Three aspects of the isomerization reaction of cyclopropane to propylene were explored, in order to evaluate the suitability of this rearrangement for use as a model reaction in studying the effects of pore diffusion on the rates of chemical change in porous solids. First, kinetic data for this reaction were extended from 555°C to 620°C, with good agreement being obtained with data of others at temperatures below 555°C For the results of this work, as well as for all other published results, the first order homogeneous rate constant at infinite pressure can be represented by log₁₀ k =15.38 [formula omitted] (T in degrees Kelvin) with an accuracy of ± 15% over the temperature range 470°- 620°C. Second, the isomerization was shown to proceed homogeneously in the presence of Pyrex surfaces, even with 60-fold changes in-the surface to volume ratio. Third, the only side reaction of any importance was the decomposition of propylene, which was found to be about 20-50 times slower than the cyclopropane isomerization. These results indicate that the cyclopropane reaction is a satisfactory one for the purposes of studying diffusion controlled processes, but the propylene pyrolysis may restrict the range of desirable experimental conditions. / Applied Science, Faculty of / Chemical and Biological Engineering, Department of / Graduate

Surgery to correct cam femoroacetabular impingement (FAI) is increasingly popular. Despite this, no known study has used motion analysis and ground reaction forces to quantify the outcome of surgery for FAI. The goal of this study was to compare the preoperative and postoperative lower-extremity joint kinematic and kinetic measurements of cam FAI patients during activities of daily living with use of a high-speed motion capture system and force platforms. We hypothesized that the lower-extremity joint mechanics of FAI patients during level walking and maximal squatting would resemble more those of healthy control subjects, after surgery. Ten patients with unilateral symptomatic cam FAI, who underwent corrective surgery using an open or combined technique, performed walking and maximal depth squatting trials preoperatively and postoperatively. Thirteen healthy control subjects, matched for age, sex and body mass index, provided normative data. Results showed that postoperatively, FAI patients had reduced hip ROM in the frontal and sagittal planes, produced smaller peak hip abduction and external rotation moments, and generated less peak hip power compared to the control group during level walking. During maximal squatting, postoperative FAI patients squatted to a greater depth, and had larger knee flexion and ankle dorsiflexion angles, as well as the sum of all joint angles of the affected limb at maximal depth compared to the preoperative values. The lower-extremity joint and pelvic mechanics of FAI patients did not fully return to normal after surgery. Although surgery seemed to reduce hip pain and restore a normal femoral head-neck offset, it further impaired muscle function as a result of muscle incisions. More research is needed to determine the effects of muscle incisions, which could help improve surgical techniques and develop better rehabilitation programs for FAI patients.

The purpose of this study was to examine the effects of body mass and sex on the joint biomechanics of the lower extremity during stair ascent and descent. Nineteen normal weight (8M and11F; BMI: 22.1 ± 1.8 kg/m2), 18 overweight (14M and 4F; BMI: 27.4 ± 1.3 kg/m2) and 8 obese subjects (3M and 5F; BMI: 33.3 ± 2.5 kg/m2) were recruited. Joint mechanical loading presented by joint moment of force and peak joint angles at the hip, knee, and ankle during stair climbing were recorded and analyzed using a motion analysis system with 10 cameras and 4 force plates. The MANOVA and linear regression analysis found a significantly larger knee extensor moment (p=0.026) among the overweight compared to the normal weight participants during descent. Sex differences were found in the peak joint angles, as the females abducted their knees more than the males (p=0.002; r(51) = 0.51) during descent.

The rate constants of the abstraction reaction Mu + HBr —• MuH + Br were measured using the well established μSR technique at TRIUMF. Measurements were made at various temperatures between 170 and 480 K, and fit to the Arrhenius equation both with and without an additional T½ dependence. The rate constants obtained were k(T) = (5.101 ± 0.106) x 10⁻¹¹ exp{-(0.560 ± 0.110) kcal mol⁻¹/RT} and k(T) = (0.183 ± 0.005) x 10⁻¹¹T½exp{-(0.286± 0.014) kcal mol⁻¹/RT} cm³ molecule⁻¹ s⁻¹. The low activation energy for such an exothermic reaction indicates that the barrier on the Mu + HBr surface is early. Kinetic isotope effects of the H/Mu + HBr reactions along with a lack of curvature in the Mu + HBr Arrhenius plot suggest that tunneling is relatively unimportant down to 170 K. / Science, Faculty of / Chemistry, Department of / Graduate

