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Isoprene Oxidation Mechanisms and Secondary Organic Aerosol Formation Under HO2-Dominated Conditions
Get PDFIsoprene, a volatile hydrocarbon emitted by plants, represents the single most abundant source of non-methane organic carbon to the atmosphere. After its rapid oxidation by OH radicals in the troposphere, isoprene may follow any of a number of complex reaction mechanisms to form more highly functionalized products, depending in large part on the relative abundance of reactive radicals such as HO2 and NO; some of these products can be sufficiently water-soluble, non-volatile, and/or reactive to partition into atmospheric particles and contribute to the creation of secondary organic aerosol (SOA). In this work, I explore the gas-phase oxidation mechanisms and SOA formation potential of second- and later-generation products formed in the HO2-dominated reaction cascade, which predominates in remote regions and is estimated to account for over >40% of isoprene oxidation. Pure standards of significant isoprene products, such as isoprene epoxydiols (IEPOX) and C4 dihydroxycarbonyl compounds, are synthesized, and the rates and product yields of their gas-phase reactions with OH are measured by CF3O- chemical ionization mass spectrometry in environmental chamber experiments. Results are compared to field observations from the Southern Oxidant and Aerosol Study in the Southeastern United States, where significant concentrations of these compounds were detected, and are integrated into a global chemical transport model to investigate their effects throughout the atmosphere. Further, the results from these and other gas-phase kinetic and product studies are incorporated into an explicit isoprene oxidation mechanism, designed to simulate the effects of isoprene chemistry on oxidant concentrations and to produce accurate representations of products known to be involved in condensed phase processes, including IEPOX. Finally, additional chamber experiments with synthetic IEPOX and inorganic seed aerosol are performed to derive particle uptake coefficients and examine the effects of particle pH, liquid water content, and chemical composition on IEPOX-SOA formation, using aerosol mass spectrometry and differential mobility analysis. The gas- and particle-phase reaction rates and product yields reported herein, along with the explicit model, provide important constraints on the fate of isoprene-derived carbon in the atmosphere and on the influence the HO2-dominated isoprene oxidation pathway exerts on SOA and oxidant budgets.</p
Spontaneous Pattern Formation in Photoelectrodeposited Semiconductor Films
Get PDFThe ability to manipulate matter with ever-increasing precision has enabled the fabrication of nanoscale structures with unprecedented utility. Scalable patterning technologies have dramatically transformed diverse application spaces such as computing and photonics, in part due to diminishing cost per unit area. The work in this thesis presents a template-free, bottom-up technique based on photoelectrodeposition which allows the direct fabrication of periodically nanostructured thin films of semiconductor material over large areas.
First, we examine the effects of wavelength, polarization and incidence angle of illumination on the film morphology. We develop an understanding of the pattern formation to be the result of interference of light scattered across the surface of the growing interface. We also examine the morphological effects of more complex illumination conditions. For example, when deposited under two different illumination wavelengths, the period of patterned films self-optimizes to concentrate light absorption to the tips of the nanostructures . Additionally, we find that the relative polarization angles and phases of two illumination sources can be tuned to produce film morphologies ranging from isotropic mesh-type patterns to orthogonally arranged, intersecting lamellar structures with independent periodicities.
We deepen our understanding of these observations by building a probabilistic computational model that correlates the local light absorption with a local growth probability at the interface of the film with few material parameters. We find that this model is able to reproduce experimentally observed morphological features for all illumination conditions investigated in this work. Through Fourier analysis, we find quantitative agreement between the simulated and experimental periods. Separately, we use electrodynamic simulations on idealized lamellar structures to understand the effect of two coincident illumination sources on the spatial absorption profile.</p
Constraining Substellar Magnetic Dynamos using Brown Dwarf Radio Aurorae
Get PDFBrown dwarfs share characteristics with both low-mass stars and gas giant planets, making them useful laboratories for studying physics occurring in objects throughout this low mass and temperature range. Of particular interest in this dissertation is the nature of the engine driving their magnetic fields. Fully convective magnetic dynamos can operate in low mass stars, brown dwarfs, gas giant planets, and even fluid metal cores in small rocky planets. Objects in this wide mass range are capable of hosting strong magnetic fields, which shape much of the evolution of planets and stars: strong fields can protect planetary atmospheres from evaporating, generate optical and infrared emission that masquerade as clouds in the atmospheres of other worlds, and affect planet formation mechanisms. Thus, implications from understanding convective dynamo mechanisms also extend to exoplanet habitability.
