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Accounting for Aerosol Scattering in the Remote Sensing of Greenhouse Gas
Get PDFThis thesis includes three different projects related to the remote sensing of Earth's atmosphere. The first part, comprising Chapter 2 and Chapter 3, focuses on the retrieval of Level 1 product, particularly the effect of aerosol scattering in the remote sensing of greenhouse gases. In Chapter 2, we study the aerosol induced bias in the retrieval of column averaged CO2 mixing ratios (XCO2). Ground based remote sensing data from the California Laboratory for Atmospheric Remote Sensing Fourier Transform Spectrometer (CLARS-FTS) are used. We employ a numerical radiative transfer model to simulate the impacts of neglecting aerosol scattering on the CO2 and O2 slant column densities (SCDs) operationally retrieved from CLARS-FTS measurements. These simulations show that the CLARS-FTS operational retrieval algorithm likely underestimates CO2 and O2 abundances over the LA basin in scenes with moderate aerosol loading. The bias in the CO2 and O2 abundances due to neglecting aerosol scattering cannot be canceled by ratioing each other in the derivation of the operational product of XCO2. We propose a method for approximately correcting the aerosol-induced bias. Results for CLARS XCO2 are compared to the direct-sun XCO2 retrievals from a nearby Total Carbon Column Observing Network (TCCON) station.
In Chapter 3, we explain why large XCO2 retrieval errors are found over deserts in the space borne Orbiting Carbon Observatory-2 (OCO-2) data. We argue that these errors are caused by the surface albedo being close to a critical surface albedo (αc). Over a surface with albedo close to αc, increasing the aerosol optical depth (AOD) does not change the continuum radiance. The spectral signature caused by changing the AOD is identical to that caused by changing the absorbing gas column. The degeneracy in the retrievals of AOD and XCO2 results in a loss of degrees of freedom (DOF) and information content (H). We employ a radiative transfer model to study the physical mechanism of XCO2 retrieval error over a surface with albedo close to αc. Based on retrieval tests over surfaces with different albedos, we conclude that over a surface with albedo close to αc, the XCO2 retrieval suffers from a significant loss of accuracy.
In the Appendix, we put in a Chapter based on my work with Prof. Andrew Thompson on ocean The second part, mainly in Chapter 4, focuses on the application of Level 2 product. In this Chapter, we examine the uncertainties in middle atmospheric HOx chemistry by comparing the Aura Microwave Limb Sound (MLS) OH and HO2 measurements with the simulations of the Caltech-JPL KINETICS photochemical model. The model using the standard chemical kinetics underestimates OH and HO2 concentrations in the mesosphere. To resolve the discrepancies, we use MLS OH and HO2 measurements as benchmark to adjust the involved chemical rate coefficients within reasonable uncertainty ranges with an optimal estimation algorithm. The results show that four key reaction rate constants and the O2 cross section at Lyman-α (121.6 nm) are the most sensitive parameters for determining the HOx profiles. We conclude that the rate coefficient of H + O2 + M → HO2 + M requires a very large adjustment beyond the uncertainty limits recommended in the NASA Data Evaluation, which suggests the need for future laboratory measurements. An alternative explanation is that radiative association plays a significant role in this process, i.e. H + O2 → HO2 + hv, which has never been measured or computed.
In the Appendix, we put in a Chapter based on my work with Prof. Andrew Thompson on ocean submesoscale turbulence.</p
Studies of the N-end Rule Pathway in Bacteria and Mammals
Get PDFMany intracellular proteins are either conditionally or constitutively short-lived, with in vivo half-lives that can be as brief as a minute or so. The regulated and processive degradation of intracellular proteins is carried out largely by the ubiquitin (Ub)-proteasome system (UPS), in conjunction with molecular chaperones, autophagy, and lysosomal proteolysis. The N-end rule pathway, the first specific pathway of UPS to be discovered, relates the in vivo half-life of a protein to the identity of its N-terminal residue. Physiological functions of the N-end rule pathway are strikingly broad and continue to be discovered. In bacteria and in eukaryotic organelles mitochondria and chloroplasts all nascent proteins bear the pretranslationally formed N-terminal formyl-methionine (fMet) residue. What is the main biological function of this metabolically costly, transient, and not strictly essential modification of N-terminal Met, and why has Met formylation not been eliminated during bacterial evolution? One possibility is that the formyl groups of N-terminal Met in Nt formylated bacterial proteins may signify a proteolytic role of Nt-formylation. My colleagues and I addressed this hypothesis experimentally, as described in Chapter 3 of this thesis.