The etching of silicon by atomic and molecular chlorine and bromine was studied as a function of etchant pressure and reaction temperature. Various types of silicon were employed in the etching experiments including intrinsic and n-type polycrystalline silicon as well as the (100) face of intrinsic single crystal silicon. The pressures of Cl₂ and Br₂ varied from 0.1 to 30 Torr and the partial pressure of Cl and Br atoms was between 0.08 and 0.2 Torr. Temperatures of between 365 and 600°C were required for CI₂ and Br₂ etching, while lower temperatures of 25 to 470°C were sufficient for the more reactive Cl and Br atoms. The reaction between silicon and Br atoms was shown to be first order with respect to the partial pressure of atoms and a first order dependence was assumed for Cl atom etching. The rate constants were determined for the Cl and Br atom etching of intrinsic and n-type polycrystalline silicon, with a dopant concentration of 5x10¹⁸ atoms cm⁻³. The reactivity of Cl atoms with n-type silicon was approximately 90 times greater than with intrinsic silicon. This enhancement in reaction rate is primarily due to an increase in the preexponential factor in k₁, with the activation enthalpy for the process remaining unchanged at approximately 28 kJ mol⁻¹. For Br atom etching, the reaction rate for the n-type silicon was over 300 times greater than for intrinsic silicon and was characterized by activation enthalpies of 55 and 63 kJ mol⁻¹ respectively. The enhancement in reactivity can also be attributed principally to an increase in the preexponential factor. The preexponential factors for the rate constants are larger than those expected, based on the collision frequencies of Cl and Br atoms. This is interpreted as evidence for a preadsorption step in these reactions. The reactions of silicon with CI₂ and Br₂ were found to display a complex pressure dependence. The etch rates varied linearly with (etchant pressure)¹′² and the intercepts from a linear regression of the data were slightly negative. To account for the half order pressure dependencies observed in these etching reactions, a reversible dissociative adsorption mechanism is proposed whereby Br₂ (or CI₂) is dissociatively adsorbed, in a reversible reaction, onto the silicon surface yielding two atoms bound to the surface. This step is then followed by a first order reaction leading to the formation of a species which is either gaseous product or some precursor which forms that product in a subsequent non rate-determining step. From the slopes of etch rate versus (pressure)¹′² plots, composite half order rate constants were calculated and from the intercepts it was possible to evaluate the rate constant for dissociative adsorption of the halogen molecules. At high etchant pressures, where the reaction was half order with respect to Br₂ (or CI₂), a half order "composite" rate constant characterized the etching reaction. Values for the half order rate constant were determined for a number of wafers at various temperatures. From the temperature dependencies of these rate constants, activation enthalpies of 131±8 and 116±7 kJ mol⁻¹ were calculated for Br₂ and CI₂ etching of intrinsic polycrystalline silicon respectively. A value of 121±7 kJ mol⁻¹ was deterrnined for the Br₂ etching of silicon (100). Higher reaction rates were observed for the etching of n-type polycrystalline silicon, with greater enhancements observed for Br₂ relative to Cl₂ etching. The enhancements in etch rates were found to be principally due to a lower activation enthalpy for the half order rate constant. An activation enthalpy for the composite rate constant of 82±3 kJ mol⁻¹ was determined for Cl₂ etching of n-type silicon with a dopant atom concentration of 5x10¹⁸ atoms cm⁻³. Br₂ etching of the same wafer yielded an activation enthalpy of 86±3 kJ mol⁻¹. At low pressures, the reaction becomes first order and the temperature dependence of the corresponding first order rate constant yielded activation enthalpies of 109 and 83 kJ mol⁻¹ for intrinsic and n-type polycrystalline silicon. / Science, Faculty of / Chemistry, Department of / Graduate

