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Part I: Structure of Central and Southern Mexico from Velocity and Attenuation Tomography. Part II: Physics of Small Repeating Earthquakes
Get PDFIn part I, the 3D velocity and attenuation structure of the Cocos subduction zone in Mexico is imaged using earthquakes recorded by two temporary seismic arrays and local stations. Inversion results reveal low-attenuation and high-velocity Cocos slab. The slab dip angle increases from almost flat in central Mexico near Mexico City to about 30 degrees in southern Mexico near the Isthmus of Tehuantepec. High attenuation and low velocity in the crust beneath the Trans-Mexico Volcanic Belt correlate with low resistivity, and are probably related to dehydration and melting process. The most pronounced high-attenuation, low-Vp and high-Vp/Vs anomaly is found in the crust beneath the Veracruz Basin. A high-velocity structure dipping southward from the Gulf of Mexico near the Isthmus of Tehuantepec coincides with a discontinuity from a receiver functions study, and provides an evidence for the collision between the Yucatan Block and Mexico in the Miocene.
In part II, we show that a model of small repeating earthquakes based on laboratory-derived rate and state friction laws reproduces the observed scaling between the recurrence time and seismic moment. In the model, a small fault patch governed by velocity-weakening friction is surrounded by a much larger velocity-strengthening region. For a fixed set of friction parameters, the observed scaling is reproduced by varying the size of the velocity-weakening patch. We further investigate the behavior of small repeating earthquakes in related models under different scenarios, including several forms of the state evolution equations in rate- and state-dependent friction laws, rectangular velocity-weakening patch geometries, quasi-dynamic vs. fully dynamic representation of inertial effects, and 2D vs. 3D simulations. We find that the simulated scalings between the recurrence time and seismic moment for these different scenarios are similar while differences do exist. We propose a theoretical model for the scaling between the recurrence time and seismic moment of small repeating earthquakes. The obtained theoretical insight is used to find the combinations of fault properties that allow the model to fit the observed scaling and range of the seismic moment and recurrence time.</p
Deformation Mechanisms in Nanoscale Single Crystalline Electroplated Copper Pillars
Get PDFScientific research in nanotechnology has enabled advances in a diverse range of applications, such as: electronics, chemical sensing, and cancer treatment. In order to transition these nanotechnology-driven innovations out of the laboratory and into real-world applications, the resilience and mechanical reliability of nanoscale structures must be well understood in order to preserve functionality under real-world operating environments. Understanding the mechanical properties of nanoscale materials is especially important because several authors have shown that single crystalline metal pillars produced through focused-ion-beam milling have unique properties when the pillar diameter, D, approaches nanotechnology-relevant dimensions. The strength, σ, of these pillars is size-dependent and is well described through a power-law relation showing that smaller is stronger: σ∝D^(-n), where n is the exponent and is found to be 0.5≤n≤1.0 in face-centered-cubic metals. In this work, the fundamental deformation mechanisms governing the size-dependent mechanical properties are investigated through uniaxial compression and tension tests of electroplated single crystalline copper pillars with diameters between 75 nm and 1000 nm. At larger pillar diameters, D >125 nm, these copper pillars are shown to obey a similar size-dependent regime, demonstrating that the “smaller is stronger” phenomenon is a function of the pillar microstructure, as opposed to the fabrication route. Furthermore, the dominant dislocation mechanism in this size-dependent regime is shown to be the result of single-arm, or spiral, sources. At smaller pillar diameters, D≤125 nm, a strain-rate-dependent mechanism transition is observed through both the size-strength relation and also quantitative, experimental measures of the activation volume. This new deformation regime is characterized by a size-independent strength and is governed by surface dislocation nucleation, a thermally activated mechanism sensitive to both temperature and strain-rate. Classical, analytical models of surface source-nucleation are shown to be insufficient to describe either the quantitative strength or the nucleation site preference. As a result, a combination of atomistic chain-of-states simulations and semi-analytical continuum models are developed in order to achieve a realistic, intuitive understanding of surface nucleation processes
The Role of Pesticide-Induced Aldehyde Dehydrogenase Inhibition in the Pathogenesis of Parkinson’s Disease
Get PDFParkinson’s disease (PD) is a neurodegenerative disorder particularly characterized by the loss of dopaminergic neurons in the substantia nigra pars compacta. Its etiology is unknown but likely includes both genetic and environmental factors. Since pesticide use has been associated with PD occurrence, we conducted a screen to identify pesticides that impair the ubiquitin-proteasome system (UPS), a degradative process implicated in PD pathogenesis. Benomyl was identified as a UPS inhibitor in this screen and became the focus of this dissertation.