Among the multitude of biological functions of the mammalian Arg/N-end rule pathway are its roles in the brain, including the regulation of synaptic transmission and the regulation of brain’s G-protein circuits. This regulation is mediated, in part, by the its Ate1-mediated arginylation branch of the Arg/N-end rule pathway. One role of the Ate1 arginyltransferase (R-transferase) is to mediate the conditional degradation of three G-protein down-regulators, Rgs4, Rgs5, and Rgs16. Ate1-/- mice, which lack the Ate1 R-transferase, exhibit a variety of abnormal phenotypes. Chapter 4 describes our studies of neurological abnormalities in Ate1-/- mice (and also in mice that express Ate1 conditionally, upon the addition of doxycycline), with an emphasis on the propensity of these mice to epileptic seizures. </p
Naturalness Confronts Nature: Searches for Supersymmetry with the CMS Detector in pp Collisions at √s = 8 and 13 TeV
Get PDFIn this thesis, we present two inclusive searches for supersymmetric particles at 8 and 13 TeV using the razor variables and guided by the principle of naturalness. We build a framework to explore the natural supersymmetry parameter space of gluino and top squark masses and branching ratios, which is a unique attempt to cover this parameter space in a more complete way than ever before using LHC data. With this approach, the production of top squarks and gluinos are excluded below 700 GeV and 1.6 TeV, respectively, independent of the branching ratios, constituting one of the tightest constraints on natural supersymmetry from the LHC. Motivated by the need to mitigate the effects of multiple interactions per bunch crossing (pileup), an essential feature of present and future hadron colliders, in this thesis we also study the precision timing capabilities of a LYSO-based sampling calorimeter, and achieve a time resolution of 30 ps in electron test beam measurements. The achieved resolution corresponds to the precision needed to significantly reduce the inclusion of pileup particles in the reconstruction of the event of interest. This study is foundational in building an R and D program on precision timing for the high-luminosity LHC and other future hadron colliders. We also propose alternative simplified models to study Higgs-plus-jets events at the LHC, and reinterpret an excess observed at 8 TeV in the context of these models. Finally, we discuss a search for narrow resonances in the dijet mass spectrum at 13 TeV using the data-scouting technique at CMS, which records a smaller event format to increase the maximum recordable rate. For the benchmark models with a vector or axial-vector mediator that couples to quarks and dark matter particles, the dijet search excludes mediator masses from 0.5 TeV up to 2.7 TeV largely independent of the dark matter particle mass, which constitutes a larger exclusion than traditional mono-X searches at the LHC. In the plane of the dark matter-nucleon interaction cross section versus dark matter mass, the dijet search is also more sensitive than direct detection experiments for spin-dependent cross sections
Anomalous Thermodynamics of Nonideal Gas Physisorption on Nanostructured Carbons
Get PDFMesoporous and microporous adsorbents play critical roles in gas storage and separation applications. This thesis describes previously unexplored anomalous thermodynamics in the field of gas physisorption and their impact on energy relevant gases including methane, ethane, krypton and carbon dioxide. Physisorption occurs when an adsorbent induces gas molecules to form a locally densified layer at its surface due to physical interactions. This increases gas storage capacity over pure compression and its efficacy is dependent on the surface area of the adsorbent and the isosteric heat of adsorption. The isosteric heat of adsorption is the molar change in the enthalpy of the adsorptive species upon adsorption and serves as a measure of adsorbent-adsorbate binding strength.
Unlike conventional adsorbate-adsorbent systems, which have isosteric heats of adsorption that decrease with surface loading, zeolite-templated carbon is shown to have isosteric heats of methane, ethane and krypton adsorption that increase with surface loading. This is a largely beneficial effect that can enhance gas storage and separation. The unique nanostructure and uniform pore periodicity of the zeolite-templated carbon promote lateral interactions among the adsorbed molecules that cause the isosteric heats of adsorption to increase with loading. These results have been tested and corroborated by developing robust fitting techniques and thermodynamics analyses. The anomalous thermodynamics are shown to result from cooperative adsorbate-adsorbate interactions among the nonideal species and are modeled with an Ising-type model.
