12023 research outputs found
Sort by
Surrogate Models of Gravitational Waves from Numerical Relativity Simulations of Binary Black Hole Mergers
Get PDFThe advanced LIGO detectors have made multiple detections of gravitational waves from the mergers of binary black hole systems, bringing us into the era of gravitational wave astronomy. From such gravitational wave detections, we can put constraints on deviations from general relativity (GR), as well as measure the masses and spins of the black holes involved in the mergers. Such measurements require knowledge of the gravitational waveforms predicted by GR for all relevant masses and spins. Numerical relativity (NR) simulations are now sufficiently robust that we can accurately simulate binary black hole mergers and obtain the waveform for all but the most extreme parameters, but they are too computationally expensive for a dense coverage of the parameter space. NR surrogate models rapidly and accurately interpolate the waveforms from a set of NR simulations over a subset of parameter space. Using the Spectral Einstein Code (SpEC), we have built several NR surrogate models for various subsets of the parameter space, culminating in a model which includes all 7 intrinsic parameter dimensions. The surrogate model waveforms are nearly as accurate as NR waveforms, and can be evaluated in milliseconds whereas a single NR simulation can take weeks.</p
Insect Sisyphus
No full textWe were driving along America’s femoral artery, the Interstate 10. Our excited car bounded ahead at just above the escape velocity required to break away from the massive cluster of Los Angeles and its satellite cities. Tendrils of strip malls and suburbs emanating from these cities branch out toward the empty desert for miles and miles, and we were nearly out of their grasp
Maximum Entropy Reconstruction for Gas Dynamics
Get PDFWe present a method for selecting a unique and natural probability distribution function (PDF) which satisfies a given number of known moments and apply it for use in the closure of moment-based schemes for approximately solving the Boltzmann equation in gas dynamics.
The method used for determining the PDF is the Maximum Entropy Reconstruction (MER) procedure, which determines the PDF with maximum entropy which satisfies a given set of constraining moments. For the five-moment truncated Hamburger moment problem in one dimension, the MER takes the form of the exponential of a quartic polynomial. This implies a bimodal structure which gives rise to a small-amplitude packet of PDF-density sitting quite far from the mean. This is referred to as the Itinerant Moment Packet (IMP). It is shown by asymptotic analysis that the IMP gives rise to a solution that, in the space of constraining moments, is singular along a line emanating from, but not including, the point representing thermodynamic equilibrium. We use this analysis of the IMP to develop a numerical regularization of the MER, creating a procedure we call the Hybrid MER (HMER). Compared with the MER, the HMER is a significant improvement in terms of robustness and efficiency while preserving accuracy in its prediction of other important distribution features, such as higher order moments.
We apply the one-dimensional HMER to close a fourth order moment system derived from the Boltzmann equation by using a specific set of moment constraints which allow the full, three-dimensional velocity PDF to be treated as a product of three independent, one-dimensional PDFs. From this system, we extract solutions to the problem of spatially homogeneous relaxation and find excellent agreement with a standard method of solution. We further apply this method to the problem of computing the profile within a normal shock wave, and find that solutions exist only within a finite shock Mach number interval. We examine the structure of this solution and find that it has interesting behavior connected to the singularity of the MER and the IMP. Comparison is made to standard solution methods. It is determined that the use of the MER in gas dynamics remains uncertain and possible avenues for further progress are discussed.</p
Transverse Photonic Doppler Velocimetry for Plate Impact Experiments
Get PDFHigh-pressure shock waves propagate in materials when automobiles collide, projectiles impact against bunkers, and mining charges detonate beneath Earth's surface. It is difficult to quantify the behavior of materials experiencing such sudden and high pressures. Specialized interferometry techniques have enabled the study of rapid, high-strain-rate deformation during controlled plate impact testing.
Transverse motion during plate impact experiments is currently measured with the transverse displacement interferometer (TDI). However, the TDI does not take advantage of modern telecommunications technology and data analysis techniques that allow for the measurement of high velocities (in the km/s range) with fine time resolution. We designed and developed a transverse photonic Doppler velocimetry (TPDV) technique for plate impact experiments based entirely on fiber optic components. The TPDV system uses light diffracted from a grating to capture transverse motion. This signal is frequency upshifted to achieve more fringes per unit time. Data is analyzed using spectral analysis techniques to detect micrometer displacements on a nanosecond to microsecond timescale.
