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Mapping the Diffuse Universe: Integral Field Spectroscopy of Galaxy Environments
Get PDFThe population of galaxies we see today is the result of billions of years of gas inflows, outflows, mergers, and feedback. To develop any holistic picture of the origin and evolution of galaxies, we thus need to understand their environments. The circumgalactic and intergalactic media (CGM and IGM) - the gas around and between galaxies, respectively - represent a large part of this environment. However, this gas is extremely faint and thus difficult to observe, and only recently have we been able to image it directly. This thesis presents instrumental and observational work focused on revealing galaxy environments in the early universe.
Chapter 1 presents a brief history of our understanding of galaxies and an overview of our current picture of galaxy formation, including the role played by galaxy environments. In particular, it focuses on presenting the evolution of baryonic structures within a cosmological density field dominated by dark matter.
Chapter 2 presents instrumental work on the Keck Cosmic Web Imager (KCWI, Morrissey et al. 2018), a new integral field spectrograph (IFS) for the Keck-2 10m telescope designed to study faint, extended emission. As an introduction, I discuss the advantages and disadvantages of integral field spectroscopy for the application of studying galaxy environments, as well as an overview of the prototype instrument - the Palomar Cosmic Web Imager (PCWI, Matuszewski et al. 2010). This chapter focuses primarily on engineering work during the development and testing of KCWI, though I conclude with a brief comparison of PCWI and KCWI performance in measuring the CGM around a high-redshift QSO.
Chapter 3 presents the development of a software package designed to extract and analyze faint, extended emission in PCWI and KCWI data: CWITools. Although software is often an afterthought in astronomical and observational work, it is likely to become a primary barrier to conducting large IFS surveys of the CGM and IGM. This semi-automated analysis pipeline is presented and released publicly to empower future PCWI and KCWI studies.
Chapter 4 presents the FLASHES (Fluorescent Lyman-α Structures in High-z Environments) pilot survey, published as O'Sullivan et al. 2020. The FLASHES pilot survey is an IFS study of extended HI Lyman-α emission in the environments of 48 z = 2.3 - 3.0 QSOs. The FLASHES Survey is the core project of this thesis, enabled by the instrumentation in Chapter 2 and the analysis pipeline developed in Chapter 3. The pilot survey represents the first statistically significant (N ≳ 30) sample of direct CGM observations in its redshift range. As such, it provides the first direct constraints on the 2D morphology, surface brightness profiles, and spatially resolved kinematics of the CGM during this period.
Chapter 5 presents the first FLASHES follow-up study; deep IFS observations targeting extended Lyα 1216Å, NV 1240Å, CIV 1549Å, and HeII 1640Å emission from a subset of FLASHES pilot targets (O'Sullivan et al., in prep). Emission from metals in the CGM is expected to be an order of magnitude or more fainter than its Lyα, yet is a crucial ingredient in understanding the composition of the gas. Detecting this emission still requires multiple hours on 10m class telescopes. As such, large surveys of the multi-phase CGM remain extremely difficult to conduct. In this chapter, I present detections and upper limits of CGM metal emission around 8 FLASHES targets.
Chapter 6 presents engineering work on FIREBall-2 (the Faint Intergalactic Redshifted Emission Balloon, second generation), a high-altitude UV telescope and IFS targeting CGM emission in the low-redshift universe (z ≃ 0.7). FIREBall-2 is an ambitious project deploying a novel, electron-multiplying CCD designed to achieve ≳ 50% quantum efficiency in the UV. This technology represents an order of magnitude increase in sensitivity from the microchannel plates used in the GALEX space telescope. FIREBall-2 serves as both an observational project in its own right, studying the low-z CGM, and a pathfinder mission for future UV space missions.
Finally, Chapter 7 summarizes the contributions from this thesis and present a brief outlook on a few topics related to observations of galaxy environments.</p
Frameworks for High Dimensional Convex Optimization
Get PDFWe present novel, efficient algorithms for solving extremely large optimization problems. A significant bottleneck today is that as the size of datasets grow, researchers across disciplines desire to solve prohibitively massive optimization problems. In this thesis, we present methods to compress optimization problems. The general goal is to represent a huge problem as a smaller problem or set of smaller problems, while still retaining enough information to ensure provable guarantees on solution quality and run time. We apply this approach to the following three settings.
First, we propose a framework for accelerating both linear program solvers and convex solvers for problems with linear constraints. Our focus is on a class of problems for which data is either very costly, or hard to obtain. In these situations, the number of data points m available is much smaller than the number of variables, n. In a machine learning setting, this regime is increasingly prevalent since it is often advantageous to consider larger and larger feature spaces, while not necessarily obtaining proportionally more data. Analytically, we provide worst-case guarantees on both the runtime and the quality of the solution produced. Empirically, we show that our framework speeds up state-of-the-art commercial solvers by two orders of magnitude, while maintaining a near-optimal solution.