As a second theme of this thesis, the study of nonideal gas adsorption has enabled the development of a Generalized Law of Corresponding States for Physisorption. A predictive understanding of high-pressure physisorption on a variety of adsorbents would facilitate the further development of tailored adsorbents and adsorption analysis. Prior attempts at developing a predictive understanding, however, have been hindered by nonideal gas effects.
By approaching physisorption from both empirical and fundamental perspectives, a Generalized Law of Corresponding States for Physisorption was established that accounts for a number of nonideal effects. This new Law of Corresponding States allows one to predict adsorption isotherms for a variety of classical gases from data measured with a single gas. In brief: "At corresponding conditions on the same adsorbent, classical gases physisorb to the same fractional occupancy."
Corresponding conditions are met when the reduced variables of each nonideal gas are equivalent, and fractional occupancy gives the fraction of occupied adsorption sites. This Law of Corresponding States for Physisorption is determined using monolayer, BET and Dubinin-Polanyi adsorption theories along with measured adsorption isotherms across a number of conditions and adsorbents. Furthermore, the anomalous cooperative adsorbate-adsorbate interactions discussed in this thesis are shown to be consistent with the Generalized Law of Corresponding States for Physisorption.</p
Computational Investigation of Small Molecule Catalysis by Cobalt, Rhodium, and Iridium Molecular Catalysts
Get PDFGlobal energy demands are predicted to increase through 2040. In the spirit of meeting these demands, work focusing on increasing the efficiency of existing energy technologies, as well as improving energy storage is necessary. This work takes a catalytic approach to these challenges, focusing on Co, Rh, and Ir catalysts with pincer and bipyridine ligands. Density functional theory (DFT) can be used in order to gain a deeper understanding of how these catalysts behave. In the realm of improving existing technologies, the mechanism for oxidation of methane to methanol by Phebox Ir (Phebox = bis(oxazolinyl)phenyl) is investigated with a focus on understanding how subtle substitutions to the ligand can help or hinder this reaction. It is shown that in this catalyst, two unwanted intermediates on the potential energy surface (an IrIV state leading to catalyst deactivation and an IrV state leading to over-oxidation) can potentially be avoided by adding trifluoromethyl groups to the ligand. For production of fuels from solar energy, two reactions are studied. Experimentally, CO2 reduction to formate by (POCOP)Ir (POCOP = C6H3-2,6-[OP(tBu)2]2) has been shown to selectively occur at moderate potentials. The mechanism by which this catalyst reduces CO2 is elucidated. In particular, the impressive product selectivity afforded this catalyst for formate over hydrogen production is rooted in kinetics: high barriers for protonation inhibit the creation of H2 adducts. In addition to this, substitutions to the ligand and metal center are investigated to further illuminate the relationship between kinetics and thermodynamics. Hydrogen evolution in Cp*Rh(bpy) (bpy = 2,2'-bipyridine, Cp* = pentamethylcyclopentadienyl) is investigated, centering on unexpected protonation at the Cp* ligand rather than the metal center. This state is on the path for hydrogen evolution in the case of using weak acids, but in the presence of strong acids, the path through the traditional hydride is most likely. Finally, the attachment of these catalysts to electrode surfaces is discussed with the aim of making molecular catalysts a more viable option in industry It is shown that chlorine present in the attachment process enables easy catalyst dissociation from the surface. Several non-halogen options are discussed as replacements. Throughout the thesis two themes emerge: the constant interaction between thermodynamics and kinetics to control mechanistic paths and products, and the ability of small modifications to have huge impacts on catalytic cycles
Highly Multiplexed Single Cell In Situ RNA Detection
Get PDFIdentifying the genetic basis of cellular function and identity has become a central question in understanding the functioning of complex biological systems in recent years. Single cell sequencing techniques have provided a great deal of insight into the transcriptional profiles of various cell types. However, single cell RNAseq studies require cells to be removed from their native environments resulting in the loss of spatial relationships between cells and suffer from low detection efficiency. Moving forward, a central question in further understanding large biological systems consisting of many disparate cell types will be how do these cells interact with each other to form functional tissues. To accomplish this goal, a method that keeps the tissue architecture intact is required. Single molecule fluorescence in situ hybridization (smFISH) is one such technique, but suffers from a lack of multiplex measurement capability as only a very few genes can be measured in any given sample and has low signal to noise ratio. Here I present a method that overcomes the low signal to noise ratio by using an amplification technique known as single molecule hybridization chain reaction (smHCR). smHCR coupled with the existing sequential FISH (seqFISH) method, which overcomes the inherent multiplexing limit of smFISH, provides a powerful tool to measure the copy numbers of 100’s of genes in single cell in situ.
