Browsing by Subject "kinetics"
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Item Carbon Dioxide Sequestration in Sedimentary Reservoirs: Fundamental and Applied Considerations(2015-05) Tutolo, BenjaminGreenhouse gas emissions and their associated changes to Earth’s climate, hydrologic, and ecological systems are amongst the most pressing issues facing society in the twenty-first century. In this thesis, I explore fundamental and applied aspects of one of the proposed methods for transitioning from a fossil fuel-burning, greenhouse gas emitting society to a renewable energy-based society: Carbon Capture, Utilization, and Storage (CCUS). CCUS involves capturing carbon dioxide (CO2 ) from point sources, such as coal-fired power plants, injecting it deep underground into permeable, porous geologic formations, and, potentially, utilizing the injected CO2 to extract geothermal energy from the subsurface. CCUS is an inherently multi-faceted problem, with researchers and practioners ranging in fields from the Earth sciences to engineering, economics, and public policy, amongst other fields. Within the Earth sciences alone, researchers must focus on a variety of processes, including (but not limited to): the thermodynamics and kinetics of geochemical reactions; the flow and transport of CO2 , reservoir brines, dissolved solutes, and heat; and the evolution of porosity and permeability with the progression of geochemical reactions and mechanical stresses. Here, my co-authors and I offer perspectives and advancements within these sub-fields of the Earth sciences. Specifically, Chapters 2 and 3 focus on the thermodynamics of relevant chemical reactions; Chapters 4 and 5 focus on experimental observations of coupled fluid flow, chemical reactions, and porosity/permeability changes; and Chapter 6 focuses on placing laboratory-scale observations of these coupled processes into the reservoir scale. Together, these chapters offer a glimpse of the immensely multi-faceted nature of CCUS research.Item High-Temperature Chemistry of Polypropylene Pyrolysis: Millisecond Reaction Kinetics and Visualization(2023-06) Sidhu, NathanThe ubiquity of plastics in modern life is evident by the rapid and continual growth of global plastic production. Polypropylene is one of the most widely produced and used plastic materials, accounting for approximately 20% of global polymer production. Billions of tons of plastic waste have been produced as a byproduct of the widespread use of plastics and are insufficiently managed under the current linear plastic economy, with the majority of plastic waste accumulating in landfills or the environment. To allow for the continued use of plastics in a sustainable fashion, a transition must be made towards a circular plastic economy, wherein end-of-life plastics are recycled in a closed loop, fully regenerating the original polymers. To realize a circular plastic economy, new recycling techniques must be developed. Pyrolysis, the thermal conversion of a material in an inert atmosphere, is a high-potential technology to help enable a circular plastic economy. Currently, the fundamental understanding of plastic pyrolysis is limited but will be essential for the development of industrially relevant waste management solutions. The quantification of the intrinsic reaction kinetics of plastic pyrolysis is an ongoing challenge, owing to the complexity of pyrolysis chemistry and the limitations of existing analytical techniques. In this work, a new Pulse-Heated Analysis of Solid Reactions (PHASR) technique was developed that is uniquely capable of operation under reaction-controlled conditions absent transport limitations to measure the millisecond intrinsic kinetics of polyolefin pyrolysis. The capabilities of this reactor to pyrolyze polyolefins under kinetically limited, isothermal conditions with millisecond scale control were extensively validated. A second, Visual PHASR reactor system was developed that enables in situ observation of reaction polyolefins via high-speed photography. Observations of reacting polyolefins revealed the presence of reaction phenomena, including a potential Leidenfrost effect. The intrinsic millisecond reaction kinetics of polypropylene pyrolysis were successfully quantified. The overall reaction kinetics were described by a lumped first-order consumption model with an activation energy of 242.0 ± 2.9 kJ mol-1 and a pre-exponential factor of 35.5 ± 0.6 ln(s-1). Additionally, the production of the solid residues formed during polypropylene pyrolysis was investigated, revealing a secondary kinetic regime.Item Macromolecular Crowding Effects on Cellular NADH-enzyme Binding Kinetics(2017-08) Wilson, ShaneReduced nicotinamide adenine dinucleotide (NADH) is a major cofactor for a large number of biological enzymes that are essential in a myriad of metabolic