Background: Knee joint motion and quadriceps activity play a crucial role in all lower limb tasks, especially those which are highly dynamic and weight-bearing. Due to anatomical differences between men and women such as height, leg length, and hip width, alignment and mechanics of the lower limb are different between males and females. An anatomical variable which is associated with alignment in the lower limb is the quadriceps muscle angle (q-angle). The purpose of this study is to determine if there is a relationship between q-angle, activity of the quadriceps and hamstring muscles and the kinetics and kinematics of the knee during stairclimbing. An investigation on the reliability of q-angle measurements was also made prior to the primary study. Methods: To test the interclass reliability of q-angle measurements, three individuals measured the q-angle on 20 subjects. The primary researcher measured the same twenty individuals on three separate days to determine intra-rater reliability. The primary study involved 10 male and 10 female subjects completing 20 stair-climbing trials (10 ascent, 10 descent). Kinematic and kinetic data were collected on the lower limbs as well as electromyography (EMG) on two quadriceps muscles and one hamstring muscle. Knee joint peak and occurrence of peak moments, average EMG amplitude and peak and occurrence of peak EMG were analyzed by gender and high and low q-angle. A two way analysis of variance (ANOVA) was used to test the statistical significance of each measured variable (alpha = 0.05). Results & Discussion: The inter-rater reliability for q-angle was low (0.27-0.78) but the intrarater reliability showed q-angle measurements to be very reliable (0.80-0.95). For study 2, it was found that females had increased vastus lateralis and vastus medialis peak EMG and average EMG amplitudes for stair ascent and descent compared to males. Furthermore, for descent only, females demonstrated having delayed occurrence of peak EMG for vastus lateralis and biceps femoris, and exhibited an increased peak knee extension moment and a decreased peak knee adduction moment compared to males. For q-angle, there was a significant difference found for biceps femoris occurrence of peak EMG during descent, with the high q-angle group having delayed occurrence of peak. For ascent, the high q-angle group had significantly increased average vastus lateralis EMG and an earlier occurrence of knee abduction moment. Q-angles were found to be higher for women compared to men. Conclusion: This study confirms that gender differences do exist in knee moment and thigh EMG parameters with stair ascent and stair descent. With the high incidence of significant findings for the quadriceps muscle, further investigation is warranted to determine if a relationship does exist between q-angle and knee joint function. It would also be recommended that hip mechanics be included in future studies due to the difference seen in adduction moments at the knee.

Under the assumption of mass-action kinetics, systems of chemical reactions can give rise to a wide variety of dynamical behaviour, including stability of a unique equilibrium concentration, multistability, periodic behaviour, chaotic behaviour, switching behaviour, and many others. In their canonical papers, M. Feinberg, F. Horn and R. Jackson developed so-called Chemical Reaction Network theory which drew a strong connection between the topological structure of the reaction graph and the dynamical behaviour of mass-action systems. A significant amount of work since that time has been conducted expanding upon this connection and fleshing out the theoretical underpinnings of the theory. In this thesis, I focus on three topics within the scope of Chemical Reaction Network theory. 1. Linearization: It is known that complex balanced systems possess within each invariant space of the system a unique positive equilibrium concentration and that that concentration is locally asymptotically stable. F. Horn and R. Jackson determined this through the use of an entropy-like Lyapunov function. In Chapter 4, I approach this problem through the alternative approach of linearizing the mass-action system about its equilibrium points. I show that this approach reproduces the results of F. Horn and R. Jackson and has the advantage of being able to give explicit exponential bounds on the convergence near equilibria. 2. Persistence: A well-known limitation of the theory is that the stabilities of the positive equilibrium concentrations guaranteed are locally limited. The conjecture that the equilibrium concentrations of complex balanced systems are global attractors of their respective invariant spaces has become known as the Global Attractor Conjecture and has received significant attention recently. This theory has been significantly aided by the realization that trajectories not tending toward the set of positive equilibria must tend toward the boundary of the positive orthant; consequently, persistence is a sufficient condition to affirm the conjecture. In Chapter 5, I present my contributions to this problem. 3. Linear Conjugacy: It is known that under the mass-action assumption two reaction networks with disparate topological structure may give rise to the same set of differential equations and therefore exhibit the same qualitative dynamical behaviour. In Chapter 6, I expand the scope of networks which exhibit the same behaviour to include ones which are related by a non-trivial linear mapping. I have called this theory Linear Conjugacy theory. I also show how networks exhibiting a linear conjugacy can be found using the mixed integer linear programming (MILP) framework introduced by G. Szederkenyi.