The mouse brain contains 100,000,000 cells arranged into distinct anatomical structures. While cell types have been previously characterized by morphology and electrophysiology, single cell RNA sequencing has recently identified many cell types based on gene expression profiles. On the other hand, the Allen Brain Atlas (ABA) provides a systematic gene expression database using in situ hybridization (ISH) of the entire mouse brain, but lacks the ability to correlate the expression of different genes in the same cell. Using the smHCR-seqFISH technique to measure the expression profiles of up to 249 genes in single cells in coronal brain sections, we have identified distinct cell clusters based on the expression profiles of 15000 cells and observed spatial patterning of cells in the hippocampus. In the dentate gyrus, we resolved lamina-layered patterns of cell clusters with a clear separation between the granule cell layer and the sub-granular zone. In CA1 and CA3, the data revealed distinct subregions, each with unique combinations of cell clusters. Particularly, we observed that the dorso-lateral CA1 is almost completely cellular homogeneous with increasing cellular heterogeneity on the dorsal to ventral axis. Together, these results demonstrate the power of highly multiplex in situ analysis to the brain, with further application to a wide range of biological systems.</p
Towards a Hydrobromic Acid Splitting Device Using Earth-Abundant Materials
Get PDFThis thesis disembarks from the traditional approach of tailoring a system to the water splitting reaction. As detailed in Chapter 2, this thesis predicts that two silicon photoelectrons connected in parallel are ideally suited to electricity storage in an integrated light collector and chemical storage device driving the splitting of hydrobromic acid (2HBr -> H2 + Br2). The predicted dual photoelectrode system could potentially obtain high solar-to-hydrogen conversion efficiencies of up to an ηSTH, HBr of 12 %, whereas an equivalent water splitting system is not possible due to the small band gap of silicon. Unfortunately, silicon possesses low catalytic activity for both the hydrogen evolution half-reaction and the bromide oxidation half-reaction. In the past, the electrocatalysis of silicon has been aided by using Pt/Ir alloys to act as both a protective and electrocatalytic layer. Herein, efforts are detailed to replace these precious metals, where possible, by using only earth-abundant materials to decrease the cost of a module. Our hope is that efforts along this path will aid the field of artificial photosynthesis as a whole.
We begin by further testing a chemical insight previously noted within our group and discover a surprisingly high activity electrocatalyst for the hydrogen evolution reaction by cobalt phosphide (CoP) nanoparticles, detailed in Chapter 3. Falling on a traditional technique of increasing the surface area of particular facets, we nanostructured our crystalline CoP to increase its surface area of exposed (111) facets and hoped it would increase our catalytic activity; however, we found that simple structuring resulted in poor adhesion of nanostructures and poorer activity than our multi-faceted CoP nanocrystals (see the appendix to find out more). Our original catalysis efforts spurred a flurry of activity in the literature, and consequently, alternative devices that are more scalable arose. We detail the developments occurring since our work in the last appendix.
Now, with a potential catalyst in hand, comes the difficulty of balancing the delicate interplay between light absorption and catalysis, as detailed in Chapter 4. While CoP is active for HER, our particles possess a relatively low turnover frequency compared to hydrogenase or platinum, and thus require high mass loadings of material (2 mg/cm2) to obtain competitive extrinsic performance. Planar electrodes are incompatible with our particles because of substantial light absorption by the thick catalyst overlayer. By structuring our photoelectrode, we abnegate our catalyst limitations by exploiting the properties of microwires. High-aspect ratio microwires have shown promise as potentially low-cost materials for future photovoltaic applications as well as photocathodes functioning as part of an energy storage device. We discuss how to integrate our materials with silicon microwires (the wires were grown by an unscalable process to serve in place of functional CVD wires with radial emitters) to prototype a candidate photocathode. While a parasitic resistance limited the overall efficiency of the photocathode candidate, it still had promising stability. The parasitic resistance was addressed by electrodepositing the cobalt phosphide, thereby giving us a promising efficiency limited by the quality of the p-n junction.