How the convective dynamos driving these fields operate remains an important open problem. While we have extensive data to inform models of magnetic dynamo mechanisms in higher mass stars like our Sun, the coolest and lowest-mass objects that probe the substellar-planetary boundary do not possess the internal structures necessary to drive solar-type dynamos. A number of models examining fully convective dynamo mechanisms have been proposed but they remain unconstrained by magnetic field measurements in the lowest end of the substellar mass and temperature space. Detections of highly circularly polarized pulsed radio emission provide our only window into magnetic field measurements for objects in the ultracool brown dwarf regime, but these detections are very rare; until this dissertation, only one attempt out of ~60 had been successful.
The work presented in this dissertation seeks to address this problem and examines radio emission from late L, T, and Y spectral type brown dwarfs spanning ~1-6 times the surface temperature of Earth and explores implications for fully convective magnetic dynamo models. </p
Slow Drive of Many-Body Localized Systems
Get PDFWe investigate a many-body localized 1d spin chain with a Hamiltonian consisting of classical disordered Ising and a small transversal field. An existing perturbative diagonalization by Imbrie is simplified and reinterpreted in order to prove the anticipated form of the Lieb-Robinson bound and the area law in an eigenstate. We also show how to approximately reduce Imbrie’s unitary to a finite depth circuit. The concept of resonances in Imbrie’s work can be given a physical meaning as an avoided crossing of levels as functions of a magnetic field. For a slow drive of this field, we discuss the proofs of validity for an efficient classical simulation of such disordered systems, both isolated and in contact with the environment. Our results are applicable to Floquet systems and describe an unexpected mechanism of heating up over long times. We also revisit noisy quantum adiabatic annealers like the D-wave machine and find a nontrivial physics that can possibly be observed in them.</p
Chemical Controls on the Dissolution Kinetics of Calcite in Seawater
Get PDFCalcium carbonate minerals are abundant on the earth’s surface. Delivery of alkalinity to the oceans is balanced by the production and burial of calcium carbonate in marine sediments, which results in a large reservoir of sedimentary calcium carbonate both in the ocean and in terrestrial rocks. Alkalinity also provides oceanic buffering capacity, which today results in about 60 times more dissolved carbon dioxide in the world oceans than is present as carbon dioxide gas in the atmosphere. Because calcium carbonate formation removes alkalinity from the oceans, calcium carbonate precipitation leads to the outgassing of carbon dioxide from the ocean into the atmosphere. Likewise, the dissolution of calcium carbonate adds alkalinity to the oceans, leading to an increased buffering capacity and a drawdown of atmospheric carbon dioxide concentration.
Calcium carbonate precipitation in the form of calcite and aragonite is almost exclusively mediated by biological organisms such as corals, coccoliths, and foraminifera, which use these minerals as components in their shells. calcium carbonate is overproduced by organisms in the ocean relative to the flux of alkalinity delivered to the oceans by rivers. Thus, a significant portion of calcium carbonate must be dissolved back into seawater for the ocean alkalinity cycle to come into steady state. Because of the link between alkalinity and carbon dioxide, the ocean alkalinity cycle has a direct effect on atmospheric carbon dioxide concentration especially on timescales less than 100,000 years.
How fast calcium carbonate dissolves back into seawater is thus a crucial rate in determining the response of the oceanic system to perturbations in either alkalinity or carbon dioxide input to the ocean-atmosphere system. We are testing the kinetics of this system with the large amount of carbon dioxide emitted from fossil fuel burning, about one third of which has dissolved into the surface ocean. This process is known as ocean acidification, as carbon dioxide is an acid, soaking up buffering capacity and dropping ocean pH. This carbon dioxide will eventually be neutralized through the dissolution of carbonate rich deep-sea sediments, but the process will take a long time. This thesis makes new measurements calcite dissolution in seawater, in an attempt to build an understanding of the chemical processes responsible for dissolution kinetics.
I first introduce the new method, in which carbon-13 labeled calcium carbonate is dissolved in undersaturated seawater. Mass loss is directly traced by measuring the appearance of carbon-13 in seawater over time. The dissolution rate of calcite is a highly nonlinear function of calcite saturation state.
