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Spectroscopy of Galaxies: Evolution of Escape Fractions, Metallicity Gradients and Stellar Metallicity
Get PDFWe use spectroscopic observations to investigate galaxies from the age of reionization to the peak of star formation, and the local universe. This thesis presents three projects to better understand characteristics of galactic feedback, i.e., how it regulates galactic gas flows.
We used deep absorption line spectroscopy to estimate the escape fractions fesc of star-forming gravitationally-lensed galaxies at z ≃ 5. The approach is to measure the covering fraction of neutral hydrogen in a galaxy from the amount of non-ionizing UV radiation absorbed by low-ionization metal species. With the boost of signal by gravitational lensing, we observed four 4 < z < 5 star-forming galaxies with DEIMOS, doubling the sample size of existing observations at the redshift range. We found that the escape fractions across our sample varies from galaxy to galaxy and appear to have no significant evolution over time. We inferred a median absolute escape fraction of Lyman continuum photons of 19 ± 6%. Accounting for possible biases and uncertainties, the absolute escape fraction could be reduced to no less than fesc,abs ~ 11%. Moreover, we spatially resolved and detected variation of escape fraction within a galaxy for the first time. The significant variations within the galaxy suggest that the escape fraction is governed by small-scale structure. We found a tentative anti-correlation between the star-formation rate (local or integrated) and the inferred escape fraction. This supports that the escape fraction is associated with the delay time after an episode of star formation. Feedback seems to be more effective in governing both a low SFR and a smaller HI covering fraction.
Spatially resolved spectroscopic observations of galaxies at the peak era of star-formation activities are effective in providing insight into the primitive disks. Specifically, we used metallicity gradients to provide constraints on the amount and extent of feedback produced in star-forming galaxies. We observed 15 star-forming galaxies at z ~ 2 with OSIRIS to obtain their kinematic properties and gas-phase metallicity gradients. With helps from AO correction and gravitational lensing, the typical spatial resolution in our study is less than a half-light radius of a typical L* galaxies at z ≃ 2. Combining with the sample in Jones et al., 2013, we approximately tripled the existing metallicity gradient measurements. We found a lower fraction of rotationally-supported systems than reported from larger kinematic surveys with coarser spatial resolution, which might be partially due to a our improved spatial resolution. We demonstrated that a high spatial resolution is crucial for an accurate diagnosis of the kinematic properties and dynamical maturity of z ≃ 2 galaxies.
As for metallicity gradients, we found a much higher fraction of z ≃ 2 galaxies having weak or flat metallicity gradients than in previous studies. We correlated the metallicity gradient with the total metallicity and found that all galaxies with low total metallicities have flat gradients (< 0.1 dex per kpc-1). For galaxies with high metallicities ([N II]/Hα > 0.1), there is a divergence between isolated or rotationally-supported and dynamically-immature systems with the latter showing zero gradients irrespective of the integrated metallicity. The results indicate that relatively strong feedback (e.g. high mass loading factors or high SN energy output) is required in order to explain the majority of the observed flat gradients.
In the second part of the thesis, we observed quiescent galaxies at z < 1 and archaeologically constrained galactic feedback via its cumulative influence on stellar metallicities. First, we present the stellar mass-[Fe/H] relationship in the Cl0024+17 galaxy cluster at z ~ 0.4. We derived the metalliticies via full spectrum stellar population synthesis modeling of individual quiescent galaxies. Our results provide the metallicities of the lowest galaxy mass (M* = 109.7M⊙) at which individual stellar metallicity has been measured beyond the local universe. We found that the mass-[Fe/H] relationship evolves with the redshift at which the galaxy is observed today. Furthermore, we found an even stronger evolution of the mass-[Fe/H] relation with the time at which the galaxy formed (rather than the time at which it is observed). Galaxies that formed earlier have lower Fe abundance than galaxies that formed later.
