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On the Stability of Supersonic Boundary Layers with Injection
Get PDFThe problem of supersonic flow over a 5 degree half-angle cone with injection of gas through a porous section on the body into the boundary layer is studied experimentally. Three injected gases are used: helium, nitrogen, and RC318 (octafluorocyclobutane). Experiments are performed in a Mach 4 Ludwieg tube with nitrogen as the free stream gas. Shaping of the injector section relative to the rest of the body is found to admit a "tuned" injection rate which minimizes the strength of shock waves formed by injection. A high-speed schlieren imaging system with a framing rate of 290 kHz is used to study the instability in the region of flow downstream of
injection, referred to as the injection layer. This work provides the first experimental data on the wavelength, convective speed, and frequency of the instability in such a flow. The stability characteristics of the injection layer are found to be very similar to those of a free shear layer. The findings of this work present a new paradigm for future stability analyses of supersonic flow with injection
Organic Matter Sulfurization in the Modern Ocean
Get PDFOnly a tiny fraction of the carbon fixed by primary producers in the surface ocean is preserved in sediments, but this organic matter (OM) burial is one of the main processes linking the short and long-term carbon cycles, giving it important roles in global biogeochemistry. OM-rich deposits often contain abundant organic S (OS), and sulfur incorporation is thought to make OM less available for heterotrophs and more likely to be preserved. Still, we have few constraints on the significance of sulfurization for OM burial in the modern ocean, and fewer on how that flux might have differed in the past. This thesis applies a new generation of analytical tools for S-isotope analysis to investigate the timescales and mechanisms of OM sulfurization in the modern ocean. By measuring the δ34S values of minor S phases and individual S-bearing organic compounds as well as major sedimentary phases, we are able to make progress on long-standing questions about the distribution of S isotopes among organic and inorganic S phases in sediments.
Chapters 2 and 3 focus on Cariaco Basin, where a large proportion of the OS in sediments appears to derive from OM sulfurization in particles sinking through the water column. Rapid sulfurization likely involves polysulfides and is associated with high primary productivity and OM export. In the sediments, low-molecular-weight organosulfur compounds accumulate over longer timescales and have low and distinctive δ34S values. Chapter 4 presents records from Santa Barbara Basin, where OS appears to be exchanging with less abundant porewater sulfide and controlling its δ34S value. As in many environments, pyrite in these sediments is more 34S-depleted than either OS or sulfide. We attribute this pattern to pyrite formation within sulfide-generating microenvironments prior to equilibration between OS and sulfide in porewater. Chapter 5 tests the feasibility of the proposed OS–sulfide exchange and confirms that sulfide δ34S can reflect equilibrium with natural OM. We also find evidence that sulfurization of thiols may involve an interim polysulfide that includes the thiol S atom, providing a mechanism to mix biogenic S into proto-kerogen and potentially helping explain differences between the global pyrite and OS S-isotope records.</p
Noncovalent Immobilization of Electrocatalysts on Carbon Electrodes via a Pyrenyl Ligand
Get PDFThere are many problems that need to be overcome if solar energy is to be viable on a global scale. Photons must be harvested and stored in a usable to allow efficient use of energy throughout the day. The functionalization of electrode surfaces with molecular catalysts is an attractive route for assembling (photo)electrochemical devices that convert renewable energy into chemical fuels. This work focuses on one method of noncovalently attaching molecular catalysts to graphitic surfaces.
The first part describes the synthesis of a pyrene-appended bipyridine ligand that serves as the linker between the catalysts and the surface. Using this ligand, a rhodium proton-reduction catalyst and a rhenium CO2-reduction catalyst were synthesized in order to study the electrochemistry of the surface-attached species. Electrochemical and spectroscopic analysis confirm catalyst immobilization and electrocatalytically active assemblies. Bulk electrolysis of the surface-attached complexes confirm catalytic turnover formation of H2 for the rhodium complex and CO for the rhenium complex.
