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Development of Methods to Study Secondary Organic Aerosol
Get PDFSecondary organic aerosol (SOA) in the atmosphere contributes significantly to air pollution and has profound impacts on regional and global climate change, as well as human health. SOA, as opposed to directly emitted particles, refers to those particles formed from oxidation of gas-phase compounds followed by nucleation and/or gas-particle partitioning, as well as those modified by gas-phase oxidants (e.g., O3, OH radical, and NO3 radical) through heterogeneous reactions within their lifetime in the atmosphere. Investigations of SOA formation in the laboratory have been carried out in batch reactors (e.g., environmental smog chambers) and continuous flow reactors (e.g., oxidation flow reactors). Compared with the real atmosphere, the reactors in the laboratory have boundaries and defined residence times under different operation conditions. To better constrain the experimental results and derive reliable parameters for aerosol models (e.g., yields of volatile organic compounds), a full understanding of the role of the reactors on the gas-phase components and suspended particles is needed.
In this thesis research, a number of studies were carried out to understand the role of the reactor itself on the behavior of SOA-forming systems. This includes the effect of the Teflon-walled Caltech Environmental Chamber on vapor molecules and characterization of the newly-built Caltech PhotoOxidation Flow Tube reactor (CPOT) for atmospheric chemistry studies.
Vapor-wall interactions in Teflon-walled environmental chambers have been studied; however, conflicting results existed in the literature concerning the basic timescales of vapor-wall loss in environmental chambers. The competition between vapor-particle and vapor-wall interactions determines the fate of vapor molecules in the reactor. A unified theory and empirical equations have been developed in this thesis to explain the observed vapor-wall interaction timescales. About 100 compounds have been studied to verify this theory. In characterizing the flow reactor performance, computational fluid dynamics (CFD) simulations have been combined with residence time distribution (RTD) experiments, revealing, among others, the importance of the inlet design of the reactor and the effect of temperature gradients on radial mixing in the reactor. An axial-dispersed plug flow reactor (AD-PFR) model framework was developed as a basis on which to simulate photochemistry occurring in the CPOT. An analytical solution for the cumulative RTD, which uses data during the transition period to a steady state, can be applied to diagnose the dispersion condition inside the flow rector.
Since SOA formation involves interactions among gas-phase molecules, particle surfaces, and particle bulk phases, a state-of-the-art experimental technique (field-induced droplet ionization mass spectrometry, FIDI-MS) and a comprehensive model coupling gas-surface-aqueous multiphase transport and chemical reactions have been applied to investigate the gas-phase OH-initiated oxidation of pinonic acid (PA) at the air-water interface. The interfacial oxidation mechanism has been found to differ from that of homogeneous reactions, and the kinetics depend on both OH diffusion from gas-phase to the interface and aqueous-phase reaction of pinonic acid + OH. The model calculation shows that, under typical ambient OH levels, PA is oxidized exclusively at the air-water interface of droplets with a diameter of 5 µm, demonstrating the critical importance of air-water interfacial chemistry in determining the fate of surface-active species.</p
Black Hole Simulations: From Supercomputers to Your Laptop
Get PDFIn this thesis, I will present various advancements in the modeling of binary black holes (BBHs): two black holes (BHs) that are in orbit around each other. The BHs lose energy to gravitational waves, causing them to spiral towards each other until they eventually merge and leave behind a single BH. BBHs are primary sources for ground based detectors such as the Laser Interferometer Gravitational-Wave Observatory (LIGO).
As the BHs are about to merge, they are moving at about half the speed of light and the spacetime is highly dynamical. All analytical methods break down at this stage, and numerical relativity (NR) simulations of the full Einstein’s equations are necessary. These simulations, however, are very expensive, with each simulation taking a month on a supercomputer. For direct data analysis applications with LIGO, we need a model that can be evaluated in a fraction of a second. Therefore, several approximate but fast models that are calibrated to NR simulations have been developed over the years.
Surrogate modeling provides a more powerful alternative: trained directly against the NR simulations without added assumptions, these models can reproduce the simulations as accurately as the simulations themselves, while taking only a fraction of a second to evaluate on a laptop. In short, surrogate models take BBH NR simulations from supercomputers to your laptop, without a loss of accuracy.