Detailed chemical kinetic models are important to the understanding and prediction of combustion properties. Better estimations require an accurate description of thermochemistry and kinetic rate parameters. This study identifies important reaction pathways at the low temperature chemistry of branched conventional and alternative fuels. Rate constants and branching ratios for important reactions are provided and important phenomena are investigated. The thermochemistry and kinetics of the 2-methylhexane model, an important component in gasoline surrogate, is updated using recent group values and rate rules from the literature. New reactions, such as hydroperoxyalkylperoxy (OOQOOH) alternative isomerization, are also added to the model. The results show that both conventional and alternative isomerization of OOQOOH radicals significantly affect the model reactivity. The kinetics of a biofuel; iso-butanol, is also investigated in this study to understand alcohol combustion chemistry and identify sensitive reactions that require more attention. The results indicate that iso-butanol is sensitive to the chain propagation reaction of α-RO2 radical and the water elimination of γ-QOOH. Because both reactions decrease model reactivity, accurate rate constants are needed to correctly determine fuel reactivity. In light of the above mentioned kinetic modeling studies, high levels computational chemistry calculations were performed to provide site-specific rates rules for OOQOOH conventional isomerization considering all possible reaction sites. This is also one of the first studies to investigate the effect of chirality on calculated rate constants. Results indicate that chirality is important when two chiral centers exist in the reactant. OOQOOH alternative isomerization rate constants are usually assigned in analogy to the isomerization of an alkylperoxy (RO2) radical which may introduce some uncertainty. To test the validity of using analogous rates, this study calculates the rate constants for selected alternative isomerization reactions. The effect of intramolecular hydrogen bonding in the calculated energies and rate constants for different reaction pathways is investigated. The result shows that alternative isomerization is a competing pathway only when it proceeds via a less strained transition state relative to the conventional isomerization transition state. A detailed analysis of the hydrogen bonding effect helped to identify cases where assigning rates in analogy may not be valid.

Decay kinetics of bacteria in biological wastewater treatment systems are vital to efficient design and operation of treatment plants.  Of special concern are decay characteristics of fecal indicator organisms, which can aid design of wastewater treatment processes to eliminate fecal pathogens.  This study focuses on characterizing the decay of three strains of the key fecal indicator bacterium, Escherichia coli, and comparing microbial techniques for quantifying decay rates.  Traditional metrics for monitoring decay include volatile solids and plate counts, which may not provide the full picture of specific decay dynamics. In particular, the viable-but-not-culturable growth phase is challenging to assay.  Recently, more specific molecular techniques have been developed, such as DNA and RNA extraction with qPCR and RT-qPCR, ATP assays and live/dead cell-staining.  However, these assays have not been widely accepted or bench-marked against traditional techniques.  It is expected that molecular assays will generate kinetic constants that better reflect the viability and activity of the bacteria as they decay, generating a more integrated understanding of the decay process.  Cells grown in pure culture were spiked into microreactors and subjected to a variety of time/temperature treatments in both buffered pure culture and sludge matrices.  These scenarios were intended to mimic on a small scale typical waste treatment processes, more specifically pasteurization, thermophilic digestion and land application.  Results indicate decay curves similar to traditional curves but with constants that vary with respect to the strains and the characterization methods used.  The foundation laid by this work can be utilized in further studies involving other organisms in a variety of environmental scenarios. / Master of Science