Next, I show that this tracer can tell us about the balance of precipitation and dissolution at the mineral surface. I use this balance to constrain mass fluxes due to precipitation and dissolution as a function of saturation state. I also show that the enzyme Carbonic Anhydrase (CA), which rapidly equilibrates carbon dioxide and carbonic acid, greatly enhances the rate of calcite dissolution especially near equilibrium. A model of dissolution is presented in which CA is most effective in the region where dissolution proceeds via etch pit nucleation at surface defects.
The dissolution behavior of biogenic carbonates is also investigated using the carbon-13 method. I cultured coccoliths, foraminifera, and soft corals in carbon-13-labeled seawater so that their skeletons incorporated the carbon-13 tracer. These skeletons were then used in dissolution experiments. I show that both magnesium and organic matter contained within the calcite lattice have large effects on the dissolution behavior of biogenic carbonates. Magnesium content generally increases dissolution rate, and it is hypothesized that highly soluble magnesium-rich phases are preferentially removed from dissolving carbonates. Organic content generally decreases dissolution rate. It is hypothesized that organic matrices within the calcite lattice promote re-precipitation reactions, due to the balance of dissolution and precipitation rates in our data, and their promotion of precipitation during biomineralization.
I then analyze in 2- and 3-dimensions dissolved foraminiferal tests to locate where and how mass is being lost. It is shown that dissolution proceeds along specific layers, that are consistent with the size and location of Mg-rich carbonate spherules that are initially deposited during chamber formation. Surface topography generation of foraminiferal tests shows that sub-micron features are formed rapidly and then quickly eroded into larger pits and channels. These larger channels then propagate and cover the test surface at higher amounts of mass loss.
Finally, the involvement of CA in carbonate dissolution necessitates the measurement of CA activity in the environment, especially in carbonate-rich ecosystems such as reefs, carbonate-rich sediments, and carbonate-rich marine particles. To this end, I survey a number of available techniques for measuring CA activity. In the end, it is shown that the most effective method is based on measuring the depletion of oxygen-18 from carbon-13- and oxygen-18-labeled DIC, as measured by membrane inlet mass spectrometry (MIMS). This method is promising and shows about 0.1 nM CA present in unfiltered surface seawater collected from San Pedro Basin.</p
Optimal Design of Materials for Energy Conversion
Get PDFThe efficiency of fuel cells, batteries and thermochemical energy conversion devices depends on inherent material characteristics that govern the complex chemistry and transport of multiple species as well as the spatial arrangement of the various materials. Therefore, optimization of the spatial arrangement is a recurrent theme in energy conversion devices. Traditional methods of synthesis offer limited control of the microstructure and there has been much work in advanced imaging for these uncontrolled microstructures and optimizing gross features. However, the growing ability for directed synthesis allows us to ask the question of what microgeometries are optimal for particular applications. Through this work, we study problems motivated by metal oxides used in solar-driven thermochemical conversion devices designed to split water or carbon dioxide into fuels. We seek to understand the arrangement of the solid and porous regions to maximize the transport given sources and sinks for the gaseous oxygen and vacancies. Three related problems are investigated with the common theme of understanding the role of microstructure design.
We derive the transport equations for electrons and oxygen vacancies through ceria under an externally-applied electric potential in an oxygen environment using various balance laws and constitutive equations. From this, we obtain various thermodynamic potentials that take into consideration the thermal, chemical, and mechanical state of the material. Accordingly, we obtain a system of partial differential equations describing ambipolar diffusion. We present the applicability of strain-engineering as a way to design systems to improve the behavior of thermochemical conversion devices. We look at an idealized thin film of mixed conductor attached to an inert substrate with a thermal mismatch as a way to induce strain into the film. The resulting impact on equilibrium non-stoichiometry is analyzed using data describing non-stoichiometry in ceria as a function of oxygen pressure and temperature.
The optimal design of material microstructure for thermochemical conversion is addressed from two standpoints: the mathematical homogenization of associated transport models, and from topology optimization. We present the homogenization of coupled transport through porous media consisting of linearized Stokes flow, convective diffusion, and diffusion in the solid phase with interface reaction. Depending on the strength of the interface chemistry, different forms of effective behavior are described at the macroscale, and we gain insight into the impact cell-design and pore shape has on the behavior.