Second, we propose a novel approach for distributed optimization which uses far fewer messages than existing methods. We consider a setting in which the problem data are distributed over the nodes. We provide worst-case guarantees on the performance with respect to the amount of communication it requires and the quality of the solution. The algorithm uses O(log(n+m)) messages with high probability. We note that this is an exponential reduction compared to the O(n) communication required during each round of traditional consensus based approaches. In terms of solution quality, our algorithm produces a feasible, near optimal solution. Numeric results demonstrate that the approximation error matches that of ADMM in many cases, while using orders-of-magnitude less communication.
Lastly, we propose and analyze a provably accurate long-step infeasible Interior Point Algorithm (IPM) for linear programming. The core computational bottleneck in IPMs is the need to solve a linear system of equations at each iteration. We employ sketching techniques to make the linear system computation lighter, by handling well-known ill-conditioning problems that occur when using iterative solvers in IPMs for LPs. In particular, we propose a preconditioned Conjugate Gradient iterative solver for the linear system. Our sketching strategy makes the condition number of the preconditioned system provably small. In practice we demonstrate that our approach significantly reduces the condition number of the linear system, and thus allows for more efficient solving on a range of benchmark datasets.</p
A Very Wide Bandwidth SIS Heterodyne Receiver Design for Millimeter and Submillimeter Astronomy
Get PDFThis text describes in some detail the design and operational history of an instrument used as the front-end receiver for a fast, broadband, high-resolution spectrometer for the 1.3 millimeter wavelength atmospheric window. Using only a single superconductor-insulator-superconductor (SIS) tunnel junction as its heterodyne detector, the receiver’s novel design achieved then unprecedented RF and IF bandwidths and incorporated several innovations which have since been widely adopted within the millimeter and submillimeter wave research communities. Although intended as a relatively simple technology demonstrator and starting point for more refined and sophisticated designs, the receiver turned out to be a useful astronomical instrument in its own right, and it was deployed as a de facto facility instrument for several years at the Caltech Submillimeter Observatory. Also described are the author’s contributions to another important aid to research and design efforts: the SuperMix software library for the analysis and optimization of high-frequency circuitry, especially developed to aid in the design of systems involving SIS and other superconducting elements. Finally, the text may serve as a useful introduction to the theory behind and methodology for modeling and design of SIS heterodyne mixers.</p
Part I: The Equations of Plasma Physics and the Richtmyer-Meshkov Instability in Magnetohydrodynamics. Part II: Evolution of Perturbed Planar Shockwaves.
Get PDFPart I: Mitigating the Richtmyer-Meshkov instability (RMI) is critical for energy production in inertial confinement fusion. Suitable plasma models are required to study the hydrodynamic and electromagnetic interactions associated with the RMI in a conducting medium. First, a sequence of asymptotic expansions in several small parameters, as formal limits of the non-dissipative and non-resistive two-fluid plasma equations, leads to five simplified plasma/magnetohydrodynamics (MHD) systems. Each system is characterized by its own physical range of validity and dispersion relations, and includes the widely used magnetohydrodynamic (MHD) and Hall-MHD equations. Next we focus on the RMI in MHD. Using ideal MHD, it has been shown that the RMI is suppressed by the presence of an external magnetic field. We utilize the incompressible, Hall-MHD model to investigate the stabilization mechanism when the plasma ion skin depth and Larmor radius are nonzero. The evolution of an impulsively accelerated, sinusoidally perturbed density interface between two conducting fluids is solved as a linearized initial-value problem. An initially uniform background magnetic field of arbitrary orientation is applied. The incipient RMI is found suppressed through oscillatory motions of the interface due to the ion cyclotron effect. This suppression is most effective for near tangential magnetic fields but becomes less effective with increasing plasma length scales. The vorticity dynamics that facilitates the stabilization is discussed.
