A full length cDNA clone of Brassica napus 3-oxoacyl-ACP reductase (β-ketoacyl-ACP reductase; E.C. 1.1.1.100; βKR) and the Escherichia coli gene for the same enzyme, have been over-expressed in E. coli. Both the Brassica napus seed and Escherichia coli βKR proteins have been purified by a rapid two-step, single chromatography matrix method. Glutaraldehyde cross-linking studies show the plant βKR is expressed as a tetramer and the E. coli enzyme is expressed as a dimer. The secondary structure of the two proteins was predicted via analysis of circular dichroism spectra, which also show dilution dependent unfolding of a-helical structure in the plant enzyme, a possible explanation for the dilution inactivation of βKRs. Ultrafiltration substrate binding studies and a bireactant initial velocity study show that Brassica napus βKR employs a fixed order ternary complex mechanism with NADPH binding to the enzyme first. One-dimensional western blot analysis indicates two isoforms of βKR (28 kDa and 31 kDa) in crude B. napus seed extracts. Further analysis using two- dimensional western blots demonstrates the presence of four major isoforms. Comparison with 2D blots from B. campestris suggests that one of the major isoforms has originated from that source. The crystal structure of the E. coli βKR enzyme is also discussed.

No description available.

This work focuses on tracking formic acid adsorption as formate onto polycrystalline gold and its subsequent catalyzed oxidation to carbon dioxide. Formic acid oxidation is notoriously dependent on supporting electrolyte composition, a dependency that is little characterized. Additionally, the mechanism of oxidation is in disagreement in the literature. As such, the two preceding topics are the primary focus of this work, and are studied in HClO4 and H2SO4 solutions. Cyclic voltammetry experiments supplemented by mathematical modelling and fitting of data were used. Solution pH and adsorption of supporting electrolyte anions onto Au(poly) were very influential factors in determining formate coverages on Au(poly). This alone explains the effect of supporting electrolyte on this reaction. The coverage of adsorbed formate was found to be singularly responsible for determining the rate of formic acid oxidation. This implies a chemical rate limiting step for oxidation, leaving the oxidation rate constant independent of potential. Another segment of this work focuses on the statistical mechanics of lattice gases, namely the role of sites available for adsorption on the activity. This topic is central to the modelling of multiple adsorbing species in competition for the same adsorption sites. Activity for interaction-free lattice gases in the thermodynamic limit was found to be coverage of adsorbates over coverage of sites available for adsorption. This relationship was exploited to simulate coadsorption of two species, the first obeying the Langmuir isotherm and the second following the hard hexagon isotherm. This system was originally considered as a possible model for coadsorption of formate and sulfate in H2SO4 solutions, but did not match with data. / Graduate / 0494 / jstrobl@uvic.ca