Lastly, we measured magnesium (Mg) abundances and extended the observed redshift to z ~ 0.55. We found that while the mass-[Fe/H] relation evolves significantly over the observed redshift range, the mass-[Mg/H] relation does not. This is due to the shorter star formation histories of quiescent galaxies at higher redshifts. Fe is mainly produced in Type Ia SN. It has a longer recycling time than Mg, which is mainly produced in core-collapse SN. Using core-collapse SN elements as a metal indicator lessens the complication of delayed recycling time and allows us to effectively use galactic chemical models with instantaneous recycling to quantify average outflows that these galaxies experience over their lifetime. We found that the average mass-loading factor η is a power-law function of galaxy stellar mass, η ∝ M*-0.21±0.09, consistent with the results of other observational methods and with the predictions where outflow is caused by star formation feedback in turbulent disks.</p
Proteomics Profiling and Functional Characterization of Caenorhabditis elegans Excreted/Secreted Proteins
Get PDFExcretory-secretory products (ESPs) are first characterized and defined in parasitic nematode proteomics studies as the combination of various biomolecules that are continuously excreted or secreted into the environment throughout the whole life cycle. ESPs are particularly interesting to many scientists as anti-parasitic vaccine candidates and
as promising drug targets since large portions of ESPs are active enzymes that potentially function directly at the parasite-host or worm-environment interfaces. However, majority of the parasites lack whole genome sequence knowledge and genome-editing tools. Thus, the number of ESPs identified is limited and many functions of ES proteins cannot be elucidated. Therefore, we use the most studied nematode, Caenorhabditis elegans, as the model to characterize the composition of excreted/secreted proteins with the help of nanoliquid chromatography coupled with tandem mass spectrometry (nanoLC-MS/MS). We characterized more than 509 excreted/secreted proteins with mix-staged worms, including many metalloproteases, cysteine proteases, and lysozymes. Proteases and proteases inhibitors are a major group in C. elegans ESPs. We performed stable isotope dimethylvlabeling quantitative proteomics and compared C. elegans ESPs on different bacteria diets. Lysozymes are not only enriched in C. elegans ESPs but are also up-regulated in response to pathogen and bacteria.
Comparative studies of expression profiles of developmental life stages and pathogen infections elucidate the dynamics in regulating ESP components. We successfully identified stage-specific ESP groups associated with L1, L3, adult, L2 dauer, and postdauer. We demonstrated that proteases activities are down regulated by increased protease inhibitor expressions, while during dauer exit proteases expressions are increased. The comparison between dauer excretome/secretome and RNA-seq dauer expression profiles revealed 91 ESP encoding genes that are highly expressed in dauers. We performed dauer formation assay to these dauer-associated gene mutants. The great prediction rate confirmed that our comparative method is the simplest way to quickly pick out candidates for functional assays. Similarly, we employed this comparative method to pathogeninduced transcriptomes. We reported a group of genes that are associated with Serratia marcescens infection and a group of bacterial pathogens responding genes. We confirmed the roles of C. elegans ESPs in immuoregulation by infection assays with various pathogens. Lysosomes and cysteine protease inhibitor are among the most important genes in innate immune response pathway of C. elegans defending pathogen infection.
The recent discovery of a C. elegans sibling species, Caenorhabditis inopinata, allows the deeply comparative study for evolutional interpretation. The excretome/secretome of C. inopinata has not been characterized. We took advantage of the sensitive and highthroughput technique of nanoscale liquid chromatography coupled to tandem mass spectrometry (nano LC-MS/MS) to directly characterize the protein components of C. inopinata excretome/secretome. Functional annotations reveal several protein families, including C-type lectins, Cathepsin Z, Cathepsin B family, transthyretin, and saposin-like families, suggesting ESPs play critical roles in regulating innate immune response. We compared C. inopinata excretome/secretome with C. elegans. The structures are highly conserved across species, suggesting the sibling species share common mechanism to respond to environmental stimuli.</p
On the Manipulation of a Turbulent Boundary Layer by Unsteady Boundary Conditions