The topology optimization of a model energy-conversion reactor is then presented. We express the problem of optimal design of the material arrangement as a saddle point problem and obtain an effective functional which shows that regions with very fine phase mixtures of the material arise naturally. To explore this further, we introduce a phase-field formulation of the optimal design problem, and numerically study selected examples. We find that zig-zag interfaces develop to balance mass transport and interface exchange. </p
Controlling Deformability in Metallic Glass Nanopillars and Nanolattices
Get PDFMetallic glasses offer desirable mechanical properties, including high strength, hardness, and elasticity. In bulk, they suffer from catastrophic failure upon mechanical loads. However, ductility may emerge upon (1) reducing the characteristic dimension of the metallic glass to the nanoscale or (2) irradiating the metallic glass. These two methods of controlling metallic glass deformability are investigated through a host of mechanical experiments on metallic glass nanopillars and nanolattices before and after irradiation. The mechanical experiments are conducted inside a scanning electron microscope to allow simultaneous mechanical loading and visualization of nanoscale deformation behavior.
Such experiments reveal that helium irradiation of electrodeposited Ni73P27 metallic glass tensile nanopillars increases plasticity by a factor of two with no sacrifice in strength. Other tensile experiments on Zr-Ni-Al metallic glass nanopillars in as-sputtered and annealed states reveal substantial ductility, highly dependent upon both the nanopillar size and processing conditions. Molecular dynamics simulations, transmission electron microscopy, and synchrotron x-ray diffraction are used to explain the observed mechanical behavior through changes in free volume and short-range order.
Larger nanolattice structures are fabricated to contain hollow beams of metallic glass, with beam wall thicknesses in the nanoscale size range that may allow proliferation of the beneficial “smaller is more ductile” size effect observed in metallic glass nanopillars. Compression experiments on Zr-Ni-Al metallic glass nanolattices reveal enhanced deformability as the nanolattice wall thickness is reduced and upon irradiation. This work points to metallic glass nanolattices as promising candidates for radiation-intensive applications and demonstrates that by fabricating the metallic glass in a nanolattice architecture the beneficial nanoscale size effect in deformability can be preserved.</p
Experiments on Gas Phase Chemistry with High Sensitivity Laser Spectroscopy
Get PDFGas phase chemistry is important to many environments on Earth and beyond. The Earth’s atmosphere is dominated by free radical reactions that, when perturbed by pollution, can lead to serious environmental problems like stratospheric ozone depletion and urban smog. Outside Earth, many other planetary atmospheres are affected by gas phase, radical chemistry, including the atmosphere of Saturn’s Moon Titan. Gas phase chemistry in interstellar clouds can synthesize the molecular building blocks of our universe. Studying gas phase chemistry has also led to basic chemical knowledge of how chemical reactions proceed and how intermolecular forces work.
This work is dedicated to studying gas phase chemical reactions with high-sensitivity laser spectroscopy. Laser spectroscopy can be a sensitive and selective way to detect gas phase species. Since laser pulses can both create reactants and detect the products, laser techniques allow the study of chemical kinetics in real time. Consequently, many different laser techniques have been developed to study gas phase chemistry. This thesis is divided into two sections: a longer first section on my work at the California Institute of Technology in Pasadena, CA and a smaller second section based on my work at the Université de Rennes 1 in Rennes, France. These two sections, while on different topics – atmospheric chemical reactions and collisional rotational energy transfer at ultra-low temperatures – are united by their study of gas phase with laser spectroscopy, which shows the breadth of this experimental approach. This thesis will both look at kinetics (the rate of chemical reactions) and product yield of chemical reactions, both key pieces of information to modeling gas phase reactions.
The first part of this work outlines my work at the California Institute of Technology, studying atmospheric radical chemistry with cavity-ringdown spectroscopy (CRDS). Chapter 1 put this work in a broader picture of current scientific work on Earth’s atmosphere. Chapter 2 provides a detailed description of our cavity-ringdown spectrometer and temperature-controlled flow cell. Next, I discuss work on three important atmospheric reactions: the isomerization of simple alkoxy radicals (Chapter 3), the reaction of HO₂ with NO (Chapter 4), and the reaction of OH with NO2 (Chapter 5).