We demonstrated the TPDV technique's capabilities with normal impact of single crystalline y-cut alpha-quartz against borosilicate. We simultaneously collected photonic Doppler velocimetry (PDV) measurements of longitudinal displacements. Finally, we compared our longitudinal and transverse experimental results to theoretical calculations. Our data's orthogonal velocity jumps showed that the TPDV technique accurately detected transient velocities and the magnitudes of longitudinal and shear waves.
Our TPDV technique will facilitate the study of deformation and failure of materials during normal and pressure-shear plate impact. Comprehending shock-wave dominated deformation in materials is important for the design of aerospace structures, understanding planetary impact, and creating shock-mitigating materials.</p
Microbial Evolution and the Rise of Oxygen: The Roles of Contingency and Context in Shaping the Biosphere through Time
Get PDFWe are shaped by our environment, but we then shape it in turn. This interplay between life and the Earth, and how these interactions have shaped both parties through time, is the heart of the discipline of geobiology. My research is fundamentally motivated by a desire to understand how life and the Earth have changed together through time to reach the state that they’re at today, and to understand from this history how the coevolution of planet and life may be different on other worlds. The focus of my work has been on how the structure and productivity of the biosphere across time and space has been shaped by the metabolic opportunities provided by the environment—as a result of both biotic and abiotic factors—and the metabolic pathways that are available to life, as a result of evolutionary contingency in the evolution of pathways and their inheritance and horizontal transfer.
The biosphere on Earth today is incredibly productive due to the coupled dominant metabolisms of oxygenic photosynthesis and aerobic respiration, yet these can’t always be assumed to have been present—considering life more broadly, for instance in the context of the early Earth and other planets, we have to grapple with how evolutionary contingency and planetary environments interact to constrain the metabolic opportunities and rates of productivity available to the biosphere. In this dissertation, I broadly consider how the size and structure of Earth’s biosphere has changed through time as surface environments evolve and metabolic innovations accumulate. These investigations make use of information gleaned from the rock record of the early Earth, as well as the biological record of the history of life as preserved in the genomes, biochemistry, and ecology of extant organisms. These coupled records provide opportunities for constraining estimates of the opportunities for life throughout Earth history and elsewhere in the universe.</p
Targeting Undruggable Oncoprotein Epitopes with Protein Catalyzed Capture Agents
Get PDFThe protein catalyzed capture (PCC) agent platform provides a new strategy to develop peptide-based ligands for difficult protein targets. This approach utilizes the target-guided in situ click reaction to allow the protein of interest to assemble its own binder. Developing a PCC agent begins with an epitope targeting strategy to develop anchor candidates against a specific region of interest on the target protein. This approach has been used to target diverse epitopes including unstructured hydrophobic regions, allosteric enzyme sites, and single amino acid point mutations. The process can then be iterated to expand a monoligand into a multiligand binder with affinity and selectivity that rivals monoclonal antibodies.
One disease-associated protein of particular importance is the serine/threonine kinase Akt. Akt is a key regulator of signal transduction pathways and is implicated in many disease such as cancer, diabetes, and neurodegeneration. Several ligands for Akt have been developed recently with the PCC agent screening approach. PCC agents now exist that can alter Akt enzymatic activity, detect its position in the cell, identify mutations within the protein, and even cause its destruction within the cell. The first part of this thesis summarizes the prior efforts to develop PCC agents against Akt and then describes new applications for these reagents while the latter part describes efforts to develop new PCC agents against another interesting target.