The second part describes three new complexes utilizing the same pyrene-appended bipyridine ligand. These are [Ru(P)(4,4’-dimethyl-2,2’-bipyridine)2]Cl2, [Cp*Ir(P)Cl]Cl, and [Mn(P)(CO)3Br]. Once again, spectroscopic and electrochemical analyses confirmed successful immobilization of these complexes on high surface area carbon electrodes. The iridium complex was found to be unstable with respect to redox cycling due to ligand exchange. The ruthenium complex exhibited very high stability over long periods of redox cycling. The manganese complex was found to catalytically produce CO during bulk electrolysis
Coupling Textural, Magnetic, and Modeling Techniques to Understand Precambrian Paleoenvironments
Get PDFThe oxygenation of our planet is perhaps the greatest transition in its history, dramatically affecting geochemical cycles and the evolution of life. Major first-order questions still remain about late Archean and Proterozoic environments, even as newly developed geochemical techniques provide additional constraints and create subtle conundrums. I apply a new approach to classic localities to understand Precambrian redox character and paleoenvironmental conditions by combining textural observations from optical and electron microscopy, isotopic measurements, and (synchrotron-based) x-ray spectroscopy with scanning magnetic microscopy and bulk rock magnetic experiments. Models paired with data from the literature provide additional context for these measurement results.
The first portion of this dissertation focuses on understanding the predominant microbial metabolism recorded in the 2.72 Ga Tumbiana Formation stromatolites. I proposed that these stromatolites formed in shallow, anoxic waters and record a global signature of unique autotrophy distinct from younger systems dominated by oxygenic photosynthesis. The next portion of this dissertation uses the redox sensitivity of iron as a tool to investigate paleoredox conditions of the 1.45 Ga lower Belt Supergroup during a potentially transitional time-period in surface environments. Observations of primary mineralogy in early diagenetic pyrite and detrital iron oxides suggest an oxygenated water-column overlying anoxic, sulfidic pore-fluids very similar to the modern. The final portion of this dissertation assesses the effects of prevalent secondary overprints on the use of iron as a paleoredox proxy. Theoretical data-driven models combined with trends from the Belt Supergroup highlight the mobility of iron during progressive burial metamorphism as well as in diagenetic transformations and reactions with infiltrating fluids. Applying coupled techniques, specifically including textural methods, is vital for untangling secondary alterations from primary records of environmental conditions during the Precambrian.
Classical Force Field Simulations of Biological Processes and Quantum Chemical Computations of Homogeneous Catalysts
Get PDFComputational chemistry methods and tools have enabled studies of biological processes and chemical reactions to get insights from detailed atomic structures and reaction mechanisms. In this thesis, two biological problems are attacked by the classical force fields simulations and two homogeneous catalysis problems are studied by quantum chemical calculations. In all four problems, new insights have been revealed by the computational results.
Chapter 1 briefly reviews the computational chemistry theories and methods developed and popularized in the past few decades. Chapter 2 addresses the protein-protein interaction problem in the onset of meningitis where E. coli OmpA interacts with FcγRI α-chain (FcγRIa) to invade macrophages. Computationally predicted three-dimensional structure of the OmpA-FcγRIa complex showed the role of three N-glycans in FcγRIa in the interaction. Chapter 3 studies the molecular origin of the bitter aftertaste of a kind of natural sweetener called steviol glycosides. By examining the predicted binding complexes between the human bitter taste receptors 2R4 and 2R14 which could be activated by steviol glycosides, a general activation model is proposed to explain the structure-function relationship and to predict new natural sweeteners with less bitterness. Chapter 4 investigated the reaction mechanisms of methane to methanol conversion by a biomimetic tricopper cluster compound. An unusual exchange-stabilized multiradical state is found to be responsible for the hydrogen abstraction reactivity and a methyl radical rebound mechanism is proposed for methane oxidation. Calculations also show interesting spin crossing during the reaction cycle with high spin state forbidden for methyl rebound. Chapter 5 examines the reaction mechanisms in olefin hydrosilylation by the Pt-based Karstedt’s catalyst. An unexpected rate-determining step of agostic bond dissociation is found in between the elementary reaction steps proposed previously. The regioselectivity of the products are studied. An alternative reaction cycle which is kinetically unflavored is proposed. Oxygen stability is studied.</p
A Core Mitophagic Machinery Promotes Selective Degradation of Paternal Mitochondria in Mouse Embryos and MEF Cells
Get PDFThe maternal mode of mitochondrial inheritance is conserved across mammalian species; however, little is known about how mitochondria from the sperm are eliminated from early mammalian embryos. Mitophagy, the regulated degradation of mitochondria in the lysosome, has been proposed as a possible mechanism. Mitophagy is an important means by which the cell responds to changes in mitochondrial fitness, and has been observed under a number of physiological and non-physiological circumstances, including, but not limited to, hypoxia, mitochondrial depolarization, mitochondrial fission, and erythrocyte differentiation.