Neste trabalho apresenta-se uma modelagem e a simulação de chamas difusivas turbulentas de etanol. A pesquisa trata da simulação da mistura molecular envolvendo reações químicas e combustão. Como os modelos de cinética química detalhada podem tornar-se computacionalmente proibitivos, por possuírem inúmeras reações e várias espécies, modelos cinéticos reduzidos são adotados. O mecanismo de oxidação do etanol utilizado possui 372 reações elementares e 56 espécies. Para diminuir a rigidez do sistema de equações rea- tivas resultantes, desenvolveu-se um mecanismo reduzido através do Método de Redução Sistemático, que usa as hipóteses de equilíbrio parcial e de regime permanente. A técnica Reaction Difusion Manifolds (REDIM), que aplica o conceito de variedade invariante, também foi implementada. A formulação Euleriana é utilizada para resolver as equações governantes da fase gasosa, que incluem as equações de Navier-Stokes, fração de mistura, fração mássica das espécies e temperatura. O efeito das gotas, fase líquida, é considerado pela introdução de termos fonte apropriados nas equações da fase gasosa. A Simulação em Grandes Escalas é utilizada para representar o fluxo turbulento com o modelo submalha de Smagorinsky para modelar a viscosidade turbulenta. Na simulação numérica adota-se o método de diferenças finitas com um sistema não oscilatório do tipo Total Variation Diminishing (TVD). O domínio é um queimador tridimensional com malha não uniforme para garantir a eficiência e precisão nos resultados em regiões onde o refinamento faz-se necessário. Para validar o modelo, além dos resultados numéricos para chamas difusivas de etanol, também realiza-se testes numéricos para chamas difusivas de metano e metanol, e os resultados obtidos comparam favoravelmente com dados encontrados na literatura. / This work presents the modeling and simulation of turbulent diffusion flames of etha- nol. The study addresses the simulation of the molecular mixing, chemical reactions and combustion. Since detailed chemical kinetics models may be computationally prohibitive, reduced kinetic models are adopted. The ethanol oxidation mechanism consists of 372 elementary reactions and 56 species. To decrease the stiffness of the reactive system of equations, a reduced mechanism is developed using the Systematic Reduction Method, based on the partial equilibrium and steady-state approximations. The Reaction Diffusion Manifolds (REDIM) technique, which applies the concept of invariant manifolds to treat the influence of the transport processes on the reduced model, is also employed. The Eule- rian formulation is used to solve the governing equations of the gas phase, which includes the Navier-Stokes, mixture fraction, species mass fraction and temperature equations. The effect of the drops, the liquid phase, is considered by introducing appropriate source terms in the equations of the gas phase. Large-Eddy Simulation is used to represent the turbulent flow with the Smagorinsky model for the turbulent viscosity. The numerical simulations are carried out using the finite difference method with a non oscillatory Total Variation Diminishing (TVD) scheme. The burner is a three-dimensional domain with nonuniform mesh to ensure efficiency and accuracy in regions where mesh refinement is necessary. To validate the model, besides the numerical results for diffusive flames of ethanol, numerical tests for methane and methanol diffusive flames are also carried out and the results compare favourably with data in the literature.

Neste trabalho apresenta-se uma modelagem e a simulação de chamas difusivas turbulentas de etanol. A pesquisa trata da simulação da mistura molecular envolvendo reações químicas e combustão. Como os modelos de cinética química detalhada podem tornar-se computacionalmente proibitivos, por possuírem inúmeras reações e várias espécies, modelos cinéticos reduzidos são adotados. O mecanismo de oxidação do etanol utilizado possui 372 reações elementares e 56 espécies. Para diminuir a rigidez do sistema de equações rea- tivas resultantes, desenvolveu-se um mecanismo reduzido através do Método de Redução Sistemático, que usa as hipóteses de equilíbrio parcial e de regime permanente. A técnica Reaction Difusion Manifolds (REDIM), que aplica o conceito de variedade invariante, também foi implementada. A formulação Euleriana é utilizada para resolver as equações governantes da fase gasosa, que incluem as equações de Navier-Stokes, fração de mistura, fração mássica das espécies e temperatura. O efeito das gotas, fase líquida, é considerado pela introdução de termos fonte apropriados nas equações da fase gasosa. A Simulação em Grandes Escalas é utilizada para representar o fluxo turbulento com o modelo submalha de Smagorinsky para modelar a viscosidade turbulenta. Na simulação numérica adota-se o método de diferenças finitas com um sistema não oscilatório do tipo Total Variation Diminishing (TVD). O domínio é um queimador tridimensional com malha não uniforme para garantir a eficiência e precisão nos resultados em regiões onde o refinamento faz-se necessário. Para validar o modelo, além dos resultados numéricos para chamas difusivas de etanol, também realiza-se testes numéricos para chamas difusivas de metano e metanol, e os resultados obtidos comparam favoravelmente com dados encontrados na literatura. / This work presents the modeling and simulation of turbulent diffusion flames of etha- nol. The study addresses the simulation of the molecular mixing, chemical reactions and combustion. Since detailed chemical kinetics models may be computationally prohibitive, reduced kinetic models are adopted. The ethanol oxidation mechanism consists of 372 elementary reactions and 56 species. To decrease the stiffness of the reactive system of equations, a reduced mechanism is developed using the Systematic Reduction Method, based on the partial equilibrium and steady-state approximations. The Reaction Diffusion Manifolds (REDIM) technique, which applies the concept of invariant manifolds to treat the influence of the transport processes on the reduced model, is also employed. The Eule- rian formulation is used to solve the governing equations of the gas phase, which includes the Navier-Stokes, mixture fraction, species mass fraction and temperature equations. The effect of the drops, the liquid phase, is considered by introducing appropriate source terms in the equations of the gas phase. Large-Eddy Simulation is used to represent the turbulent flow with the Smagorinsky model for the turbulent viscosity. The numerical simulations are carried out using the finite difference method with a non oscillatory Total Variation Diminishing (TVD) scheme. The burner is a three-dimensional domain with nonuniform mesh to ensure efficiency and accuracy in regions where mesh refinement is necessary. To validate the model, besides the numerical results for diffusive flames of ethanol, numerical tests for methane and methanol diffusive flames are also carried out and the results compare favourably with data in the literature.