Part II: We consider the evolution of a planar gas-dynamic shock wave subject to smooth initial perturbations in both Mach number and shock shape profile. A complex variable formulation for the general shock motion is developed based on an expansion of the Euler equations proposed by Best [Shock Waves, {1}: 251-273, (1991)]. The zeroth-order truncation of Best's system is related to the well-known geometrical shock dynamics (GSD) equations while higher-order corrections provide a hierarchy of closed systems, as detailed initial flow conditions immediately behind the shock are prescribed. Solutions to Best's generalized GSD system for the evolution of two-dimensional perturbations are explored numerically up to second order in the weak and strong shock limits. Two specific problems are investigated: a shock generated by an impulsively accelerated piston with a corrugated surface, and a shock traversing a density gradient. For the piston-driven flow, it is shown that this approach allows full determination of derivative jump conditions across the shock required to specify initial conditions for the retained, higher-order correction equations. In both cases, spontaneous development of curvature singularity in the shock shape is detected. The critical time at which a singularity occurs follows a scaling inversely proportional to the initial perturbation size. This result agrees with the weakly nonlinear GSD analysis of Mostert et al. [J. Fluid Mech., {846}: 536-562, (2018)].</p
Novel, Rapid and Cost-effective Methods for Concentration, Detection and Monitoring of Waterborne Pathogens in Resource-Limited Settings
Get PDFWaterborne pathogenic organisms including bacteria, viruses, protozoa and helminths, are responsible for a series of diseases which is a major public health concern worldwide. This issue is extremely severe in developing regions due to the scarcity of clean water supply and poor sanitation. Therefore, point-of-use (POU) detection and quantification processes as well as a monitoring program of waterborne pathogens are needed to ensure the safety of water and protect human health. However, the polymerase chain reaction (PCR) technology and its related detection platforms rely on complicated thermal cycling, centralized laboratory equipment and trained personnel, thus making PCR-based systems incapable of POU testing of environmental waters. In this dissertation, we develop a portable 3D-printed system with super-absorbent polymer (SAP) microspheres for sample enrichment, and a membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) system for absolute quantification of pathogens. We also explored the interactions between microbial indicator of Escherichia coli (E. coli) and waterborne pathogen Vibrio Cholerae (V. Cholerae). The main results are as follows:
1. The application of detection and quantification methods is often hindered by the low pathogen concentrations in natural waters. Rapid and efficient sample concentration methods are urgently needed. Here we present a novel method to pre-concentrate microbial pathogens in water using a portable 3D-printed system with super-absorbent polymer (SAP) microspheres, which can effectively reduce the actual volume of water in a collected sample. The SAP microspheres absorb water while excluding bacteria and viruses by size exclusion and charge repulsion. The 3D-printed system with optimally-designed SAP microspheres could rapidly achieve a 10-fold increase in the concentration of E. coli and bacteriophage MS2 within 20 minutes with concentration efficiencies of 87% and 96%, respectively. Fold changes between concentrated and original samples from qPCR and RT-qPCR results were found to be 11.34-22.27 for E. coli with original concentrations of 104-106 cell·mL-1; and 8.20-13.81 for MS2 with original concentrations of 104-106 PFU·mL-1. Furthermore, SAP microspheres can be reused 20 times without performance loss thereby significantly decreasing the cost of our concentration system.
2. Following sample concentration, accurate quantification methods for waterborne pathogens are needed, especially at the point of sample collection. The surge of COVID-19 in late 2019 called for a more urgent need for a rapid and cost-effective quantification of SARS-CoV-2 in environmental waters. Quantification results contribute to wastewater-based epidemiology (WBE) which helps the monitoring of prevalent infections within a community and early detections of contamination. Here we demonstrated the usage of our portable membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) system for absolute quantification of SARS CoV-2 in wastewater samples within a one-hour timeframe for point-of-use (POU) testing and data management. The limit of detection (LOD) of mgLAMP for SARS-CoV-2 quantification in Milli-Q water was observed to be down to 1 copy/mL, and that in surface water collected from Kathmandu, Nepal was down to 100 copies/mL. Both were 100-fold lower than that of RT-qPCR in corresponding matrices. Compared to alternative detection methods, our platform has a very high level of tolerance against inhibitors thanks to the restriction of the hydrogel matrix. This enables the highly sensitive detection in either clinical or environmental samples.
3. Regular environmental surveillance of waterborne pathogens is key to ensure the safety of water and protect public health. Due to the diversity of pathogenic bacteria in environmental waters, regular monitoring of so many pathogens for individuality is impractical. Therefore, microbial indicators are used to gauge the total pathogen concentration; and manage waterborne health risks. In this study, the interactions of V. cholerae, the etiologic agent of reemerging cholera, with E. coli, the most commonly used indicator for waterborne pathogens. Specifically, we investigated through evaluating the survival and growth of both bacteria under different temperature and nutrition deprivation using plate culturing and real-time polymerase chain reaction (qPCR). During co-growth, it was challenging for V. Cholerae to maintain initial population advantages as E. coli consumes nutrition more effectively. Whereas during co-existence, V. Cholerae soon fell into a viable-but–non-culturable state under environmental stress in 3-5 days while E. coli stay viable more than 14 days. We found that V. cholerae interacts with E. coli differently depending on the composition of the water that is sampled and analyzed. This suggests that bacterium-bacterium interactions influenced by the intrinsic chemical and biological parameters of ambient water will be a contributing mechanism in regulating the proliferation of V. cholerae.