Here we examine the core component of mitophagy proteins involved in three physiological states: respiration-induced mitophagy in cultured mouse fibroblasts, mitophagy of dysfunctional mitochondria in the absence of mitochondrial fusion, and degradation of paternal mitochondria in pre-implantation mouse embryos. We find that a common pathway is used for elimination of mitochondria, involving mitochondrial depolarization, and the E3 ubiquitin ligases PARKIN and MUL1. We find that PARKIN and MUL1 play partially redundant roles in elimination of paternal mitochondria that is also dependent on PINK1 kinase, the fission factor, FIS1, and the autophagy receptor, p62. We find that p62 is specifically recruited to defective mitochondria in fusion deficient cells by a mechanism independent of ubiquitin binding. Our results elucidate the molecular mechanism of strict maternal transmission of mitochondria and uncover a collaboration between MUL1 and PARKIN in mitophagy.</p
Optimization of NEMS for Frequency Shift Sensing Applications
Get PDFThis thesis has two areas of focus: the application of the dynamic similarity principle in microelectromechancial systems (MEMS) and nanoelectromechanical systems (NEMS) and the study of anomalous phase noise (APN) in MEMS and NEMS. In the first portion of the thesis, we employ the dynamic similarity principle to predict the quality factor due to gas damping in MEMS and NEMS. In the second portion of the thesis, we provide a theoretical framework for sources of phase noise in MEMS and NEMS and describe the measurements that we made to quantify the temperature dependence of anomalous phase noise in silicon doubly clamped beams
DNA-Mediated Charge Transport Signaling Within the Cell
Get PDFDNA possesses the curious ability to conduct charge longitudinally through the π-stacked base pairs that reside within the interior of the double helix. The rate of charge transport (CT) through DNA has a shallow distance dependence. DNA CT can occur over at least 34 nm, a very long molecular distance. Lastly, DNA CT is exquisitely sensitive to disruptions, such as DNA damage, that affect the dynamics of base-pair stacking. Many DNA repair and DNA-processing enzymes are being found to contain 4Fe-4S clusters. These co-factors have been found in glycosylases, helicases, helicase-nucleases, and even enzymes such as DNA polymerase, RNA polymerase, and primase across the phylogeny. The role of these clusters in these enzymes has remained elusive. Generally, iron-sulfur clusters serve redox roles in nature since, formally, the cluster can exist in multiple oxidation states that can be accessed within a biological context. Taken together, these facts were used as a foundation for the hypothesis that DNA-binding proteins with 4Fe-4S clusters utilize DNA-mediated CT as a means to signal one another to scan the genome as a first step in locating the subtle damage that occurs within a sea of undamaged bases within cells.