While high-catalytic activity for the HER in acidic solutions using earth-abundant materials represents a significant advance, the photocathode is just one component of what is necessary for a complex system of splitting hydrobromic acid. Silicon, by its virtue of being a small band gap material, is easily passivated in aqueous solutions by the formation of a silicon oxide. In the past, our colleagues had shown that a monolayer of graphene could occasionally provide protection in a test solution, but batch-to-batch variability provided a considerable challenge. The putative hypothesis offered for the degradation argued defects in the crystalline graphene at grain-boundaries were the culprit. In Chapter 5 we present a method to passivate defects in the graphene crystal by light fluorination and observe a considerable enhancement in stability relative to typical graphene-protected silicon photoanodes. We had hoped that catalysis for bromide oxidation would be aided by the near-perfect graphene liquid junction, but electrodeposited Pt was required to effect photoxidation. A cursory stability test shows promising stability for one-half of an hour, but we would like to avoid using Pt. Finally, we also turned our attention to protecting silicon surfaces from oxidation by exploiting covalent silicon surface chemistry, accessible via a two-step chlorination/alkylation procedure, and explored the deposition of potentially protective thin-film metal oxides (see the appendix).</p
Optics for High-Efficiency Full Spectrum Photovoltaics
Get PDFWhile the price of solar energy has dropped dramatically in the last few years, costs must be further reduced to reach wide-scale adoption. One strategy to decrease cost is to increase efficiency. Photovoltaic energy conversion is most efficient for a narrow frequency range. Lack of absorption of low energy photons and thermalization of high-energy photons leads lead to a loss of over 40% of incident solar power on a silicon cell. Current-matching and lattice-matching restrictions limit the efficiency of traditional monolithic multijunction solar cells. In order to avoid these limitations and realize ultrahigh efficiency (close to 50%), this thesis explores use of optical elements to split broadband sunlight into multiple spectral bands that can each be sent to physically separated solar cells tuned to best convert that band.
Design of a holographic diffraction grating based spectrum-splitting system resulted in a simulated module efficiency of 37%, meeting the efficiency of state-of-the-art modules. One of four holographic grating stacks is experimentally characterized. Next, a design incorporating dichroic filters, seven subcells with bandgaps spanning the solar spectrum, and concentrators with efficiency potential exceeding 45% module efficiency is presented. While prototyping this design, we also used on-going cost-modeling to ensure that our design was on-track to be a high-volume technology with low lifetime energy cost.
Finally, high-contrast gratings are used as resonant, dielectric spectrally selective mirrors in a tandem luminescent solar concentrator and as alternatives to Bragg reflectors. Gratings can have omnidirectional, high reflectivity by appropriately offsetting grating resonances in nano-patterned subwavelength thickness high-refractive index material. Subwavelength feature sizes suppress diffraction, and the high-refractive index of the grating layer leads to relatively angle-insensitive reflectance. Gratings can be fabricated by nanoimprint lithography, making them a scalable and economical option for photovoltaic applications. Simulations show hemispherically average reflectivity near 90% possible from a single subwavelength thickness layer. These properties are well suited for a variety of applications including multiple spectrum-splitting device architectures.</p
Electronically Tunable Light Modulation with Graphene and Noble Metal Plasmonics
Get PDFGraphene is a monolayer of carbon atoms constructing a two-dimensional honeycomb structure, and it has an excellent carrier mobility and a very high thermal conductivity. Remarkably, it has been experimentally demonstrated that a monolayer graphene exhibits an exotic optical properties. To be specific, the plasmonic dispersion relation of a transverse magnetic graphene plasmon is electronically tunable by adjusting carrier density in graphene with external gate bias, and graphene plasmonic nano cavities have been utilized to modulate mid-infrared light.
In this thesis, we present how to efficiently modulate mid-infrared light by combining graphene plasmonic ribbons with noble metal plasmonic structures.