In this thesis, I will present several state-of-the-art surrogate models including (i) the first NR based surrogate model to span the full range of frequencies for ground based detectors, (ii) the first surrogate model for the mass, spin, and kick velocity of the final black hole after merger, and (iii) extension of an existing precessing surrogate model to higher mass ratios. In addition, I will present some work in improving the BBH initial data used in NR simulations, as well as in understanding the systematic biases introduced by approximate waveform models in LIGO data analysis.
As we head into the imminent era of high-precision gravitational wave astronomy, accurate yet fast models such as surrogate models will play a crucial role in maximizing the science output of our detectors.</p
Searching for the Cosmic Dawn with the Hyperfine Structure Transition of Hydrogen
Get PDFThe 21 cm hyperfine structure transition of neutral hydrogen promises to open a window into the first billion years of the Universe (z > 6). With the exception of rare lines of sight towards exceptionally distant and luminous galaxies, this period of the universe's history remains largely unexplored. During this time the 21 cm transition is expected to be detectable as a 10--100 mK perturbation in the thermal Cosmic Microwave Background (CMB) spectrum.
Due to the large field of view of low frequency radio telescopes (typically composed of dipole antennas) and the fact that the line of sight distance can be inferred from the measured frequency of the transition, the ultimate goal of 21 cm cosmology is to produce three dimensional tomographic maps of the 21 cm brightness temperature. In this way, the formation of the first stars and galaxies will be revealed through their influence on the neutral gas around them.
This thesis saw the construction of the Owens Valley Radio Observatory Long Wavelength Array (OVRO-LWA), a new low frequency (27--85 MHz) radio telescope located near Bishop, California. Composed of 288 crossed-dipole antennas, the OVRO-LWA is capable of imaging the entire visible hemisphere in a single 13 s snapshot image with 8 arcmin angular resolution.
The primary challenges faced by efforts to detect the highly redshifted 21 cm transition are seeing past the blinding glow of foreground radio emission that is five orders of magnitude brighter than the cosmological emission, and calibrating the instrument to a level where it's possible to make the separation between foreground emission and the 21 cm signal. In this thesis I will present foundational work using the OVRO-LWA to place upper limits on spatial fluctuations of the 21 cm transition during the Cosmic Dawn---the period of first star formation.
In this thesis I present the highest angular resolution maps of the full sky below 100 MHz, and generated with a new widefield imaging technique that is specialized for drift scanning interferometers. These sky maps are a 10-fold improvement in angular resolution over existing maps at comparable frequencies, and are publicly available now for use in modeling and subtracting the contamination of foreground emission in 21 cm experiments.
Using a 28 hr integration with the OVRO-LWA, I place to-date the most constraining upper limits on the amplitude of the 21 cm spatial power spectrum at the Cosmic Dawn, and the first limits at z > 18. Although the current constraints Δ212 ≲ (104mK)2 do not meaningfully restrict the parameter space of models of early star formation, they do inform the design and calibrations necessary for future measurements to push towards a detection of the high-redshift 21 cm transition. In making this measurement I demonstrate the application of a new foreground filter that accounts for the full covariance of the foreground emission, and provide an updated measurement of the foreground angular covariance. Finally, I interpret the limiting factors in this measurement and determine the instrumental calibration and characterization requirements the OVRO-LWA will need to achieve in order to make a detection of the 21 cm power spectrum of the Cosmic Dawn.</p
Essays on Economics of Groundwater Resource Management
Get PDFThis thesis examines groundwater management regimes in California and discusses how to implement an optimal aquifer management scheme.
Chapter 2 examines the effectiveness of adjudication, a legal settlement among groundwater pumpers, in managing groundwater basins in Southern California. As a form of self-governance, adjudication generally leads to higher water level in the adjudicated basins than the unregulated ones. However, its rigid rules impair dynamic efficiency. Compared with the competitive pumpers, pumpers in the adjudicated basins actually have a less counter-cyclical extraction pattern in response to surface water availability.
Chapter 3 examines how surface water trading intensifies groundwater depletion in California's Central Valley. A surface water market only mitigates the groundwater over-extraction problem when pumping costs are very high, while market failure arises when the pumping costs are low. I build an agricultural water use model to connect the efficacy of the surface water market with crop patterns response to surface water supply variation. The data suggest that the Central Valley is in a low pumping cost regime where the farmers pump groundwater to replace whatever surface water they sell. Therefore, the surface water trade is inefficient because it depletes groundwater resources and should be curtailed until the commons problem is addressed.