The second, and smaller, part of this work, contains one chapter – chapter 6 – on work done at the Université de Rennes 1, which describes work on the rotational energy transfer in collisions between CO and Ar at temperatures from 293 to 30 K with infrared-vacuum ultraviolet double resonance CRESU experiments. </p
Discovery and Development of Small-Molecule Modulators for the Sulfation of Glycosaminoglycans and Studying the Role of O-GlcNAc on CREB through Semisynthesis
Get PDFGlycosaminoglycans (GAGs) are sulfated polysaccharides that play key roles in many cellular processes, ranging from viral invasion and cancer metastasis to neuronal development. Their diverse biological activities stem from their complex sulfation patterns, which are tightly regulated in vivo. For instance, the GAG chondroitin sulfate (CS) has been shown to undergo regiochemical sulfation during development and after spinal cord injury. However, few tools exist to modulate specific GAG sulfation patterns and study their importance in different biological contexts. Here, we identified the first cell-permeable small molecule that can selectively inhibit GAG sulfotransferases and modify the fine structure of GAGs. We demonstrate that the inhibitor reduces GAG sulfation in vitro and in cells and reverses CS-E-mediated inhibition of neuronal outgrowth. This small molecule may serve as a useful lead compound or chemical tool for studying the importance of CS and other GAGs in normal biology and disease.
The β-N-acetyl-D-glucosamine (O-GlcNAc) post-translational modification plays a major role in many diseases such as cancer, diabetes, and neurodegenerative disorders, but much is still unknown about its molecular-level influence on protein structure and function. Although post-translational modifications have been known to induce important structural changes in proteins, notably, no structures of O-GlcNAcylated proteins exist. The challenge of obtaining homogeneous glycoproteins bearing the GlcNAc sugar at defined sites has hindered the structural and biochemical studies of this modification. Here we have utilized a semisynthetic approach to generate a homogeneously O-GlcNAcylated form of cyclic-AMP response element binding protein (CREB) for structural and functional studies.</p
Terahertz and Microwave Spectroscopy of Liquids and Hydrogen-Bonded Clusters
Get PDFThe microwave (MW, 0.3-100 GHz) and terahertz (THz, 0.1-10 THz) regions of the electromagnetic spectrum are replete with a rich set of molecular motions, including soft inter- and intramolecular vibrations, torsions, and rotations. At room temperature these motions are well populated, and play an active role in condensed-phase chemistry on Earth. This work details the development of one MW and two THz spectrometers along with their application to the study of liquids and hydrogen-bonded clusters.
In the first section, we cover the design and construction of a chirped pulse Fourier transform microwave (CP-FTMW) spectrometer. The instrument relies on a compact, inexpensive direct digital synthesis board to generate 2 GHz, 1 microsecond chirped pulses that, after amplification, polarize the rotational states of gas-phase molecules in a pulsed supersonic jet. In an initial demonstration, the CP-FTMW instrument is used to collect the 8-18 GHz rotational spectra of the ethanol-water and ethanol-methanol dimers. These data reveal evidence of quantum tunneling, and a complicated interplay between weak and strong hydrogen-bonds in both dimers.
Next, we describe the ongoing development of a decade spanning high precision THz frequency comb, using THz time-domain spectroscopy. The instrument is capable of generating ~28000 comb teeth from 0.15-2.4 THz with a fractional precision of 1.8x10-9 and a Doppler-limited accuracy of 6.1x10-8. Further prospects for studies of intermolecular interactions in jet-cooled molecular clusters are also discussed.
In the last section, we move to condensed-phase studies of THz orientational and vibrational motions of liquids. The liquids are excited with one or two intense time-delayed ultrafast THz pulses and probed with a non-resonant 40 fs Raman pulse. Initially, we use this approach to measure the picosecond molecular orientational alignment and decay timescales in several aromatic liquids. By adding a second THz pulse to the experiment and adjusting the delays between the three pulses, we control the orientational alignment of the molecules, and acquire phase-coherent 2D-THz-THz-Raman spectra in the time domain. The 2D responses of liquid CHBr3, CCl4, and CCl2Br2 show off-diagonal peaks from coupling between thermally-populated vibrational modes. In an extended bandwidth measurement, we observe photon-echo signals from liquid CHBr3 and a complicated pattern of dipole forbidden transitions. The molecular origins of the forbidden transitions are still under investigation, but are likely due to nonlinearities in the condensed-phase dipole moment surface. Coherence transfer, vibrational anharmonicity, and intermolecular coupling are also considered in this analysis.</p