First, we propose and demonstrate electronically tunable resonant perfect absorption in graphene plasmonic metasurface enhanced by noble metal plasmonic effect, which results in modulating reflecting light. In this device, we improve coupling efficiency of free-space photons into graphene plasmons by reducing wavevector mismatching with a low permittivity substrate. In addition, the graphene plasmonic resonance is significantly enhanced by plasmonic light focusing effect of the coupled subwavelength metallic slit structure, which results in strongly fortifying resonance absorption in the graphene plasmonic metasurface. In the proposed device, theoretical calculation expects that perfect absorption in the graphene plasmonic metasurface is achievable with low graphene carrier mobility. We also present an analytical model based on surface admittance in order to fully understand how this enhancement occurs.
In the second device, we propose and demonstrate a transmission type light modulator by combining graphene plasmonic ribbons with subwavelength metal slit arrays. In this device, extraordinary optical transmission resonance is coupled to graphene plasmonic ribbons to create electrostatic modulation of mid-infrared light. Absorption in graphene plasmonic ribbons situated inside metallic slits can efficiently block the coupling channel for resonant transmission, leading to a suppression of transmission. This phenomenon is also interpreted by anti-crossing between the graphene plasmonic resonance in the ribbons and the noble metal plasmonic resonance in the subwavelength metal slit arrays.
Finally, we devise a platform to demonstrate graphene plasmonic resonance energy transport along graphene plasmonic ribbons. In this device, two metal-insulator-metal waveguides are connected by a subwavelength metal slit, and graphene plasmonic ribbons are located inside this slit. Due to the large impedance mismatch at the junction, light coupling efficiency across the junction is poor. If the graphene plasmonic ribbons are tuned to support strong graphene plasmonic resonances, the light energy can be transferred via graphene plasmons along the ribbons, and it leads to significant improvement in the light coupling efficiency across the junction. In addition to enhanced light coupling efficiency, we also present how to totally suppress the transmission by inducing a Fano resonance between a non-resonant propagation mode across the junction and a resonant graphene plasmonic transport mode, which can be utilized to efficiently modulate light in a noble metal plasmonic waveguide with the graphene plasmon resonance energy transfer.</p
Insights into the Mechanism of Biological Nitrogen Fixation through Characterization of the Nitrogenase Molybdenum-Iron Protein
Get PDFNitrogen fixation, the process of converting dinitrogen to ammonia, is performed industrially and biologically by the Haber-Bosch process and nitrogenase, respectively. The resulting ammonia is largely used as fertilizer. Since there is a finite amount of ammonia produced by nitrogenase, we are heavily dependent on the Haber-Bosch process – only two-fifths of the world’s population could be fed without it. Although the importance of the Haber-Bosch process cannot be overstated, our dependence on it has several drawbacks, including significant energy costs (~5% of the annual natural gas consumption), greenhouse gas emissions, and nitrate runoffs. By understanding the biological mechanism of nitrogen fixation, we may be able to (1) develop more efficient nitrogen fixing catalysts to replace those in the Haber-Bosch process or (2) express de novo nitrogen fixing proteins in plants so crops can essentially fertilize themselves. The projects described in this thesis aim to contribute to our understanding of the mechanism of biological nitrogen fixation through structural studies of nitrogenase. Nitrogenase consists of the iron and molybdenum-iron (MoFe) proteins, the latter of which contains the active site, the FeMo-cofactor. Throughout my work, I compare the MoFe proteins from Azotobacter vinelandii (Av1) and Clostridium pasteurianum (Cp1), the two most structurally divergent molybdenum nitrogenases known. Determining the similarities and differences between these proteins may aid our understanding of biological nitrogen fixation. My first project (Chapter III) compares a 1.08 Å Cp1 X-ray structure to a previously published 1.0 Å Av1 structure. I determined that the center atom of the Cp1 FeMo-cofactor is carbon, showing conservation of cofactor structure among molybdenum nitrogenases. Next, I compared substrate pathways in Av1 and Cp1 via Xe pressurization and identification of small molecule binding sites (Chapter IV). My most significant results include the structural and electronic characterization of a reversible protonated resting state of Av1 and Cp1 (Chapter VII).</p