Neste trabalho apresenta-se uma modelagem e a simulação de chamas difusivas turbulentas de etanol. A pesquisa trata da simulação da mistura molecular envolvendo reações químicas e combustão. Como os modelos de cinética química detalhada podem tornar-se computacionalmente proibitivos, por possuírem inúmeras reações e várias espécies, modelos cinéticos reduzidos são adotados. O mecanismo de oxidação do etanol utilizado possui 372 reações elementares e 56 espécies. Para diminuir a rigidez do sistema de equações rea- tivas resultantes, desenvolveu-se um mecanismo reduzido através do Método de Redução Sistemático, que usa as hipóteses de equilíbrio parcial e de regime permanente. A técnica Reaction Difusion Manifolds (REDIM), que aplica o conceito de variedade invariante, também foi implementada. A formulação Euleriana é utilizada para resolver as equações governantes da fase gasosa, que incluem as equações de Navier-Stokes, fração de mistura, fração mássica das espécies e temperatura. O efeito das gotas, fase líquida, é considerado pela introdução de termos fonte apropriados nas equações da fase gasosa. A Simulação em Grandes Escalas é utilizada para representar o fluxo turbulento com o modelo submalha de Smagorinsky para modelar a viscosidade turbulenta. Na simulação numérica adota-se o método de diferenças finitas com um sistema não oscilatório do tipo Total Variation Diminishing (TVD). O domínio é um queimador tridimensional com malha não uniforme para garantir a eficiência e precisão nos resultados em regiões onde o refinamento faz-se necessário. Para validar o modelo, além dos resultados numéricos para chamas difusivas de etanol, também realiza-se testes numéricos para chamas difusivas de metano e metanol, e os resultados obtidos comparam favoravelmente com dados encontrados na literatura. / This work presents the modeling and simulation of turbulent diffusion flames of etha- nol. The study addresses the simulation of the molecular mixing, chemical reactions and combustion. Since detailed chemical kinetics models may be computationally prohibitive, reduced kinetic models are adopted. The ethanol oxidation mechanism consists of 372 elementary reactions and 56 species. To decrease the stiffness of the reactive system of equations, a reduced mechanism is developed using the Systematic Reduction Method, based on the partial equilibrium and steady-state approximations. The Reaction Diffusion Manifolds (REDIM) technique, which applies the concept of invariant manifolds to treat the influence of the transport processes on the reduced model, is also employed. The Eule- rian formulation is used to solve the governing equations of the gas phase, which includes the Navier-Stokes, mixture fraction, species mass fraction and temperature equations. The effect of the drops, the liquid phase, is considered by introducing appropriate source terms in the equations of the gas phase. Large-Eddy Simulation is used to represent the turbulent flow with the Smagorinsky model for the turbulent viscosity. The numerical simulations are carried out using the finite difference method with a non oscillatory Total Variation Diminishing (TVD) scheme. The burner is a three-dimensional domain with nonuniform mesh to ensure efficiency and accuracy in regions where mesh refinement is necessary. To validate the model, besides the numerical results for diffusive flames of ethanol, numerical tests for methane and methanol diffusive flames are also carried out and the results compare favourably with data in the literature.