In an epidemiologic study, we used state-mandated Pesticide Use Reports to estimate chronic exposures and observed 65-92% increased PD risk in a population exposed to the fungicide benomyl. In experimental models, we found that benomyl induced selective dopaminergic neuronal loss in vitro with primary mesencephalic cultures and selective aminergic neuronal loss in a novel in vivo zebrafish system. Benomyl is readily metabolized to S-methyl N-butylthiocarbamate and its sulfoxide, a potent aldehyde dehydrogenase (ALDH) inhibitor. These thiocarbamates inhibited ALDH activity in primary neurons at submicromolar concentrations leading to accumulation of the dopamine metabolite 3,4-dihydroxyphenylacetaldehyde, the proposed neurotoxicant. This model for PD etiology via ALDH inhibition may help explain the selective vulnerability of dopaminergic neurons in PD.
To follow up on this finding, we developed a novel ex vivo neuronal assay to screen other pesticides for ALDH inhibitory activity. All dithiocarbamates tested (e.g., mancozeb, maneb, ziram), two dicarboxymides (captan, folpet), and two imidazoles (benomyl, triflumizole) inhibited ALDH activity, potentially via metabolic byproducts (e.g., carbon disulfide, thiophosgene). Exposures to ALDH-inhibiting pesticides (i.e., positive hits) applied in our study area were associated with dose-dependent twofold to fourfold increases in PD risk. Genetic variation in the ALDH2 gene potentiated this risk considerably (up to sixfold) for people working where these pesticides were sprayed liberally.
This is the first report of a pesticide that damages dopaminergic neurons by inhibiting ALDH activity. The identification of multiple ALDH-inhibiting pesticides associated with increased PD risk supports the potential of ALDH as a novel therapeutic target and a subject for consideration by regulators and policymakers.</p
High-Order Integral Equation Methods for Diffraction Problems Involving Screens and Apertures
Get PDFThis thesis presents a novel approach for the numerical solution of problems of diffraction by infinitely thin screens and apertures. The new methodology relies on combination of weighted versions of the classical operators associated with the Dirichlet and Neumann open-surface problems. In the two-dimensional case, a rigorous proof is presented, establishing that the new weighted formulations give rise to second-kind Fredholm integral equations, thus providing a generalization to open surfaces of the classical closed-surface Calderon formulae. High-order quadrature rules are introduced for the new weighted operators, both in the two-dimensional case as well as the scalar three-dimensional case. Used in conjunction with Krylov subspace iterative methods, these rules give rise to efficient and accurate numerical solvers which produce highly accurate solutions in small numbers of iterations, and whose performance is comparable to that arising from efficient high-order integral solvers recently introduced for closed-surface problems. Numerical results are presented for a wide range of frequencies and a variety of geometries in two- and three-dimensional space, including complex resonating structures as well as, for the first time, accurate numerical solutions of classical diffraction problems considered by the 19th-century pioneers: diffraction of high-frequency waves by the infinitely thin disc, the circular aperture, and the two-hole geometry inherent in Young's experiment
A Dark-Matter Search Using the Final CDMS II Dataset and a Novel Detector of Surface Radiocontamination
Get PDFSubstantial evidence from galaxies, galaxy clusters, and cosmological scales suggests that ~85% of the matter of our universe is invisible. The missing matter, or "dark matter" is likely composed of non-relativistic, non-baryonic particles, which have very rare interactions with baryonic matter and with one another. Among dark matter candidates, Weakly Interacting Massive Particles (WIMPs) are particularly well motivated. In the early universe, thermally produced particles with weak-scale mass and interactions would `freeze out’ at the correct density to be dark matter today. Extensions to the Standard Model of particle physics, such as Supersymmetry, which solve gauge hierarchy and coupling unification problems, naturally provide such particles.
Interactions of WIMPs with baryons are expected to be rare, but might be detectable in low-noise detectors. The Cryogenic Dark Matter Search (CDMS) experiment uses ionization- and phonon- sensitive germanium particle detectors to search for such interactions. CDMS detectors are operated at the Soudan Underground Laboratory in Minnesota, within a shielded environment to lower cosmogenic and radioactive background. The combination of phonon and ionization signatures from the detectors provides excellent residual-background rejection.