Chapter 4 studies optimal groundwater aquifer management. I solve the dynamic optimization problem for groundwater extraction by a social planner when when farmers are heterogeneous and the surface water supply is uncertain. To implement the optimal pumping plan, the farmers must be allocated pumping rights each period equal to the socially optimal extraction. An incentive compatibility issue arises if farmers have heterogeneous access to groundwater. Those who overlie the deepest part of the aquifer might delay regulation because they will get more water as others exit. A larger amount of farmers must be included in the decision set to resolve this political conflict.</p
Metabolic Bi-Stability and Hysteresis in a Model Microbiome Community
Get PDFChanges in the species composition of the human microbiome are associated with a broad range of diseases, but elucidating causal mechanisms has been challenging. Some microbiome disease states persist in seemingly unfavorable conditions, e.g., the proliferation of aerobe–anaerobe communities in oxygen-exposed environments in wounds or small intestinal bacterial overgrowth. In Chapter I, using two microbes relevant to the human microbiome, we combine genome-scale mathematical modeling, bioreactor experiments, transcriptomics, and control theory to show that multi-stability and hysteresis (MSH) is a mechanism that can describe shifts to a resilient aerobe–anaerobe community. We examine the impact of changing oxygen and nutrient regimes and identify factors, including changes in metabolism and gene expression, that lead to MSH. Where MSH explains microbiome shifts, it can profoundly improve our conceptual understanding of these paradoxically persistent disease states, and thereby facilitate effective interventions.
Chapter II details a method for rapidly detecting the susceptibility and resistance of Neisseria gonorrhoeae to the antibiotic ciprofloxacin. Antimicrobial-resistant Neisseria gonorrhoeae is an urgent public-health threat, with continued worldwide incidents of infection and rising resistance to antimicrobials. Traditional culture-based methods for antibiotic susceptibility testing are unacceptably slow (1–2 days), resulting in the use of broad-spectrum antibiotics and the further development and spread of resistance. Critically needed is a rapid antibiotic susceptibility test (AST) that can guide treatment at the point-of-care. In our approach, we explore the use of RNA signatures, which are among the first cellular responses to drug exposure, as an indicator of antibiotic susceptibility. Using RNA sequencing, we identified antibiotic-responsive transcripts. Significant shifts (>4-fold change) in transcript levels occurred within 5 minutes of antibiotic exposure. We designed assays for responsive transcripts with the highest abundances and fold changes, and validated gene expression using digital PCR. Using the top two markers (porB and rpmB), we correctly determined the antibiotic susceptibility and resistance of 49 clinical isolates after 10-min exposure to ciprofloxacin. RNA signatures are therefore promising as an approach on which to build rapid AST devices for N. gonorrhoeae at the point-of-care, which is critical for disease management, surveillance, and antibiotic stewardship efforts.</p
Chemical Tools for Protein Imaging in Live Bacterial Cells
Get PDFBacteria spatially and temporally localize their proteins to carry out fundamental cellular processes. Methods for visualizing protein subcellular localization have been critical to our understanding of prokaryotic cell biology. Fluorescent reporters have been instrumental for imaging bacterial proteins in live cells. Small-molecule fluorescent dyes, which have favorable spectral properties, including high brightness and photostability, are attractive in labeling proteins of interest. Here we present a method to site-specifically label the N-termini of bacterial protein targets in situ for fluorescence imaging in bacterial cells. The method uses the eukaryotic enzyme N-myristoyltransferase to ligate target proteins, bearing a nonapeptide recognition sequence, with an azide-bearing fatty acid. Subsequent strain-promoted azide–alkyne cycloaddition with fluorophores enable tagging of chemotaxis and cell division proteins in live cells. We describe using a reactive BODIPY fluorophore for visualization of the chemotaxis proteins Tar and CheA and the division proteins FtsZ and FtsA. Next we integrate a single copy of the gene encoding the protein target into the chromosome via Tn7 transposon mutagenesis and use the method to fluorescently label a bacterial chemoreceptor. Finally, we describe the preparation of photoswitchable rhodamine spirolactam dyes for super-resolution imaging in live bacterial cells. Our work highlights the utility of using photoswitchable molecules to label intracellular protein targets. The ability to tag proteins, perform super-resolution imaging, and visualize proteins in space and time will prove broadly useful
Adaptive and Reconfigurable Architected Materials Driven by Electrochemistry
Get PDFArchitected materials are a new class of engineered materials with carefully controlled internal structures that give rise to properties that differ from or surpass those of their constituent materials. Recent advances in additive manufacturing provide an extraordinary opportunity to rationally design the structure and the chemical composition of architected materials across multiple length scales to optimize properties and functionalities for a variety of applications. These functional architected materials are capable of decoupling critical trade-offs, such as strength vs. density, to reach new regions of the material property space, and enabling exotic properties that rarely exist in classical materials such as negative refraction and negative thermal expansion.