Les procédés industriels de fabrication de composites carbone/carbone consistent en la densification d’un substrat poreux (préforme) par dépôt de précurseurs gazeux. L’objectif de ce travail a été de développer et valider un mécanisme cinétique détaillé modélisant les réactions hétérogènes de dépôt de pyrocarbone par pyrolyse de propane. Les expérimentations ont été réalisées en utilisant un dispositif adapté à l’étude cinétique de réactions hétéro-homogènes. Des analyses par chromatographie ont permis de doser 29 espèces gazeuses, la vitesse de dépôt étant déterminée par pesée. Nous avons étudié l’influence des paramètres opératoires suivants : température (900-1050°C ); temps de passage (0,5-4 s), ratio S/V (20-170 cm-1) et composition de l’alimentation du réacteur (ajout d’hydrogène, acétylène et benzène). Le mécanisme hétérogène est constitué de 275 processus élémentaires impliquant 66 sites de surface. Les paramètres cinétiques des réactions de surface ont été estimés par analogie avec des réactions gazeuses « prototypes ». Les simulations ont été réalisées en utilisant Chemkin Surface. Le modèle permet de prédire de manière quantitative la vitesse de dépôt ainsi que les fractions molaires des principales espèces gazeuses. Les fractions molaires en espèces minoritaires sont reproduites de manière semi-quantitative. L’analyse de flux a montré que le pyrocarbone est principalement formé par dépôt de radicaux méthyles et de petites espèces insaturées (acétylène, éthylène) dans nos conditions opératoires / Industrial Carbon/Carbon composite manufacturing processes consist in the densification of a porous substrate (preform) by deposition of gaseous precursors. The aim of this work was to develop and validate a detailed kinetic mechanism modeling heterogeneous reactions of pyrocarbon deposition by propane pyrolysis. Experiments were carried out using an experimental set-up appropriate for studying the kinetics of hetero-homogeneous reactions. Chromatographic analysis were performed to quantify 29 gas phase species, the deposition rate being measured by weighing. We studied the influence of the following experimental parameters: temperature (900-1050°C), residence time (0.5-4 s), S/V ratio (20-170 cm-1) and composition of the reactor inlet (addition of hydrogen, acetylene and benzene). The heterogeneous mechanism contains 275 surface elementary steps involving 66 surface sites. Kinetic parameters of surface reactions were estimated by analogy with gas phase “prototype” reactions. Simulations were carried out using the Surface Chemkin package. The model is efficient to quantitatively predict the deposition rate as well as the mole fractions of major gas phase species. The mole fractions of minor species are semi-quantitatively predicted. The flow rate analysis demonstrates that the pyrocarbon is mostly formed by deposition of methyl radicals and small unsaturated species (acetylene, ethylene) in our experimental conditions

A one-dimensional, steady-state numerical model of the combustion of homogeneous solid propellant has been developed. The combustion processes is modeled in three regions: solid, two-phase (liquid and gas) and gas. Conservation of energy and mass equations are solved in the two-phase and gas regions and the eigenvalue of the system (the mass burning rate) is converged by matching the heat flux at the interface of these two regions. The chemical reactions of the system are modeled using a global kinetic mechanism in the two-phase region and an elementary kinetic mechanism in the gas region. The model has been applied to RDX, HMX and GAP. There is very reasonable agreement between experimental data and model predictions for burning rate, temperature sensitivity, surface temperature, adiabatic flame temperature, species concentration profiles and melt-layer thickness. Many of the similarities and differences in the combustion of RDX and HMX are explained from sensitivity analysis results. The combustion characteristics of RDX and HMX are similar because of their similar chemistry. Differences in combustion characteristics arise due to differences in melting temperature, vapor pressure and initial decomposition steps. A reduced mechanism consisting of 18 species and 39 reactions was developed from the Melius-Yetter RDX mechanism (45 species, 232 reactions). This reduced mechanism reproduces most of the predictions of the full mechanism but is 7.5 times faster. Because of lack of concrete thermophysical property data for GAP, the modeling results are preliminary but indicate what type of experimental data is necessary before GAP can be modeled with more certainty.