pathways such as glycolytic and oxidative phosphorylation pathways. In addition, NADH is intrinsically fluorescent and therefore has the potential of serving as a biomarker to monitor mitochondrial dysfunctions associated with aging, cancer, and apoptosis. In this thesis, we investigate how macromolecular crowding may affect the biochemical reaction kinetics of NADH interaction with lactate dehydrogenase (LDH) as a model system in biomimetic crowding (e.g., Ficoll-enriched buffer at 0 ̶ 400 g/L). Using noninvasive, quantitative two-photon fluorescence lifetime and associated anisotropy, we exploit the sensitivities of NADH fluorescence lifetime and rotational diffusion to protein binding. To differentiate between viscosity and crowding effects on the reaction kinetics, we also conducted complementary measurements in glycerol-enriched buffer. Additionally, we are investigating the sensitivity of cellular NADH interaction with dehydrogenases to metabolic manipulations. Our quantitative and non-invasive methodology complements the traditional biochemical and thermodynamics techniques without the destruction of live cells. Intracellular NADH also exists as a mixture of free and enzyme-bound populations at dynamic equilibrium throughout living cells, which can be imaged using fluorescence lifetime imaging for both quantitative and noninvasive assessment of cellular metabolism. 2P-fluorescence lifetime imaging microscopy (FLIM) and 2P- fluorescence anisotropy of intrinsic NADH was measured in cultured mouse embryonic cells under both resting conditions and metabolic-manipulation.Item Measuring Binding Kinetics of Therapeutic Antibodies to Membrane Receptors Using Nanohole Array SPR Biosensors(2016-04) Jordan, LukeIn the field of drug discovery, two important metrics of candidate drugs are their binding affinity and kinetics to target receptors. Dr. Moses Rodriguez and his colleagues at the Mayo Clinic have found monoclonal IgM antibodies exhibiting therapeutic effects for multiple sclerosis and amyotrophic lateral sclerosis in animal models, and therefore desired to obtain the kinetic profiles of these antibodies to their targets. Dr. Sang-Hyun Oh’s lab at the University of Minnesota specializes in designing and fabricating plasmonic devices, and have developed a nanohole array sensor coated with silicone dioxide which permits formation of cell mimicking supported lipid bilayers. The focus of this dissertation has been to build these devices and develop assays to measure the binding between these antibodies and receptors in cell extracts and supported lipid bilayers. The first antibody to measure was rHIgM22, which binds to myelin membrane. We did not know the receptor, so we used myelin extracts which would include the unknown receptors, and attached these particles to the sensor surface by passive immobilization. To reduce particle size into the sensor detection window, we extruded the particles through pores of known dimensions. After immobilization we measured binding with antibodies. Unfortunately, binding with rHIgM22 was undetectable, but a similar antibody, mouse IgM O4, which also binds to myelin and has a therapeutic effect, did bind consistently and gave KD, apparent = 2.6 ± 3.6 nM, ka = 2.5 ± 0.0l × 10^4 M^-1^s-1, and kd,slow = 6.6 ± 0.3 × 10^-5 s^-1. The second antibody to measure was rHIgM12, which binds to neuronal membranes. We found rHIgM12 binds to the gangliosides GT1b and GD1a, but not GM1. These gangliosides were incorporated into supported lipid bilayers (5 mol %) and binding to the antibodies was measured. Binding of rHIgM12 to GT1b gave KD, apparent = 24.8 ± 7.9 nM, ka = 2.19 ± 0.196 × 10^4 M^-1s^-1, and kd,slow = 4.72 ± 1.15 × 10^-4 s^-1. Binding of rHIgM12 to GD1a gave KD, apparent = 42.3 ± 20.6 nM, ka = 1.79 ± 0.516 × 10^4 M^-1s^-1, and kd,slow = 4.43 ± 1.38 × 10^-4 s^-1.Item Modeling PHS Activity in Azurin Comparing Tert-Butyl Hydrogen Peroxide with Oxygen Gas as Oxidants(2020) Evenson, Austin BMetalloproteins are common among living organisms, with one third to one half of all proteins requiring a metal ion for proper structure or function. They are associated with many key processes, such as signal transduction, nutrient storage and enzyme-mediated catalysis. One such metalloprotein, phenoxazinone synthase (PHS), is a hexameric, multicopper oxidase that creates aminophenoxazinone (APX) from ortho-aminophenol (oAP). APX is a major component of actinomycin D, an antibiotic. One way to examine the enzymatic activity of PHS is through the use of the protein azurin as a model system. Native azurin is a small copper metalloprotein, with a single Type 1 copper center, and has no PHS activity. However, it can model the reactivity of PHS through the addition of a Type 2 copper center via targeted mutagenesis. In our studies, the resulting models were then given additional