This thesis probes into the dynamic behaviors of architected materials undergoing electrochemical reactions and aims to provide an in-depth understanding of the underlying mechanisms as well as design principles generalizable for other functional architected material systems. We developed novel fabrication methods based on two-photon lithography and various physical and chemical post-processing techniques to create architected materials with multi-level design freedom including feature sizes, structural geometries, and material compositions, which resonates with the multi-faceted challenges in electrochemical systems. We demonstrated that architected materials provide a new platform to design battery electrodes that could accommodate the large volumetric changes associated with conversion-based electrode materials, while decoupling the longstanding trade-off between active material loading and transport kinetics in batteries. Furthermore, we presented a new class of electrochemically reconfigurable architected materials that could transform their structures in a programmable, reversible and non-volatile fashion, which provide new vistas for designing mechanical metamaterials with tunable phononic bandgaps and deployable micro-devices for biomedical applications.
The multi-scale and multi-physics nature of these electrochemically driven architected materials prompted us to develop a toolset of (1) in situ SEM and optical microscopy to visualize the dynamic responses, (2) coupled chemo-mechanical finite element analysis to reconstruct detailed mechanical evolution as electrochemical reactions proceed, and (3) a statistical mechanics framework to capture the transient interactions between coupled mechanical instabilities. Using these tools, we investigated lithiation-induced cooperative beam buckling in tetragonal Si microlattices: from the deformation mechanisms of individual beams and the cooperative coupling between buckling directions of neighboring beams to the lithiation rate-dependent distribution of ordered buckling domains separated by distorted domain boundaries. Results indicate that local defects and stochastic energy fluctuations play a critical role in the dynamic response of architected materials in a way analogous to that during phase transformations of classical materials. These connections have profound implications on how we could understand and design architected materials by drawing inspiration from established theories in materials science.</p
Plasma Surface Interactions in LaB₆ Hollow Cathodes with Internal Xe Gas Discharge
Get PDFThe ultimate goals of space vehicles are to move faster, further, and more reliably in the space environment. Electric propulsion (EP) has proven to be a necessary technology in the exploration of our solar system ever since its working principle was empirically tested in space in 1964. Thanks to the high exhaust velocities of ionized propellant gases, EP enables efficient utilization of the limited supply of propellant aboard spacecrafts. This technology has opened the possibility of long distance autonomous space missions.
EP devices require electron sources to ionize the propellant gas and to neutralize charges that are leaving the spacecraft. In modern EP thrusters, this is achieved by the use of hollow cathodes -- complex devices that employ low work function materials to emit electrons. Hollow cathodes using polycrystalline LaB6 inserts are attractive candidates for long duration EP based space missions. However, the physics behind LaB6 hollow cathode operation has not been studied in detail, which limits the possibility of their optimization. This work presents an integrated experimental and computational approach to investigate LaB6 hollow cathode thermal behaviour and the interplay between LaB6 insert surface chemistry and xenon plasma.