Herein we describe a role for 4Fe-4S clusters in DNA-mediated charge transport signaling among EndoIII, MutY, and DinG, which are from distinct repair pathways in E. coli. The DinG helicase is an ATP-dependent helicase that contains a 4Fe-4S cluster. To study the DNA-bound redox properties of DinG, DNA-modified electrochemistry was used to show that the 4Fe-4S cluster of DNA-bound DinG is redox-active at cellular potentials, and shares the 80 mV vs. NHE redox potential of EndoIII and MutY. ATP hydrolysis by DinG increases the DNA-mediated redox signal observed electrochemically, likely reflecting better coupling of the 4Fe-4S cluster to DNA while DinG unwinds DNA, which could have interesting biological implications. Atomic force microscopy experiments demonstrate that DinG and EndoIII cooperate at long range using DNA charge transport to redistribute to regions of DNA damage. Genetics experiments, moreover, reveal that this DNA-mediated signaling among proteins also occurs within the cell and, remarkably, is required for cellular viability under conditions of stress. Knocking out DinG in CC104 cells leads to a decrease in MutY activity that is rescued by EndoIII D138A, but not EndoIII Y82A. DinG, thus, appears to help MutY find its substrate using DNA-mediated CT, but do MutY or EndoIII aid DinG in a similar way? The InvA strain of bacteria was used to observe DinG activity, since DinG activity is required within InvA to maintain normal growth. Silencing the gene encoding EndoIII in InvA results in a significant growth defect that is rescued by the overexpression of RNAseH, a protein that dismantles the substrate of DinG, R-loops. This establishes signaling between DinG and EndoIII. Furthermore, rescue of this growth defect by the expression of EndoIII D138A, the catalytically inactive but CT-proficient mutant of EndoIII, is also observed, but expression of EndoIII Y82A, which is CT-deficient but enzymatically active, does not rescue growth. These results provide strong evidence that DinG and EndoIII utilize DNA-mediated signaling to process DNA damage. This work thus expands the scope of DNA-mediated signaling within the cell, as it indicates that DNA-mediated signaling facilitates the activities of DNA repair enzymes across the genome, even for proteins from distinct repair pathways.
In separate work presented here, it is shown that the UvrC protein from E. coli contains a hitherto undiscovered 4Fe-4S cluster. A broad shoulder at 410 nm, characteristic of 4Fe-4S clusters, is observed in the UV-visible absorbance spectrum of UvrC. Electron paramagnetic resonance spectroscopy of UvrC incubated with sodium dithionite, reveals a spectrum with the signature features of a reduced, [4Fe-4S]+1, cluster. DNA-modified electrodes were used to show that UvrC has the same DNA-bound redox potential, of ~80 mV vs. NHE, as EndoIII, DinG, and MutY. Again, this means that these proteins are capable of performing inter-protein electron transfer reactions. Does UvrC use DNA-mediated signaling to facilitate the repair of its substrates?
UvrC is part of the nucleotide excision repair (NER) pathway in E. coli and is the protein within the pathway that performs the chemistry required to repair bulky DNA lesions, such as cyclopyrimidine dimers, that form as a product of UV irradiation. We tested if UvrC utilizes DNA-mediated signaling to facilitate the efficient repair of UV-induced DNA damage products by helping UvrC locate DNA damage. The UV sensitivity of E. coli cells lacking DinG, a putative signaling partner of UvrC, was examined. Knocking out DinG in E. coli leads to a sensitivity of the cells to UV irradiation. A 5-10 fold reduction in the amount of cells that survive after irradiation with 90 J/m2 of UV light is observed. This is consistent with the hypothesis that UvrC and DinG are signaling partners, but is this signaling due to DNA-mediated CT? Complementing the knockout cells with EndoIII D138A, which can also serve as a DNA CT signaling partner, rescues cells lacking DinG from UV irradiation, while complementing the cells with EndoIII Y82A shows no rescue of viability. These results indicate that there is cross-talk between the NER pathway and DinG via DNA-mediated signaling. Perhaps more importantly, this work also establishes that DinG, EndoIII, MutY, and UvrC comprise a signaling network that seems to be unified by the ability of these proteins to perform long range DNA-mediated CT signaling via their 4Fe-4S clusters. </p
Physical, Metabolic, and Energetic Investigations of Methane-Metabolizing Microbial Communities