mutations, in order to more accurately understand the effects that the proteins’ specific structure has on the kinetics and rate of the redox reaction. One of the original models, NiR3His-Azurin, has the added Type 2 copper center. This scaffold protein was found to be active in PHS enzyme assays and is the predecessor to a “second-generation” azurin mutant: Met121Leu, which was designed to alter the reduction potential and therefore reactivity of the copper centers in azurin. In the Met121Leu mutant, a methionine near the copper active site is replaced with a leucine. This leads to an increased reduction potential, and the hypothesis that the resulting PHS activity rate will be decreased, due to a decrease in the reoxidation of the protein, a rate limiting step in the catalysis. The differences between the PHS activity of the NiR3His and Met121Leu mutants were explored by using both oxygen gas (O2) and tert-butyl hydrogen peroxide (TBHP) as oxidants. It is known that TBHP is a stronger oxidant than O2, and should cause a faster turnover of the redox reaction by the protein, thereby giving a higher rate of activity. However, O2 allows for the study of the protein using the native oxidant. Preliminary trials indicate that the Met121Leu variant is not significantly than the observable 0.0118 mMol/min Vmax for Nir3His, using both TBHP and O2 as oxidants.Item On the Intrinsic Kinetics of Polyethylene Pyrolysis(2023-05) Mastalski, IsaacGlobal plastic use has grown exponentially over the past several decades, and this has led to a concomitant increase in plastic waste. Because current plastics, and polyolefins such as polyethylene in particular, have become a necessity for modern life, it is unlikely that more sustainable, alternative plastics can displace them anytime soon, so one of the best ways to mitigate plastic waste is to develop more sustainable, alternative recycling methods. Pyrolysis, or thermal degradation under an inert atmosphere, shows great promise in this regard, since it is capable of chemically recycling plastics back to their constituent monomers or to value-added chemicals. However, knowledge of the mechanisms and reaction kinetics underlying polyethylene pyrolysis remains extremely lacking, hindering development of large-scale plastic recycling capabilities. Therefore, the primary objective of this thesis was to investigate those kinetics and shed new light on the reasons behind the vast discrepancies reported in the literature. Fundamental understanding of polyethylene pyrolysis has previously been limited due to an inability to obtain intrinsic reaction kinetics; instead, the literature presently reports only apparent kinetics, which are a combination of intrinsic kinetics and a variety of other transport and system design limitations. In this thesis, an extensive summary of these limitations in other works is presented, and a new system, known as the Pulse-Heated Analysis of Solid Reactions, or PHASR, system was developed to overcome these limitations. The PHASR system is uniquely capable of operating under “isothermal, reaction-controlled” conditions, at which intrinsic kinetics can reliably be measured. The PHASR system was validated extensively to ensure operation in this desired regime, and detailed descriptions of the reactor setup and experimental methodologies are presented. Alongside this system, a second, Visual PHASR system was developed as well, to enable visualization of polyethylene pyrolysis reaction phenomena for the first time, via integrated high-speed photographic equipment. The method of PHASR was then used to study the intrinsic kinetics of polyethylene pyrolysis. Conversion of low-density polyethylene to pyrolysis products was measured over a range of reaction temperatures (550 to 650 °C) and reaction durations (20 ms to 2.0 s), and three distinct product lumps were characterized via integrated gas chromatography and a microgram-resolution balance. Lumped intrinsic reaction kinetics were calculated using these product fractions. The results were further validated by applying a generalized Rice-Herzfeld radical reaction model to the polyethylene pyrolysis system; good agreement was found between this first principles approach and the PHASR experimental data. Additionally, extensive characterization was performed on the residues left behind in PHASR post-pyrolysis, and this helped elucidate new insights into the different reaction timescale regimes that are present during polyethylene pyrolysis.Item Polymerization Kinetics of Cyclic Esters by Metal Alkoxide Complexes and Catalytic Decarbonylation of Bio-Derived Carboxylic Acids to Commodity Alkenes(2014-05) Miranda, MariaPlastic materials are an integral part of modern life; however, nearly every plastic, or polymer, is derived from petroleum resources, which are non-sustainable, non-degradable, and