Get PDFReducing the frictional drag generated by a turbulent boundary layer (TBL) is critical for many engineering applications. Motivated by existing turbulent drag reduction methods, this study explores the possibility of sustaining wall-attached air-films and manipulating the near-wall turbulence in hydrodynamic TBL. An innovative air-retaining system is designed to sustain and dynamically modulate the wall-attached air-films in TBL. In still water, the oscillating air-films induce vortical motions in the near-region of air-films. In TBL, phenomena such as Stokes-type oscillatory motion, zero- shear-stress layer, 'inactive' turbulence and reduced viscous shear stress are observed in the vicinity region of air-films. The analysis shows that TBL momentum transfer toward the wall is suppressed and a turbulence re-laminarization mechanism is induced in the near-wall region. One potential physical mechanism points to the process of vorticity generation in the near-region of oscillating air-films, which 'pushes' the TBL near-wall vortical structures away from the wall. With this viewpoint, the phenomena mentioned above can be explained. The modified momentum transfer mechanism and turbulence re-laminarization process are shown to be the potential cause of suppressed viscous shear stress in the near-wall region. Estimated using the Clauser chart method, the turbulent wall-skin friction shows a noticeable decrease in the presence of air-films.</p
Mechanistic Investigations of Receptor Signaling via Canonical and Non-Canonical Amino Acid Mutagenesis
Get PDFThis dissertation primarily describes investigations of the mechanisms by which pentameric ligand-gated ion channels (pLGICs) activate ("gating") using canonical and non-canonical amino acid mutagenesis. Chapter 1 provides an introduction to the systems being studied, their physiological roles, and the techniques that we have used to study them. Chapter 2 describes a series of experiments comparing the roles of amino acid residues proximal to the neurotransmitter binding site in the type 3 serotonin receptor (5-HT3R) to the aligning residues of the muscle-type nicotinic acetylcholine receptor (nAChR). The findings presented in Chapter 3 assess the functional roles of proline residues in the prokaryotic pLGIC, Erwinia ligand-gated ion channel (ELIC). Chapter 4 describes an extensive investigation of salient details of 5-HT3R gating using canonical and non-canonical amino acid mutagenesis of amino acid residues at the interface of the extracellular domain and transmembrane domain of this receptor. Chapter 5 applies a photocrosslinking strategy employing the non-canonical amino acid p-azidophenylalanine to study dimerization and cofactor interactions of the estrogen receptor α.</p
Essays On Decision Theory
Get PDFThis thesis introduces some general frameworks for studying problems in decision theory. The purpose of this dissertation is two-fold. First, I develop general mathematical frameworks and tools to explore different decision theoretic phenomena. Second, I apply my developed frameworks and tools in different topics of Microeconomics and Decision Theory.
Chapter 1 introduces a notion of the classifier, to represent the different classes of data revealed through some observations. I present a general model of classification, notion of complexity, and how a complicated classification procedure can be generated through some simpler classification procedures.
My goal is to show how an individual's complex behavior can be derived from some simple underlying heuristics. In this chapter, I model a classifier (as a general model for decision making) that based on observing some data points classifies them into different categories with a set of different labels. The only assumption for my model is that whenever a data point is in two categories, there should be an additional category representing the intersection of the two categories. First, I derive a duality result similar to the duality in convex geometry. Then, using my result, I find all representations of a complex classifier by aggregating simpler forms of classifiers. For example, I show how a complex classifier can be represented by simpler classifiers with only two categories (similar to a single linear classifier in a neural network). Finally, I show an application in the context of dynamic choice behaviors. Notably, I use my model to reinterpret the seminal works by Kreps (1979) and Dekel, Lipman, and Rustichini (2001) on representing preference ordering over menus with a subjective state space. I also show the connection between the notion of the minimal subjective state space in economics with my proposed notion of complexity of a classifier.
In Chapter 2, I provide a general characterization of recursive methods of aggregation and show that recursive aggregation lies behind many seemingly different results in economic theory. Recursivity means that the aggregate outcome of a model over two disjoint groups of features is a weighted average of the outcome of each group separately.
This chapter makes two contributions. The first contribution is to pin down any aggregation procedure that satisfies my definition of recursivity. The result unifies aggregation procedures across many different economic environments, showing that all of them rely on the same basic result. The second contribution is to show different extensions of the result in the context of belief formation, choice theory, and welfare economics.
In the context of belief formation, I model an agent who predicts the true state of nature, based on observing some signals in her information structure. I interpret each subset of signals as an event in her information structure. I show that, as long as the information structure has a finite cardinality, my weighted averaging axiom is the necessary and sufficient condition for the agent to behaves as a Bayesian updater. This result answers the question raised by Shmaya and Yariv (2007), regarding finding a necessary and sufficient condition for a belief formation process to act as a Bayesian updating rule.