Adsorption at metal electrodes is usually a very fast process and it plays a most important role in many areas of industry. The thermodynamics of the process are well known for many systems. However, there is currently no good method that allows a determination of very fast kinetics of adsorption to be made. Previously, many attempts at evaluation of kinetic parameters of adsorption were made, but in moat cases, due to the inadequacy of the experimental methods used, the parameters obtained were much lower than expected. This thesis aims at providing the means for determining the kinetics of adsorption at metal electrodes. The methods herein described are based on two different experimental techniques. These techniques are: (i) fast cyclic voltammetry (FCV, potential sweep rate up to 100000 V/s) and (ii) high frequency AC and FFT SW (Fast Fourier Transform Square-wave) voltammetry (frequency up to 50 MHz) at ultramicroelectrodes (5 or 6.25 ìm in radius). A theoretical description of the adsorption process for both kinds of experiments is presented. A simulation program was written to provide a better understanding of the process and to elucidate the development of methods for determining the kinetics of adsorption. Thermodynamic and kinetic descriptions of the process are based on the Frumkin adsorption isotherm. Both the equilibrium constant and the adsorption rate constant are treated as functions of potential and the electrode coverage. Comparison of results for different systems is presented as an analysis of the dependence of the adsorption rate constant on the equilibrium constant. FCV proved to be useful in the evaluation of kinetics of chemisorption (standard rate constant in the range of 10⁶ s$\sp{-1})$ but the results for adsorption of aliphatic alcohols were unreliable. High frequency AC methods allowed the determination of kinetics of physical adsorption. It was found that the activation energy of the adsorption process can be expressed as a linear combination of the electrical component of the standard free energy of adsorption (a major contribution) and the energy of lateral interactions (a minor contribution). At the zero charge potential the rate constant reaches the maximum value of $\rm(4.6\pm0.3)10\sp9\ s\sp{-1}.$

Human T-cell lymphotropic virus type I (HTLV-I) is a retrovirus that is the causative agent of the fatal disease adult T-cell leukemia (ATL). HTLV-I silently infects over twenty million people worldwide; up to ten percent of these will develop ATL in their lifetime. There are currently no effective treatments for this disease. HTLV-I expresses its genome as polypeptides that must be processed in order to produce infectious virions. Like other retroviruses, HTLV-I encodes an aspartic acid protease to process these polypeptides into mature form. Because the protease is essential in the virus life cycle, it is an attractive target for the treatment of HTLV-I-induced ATL. The present work examines the structure and function of HTLV-I protease. A theoretical structure of the protease is presented, and the function of the C-terminal extension is considered. In order to determine which residues are involved in binding substrate, two experiments were performed: first, several residues were mutated to the corresponding residues in HIV-1 protease to determine whether HTLV-I protease can be made to process an HIV-1 protease substrate; second, an alanine scan was performed to knock out individual residues to assess their importance in binding substrate. This work builds knowledge of the structure and function of HTLV-I protease. By understanding which residues play a role in binding substrate and by developing a clearer picture of the structure of the protease, it will be possible to develop specific inhibitors for HTLV-I protease.

Systems biology is an emerging field of study that seeks to provide systems-level understanding of biological systems through the integration of high-throughput biological data into predictive computational models. The integrative nature of this field is in sharp contrast as compared to the Reductionist methods that have been employed since the advent of molecular biology. Systems biology investigates not only the individual components of the biological system, such as metabolic pathways, organelles, and signaling cascades, but also considers the relationships and interactions between the components in the hope that an understandable model of the entire system can eventually be developed. This field of study is being hailed by experts as a potential vital technology in revolutionizing the pharmaceutical development process in the post-genomic era. This work not only provides a systems biology investigation into principles governing de novo sphingolipid metabolism but also the various computational obstacles that are present in converting high-throughput data into an insightful model.

