoichiometric amounts of cyclopentene. Conversely, dehydrogenation of cyclopentene to a platinum-bound η5-cyclopentadiene resulted from the treatment of the platinum hydroxyl-dimer with super-stoichiometric amounts of cyclopentene at room temperature. This difference in reactivity with the same substrate may be due to the relative reactivities of allylic versus homoallylic C-H bonds. Further evidence of a homoallylic C-H activation mechanism was demonstrated by treating the diimine platinum hydroxyl-dimer with neo-hexene to form a cyclometalated neo-hexenyl platinum complex. The diimine palladium hydroxyl-dimer was also found to catalytically oligomerize and isomerize olefins. Furthermore, the catalytic activity was supported by the presence of oxygen and stable in the presence of water. Most likely the oligomerization proceeded through a palladium hydride that can decompose to palladium(0) complex, which can be reoxidized by oxygen. The photochemical oxidation of platinum complexes with Ru(bipy)_3^(2+) was also investigated. Finally, the coordination chemistry of the tris(triphenylphosphino)silyl ligand was explored with cobalt, ruthenium, nickel, and platinum
Axel Rover Tethered Dynamics and Motion Planning on Extreme Planetary Terrain
Get PDFSome of the most appealing science targets for future exploration missions in our solar system lie in terrains that are inaccessible to state-of-the-art robotic rovers such as NASA's Opportunity, thereby precluding in situ analysis of these rich opportunities. Examples of potential high-yield science areas on Mars include young gullies on sloped terrains, exposed layers of bedrock in the Victoria Crater, sources of methane gas near Martian volcanic ranges, and stepped delta formations in heavily cratered regions. In addition, a recently discovered cryovolcano on Titan and frozen water near the south pole of our own Moon could provide a wealth of knowledge to any robotic explorer capable of accessing these regions.
To address the challenge of extreme terrain exploration, this dissertation presents the Axel rover, a two-wheeled tethered robot capable of rappelling down steep slopes and traversing rocky terrain. Axel is part of a family of reconfigurable rovers, which, when docked, form a four-wheeled vehicle nicknamed DuAxel. DuAxel provides untethered mobility to regions of extreme terrain and serves as an anchor support for a single Axel when it undocks and rappels into low-ground.
Axel's performance on extreme terrain is primarily governed by three key system components: wheel design, tether control, and intelligent planning around obstacles. Investigations in wheel design and optimizing for extreme terrain resulted in the development of grouser wheels. Experiments demonstrated that these grouser wheels were very effective at surmounting obstacles, climbing rocks up to 90% of the wheel diameter. Terramechanics models supported by experiments showed that these wheels would not sink excessively or become trapped in deformable terrain.
Predicting tether forces in different configurations is also essential to the rover's mobility. Providing power, communication, and mobility forces, the tether is Axel's lifeline while it rappels steep slopes, and a cut, abraded, or ruptured tether would result in an untimely end to the rover's mission. Understanding tether forces are therefore paramount, and this thesis both models and measures tension forces to predict and avoid high-stress scenarios.
Finally, incorporating autonomy into Axel is a unique challenge due to the complications that arise during tether management. Without intelligent planning, rappelling systems can easily become entangled around obstacles and suffer catastrophic failures. This motivates the development of a novel tethered planning algorithm, presented in this thesis, which is unique for rappelling systems.
Recent field experiments in natural extreme terrains on Earth demonstrate the Axel rover's potential as a candidate for future space operations. Both DuAxel and its rappelling counterpart are rigorously tested on a 20 meter escarpment and in the Arizona desert. Through analysis and experiments, this thesis provides the framework for a new generation of robotic explorers capable of accessing extreme planetary regions and potentially providing clues for life beyond Earth.</p
Network Structure Optimization with Applications to Minimizing Variance and Crosstalk
Get PDFThis thesis provides a unified methodology for analyzing structural properties of graphs, along with their applications. In the last several years, the field of complex networks has been extensively studied, and it is now well understood that the way a large network is built is closely intertwined with its function. Structural properties have an impact on the function of the network, and the form of many systems has been evolved in order to optimize for given functions. Despite the great progress, particularly in how structural attributes affect the various network functions, there is a significant gap in the quantitative study of how much these properties can change in a network without a significant impact on the functionality of the system, or what the bounds of these structural attributes are. Here, we find and analytically prove tight bounds of global graph properties, as well as the form of the graphs that achieve these bounds. The attributes studied include the network efficiency, radius, diameter, average distance, betweenness centrality, resistance distance, and average clustering. All of these qualities have a direct impact on the function of the network, and finding the graph that optimizes one or more of them is of interest when designing a large system. In addition, we measure how sensitive these properties are with respect to random rewirings or addition of new edges, since designing a network with a given set of constraints may include a lot of trade-offs. This thesis also studies properties that are of interest in both natural and engineered networks, such as maximum immunity to crosstalk interactions and random noise. We are primarily focused on networks where information is transmitted through a means that is accessible by all the individual units of the network and the interactions among the different entities that comprise it do not necessarily have a dedicated mechanism that facilitates information transmission, or isolates them from other parts of the network. Two examples of this class are biological and chemical reaction networks. Such networks suffer from unwanted crosstalk interactions when two or more units spuriously interact with each other. In addition, they are subject to random fluctuations in their output, both due to noisy inputs and because of the random variance of their parameters. These two types of randomness affect the behavior of the system in ways that are intrinsically different. We examine the network topologies that accentuate or alleviate the effect of random variance in the network for both directed and undirected graphs, and find that increasing the crosstalk among different parts reduces the output variance but also contributes to a slower response