can be toxic to humans and the environment. Developing methodologies to synthesize and characterize alternative materials that are degradable, safe, and sustainable has therefore been a vibrant research area. This thesis describes two approaches towards the development of sustainable polymers and monomers (the building blocks from which polymers are made). The first aims to understand the fundamental mechanistic details of metal-catalyzed ring-opening polymerization of renewable cyclic ester monomers to degradable polyesters. The second targets the catalytic synthesis of common petroleum-based monomers from sustainable and biomass-derived carboxylic acids.Item Supporting data for Impact of macromonomer molar mass and feed composition on branch distributions in model graft copolymerizations(2021-12-07) Zografos, Aristotelis; Lynd, Nathaniel A; Bates, Frank S; Hillmyer, Marc A; hillmyer@umn.edu; Hillmyer, Marc A; University of Minnesota, Department of ChemistryThese files contain primary data along with associated output from instrumentation supporting all results reported in the referenced manuscript. Graft polymers are useful in a versatile range of material applications. Understanding how changes to the grafted architecture, such as the grafting density (z), the side-chain degree of polymerization (Nsc), and the backbone degree of polymerization (Nbb), affect polymer properties is critical for accurately tuning material performance. For graft-through copolymerizations, changes to Nsc and z are controlled by the macromonomer degree of polymerization (NMM) and initial fraction of the macromonomer in the feed (fMM0), respectively. We show that changes to these parameters can influence the copolymerization reactivity ratios and, in turn, impact the side-chain distribution along a graft polymer backbone. Poly((±)-lactide) macromonomers with NMM values as low as ca. 1 and as high as 72 were copolymerized with a small-molecule dimethyl ester norbornene comonomer over a range of fMM0 values (0.1 ≤ fMM0 ≤ 0.8) using ring opening metathesis polymerization (ROMP). Monomer conversion was determined using 1H nuclear magnetic resonance spectroscopy, and the data were fit using terminal and non-terminal copolymerization models. The results from this work provide essential information for manipulating Nsc and z, while maintaining synthetic control over the side-chain distribution for graft-through copolymerizations.Item Systems Design and Synthetic Construction of Influenza Virus for Flu Vaccine Application(2021-11) Phan, ThuInfluenza A virus (IAV) is the leading cause of annual flu epidemics, which inflicts about 250,000-500,000 deaths worldwide. The morbidity and mortality rate are much higher when a novel strain of IAV arises, resulting in flu pandemics. Vaccination has been the best prevention strategy for influenza. However, flu viruses constantly evolve and escape the established immunity, thus annual flu vaccination is required. Most current flu vaccine manufacturing platforms use multi-plasmid transfection to rescue seasonal seed viruses, the seed viruses are then used to infect either embryonic chicken eggs or cultured cells to produce viruses. Both production methods have high degrees of variability and produce viruses with a high content of non-infectious particles that reduce vaccine effectiveness. To address the need for more reliable and scalable processes, we applied systems biology and synthetic biology approaches to understand the kinetics of virus replication and to engineer cell lines that can control viral gene expression dynamics. First, we established a new data analysis pipeline using RNA sequencing to study segment-specific kinetics of all IAV RNA molecules. Using the pipeline, InVERT, to study the kinetics of IAV infection, revealed different phases of virus infection, and groups of genes whose kinetics are similar. This was the first-time IAV replication kinetics of all segments is reported. Building on that success, we then developed the second pipeline named InVERT II, which can further differentiate mRNA transcripts made by the viral replication enzyme RdRP from mRNA transcripts synthesized by host cells' RNA Polymerase II, to study the kinetics of virus rescue by transfection. With the understanding gained from the kinetics of virus infection and replication, we engineered the human cell line HEK 293T to express inducible components of IAV that not only have inducible replicative activity but also can package virus particles. This is the first proof of principle to show that mammalian cells can be engineered to produce complex negative-sense RNA viruses. Our integrative approach using both systems biology and synthetic biology has enabled the creation of a platform that could be further optimized for reliable, robust, and scalable flu vaccine manufacturing processes.