Despite a number of kinetic and spectroscopic studies, the chemical mechanisms of amine oxidation by flavoenzymes remain widely debated. The mechanisms of by Nmethyltryptophan oxidase (MTOX) and tryptophan 2-monooxygenase (TMO) were probed using a combination of pH and primary deuterium, solvent, and 15N kinetic isotope effects. Slow substrates were chosen for these studies; MTOX was characterized with N-methylglycine and TMO was characterized with L-alanine. Primary deuterium kinetic isotope effects of 7.2 and 5.3 were observed for sarcosine oxidation by MTOX and for alanine oxidation by TMO, respectively, independent of the substrate concentration and pH. Monitoring the reduction of flavin spectroscopically revealed no intermediate flavin species with both enzyme-substrate systems. Furthermore, the magnitudes of the 15N kinetic isotope effects observed with both systems suggest that nitrogen rehybridization and C-H bond cleavage are concerted. These results are consistent with both enzymes utilizing a hydride transfer mechanism for amine oxidation. The role of the iron ligands of tyrosine hydroxylase (TyrH) was also investigated. TyrH contains one iron per monomer, which is held by three conserved amino acid residues, two histidines and a glutamate. As a probe of the plasticity of the metal binding site, each of the metal ligands in TyrH was substituted with glutamine, glutamate, or histidine. The resulting proteins were characterized for metal content, catalytic activity, and dopamine binding. The H336E and H336Q enzymes retain substantial catalytic activity. In contrast, the E376Q enzyme retains about 0.4% of the wild-type catalytic activity, and the E376H enzyme has no significant activity. The H331E enzyme oxidizes tetrahydropterin in a tyrosine-independent manner. The position of the charge-transfer absorbance band for the H336E and H336Q enzyme-inhibitor complexes is shifted relative to that of the wild-type enzyme, consistent with the change in the metal ligand. In contrast, the E376H and E376Q enzymes catalyze dopamine oxidation. These results provide a reference point for further structural studies of TyrH and the other aromatic amino acid hydroxylases, and for similar studies of other enzymes containing this ironbinding motif.

The measure of chemiluminescence from the transition of the hydroxyl radical from its electronically excited state (A^2 Sigma^positive) to its ground state (X^2 Pi) is used in many combustion applications for diagnostic purposes due to the non-intrusive nature of the chemiluminescence measurement. The presence of the ultraviolet emission at 307nm is often used as an indicator of the flame zone in practical combustion systems, and its intensity may be correlated to the temperature distribution or other parameters of interest. To date, the measurement of the excited state OH, OH*, is mostly qualitative. With the use of an accurate chemical kinetics model, however, it is possible to obtain quantitative measurements. Shock-tube experiments have been performed in highly diluted mixtures of H2/O2/Ar at a wide range of pressures to evaluate the pressure-dependent rate coefficient of the title reaction. In such mixtures the main contributing reaction to the formation of OH* is, O H M = OH* M. R1 Previous work has determined the reaction rate of R1 at atmospheric conditions and accurately predicts the amount of OH* experimentally produced. At elevated pressures up to 15 atm, which are of interest to the gas turbine community, the currently used reaction rate of R1 (i.e., without any pressure dependence) significantly over predicts the amount of OH* formed. This work provides the pressure dependence of R1. The new reaction rate is able to reproduce the experimental data over the range of conditions studied and enables quantitative measurements applicable to practical combustion environments.

The tropospheric oxidation of unsaturated hydrocarbons is a central issue in atmospheric chemistry. These hydrocarbons are emitted into the atmosphere from both natural and anthropogenic sources, and their atmospheric oxidation leads to different atmospheric pollutants, including ground level ozone, photochemical smog and secondary organic aerosols. Isoprene and 1,3-butadiene represent a biogenic and an anthropogenic hydrocarbon, respectively, which primarily undergo electrophilic addition of OH radical, followed by chain propagating radical reactions. Their oxidation is the major source for ground level ozone formation in both rural and urban area and understanding their chemistry is essential for regional air quality modeling. Until recently, most of the studies of isoprene chemistry have been non-isomer specific, reflecting the reactivity of combined pathways and therefore were insensitive to specific details of the isomeric pathways. An isomeric selective approach to studying unsaturated hydrocarbon oxidation is described in this dissertation. A synthesized precursor, whose photolysis can provide a route to the formation of energy selected single isomer in the isoprene oxidation pathway, enables the study of important channels that are difficult to unravel in non isomer specific experiments. The major addition channel in OH isoprene oxidation has been studied following the isomeric selective approach and using Laser Photolysis-Laser Induced Fluorescence (LP-LIF) as the primary experimental technique. The study reveals important information about the oxidative chemistry of the δ-peroxy radicals, accounting for about 20 percent of missing carbon balance in isoprene oxidation, and isomeric specific rate constants. A similar approach was applied to study the oxidation of 1,3-butadiene, and the photolytic precursor for the dominant hydroxy alkyl isomer in the OH initiated oxidation of 1,3-butadiene was synthesized. The subsequent experiments and analysis revealed detailed information about the oxidative chemistry accounting for approximately 26 percent of the missing chemistry. Finally, non isomeric selective OH cycling experiments were carried out on the1,3-butadiene system. By analyzing the OH cycling data with the combined information obtained from the isomeric specific studies of the two isomeric channels of 1,3-butadiene oxidation, the relative branching between the two isomeric channels of OH-1,3-butadiene oxidation was determined.