Our investigation of the thermal behaviour of LaB6 cathodes led to the unexpected discovery of a thermal transient when a new insert is first used. Specifically, we observed that the cathode temperature decreases by approximately 300 degrees over 50 hours before reaching steady state. This finding suggests a beneficial dynamic evolution of the cathode's chemical state when it interacts with its own plasma. This evolution is intrinsic to cathode operation and can only be precisely understood when the multiphysic nature of the cathode is self-consistently simulated. Thus, we built a numerical platform capable of combining the plasma, thermal and chemical behavior of a discharging hollow cathode. Simulations incorporating different neutralization models, inelastic ion-surface interaction and heterogeneous chemical evolution led to two major conclusions. First, simulations predicted a significant reduction of the LaB6 work function (0.42~eV) compared to previously reported baseline values, which is of paramount importance for EP thruster efficiency and operational lifetimes. Second, simulations suggested that the interaction between xenon low energy ions (< 50 eV) and the LaB6 surface occurs following a two step neutralization mechanism. The predicted work function reduction was experimentally confirmed by photoemission spectroscopy. Furthermore, using a combination of crystallographic analysis, scanning electron microscopy and profilometry, we demonstrated that work function reduction is caused by the creation of a crystallographic texture at the LaB6 surface upon interaction with Xe plasma. In addition, we postulated the existence of a work function enhancing mechanism of secondary importance, which can be explained by forced cationic termination of plasma exposed crystals.
Our results revealed the unexpected phenomenon of work function reduction upon plasma exposure of LaB6. These findings suggest that LaB6 hollow cathodes may outperform current technologies and become the component of choice in EP thrusters for future space missions.</p
Remotely Sensing Aqueous Alteration on Mars: Innovative Statistical and Analytical Methods for Large Spectral Datasets
Get PDFLiquid water once flowed on Mars and altered the crust. Aqueous minerals and salts record a rich history of aqueous processes and environmental changes. In this dissertation, I developed and applied innovative analytical and statistical methods to large spectral datasets to better characterize aqueous alteration on Mars. The Mars Science Laboratory (MSL) Curiosity rover is investigating the sedimentary sequence at Gale crater recording a potentially global transition from clay-enriched to sulfate-enriched rocks. Volatile elements like H and Cl are important for investigating aqueous processes but are difficult to quantify in the large ChemCam laser-induced breakdown spectroscopy (LIBS) dataset. In the first part of this dissertation, I measured aqueously altered samples with LIBS in the laboratory under Mars-relevant conditions to develop analytical methods for application to ChemCam. The Murray formation, the lowest exposed strata of the sedimentary sequence, contains 2.6 ± 2.1 wt. % H2O. Carriers of H enrichment including clays, opal, Mg-sulfates, Ca-sulfates, hydrous Mn-oxides, akageneite, and jarosite are identified. Variability in the H content of the Murray formation records multiple aqueous alteration events as well as potential increases in salinity in the Gale crater lake. In the fourth chapter, I measured chlorine in Gale crater using multiple MSL instruments. Cl-enrichments correlated with increased Na2O are detected in the bedrock, in nodular textures, and at vein margins, indicating halite. The scattered, isolated occurrences of chlorides are consistent with late groundwater reworking and remobilization. Halite is concentrated in particular members of the Murray formation; the chlorides may have been emplaced as primary deposits in these members, consistent with varying salinity in the past lakewaters. In the second part of this dissertation, I adapted and applied semi-automated statistical methods called factor analysis and target transformation to the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) dataset to systematically search for hematite in stratified, candidate sedimentary outcrops. Few outcrops containing hematite are found and no obvious analogs to terrestrial iron formations are identified. Future studies will search for hematite in other geologic settings as well as other Fe-bearing phases such as Fe-phyllosilicates and Fe-sulfates to better characterize aqueous processes on Mars
Activation of Nitric Oxide and Water by Transition Metal Clusters Relevant to Active Sites in Biology
Get PDFThis dissertation discusses the synthesis, characterization, and reactivity of site-differentiated tetranuclear clusters containing Fe and Mn with NO and H2O-derived ligands. The motivation of this work was to conduct a detailed examination of structure-property relationships in well-defined molecular systems focused on unique features of multinuclear systems, such as bridging ligands, neighboring metal identity, and cluster oxidation state. Reactivity towards NO and H2O-derived ligands was targeted due to their relevance to biological multinuclear transition metal active sites that promote multi-electron small molecule transformations.