In the context of choice theory, I consider the standard theory of discrete choice. An agent chooses randomly from a menu. The outcome of my model is the average choice (mean of the distribution of choices) rather than the entire distribution of choices. Average choice is easier to report and obtain than the entire distribution. However, an average choice does not uniquely reveal the underlying distribution of choices. In this context, I show that (1) it is possible to uniquely extract the underlying distribution of choices as long as the average choice satisfies weighted averaging axiom, and (2) there is a close connection between my weighted averaging axiom and the celebrated Luce (or Logit) model of discrete choice.
Chapter 3 is about the aggregation of the preference orderings of individuals over a set of alternatives. The role of an aggregation rule is to associate with each group of individuals another preference ordering of alternatives, representing the group's aggregated preference. I consider the class of aggregation rules satisfying the extended Pareto axiom. Extended Pareto means that whenever we partition a group of individuals into two subgroups, if both subgroups prefer one alternative over another (as indicated by their aggregated preferences), then the aggregated preference ordering of the union of the subgroups also prefers the first alternative over the second one.
I show that (1) the extended Pareto is equivalent to my weighted averaging axiom, and (2) I derive a generalization of Harsanyi's (1955) famous theorem on Utilitarianism. Harsanyi considers a single profile of individuals and a variant of Pareto to obtain Utilitarianism. However, in my approach, I partition a profile into smaller groups. Then, I aggregate the preference ordering of these smaller groups using the extended Pareto. Hence, I obtain Utilitarianism through this consistent form of aggregation. As a result, in my representation, the weight associated with each individual appears in all sub-profiles that contain her.
In another application, I find the class of extended Pareto social welfare functions. My result has a positive nature, compared to the claims by Kalai and Schmeidler (1977) and Hylland (1980) that the negative conclusion of Arrow's theorem holds even with vN-M preferences.
Finally, in Chapter 4, I derive a simple subjective conditional expectation theory of state-dependent preferences. In many applications such as models for buying health insurance, the standard assumption about the independence of the utility and the set of states is not a plausible one. Hence, I derive a model in which the main force behind the separation of beliefs and state-dependent utility comes from the extended Pareto condition. Moreover, I show that, as long as the model satisfies my strong minimal agreement condition, we can uniquely separate beliefs from the state-dependent utility.</p
Dynamic Earthquake Source Modeling and the Study of Slab Effects
Get PDFIn this Thesis, I report my Ph.D. research on two major issues that are devoted towards constructing more realistic earthquake source model using computational tools: (1) constructing physically consistent dynamic rupture models that include complexities in fault geometry as well as heterogeneous stress and frictional properties inferred from observations; (2) study the effect of subducting slab structure on earthquakes that occur inside it with a special focus on the teleseismic waveforms.
Fault step over is one of the most important geometric complexities that control the propagation and arrest of earthquake ruptures. In Chapter 2, we study the role of seismogenic depth and background stress on physical limits of earthquake rupture across fault step overs. We conclude that the maximum step over distance that a rupture can jump is approximately proportional to seismogenic depth. We also conclude that the pre-stress conditions have a fundamental effect on step over jump distance while the critical nucleation size has a secondary effect.
Seismic wave carries information of source as well as structures along the path it travels. It was found that seismic waves generated by shallow events in subduction zones whose ray path coincide with the down going slab structure display waveform complexities that feature multipathing. In Chapter 3, we study deep earthquakes whose depth phases sample the slab structure on their way up to the surface. Differential travel time sP-P analysis shows a systematic decrease of up to 5 seconds from Europe to Australia and then to Pacific which is indicative of a dipping high velocity layer above the source region. Finite-difference simulations showed that a slab shaped structure that follows the Benioff zone at shallow depth and steepens beyond 400 km produces a model that can account for the sP-P differential travel times of 5 seconds for oceanic paths. In Chapter 4, we design a slab operator that can be applied on the 1D synthetics to generate 2D synthetics with slab structure. We hope this operator can be used for generating more accurate Green's functions that could potentially serve earthquake source inversion.
In Chapter 5, we design a dynamic rupture model of the Mw 7.8 Gorkha, Nepal earthquake. We employ a novel approach of integrating kinematic inversion results which provide low frequency stress distribution and stochastic high frequency stress motivated by earthquake cycle models and observations. By doing this, we are able to reproduce the observed frequency dependent rupture processes, in particular the concentration of high-frequency radiation in the down-dip part of the rupture.