Chapter 1 provides a summary of the technology and describes how it has be utilized thus far. Chapter 2 describes how a PCC agent was used as an imaging probe capable of detecting Akt membrane localization. Chapter 3 provides several examples of the modularity of PCC agents and demonstrates how they can be used to influence a target protein in cells. A pair of allosteric Akt modulators were functionalized with a cell penetrating peptide for cellular delivery and were subsequently used to activate or inhibit Akt enzymatic activity. PCC agents can also be used as a targeting moiety to deliver a specific signal to a protein. When functionalized with a degradation tag the Akt-binding capture agents caused the protein to be degraded. This provides another demonstration of the usefulness of Proteolysis Targeting Chimeric Molecules, or PROTACs, in destroying disease-associated proteins. Finally, Chapter 4 describes the development of PCC agents against the oncoprotein K-RasG12D and how these molecules can be used to target this protein in new ways.</p
Essays on the Political Economy of Subnational Public Finances
Get PDFThis dissertation is comprised of three essays addressing the connections between democracy and public finance at the subnational level. Chapter 2 focuses on variation within public expenditure, revenue, and debt at the state level in the United States for the period 1977-2011 seeking to uncover whether there is evidence of efforts by incumbents to manipulate state public finances to influence election outcomes. I find that total public expenditure increased the year before elections, especially during the period 1977-1994, but it is mostly driven by intergovernmental expenditure. Meanwhile, for later years there is a sizable reduction in tax revenue during electoral years, which results a debt increase. In Chapter 3, I extend the literature of political budget cycles at the subnational level to include pension funding. I explore the relationship between state pension funding and gubernatorial elections in the United States for the years 2001-2014. I show that one is more likely to observe the government and other employers undercontributing to pension funds during the pre-electoral year. I also found fluctuations in the pension fund's portfolio composition depending on how close a gubernatorial election is. Finally, in Chapter 4, I investigate whether the credit rating agencies (Fitch, Moody's, and Standard and Poor's) adjust the timing of their ratings as a function of the electoral calendar. I collect a novel database using credit ratings of Mexican states, and estimate panel models for gubernatorial elections in Mexico for 2005-2015. My results indicate that credit rating agencies delay announcing rating downgrades until after elections, especially when elections are very competitive.</p
Convection in Planetary Atmospheres: Titan's Haze, Saturn's Storm and Jupiter's Water
Get PDFAtmospheric convection is a profound topic. Numerous books have been written on the consequences of convection. Yet, the picture of convection is still far from complete because of its high nonlinearity, multi-scale coupling and complex interactions with other systems. The theme of my dissertation is to investigate three aspects of atmospheric convection on three different planets. This dissertation is multi-disciplinary and includes scientific topics like photochemistry, dynamics and radiation, and methodologies like information retrieval, theoretical calculation and dynamic modeling.
Chapter 1 and 2 study Titan. It focuses on how to infer the strength of convection from the vertical distribution of chemical species. In a photochemical model, convection is parameterized as eddy diffusion and the strength of convection is proportional to eddy diffusivity. We developed an inversion method to retrieve the vertical profile of eddy diffusivity directly from the Cassini observations and found out a stable layer in the atmosphere which may give rise to the detached haze layer on Titan. In addition, new observation from Cassini/CIRS limb sounding came a few month later. C3H6 was detected for the first time in the stratosphere. Our new photochemical model with the updated eddy diffusion profile successfully explained the observed vertical distribution of C3H6. Chapter 2 explains the modeling result and does a systematic study on all C3-hydrocarbons.
Chapter 3 studies Saturn. It investigates the role of convection on regulating Saturn’s giant storms. Six giant storms, called Great White Spots, have erupted on Saturn since 1876 at intervals of about 30 years. The most recent one occurred on Dec. 5th, 2010 at planetographic latitude 37.7°N. It produced intense lightning, created enormous cloud disturbances and wrapped around the planet in 6 months. We proposed the water-loading mechanism to explain the periodicity. Moist convection is suppressed for decades due to the larger molecular weight of water in a hydrogen-helium atmosphere. We show that this mechanism requires the deep water vapor mixing ratio to be greater than 1.0%, which implies Saturn’s O/H to be at least 10 times the solar value.