Natural and synthetic estrogens are some of the most potent hormones detected in the environment. Agriculture fields often release higher concentrations of natural estrogens to the environment, but wastewater treatment plants (WWTPs) commonly release higher concentrations of synthetic estrogens. Estrogens can disrupt endocrine functions in wildlife and humans. Less attention has been paid to the fate and occurrence of estrogens in agricultural operations than WWTPs. Their fate is influenced by major mechanisms such as sorption and biodegradation. Sorption typically accounts for less than 10 percent of estrogen removal in WWTPs. However, biodegradation is a primary method for estrogen loss at high ammonia concentration in the agricultural and municipal operation. Less attention has been paid to the biodegradation kinetics of estrogens in the field application. Therefore, this dissertation focused on the occurrence of estrogens in agricultural fields and their biodegradation by a mixed culture and a pure culture. The estrogens in turkey litter amended fields might be biodegraded to some degree by turkey litter borne bacteria. The estrogen biodegradation by a mixed culture showed different mechanisms for each estrogen. E1 and E2 were easily degraded as a carbon source of the mixed culture. E3 and EE2 were favorable for cometabolic degradation by AOB. EE2 was not readily biodegraded by the mixed culture due to a steric hindrance of enzyme expression and EE2 metabolism in the ethynylgroup of EE2. The cometabolic kinetics of individual estrogen was evaluated by using a pure culture. The cometabolism of estrogen was demonstrated by a reductant model. This model appropriately estimated the cometabolic kinetics of individual estrogens. In addition, the effect of antibiotics on the hormone degradation was investigated in Sequencing Batch Reactors (SBRs). No significant difference was detected for the removal efficiency of target compounds in the SBRs in presence or absence of antibiotics (oxytetracycline and chlortetracycline) during long sludge retention time (SRT). However, the effluent organic matter (EfOM) was less decomposed with the presence of antibiotics, especially causing less degradation of the humic-like substances in EfOM. The results indicated the flux of antibiotics to WWTPs did not affect hormone degradation, but reduced the decomposition of humic-like substance. Finally, the findings from the research provide insight into how biodegradation influences estrogen removal in agricultural fields and municipal WWTPs. The models developed in this research yielded valuable predictive values for engineered systems.

Zeolites are microporous crystalline materials, which are widely used in catalysis, adsorption, and ion-exchange processes. However, in most cases, the synthesis of novel zeolites as functional materials still relies on trial-and-error methods, which are time consuming and expensive. Therefore, the motivation for this thesis work is to understand the zeolite synthesis mechanismand further develop knowledge for manipulating zeolite properties and ultimately the rational design of porous materials. This work focused on formation of silicalite-1 (pure-silica ZSM-5) from basic aqueous solutions containing tetraorthosilicate (TEOS) as silica source, and tetrapropylammonium (TPA) cations as the organic structure-directing agent. The presence of silica precursor particles with size of 2-5 nm in these mixtures prior to and during hydrothermal treatments have been observed through dynamic light scattering (DLS), small-angle X-ray (SAXS) and transmission electron microscopy (TEM). However, to quantify composition and the molecular structure transformation of these silica precursor particles during zeolite synthesis is still a technical challenge. Another important yet unresolved question is how organocations interact with these nanoparticles and direct zeolite nuclei. Unlike many studies performed analyzing the inorganic phase (silica) present in synthesis mixtures, this study quantified the organocation-silica particle interaction and its ultimate effect on zeolite growth mainly through probing the behavior of the organocations. Pulsed-field gradient (PFG) NMR was used to capture the mobility change of organocations, and was complemented with scattering measurements (DLS, SAXS) on the silica nanoparticles. On the basis of the measurement results, the thermodynamic and kinetic properties of the organic-inorganic interaction were derived. Upon aging at room temperature, this interaction manifested as binding of TPA onto the silica particles due to electrostatic interactions, and such binding behavior can be well described by the Langmuir adsorption model. Upon hydrothermal treatment, a fraction of TPA adsorbed at room temperature dissociates from the growing silica nanoparticles and the corresponding desorption profiles were fitted well by the pseudo-second order kinetic model. The addition of tetramethylammonium (TMA) as "competitors" promoted TPA desorption kinetics and hindered silica nanoparticle growth due to stronger association of TMA with particles than that of TPA. Finally, the TPA adsorption strength increased via addition of monovalent salts with increasing ionic size whereas that of TMA shows an opposite trend. This suggests one potential route for tuning the organic-silica precursor particle interactions and thus possibly affecting some kinetics steps in the synthesis.