The 7-deazaguanosine nucleosides queuosine (Q) and archaeosine (G⁺) are two of the most structurally complex modified nucleosides found in tRNA. Q is found exclusively in the wobble position of tRNAGUN coding for the amino acids asparagine, aspartate, histidine and tyrosine in eukarya and bacteria, while (G⁺) occurs in nearly all archaeal tRNA at position 15. In archaea preQ₀ is inserted into tRNA by the enzyme tRNA-guanine transglycosylase (TGT), which catalyzes the exchange of guanine with preQ₀ to produce preQ₀-tRNA. The first objective of this study was to identify and characterize the enzyme(s) catalyzing the conversion of preQ₀-tRNA to G+-tRNA. Comparative genomics identified a protein family possibly involved in the final steps of archaeosine biosynthesis, which was annotated as TgtA2. Structure based alignments comparing TGT and TgtA2 revealed that TgtA2 lacked key TGT catalytic residues and contained an additional module. The gene corresponding to "tgtA2" from "Methanocaldococcus jannaschii (mj1022)" was cloned, expressed and the purified recombinant enzyme characterized. Recombinant MjTgtA2 was shown to convert preQ₀-tRNA to G⁺-tRNA using glutamine, asparagine or NH₄⁺ as nitrogen donors in an ATP-independent reaction. This is the only example of the conversion of a nitrile to a formamidine known in biology. QueF catalyzes the reduction of preQ₀ to 7-aminomethyl-7-deazaguanine preQ₀ in the queuosine biosynthetic pathway. The second aim of this study was the transient state kinetic analysis of substrate binding and catalysis by the enzyme QueF, as well as investigation of the effects of ligands on its quaternary structure. Gel filtration and sedimentation equilibrium analyses indicated that QueF exists as a hybrid population in a rapid equilibrium between decamer and pentamer states. Addition of preQ₀ to QueF resulted in shifting the equilibrium towards the decamer state, as did the addition of divalent metals. Potassium chloride at high concentrations was found to disrupt the quaternary structure of QueF. Intrinsic tryptophan and NADPH fluorescence was used to determine the substrate binding to QueF by stopped-flow kinetic studies. Studies on the binding of preQ₀ to QueF in conjuction with binding NADPH to the QueF mutant E78A-thioimide intermediate suggested a two-step mechanism consisting of a fast bimolecular process and a subsequent slower unimolecular process, while the binding of preQ₀ to the C55A mutant was monophasic, consisting of only the fast bimolecular process. Thioimide formation was monitored by UV-Vis; under single turnover conditions the data fit well to single exponential rise. However, at high preQ₀ concentrations two phases could be observed. The reduction of the thioimide was determined under single turnover conditions by both UV-Vis and fluorescence, and comparable rates were obtained from both techniques. These results indicate that the binding of preQ₀ and NADPH to QueF, as well as thioimide formation, are very rapid; and that reduction of the thioimide is most likely the rate limiting step. Analysis of component rates suggests structural changes occur between these steps, further limiting the overall rate.

No description available.

A comprehensive understanding of sex-specific gait patterns throughout the lifespan is important considering differences between males and females that can manifest biomechanically, and epidemiological evidence of female sex being a risk factor for some age-related pathologies such as osteoarthritis. This thesis aimed to, 1) characterize the differences in lower extremity joint kinematics and kinetics during gait between healthy women and men in different age groups, and 2) define salient inter-joint kinematic coordination strategies in healthy adult gait. Gait data from 154 asymptomatic adult participants was analyzed. Waveform principal component analysis (PCA) was applied to hip, knee and ankle joint angles and net external moments to extract major patterns of variability. Using a two-factor ANOVA, PC scores were examined for significant sex, age and interaction effects. A second series of PCA models were also developed with the PC scores of the kinematic features of each joint to model the inter-joint kinematic coordination. Demographics, anthropometrics and root mean square (RMS) of EMG waveforms for the high and low groups (85th and 15th percentile) of the retained kinematic strategies were statistically compared using a one-way ANOVA analysis. 13 PC features differed between healthy male and female gait patterns and were independent of age category. No PC features significantly differed between the age groups, and there was no significant sex by age interactions. Four different kinematic gait coordination strategies were identified, one with a significant sex-effect. Therefore, both analyses supported sex-differences in gait biomechanics and the importance of using sex-specific normative data in clinical gait studies. Additionally, the results suggest underlying kinematic differences within asymptomatic adults are concentrated in the patterns of their gait mechanics. Understanding how these strategies may link to susceptibility of injury and disease has important implications for patient-centered care and may provide important insight into age-related pathology and disease. / Thesis / Master of Applied Science (MASc) / Since variability in healthy walking gait strategies may provide evidence for early mobility decline, this thesis aimed to identify the primary walking gait strategies in a healthy adult population. This work is distinct from previous work in that it comprehensively investigates the influence of sex and age on walking gait features and simultaneously defines primary walking gait strategies in healthy adults. The results indicate an overall difference in walking strategy between healthy male and female adults but no significant differences with age, indicating that age-matching for gait studies using adult controls is not as critical as sex considerations. Additionally, the results suggest that gait differences within healthy adults are concentrated in the patterns of their gait mechanics. Understanding how these strategies may link to susceptibility of injury and disease may provide important insight into age-related mobility limitations and help improve mobility longevity in the aging population.