In summary, two platforms for environmental sample concentration and detection have been developed and tested using ambient and engineered waters. In addition, interactions between a microbial indicator, E. coli, and the pathogenic bacteria, V. Cholerae, were studied. The chapters in this thesis describe in detail: (1) A hand-pressed 3D-printed system to produce SAP microspheres was developed with the goal of achieving efficient concentrations of environmental microorganisms for subsequent analysis. The simplified concentration procedure and can be easily integrated into various detection platforms; (2) A portable membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) system was developed for absolute quantification of SARS-CoV-2 in environmental water samples within one hour, enabling a 100-fold lower detection limit compared to the gold-standard of RT-qPCR; and (3) Differences in bacterium-bacterium interactions of V. cholerae and E. coli under as a function of water composition indicated that environmental stress presented in ambient water matrices should be taken into consideration while using a microbial indicator such as E. coli to estimate the risk of waterborne pathogens. These collective advances allow for the rapid and ultrasensitive POU testing of waterborne pathogens that should provide for more effective monitoring strategies in terms of the use of indicator microorganisms.</p
Statistical Mechanics of Problems in Transcription Regulation
Get PDFAs the quantity of sequenced genome data continues to multiply, our understanding of the transcriptional regulation of genomes has lagged behind. This deficit impinges on research throughout biology, from fundamental questions of how evolution proceeds to eminently practical questions such as how antibiotic resistance arises.
In this thesis we present three threads that address the question of transcriptional regulation from distinct perspectives. The first thread focuses on the simplest nontrivial regulation motif common in bacteria. We analyze in turn a sampling of the myriad mathematical models previously proposed in the literature for this system. We attempt to shine light on the similarities and differences of the models’ predictions, clarify their microscopic interpretations, and offer guidance as to situations when one model or another should be preferred or even distinguishable.
The second thread considers a substantially more complicated genetic circuit, for which we build a minimal phenomenological model that retains intuitive microscopic meaning for all its parameters. The model neatly explains recent experimental observations of bistability in the circuit, and suggests natural generalizations to other metabolically important gene circuits with qualitatively similar architectures.
Motivation for the third thread comes from even more complicated transcriptional regulation problems with a multitude of regulatory proteins and binding sites, where even enumerating all possible DNA-protein complexes manually is a formidable challenge. Here we propose a method to tackle this complexity that uses ideas from quantum field theory to encode assembly rules for macromolecular complexes. By specifying a small set of rules, we avoid manual enumeration of the much larger set of complexes, allowing the formalism to automatically generate this set for us.</p
Unravel at the Seams
No full text[Introduction] The white needle glinted hypnotically in the firelight. Up. Down. Up. Down. Her stitches were even, as they always were, and she looked down at the bodice with detached satisfaction. Across the room, the old woman sat at her rocking chair by the fire, long knitting needles furiously flashing, dripping with jet black wool. The sound of the sewing machine’s constant whirring and the chair’s steady rocking filled the room like a heartbeat
Stabilization of Brain-Machine Interface Systems via Alignment to Baseline
Get PDFResearch in the brain-machine interface has the potential to transform the lives of individuals with limited motor capabilities to allow for greater independence. By directly accessing signals in the brain, it is possible to train a decoder to identify intended motion and allow the user to control a prosthetic limb or computer cursor by simply thinking about the motion. However, neural data recorded from implanted electrodes is highly unstable over time and across multiple sessions, leading to a severe drop in decoding performance as the test data becomes more distant from the data on which the decoder was trained. Here, we investigate a method to stabilize neural spike data from human trials of a center-out cursor control task before it is passed to a linear decoder, using the techniques of factor analysis and Procrustes alignment. We find that for highly variable human neural data from experiment dates that are far apart, the method does not help the decoder better predict cursor kinematics. However, when factor analysis weights are averaged over multiple baseline days, the performance of the decoder significantly increases with Procrustes alignment, which gives a promising method to limit recalibration and retraining of neural decoders by prolonging their higher accuracy performance over time
Constraining Earthquake Source Processes Through Physics-Based Modeling
Get PDFDetermining principles and conditions governing motion along faults is crucial for assessing how earthquake ruptures start and how large they may ultimately become. This thesis aims to shed light on the physics governing earthquake source processes by (i) developing physics-based numerical models that combine geological observations and laboratory insight with theoretical developments, and (ii) using these models to examine how different physical mechanisms and conditions are reflected in a range of geophysical observations taken together, from heat-flow constraints and seismologically determined properties of earthquakes to geodetic inferences and earthquake frequency-magnitude statistics.