In Chapter 6, I report my on going work on the spectral element method based earthquake cycle simulator. Large scale earthquake cycle simulation with consideration of complicated velocity structure and fault geometry is a great challenge for numerical modeling. I tried to push forward this boundary by extending the existing spectral element earthquake cycle simulator to enable cycle simulations on bi-material faults. This chapter includes a benchmark test in 2D that demonstrates the correctness of this new algorithm and an application of this method on bi-material fault earthquake cycle modeling.</p
Periodically Disturbed Oscillators
Get PDFBy controlling the timing of events and enabling the transmission of data over long distances, oscillators can be considered to generate the "heartbeat" of modern electronic systems. Their utility, however, is boosted significantly by their peculiar ability to synchronize to external signals that are themselves periodic in time. Although this fascinating phenomenon has been studied by scientists since the 1600s, models for describing this behavior have seen a disconnect between the rigorous, methodical approaches taken by mathematicians and the design-oriented, physically-based analyses carried out by engineers. While the analytical power of the former is often concealed by an inundation of abstract mathematical machinery, the accuracy and generality of the latter are constrained by the empirical nature of the ensuing derivations. We hope to bridge that gap here.
In this thesis, a general theory of electrical oscillators under the influence of a periodic injection is developed from first principles. Our approach leads to a fundamental yet intuitive understanding of the process by which oscillators lock to a periodic injection, as well as what happens when synchronization fails and the oscillator is instead injection pulled. By considering the autonomous and periodically time-varying nature that underlies all oscillators, we build a time-synchronous model that is valid for oscillators of any topology and periodic disturbances of any shape. A single first-order differential equation is shown to be capable of making accurate, quantitative predictions about a wide array of properties of periodically disturbed oscillators: the range of injection frequencies for which synchronization occurs, the phase difference between the injection and the oscillator under lock, stable vs. unstable modes of locking, the pull-in process toward lock, the dynamics of injection pulling, as well as phase noise in both free-running and injection-locked oscillators. The framework also naturally accommodates superharmonic injection-locked frequency division, subharmonic injection-locked frequency multiplication, and the general case of an arbitrary rational relationship between the injection and oscillation frequencies. A number of novel insights for improving the performance of systems that utilize injection locking are also elucidated. In particular, we explore how both the injection waveform and the oscillator's design can be modified to optimize the lock range. The resultant design techniques are employed in the implementation of a dual-moduli prescaler for frequency synthesis applications which features low power consumption, a wide operating range, and a small chip area.
For the commonly used inductor-capacitor (LC) oscillator, we make a simple modification to our framework that takes the oscillation amplitude into account, greatly enhancing the model's accuracy for large injections. The augmented theory uniquely captures the asymmetry of the lock range as well as the distinct characteristics exhibited by different types of LC oscillators. Existing injection locking and pulling theories in the available literature are subsumed as special cases of our model. It is important to note that even though the veracity of our theoretical predictions degrades as the size of the injection grows due to our framework's linearization with respect to the disturbance, our model's validity across a broad range of practical injection strengths are borne out by simulations and measurements on a diverse collection of integrated LC, ring, and relaxation oscillators. Lastly, we also present a phasor-based analysis of LC and ring oscillators which yields a novel perspective into how the injection current interacts with the oscillator's core nonlinearity to facilitate injection locking.</p
Modeling Rapidly Fading Supernovae as Nickel-Free Core-Collapse Explosions of Extended Helium Stars
Get PDFSupernovae are the engines of the universe, pulling material out of the furnaces of stars and spewing it out into their galaxies. As some of the most powerful explosions since the Big Bang, they influence not only the chemical but also mechanical evolution of the galaxies they inhabit. They induce star formation and produce the building blocks of planets, organisms, and ultimately, civilizations. Understanding the connections between the supernovae we observe and the stars that would have produced them is a critical piece of understanding this process.
Unfortunately, we rarely have the ability to observe the progenitor stars of supernovae directly; it is usually difficult to predict when a given star will explode, and most are in galaxies too distant to allow observation of individual stars. Instead, we typically must leverage our understanding of the explosions themselves to reveal the nature of the stars that produced them. Using analytical and numerical calculations, it is possible to predict the supernovae from certain types of stars and work backwards.