Get PDFUnderstanding the roles of microorganisms in environmental settings by linking phylogenetic identity to metabolic function is a key challenge in delineating their broad-scale impact and functional diversity throughout the biosphere. This work addresses and extends such questions in the context of marine methane seeps, which represent globally relevant conduits for an important greenhouse gas. Through the application and development of a range of culture-independent tools, novel habitats for methanotrophic microbial communities were identified, established settings were characterized in new ways, and potential past conditions amenable to methane-based metabolism were proposed. Biomass abundance and metabolic activity measures – both catabolic and anabolic – demonstrated that authigenic carbonates associated with seep environments retain methanotrophic activity, not only within high-flow seep settings but also in adjacent locations exhibiting no visual evidence of chemosynthetic communities. Across this newly extended habitat, microbial diversity surveys revealed archaeal assemblages that were shaped primarily by seepage activity level and bacterial assemblages influenced more substantially by physical substrate type. In order to reliably measure methane consumption rates in these and other methanotrophic settings, a novel method was developed that traces deuterium atoms from the methane substrate into aqueous medium and uses empirically established scaling factors linked to radiotracer rate techniques to arrive at absolute methane consumption values. Stable isotope probing metaproteomic investigations exposed an array of functional diversity both within and beyond methane oxidation- and sulfate reduction-linked metabolisms, identifying components of each proposed enzyme in both pathways. A core set of commonly occurring unannotated protein products was identified as promising targets for future biochemical investigation. Physicochemical and energetic principles governing anaerobic methane oxidation were incorporated into a reaction transport model that was applied to putative settings on ancient Mars. Many conditions enabled exergonic model reactions, marking the metabolism and its attendant biomarkers as potentially promising targets for future astrobiological investigations. This set of inter-related investigations targeting methane metabolism extends the known and potential habitat of methanotrophic microbial communities and provides a more detailed understanding of their activity and functional diversity
Imidazolium-Based Organic Structure Directing Agents for the Synthesis of Microporous Materials
Get PDFThe central theme of this thesis is the use of imidazolium-based organic structure directing agents (OSDAs) in microporous materials synthesis. Imidazoliums are advantageous OSDAs as they are relatively inexpensive and simple to prepare, show robust stability under microporous material synthesis conditions, have led to a wide range of products, and have many permutations in structure that can be explored. The work I present involves the use of mono-, di-, and triquaternary imidazolium-based OSDAs in a wide variety of microporous material syntheses. Much of this work was motivated by successful computational predictions (Chapter 2) that led me to continue to explore these types of OSDAs. Some of the important discoveries with these OSDAs include the following: 1) Experimental evaluation and confirmation of a computational method that predicted a new OSDA for pure-silica STW, a desired framework containing helical pores that was previously very difficult to synthesize. 2) Discovery of a number of new imidazolium OSDAs to synthesize zeolite RTH, a zeolite desired for both the methanol-to-olefins reaction as well as NOX reduction in exhaust gases. This discovery enables the use of RTH for many additional investigations as the previous OSDA used to make this framework was difficult to synthesize, such that no large scale preparations would be practical. 3) The synthesis of pure-silica RTH by topotactic condensation from a layered precursor (denoted CIT-10), that can also be pillared to make a new framework material with an expanded pore system, denoted CIT-11, that can be calcined to form a new microporous material, denoted CIT-12. CIT-10 is also interesting since it is the first layered material to contain 8 membered rings through the layers, making it potentially useful in separations if delamination methods can be developed. 4) The synthesis of a new microporous material, denoted CIT-7 (framework code CSV) that contains a 2-dimensional system of 8 and 10 membered rings with a large cage at channel intersections. This material is especially important since it can be synthesized as a pure-silica framework under low-water, fluoride-mediated synthesis conditions, and as an aluminosilicate material under hydroxide mediated conditions. 5) The synthesis of high-silica heulandite (HEU) by topotactic condensation as well as direct synthesis, demonstrating new, more hydrothermally stable compositions of a previously known framework. 6) The synthesis of germanosilicate and aluminophosphate LTA using a triquaternary OSDA. All of these materials show the diverse range of products that can be formed from OSDAs that can be prepared by straightforward syntheses and have made many of these materials accessible for the first time under facile zeolite synthesis conditions