We examine the behavior and observable characteristics of numerically simulated sequences of earthquakes and aseismic slip in fault models designed to reproduce well-known features of mature faults that produce large destructive earthquakes. In part, the models are consistent with the inferred low-stress, low-heat operation of mature faults, which host large earthquakes at much lower levels of stress than their expected static strength. We explore two potential explanations for such behavior, one that faults are indeed quasi-statically strong but experience dramatic weakening during earthquakes, or that faults are persistently weak, e.g., due to fluid overpressure. We find that the two classes of fault models can, in principle, be distinguished based on the amount of seismic energy radiated from earthquake ruptures. Dynamic ruptures in the form of self-healing pulses, which occur on quasi-statically strong but dynamically weak faults, result in much larger radiated energy than inferred teleseismically for megathrust events, whereas crack-like ruptures on persistently weak faults are consistent with the seismological observations. The larger radiated energy of self-healing pulses is similar to limited regional inferences for crustal strike-slip faults. Our results suggest that re-evaluating estimates of radiated energy and static stress drop would provide substantial insight into the driving physics of large earthquakes and the absolute stress conditions on faults, with potential differences between tectonic settings.
The results also have significant implications for seismic hazard, since our modeling shows that fault models that experience efficient dynamic weakening during ruptures tend to predominantly produce large earthquakes, at the expense of smaller earthquakes. Such behavior is consistent with some mature fault segments, such as several segments of the San Andreas Fault in California that have hosted large earthquakes but are currently nearly seismically quiescent. These considerations can provide physical basis for improving earthquake early warning systems. If mature faults in California are indeed governed by enhanced dynamic weakening, then our results suggest that the likelihood of an earthquake on these faults becoming substantially larger is much higher than typical expectations based on Gutenberg-Richter statistics.
By considering average fault stress before simulated earthquake ruptures, we find that critical stress conditions for earthquake occurrence depend on the size and style of motion (e.g. the degree of slip acceleration at the rupture front) during individual ruptures. In particular, the stress conditions required to propagate large earthquake ruptures can be considerably lower than those required for rupture nucleation, and standard notions of quasi-static fault strength based on laboratory studies. Our results demonstrate that the critical stress for earthquake occurrence is not governed by a simple condition such as a certain level of Coloumb stress, as commonly used in studies of stress interactions among faults and earthquake aftershocks patterns. More robust criteria for critical stress conditions would depend on the strength evolution during dynamic rupture and can be explored in numerical simulations.
Finally, evaluating the predictive power of numerical earthquake models for future hazards is a topic of great importance for physics-based seismic hazard assessment. Towards that end, we investigate the sensitivity of outcomes from numerical simulations of sequences of earthquakes and aseismic slip, including the long-term interaction of fault segments, to choices in numerical discretization and treatment of inertial, wave-mediated effects. In particular, we find that the rate of earthquake ruptures that manage to jump between two fault segments, a parameter routinely used in seismic hazard studies, is highly sensitive to numerical and physical modeling choices. These results suggest the need for developing different parameterization of seismic hazard than currently used, a task for which numerical modeling is well-suited.</p
Growth Towards Light: Translation of Optical Inputs into Mesostructured Outputs via Inorganic Phototropism
Get PDFPalm trees exhibit phototropic growth wherein physical extension of the plant guides the crown towards the time-averaged position of the sun to maximize solar harvesting. In analogous fashion, the directed growth and resultant nanoscale morphology of an evolving inorganic semiconductor deposit can be precisely defined in three-dimensional space using incoherent, uncorrelated light with spatially-invariant intensity. Maskless, photo-driven electrochemical deposition of semiconductor films generates highly ordered, periodic mesostructures with anisotropic, nanoscale features conformally over macroscale areas. This inorganic phototropic growth process does not utilize any physical nor chemical templating agents. Rather, as with natural phototropism, wherein the morphological phenotype expressed by an organism is a function of the light available in the habitat during growth, the precise mesostructures are set by the deposition illumination. Structural complexity and anisotropy result as consequences of inherent asymmetry in the light-material interactions during growth. Here, the morphological outcomes defined by specific illumination inputs are explored and the microscopic optical phenomena underpinning this physical recording of light information is interrogated via both experimental and computational methodologies