In this thesis, we present a new model for previously elusive rapidly fading supernovae, which we believe are due to the core-collapse explosions of massive stars inside extended hydrogen-free envelopes or previously ejected mass shells. This model requires not only pre-explosion stellar radii of unprecedented size for hydrogen-free stars but also a lack of radioactive nickel, which is usually present in supernovae. We show our process from simple toy models to self-consistent explosions of stellar models and compare our results to existing rapidly fading supernovae. Understanding these unusual transients will shed light on the many possible ways stars behave shortly before death and also may be critical for understanding the population of core-collapse supernovae as a whole.</p
Fluid-Structure Instability in an Internal Flow Energy Harvester
Get PDFAccess to reliable power sources in remote locations is a recurring engineering challenge for both large and small applications. The developing world struggles with power connectivity in remote villages, while sensor networks strain with power limitations of batteries or short-lived turbines. Energy harvesting based on fluid-induced vibration provides a potential robust alternative for in-situ power generation, furnishing means for a decades long supply of power. Yet, one of the main challenges in the design of flow energy harvesters is understanding the mechanisms that drive their motion. Fluid-structure interaction problems often span a large parametric space and require considerable computational resources to resolve the necessary dynamic details for reliable designs.
This thesis aims to address this challenge for a piezoelectric internal flow energy harvester developed in conjunction with NASA Jet Propulsion Laboratory for in-well, deepwater sensor and actuator systems. Through exploratory experimentation, a configuration consisting of a piezoelectric beam within a converging-diverging channel in axial flow generated considerable power at moderate flow velocities when compared to other devices of the same size. The current device, though adapted to a more robust configuration based on flextensional actuators, still maintains the same fluid-structure interaction: the instability that ensues forces the system into self-sustained oscillations that produces consistent power output for flow rates above a critical threshold.
To understand and quantify this behavior, we develop an analytical framework based on a leakage-flow type instability, which curtails the shortcomings of expensive numerical simulations once verified. The formulation consists of a quasi one-dimensional simplification of coupled fluid-structure equations, which are linearized for classical stability analysis. The stability boundary and critical property predictions are verified through a set of fully coupled fluid-structure immersed boundary direct numerical simulations. Experiments are carried out in tandem to quantify the dynamics of the harvester, specifically targeting the critical flow rate threshold. The analytical framework is expanded to include flow in the spanwise direction of the beam, and results to a simplified geometry of the harvester compared with those from experiments. Agreement between predicted critical values suggest that leakage-flow may be the principal mechanism for fluid-induced vibration within our device. The model can serve as the foundation of initial exploration of design parameters, and perhaps more powerful devices in future endeavors.</p
Silicon Neural Probes for Stimulation of Neurons and the Excitation and Detection of Proteins in the Brain
Get PDFThis thesis describes the development of a number of novel microfabricated neural probes for a variety of specific neuroscience applications. These devices rely on single mode waveguides and grating couplers constructed from silicon nitride thin films, which allows the use of planar lightwave circuits to create advanced device geometries and functions. These probes utilize array waveguide gratings to select an individual emitter from a large array of emitters using the wavelength of incoming light, allowing for spatial multiplexing of optical stimulation. These devices were tested in the laboratory and in living tissue to verify their efficacy. This technology was then modified to create steerable beam forming for stimulation of neurons using optical phase arrays. This technology was also tested for use in fluoresence lifetime imaging microscopy and the first application of pulsed light through the photonic circuits. Finally, this technology was again modified to create laminar illumination patterns for light sheet fluorescence microscopy applications. These devices were further improved by adding embedded microfluidics to the probes. The process of creating embedded microfluidic channels by the dig and seal method is described in detail, including modifications to the procedure that were added to address potential pitfalls in the fabrication process. Next, two projects which combine microfluidics with the optical devices described in the previous chapter are detailed. One project involves combining the use of optical emitters with microfluidic injections containing caged neurotransmitters to stimulate neurons is described. The other project involves microfluidic sampling of the extracellular space for neuropeptides which are detected using ring resonator biosensors. The sensitivity of these biosensors was analyzed in detail, determining both the physical limit of detection and the effect of biological noise due to non-specific binding on the sensors