Choline oxidase (E.C. 1.1.3.17) from Arthrobacter globiformis catalyzes the four-electron oxidation of choline to glycine betaine (N,N,N-trimethylglycine) via two sequential, FAD-dependent reactions in which betaine aldehyde is formed as an enzyme-bound intermediate. In each oxidative half-reaction, molecular oxygen acts as electron acceptor and is converted into hydrogen peroxide. Biochemical, structural, and mechanistic studies on the wild-type and a number of mutant variants of choline oxidase have recently been carried out, allowing for the depiction of the mechanism of alcohol oxidation catalyzed by the enzyme. Catalysis by choline oxidase is initiated by the removal of the hydroxyl proton of alcohol substrate by a catalytic base in the enzyme-substrate complex, yielding the formation of the alkoxide species. In this dissertation, the roles of His351 and conserved His466 were investigated. The results presented demonstrate that His351 is involved in the stabilization of the transition state for the hydride transfer reaction and contributes to substrate binding. His466 is likely to be a catalytic base in choline oxidase due to its dramatic effect on enzymatic activity. Comparison of choline oxidase and other enzymes within its superfamily reveals the presence of a conserved His-Asn pair within the active site of enzymes. Therefore, the role of the conserved Asn510 in choline oxidase was examined in this study. The results presented here establish the importance of Asn510 in both the reductive and oxidative half-reactions. The lost of ability to form a hydrogen bond interaction between the side chain at position 510 with neighboring residues such as His466 resulted in a change from stepwise to concerted mechanism for the cleavages of OH and CH bonds of choline, as seen in the Asn510Ala mutant. Finally, the steady-state kinetic mechanism of pyranose 2-oxidase in the pH range from 5.5 to 8.5 was investigated. It was found that pH exerts significant effects on enzyme mechanism. This study has established the involvement of the residues in the initiation of enzyme catalysis and the stabilization of the alkoxide intermediate in choline oxidase. In addition, this work demonstrates the first instance in which the kinetic mechanism of a flavin-dependent oxidase is governed by pH.

Due to their potential health impact on human beings and ecosystems, persistent trace organic compounds (TOrCs) have aroused concern from both the public and professionals. In particular, the discharge of pharmaceuticals, endocrine disrupters, disinfection byproducts and other TOrCs from wastewater treatment plants into the environment is an area of extensive current research. This work studies the fate and treatments of TOrCs, with emphases on advanced oxidation processes (AOPs). This work presents predicted removal efficiencies of a variety of engineered and natural processes for 55 frequently encountered TOrCs in treated wastewater, based on previously reported data and using existing predictive models. Correlations between physicochemical and biological properties of TOrCs and treatment performance were explored. Removal of TOrCs in all processes investigated in this study was found to be sensitive to matrix effects. Heuristic guidelines for selection of sequenced treatment processes for TOrCs management were established. A field reconnaissance of natural process of TOrCs was conducted by analyzing the occurrence and fate of a suite of TOrCs, as well as estrogenic activity in water and sediments in the Santa Cruz River, an effluent-dependent stream in Tucson, Arizona. Some TOrCs, including contributors to estrogenic activity, were rapidly attenuated with distance of travel in the river. TOrCs that have low biodegradability and low octanolwater partitioning coefficients were less removed. Results of independent experiments indicated potential indirect photodegradation of estrogenic compound by reactive species generated from photolysis of effluent organic matter. Utilizing advanced oxidation processes (AOPs) as tertiary water and wastewater treatment is an option to prevent discharge of TOrCs into the environment. Compared to conventional AOPs, the ability of generating hydroxyl radicals (•OH) without additional doses of hydrogen peroxide (H2O2) or ozone makes ultraviolet (UV) photolysis of ferric hydroxo complexes a novel AOP, especially in acidic environments. A Fe(III)/UV254 kinetic model, which combines Fenton-like mechanism, and photolyses of Fe3+, FeOH2+ and H2O2 was proposed and experimentally validated to predict Fenton-like and H2O2 direct UV254 photolysis scenarios, individually. Nevertheless, the model underestimated the ferrous ion development during Fe(III)/UV254 photolysis, perhaps due to the overprediction of the oxidation of Fe2+ by •OH. The UV/H2O2 AOP was also studied in this work. A predictive kinetic model was developed to evaluate process efficiency of oxidation of p-cresol by UV/H2O2 photolysis based on a complete reaction mechanism, including reactions of intermediates with •OH. Results of this study highlight the significance of consideration of radical scavenging effects by the byproducts from oxidation of organic matter in model prediction performance.