This dissertation presents improved techniques for phonon calibration of CDMS II detectors and the analysis of the final CDMS II dataset with 612 kg-days of exposure. We set a limit of 3.8x10^(-44) cm^2 on WIMP-nucleon spin-independent scattering cross section for a WIMP mass of 70 GeV/c^2. At the time this analysis was published, these data presented the most stringent limits on WIMP scattering for WIMP masses over 42 GeV/c^2, ruling out previously unexplored parameter space.
Next-generation rare-event searches such as SuperCDMS, COUPP, and CLEAN will be limited in sensitivity, unless they achieve stringent control of the surface radioactive contamination on their detectors. Low-penetrating radiation, such as alpha and beta particles, will mimic signal in these experiments. This dissertation also presents the design and prototyping of a novel detector for surface radiocontaminants, called the BetaCage --- a neon-gas time projection chamber built from radiopure materials and operated underground with shielding similar to CDMS II. The BetaCage will enable beta screening of materials at world-best sensitivity of 10^(-5)/cm^2/keV/day, providing a valuable tool to the physics community.</p
Atmospheric Black Carbon: Measurements in the Los Angeles Atmosphere and Aging by Condensation of Organic Aerosol
Get PDFAerosol particles in the atmosphere scatter and absorb solar radiation; an interaction that yields the largest uncertainty in models of future climate change. While most aerosols scatter light and, therefore, cool the environment, absorbing aerosol warms the environment. In particular, black carbon (BC) aerosol, the largest component of absorbing aerosol, may exhibit the second-largest forcing on climate behind greenhouse gases. In addition, the mixing state of BC aerosol, or the degree to which a BC core is coated with a scattering substance, may significantly increase the absorbing potential of BC. This thesis presents results from field and laboratory studies of BC aerosol, its mixing state in the atmosphere, and how it ages in the presence of condensing secondary organic aerosol.
A major field study, CalNex 2010, was conducted in Southern California to study air quality and climate change issues. Measurements of BC aerosol in and around the Los Angeles (LA) Basin reveal the evolution of BC aerosol from a thinly coated state near sources in the eastern LA Basin to a more thickly coated state in the outflow regions of the Basin. While the majority of BC aerosol emitted in the LA Basin remains near the surface, some BC aerosol is transported to the free troposphere through sea-breeze and mountain-flow coupling. BC aerosol above the inversion layer tends to be thickly coated, indicating that it is more aged than the BC measured near the surface.
To understand how the mixing state of BC evolves with secondary formation of species in the atmosphere, carefully controlled environmental chamber experiments were conducted. Two types of secondary organic aerosol (SOA) precursors, alpha-pinene and naphthalene, were reacted in the chamber to condense secondary products onto BC seed aerosol. The rate of growth and magnitude of absorption enhancement due to the secondary coating on BC was measured, revealing that growth of coatings is diffusion-limited. Particle composition measurements reveal that condensed SOA onto BC seed particles is nearly identical to nucleated SOA from the same parent hydrocarbon. Measurements of coating thickness and optical properties provide insight to single-particle SOA growth and volatility.</p
Cloud Computing for Citizen Science
Get PDFMy thesis describes the design and implementation of systems that empower individuals to help their communities respond to critical situations and to participate in research that helps them understand and improve their environments. People want to help their communities respond to threats such as earthquakes, wildfires, mudslides and hurricanes, and they want to participate in research that helps them understand and improve their environment. “Citizen Science” projects that facilitate this interaction include projects that monitor climate change, water quality and animal habitats. My thesis explores the design and analysis of community-based sense and response systems that enable individuals to participate in critical community activities and scientific research that monitors their environments
Eulerian Geometric Discretizations of Manifolds and Dynamics
Get PDFThis thesis explores new methods for geometric, structure-preserving Eulerian discretizations of dynamics, including Lie advection and incompressible fluids, and the manifolds in which these dynamics occur. The result is a novel method for discrete Lie advection of differential forms, a new family of structure-preserving fluid integrators, and a new set of energies for optimizing meshes appropriate for some discrete geometric operators. First, high-resolution nite volume methods are leveraged to introduce a new method for discretizing the Lie advection of discrete differential forms, along with the related contraction operator, on regular grids. Through its geometric approach, the method exactly preserves properties such as the closedness of Lie advected closed forms. This results in an extension of nite volume techniques applicable to forms of arbitrary degree. After this, attention is turned to simplicial meshes, where new meshing techniques are developed to give formal error bounds on the discrete diagonal Hodge star, an important operator for geometric computations. Utilizing weighted Delaunay triangulations, both the primal mesh and its dual are optimized simultaneously over the entire space of orthogonal primal/dual pairs. Improved accuracy of the solution of Poisson equations is demonstrated as a practical application, as well as an increase in percentage of well-centered elements. Finally, a new structure-preserving method for the incompressible Navier-Stokes equations on simplicial meshes is developed, offering in the inviscid case the exact conservation of either the discrete energy or symplectic form. This leads to capturing the correct energy decay when viscosity is added, resulting in dissipation independent of grid and time resolution
Compiling and Verifying DNA-Based Chemical Reaction Network Implementations
Get PDFOne goal of molecular programming and synthetic biology is to build chemical circuits that can control chemical processes at the molecular level. Remarkably, it has been shown that synthesized DNA molecules can be used to construct complex chemical circuits that operate without any enzyme or cellular component. However, designing DNA molecules at the individual nucleotide base level is often difficult and laborious, and thus chemical reaction networks (CRNs) have been proposed as a higher-level programming language. So far, several general-purpose schemes have been described for designing synthetic DNA molecules that simulate the behavior of arbitrary CRNs, and many more are being actively investigated.