Chapter 4 studies Jupiter. It proposes an inversion strategy for the upcoming Juno microwave observation based on the modeling results and the theoretical arguments developed in Chapter 3. We extend the Juno/MWR’s functionality by retrieving both the deep water mixing ratio and a few dynamic parameters representing subcloud meteorology. This proposition will contribute substantially to achieving the Juno/MWR objectives and shed light on the functioning of convection on planets with deep atmospheres.</p
Non-Canonical Amino Acids As Biochemical Probes of Ligand-Gated Ion Channel Structure and Function
Get PDFThis dissertation describes several different chemical-scale studies of proteins involved in cellular signaling. The primary focus of this work is on ligand-gated ion channels, an important family of membrane receptors. In each study, the incorporation of structurally diverse non-canonical amino acids have been used to attain a high level of precision in probing the mechanisms of molecular processes. The first chapter provides an introduction to the nonsense suppression methodology used to genetically encode these probes, and surveys the classes of proteins studied herein.
The second and third chapters are concerned with the mechanism of
activation of a prokaryotic receptor, Gloeobacter violaceus ligand-gated ion channel. In these experiments, novel histidine derivatives were designed, synthesized, and incorporated to test the functional importance of acid-base titration at several positions in the receptor. Then, a battery of proline analogs were used to identify necessary structural features of several critical proline residues, providing clues to conformational changes that occur during receptor activation.
The fourth chapter discusses studies of a different class of receptors, the Acid-Sensing Ion Channels. Several fluorinated aspartic acid and glutamic acid derivatives were targeted to modulate the acidity of putative proton binding sites. Attempts at preparation of these compounds for incorporation into proteins are detailed. Additional sections describe, efforts to elucidate factors in the binding selectivity of the tarantula venom psalmotoxin and selectivity of cation permeability.
In the final chapter, early efforts at developing crosslinking assays for protein-protein interactions in mammalian cells are outlined. These assays involve the introduction of orthogonal tRNA/synthetase pairs for genetically encoding photoreactive phenylalanine analogs. The most successful studies involve the ligand-dependent dimerization of the soluble nuclear receptor, estrogen receptor α. However, the ultimate goal of this work is to to probe protein-protein interactions among membrane receptors and other proteins. Progress toward extension of the photocrosslinking assay into membrane receptors is described.</p
Automatic Decomposition of Geodetic Time Series for Studies of Ground Deformation
Get PDFGeodetic measurements of surface deformation have been used for several decades to study how the Earth's surface responds to a wide range of geophysical processes. Geodetic time series acquired over a finite spatial extent can be used to quantify the time dependence of surface strain for a wide range of spatial and temporal scales. In this thesis, we present a new method for automatically decomposing geodetic time series into temporal components corresponding to different geophysical processes. This method relies on constructing an overcomplete temporal dictionary of reference functions such that any geodetic signal can be described by a linear combination of the functions in the dictionary. By solving a linear least squares problem with sparsity-inducing regularization, we can limit the total number of dictionary elements needed to reconstruct a signal. In Chapter 2, we present the development of this method in the context of transient detection, where we define transient deformation as nonperiodic, nonsecular accumulation of strain in the crust. The sparsity regularization term automatically localizes the dominant timescales and onset times of any transient signals. We apply this method to Global Positioning System (GPS) data for a slow slip event in the Cascadia subduction zone while incorporating a spatial weighting scheme that filters for spatially coherent signals. In Chapter 3, we use a combination of unique space geodetic measurements and seismic observations to study the 2014 collapse of Bárðarbunga Caldera in Iceland associated with a major eruption event. The eruption sequence, which involved deflation of a magma chamber underneath the caldera and emplacement of a dike leading to lava flow, resulted in rapid subsidence of the glacier surface overlying the caldera and wide-scale ground deformation encompassing the rift zone associated with the dike emplacement. We present a model of the collapse that suggests that the majority of the observed subsidence occurs aseismically via a deflating sill-like magma chamber. In Chapter 4, we extend upon the transient detection framework presented in Chapter 2 to study complex surface deformation over groundwater basins near Los Angeles, California. We develop a distributed time series analysis framework based on the sparse estimation techniques of Chapter 2 and apply it to an 18-year interferometric synthetic aperture radar (InSAR) time series covering the Los Angeles area. We compare long- and short-term ground deformation signals to hydraulic head data from monitoring wells to understand the mechanical link between pressure variations in subsurface aquifers and observed ground deformation