Chapter 2 discusses the synthesis of Fe-nitrosyl clusters bearing an interstitial μ4-F atom. These clusters were prepared to compare their reactivity to previously synthesized [Fe33OFeNO] clusters with an analogous structure. A redox series of the [Fe3FFe] and [Fe3FFeNO] clusters were accessed, with the nitrosyl clusters displaying five cluster oxidation states, from FeII3{FeNO}8 to FeIII3{FeNO}7. Overall, the weaker bonding of the F- ligand resulted in attenuation of the activation and reactivity of the {FeNO}7, relative to the corresponding μ4-O clusters. Furthermore, the ability of distal Fe oxidation state changes to influence the activation of NO was decreased, demonstrating lower cooperativity between metals in clusters linked by a weaker μ4-atom This represents a rare case where the effects of bridging atom ligands could be compared in isostructural multinuclear complexes and decoupled from changes in metal ion coordination number, oxidation states, or geometry.
Chapter 3 describes the synthesis of site-differentiated heterometallic clusters of [Fe3OMn], displaying facile ligand substitution at the five-coordinate Mn. This system was able to coordinate H2O and thermodynamic parameters of the proton and electron transfer processes from the MnII–OH2 to form a MnIII–OH moiety were studied. The oxidation state distribution of the neighboring Fe centers had a significant influence on these thermodynamic parameters, which was similar to the analogous parameters for mononuclear Mn systems, demonstrating that oxidation state changes in neighboring metals of a cluster can perturb the reactivity of a Mn–OHx unit nearly as much as an oxidation state change at the Mn–OHx. Subsequent experiments attempted to find spectroscopic or electrochemical evidence for formation of a terminal Mn-oxo in this system; however, that was not obtained, even in relatively extreme conditions. This established a lower limit for the bond dissociation enthalpy of the MnIII–OH of ca. 93 kcal/mol, which makes formation of a terminal Mn-oxo cluster unfavorable in most organic solvents, due to expected facile hydrogen atom abstraction of a solvent C–H bond.
The insights obtained on the reactivity of these tetranuclear metal-hydroxide clusters was applied towards stabilizing a terminal metal-oxo in a multinuclear complex, as outlined in Chapter 4. Through the use of pendant hydrogen bond donors with tert-butyl-aminopyrazolate ligands, tetranuclear Fe clusters bearing terminal-hydroxide and -oxo ligands could be stabilized and structurally characterized. A similar thermodynamic analysis of the FeIII–OH bond dissociation enthalpy was conducted, which demonstrated FeIII-oxo clusters could be accessed with a range of reactivity at the terminal-oxo ligand, based on the redox distribution of the neighboring Fe centers. The kinetics of C–H activation for the [FeII2FeIII2]-oxo cluster redox state were analyzed, demonstrating a strong dependence of the C–H bond pKa on the rate of proton coupled electron transfer.
Lastly, Chapter 5 describes the synthesis and reactivity of tetranuclear Fe clusters bearing unsubstituted pyrazolate ligands, focusing on attempts to observe evidence for a terminal Fe-oxo or Fe-imido motif. Clusters bearing a labile trifluoromethanesulfonate ligand at the five-coordinate Fe center could be prepared, and would react with oxygen atom transfer reagents to produce a terminal Fe-hydroxide cluster, which, upon dehydration, led to isolation of an octanuclear μ2-O cluster. The pathway for Fe-hydroxide formation was investigated, but could not conclusively determine whether reactivity occurred from a transient terminal Fe-oxo. Similarly, the reduced tetra-iron cluster, in the [FeII3FeIII], redox state was prepared, and demonstrated reactivity towards electron deficient aryl azides. Isolation of aryl amide clusters (Fe-NHAr) was observed, suggesting, again, formation of a reactive Fe-imido which decomposes through formal hydrogen atom abstraction. Efforts to stabilize either of these Fe=O/NR multiply-bonded species through a more acidic Fe were investigated by synthesizing the corresponding pyrazolate bridged μ4-F clusters. The [FeII4] cluster also displayed reactivity towards oxygen atom transfer reagents, and produced a similar octanuclear μ2-O cluster, but the observation of μ4-F substitution with oxygen to produce μ4-O clusters with a terminal F ligand likely precluded formation of a reactive terminal-oxo cluster. Instead, thermodynamically favorable cluster rearrangement to the [Fe3OFe] structure dominates.</p