Here, we solve two problems related to this topic. First, we present a general-purpose CRN-to-DNA compiler that can apply user-defined compilation schemes for translating formal CRNs to domain-level specifications for DNA molecules. In doing so, we develop a language in which such schemes can be concisely and precisely described. This compiler can greatly reduce the amount of tedious manual labor faced by researchers working in the field. Second, we present a general method for the formal verification of the correctness of such compilation. We first show that this problem reduces to testing a notion of behavioral equivalence between two CRNs, and then we construct a mathematical formalism in which that notion can be precisely defined. Finally, we provide algorithms for testing that notion. This verification process can be thought of as an equivalent of model checking in molecular computation, and we hope that the generality of our verification techniques will eventually allow us to apply them not only to DNA-based CRN implementations but to a wider class of molecular programs.</p
Improving Selectivity in Olefin Metathesis for Small Molecule Synthesis and Materials Applications
Get PDFThe olefin metathesis reaction has been studied extensively from the perspective of catalyst design and synthesis, as well as from that of reaction control and application in a variety of fields. Beginning with the design of enantioselective catalysts based on the “geared” C2-symmetric N-heterocyclic carbene (NHC) containing ruthenium catalysts, architectural modifications were envisioned and implemented in order to control the N-bound arene tilt angle (Chapter 2). From there, the asymmetric class of olefin metathesis reactions were explored and trends in enantioselectivities were obtained and reapplied in the further design of novel, chiral catalysts. These asymmetric catalysts were developed not only for their useful application in a range of asymmetric metathesis reactions, but also to provide insight into the spatial arrangement of the NHC ligand during the catalytic cycle.
Amidst this overall cyclical process, mechanistic understandings of the ruthenium-based olefin metathesis catalysts were garnered and integrated; and the concept of a covalentlylinked NHC ligand was born. In Chapter 3, both the cis-fused and trans-fused versions of this linked NHC were constructed, with each independent synthesis hinging on a key ringclosing metathesis reaction mediated by ruthenium catalysts. These novel NHCs were then translated into rhodium-bound complexes and their unique structural conformations were studied with X-Ray crystallography.
Chapter 4 explores the forefront of control and selectivity in olefin metathesis, specifically, in the selective reactivity of dienes in cross-metathesis reactions. The desire to synthesize conjugated dienes, thus limiting reactivity to one of two potentially reactive olefins, is both mechanistically intriguing and contains practical applications for the synthesis of linear pheromone natural products. These pheromones show great utility as a green, biorational pesticide with few ecological and biological side-effects. Thus, exploration of the general diene cross-metathesis reaction was focused on the actual synthesis of codlemone, one of the world’s most sought-after insecticides.
The potential of the olefin metathesis reaction for biomedical applications was further explored in the application of peptide-containing polynorbornenes formed from ringopening metathesis polymerization (ROMP). In order to apply synthetic materials made from ROMP in biological applications, a route towards ruthenium removal to the FDAapproved levels of 10 parts per million (ppm) was developed. Once low ppm remnant ruthenium content was obtained, the synthesis of varying monomers for crosslinking to bulk materials was explored.</p