We study diffusion-reaction-advection models describing population dynamics of aquatic organisms subject to a constant drift, with reflecting upstream and outflow downstream boundary conditions. We consider three different models: single logistically growing species, two and three competing species. In the case of a single population, we determine conditions for existence, uniqueness and stability of non-trivial steady-state solutions. We analyze the dependence of such solutions on advection speed, growth rate and length of the habitat. Such analysis offers a possible explanation of the "drift paradox" in our context. We also introduce a spatially implicit ODE (nonspatial approximation) model which captures the essential behavior of the original PDE model. In the case of two competing species, we use a diffusion-advection version of the Lotka-Volterra competition model. Combining numerical and analytical techniques, in both the spatial and nonspatial approximation settings, we describe the effect of advection on competitive outcomes. Finally, in the case of three species, we use the nonspatial approximation approach to analyze and classify the possible scenarios as we change the flow speed in the habitat.

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.

We study diffusion-reaction-advection models describing population dynamics of aquatic organisms subject to a constant drift, with reflecting upstream and outflow downstream boundary conditions. We consider three different models: single logistically growing species, two and three competing species. In the case of a single population, we determine conditions for existence, uniqueness and stability of non-trivial steady-state solutions. We analyze the dependence of such solutions on advection speed, growth rate and length of the habitat. Such analysis offers a possible explanation of the "drift paradox" in our context. We also introduce a spatially implicit ODE (nonspatial approximation) model which captures the essential behavior of the original PDE model. In the case of two competing species, we use a diffusion-advection version of the Lotka-Volterra competition model. Combining numerical and analytical techniques, in both the spatial and nonspatial approximation settings, we describe the effect of advection on competitive outcomes. Finally, in the case of three species, we use the nonspatial approximation approach to analyze and classify the possible scenarios as we change the flow speed in the habitat.

No description available.

Tripeptidyl peptidase II (TPPII) is an exopeptidase which cleaves tripeptides from theN-terminus of peptides. The exact functional role of TPPII is still a matter of investigation. Itis believed that the enzyme is primarily involved in intracellular protein degradation, where itcooperates with the proteasome and other peptidases to degrade proteins into free aminoacids. These amino acids can subsequently be used in the production of new proteins. The aimof this work was to express murine wild type TPPII using E. coli and thereafter purify theenzyme from the bacterial lysate. Methods used for the purification included protein andnucleic acid precipitation, anion exchange chromatography, hydrophobic interactionchromatography and gel filtration. The presence of TPPII was determined using activityassay, western blot and SDS-PAGE. Despite the fact that some modification is still needed,the purification yielded a total of 34μg TPPII with a purity of approximately 60%. Thispurified enzyme can be used for future functional characterization.

In this thesis, we first show that the performance of ranking and selection (R&S) procedures in steady-state simulations depends highly on the quality of the variance estimates that are used. We study the performance of R&S procedures using three variance estimators --- overlapping area, overlapping Cramer--von Mises, and overlapping modified jackknifed Durbin--Watson estimators --- that show better long-run performance than other estimators previously used in conjunction with R&S procedures for steady-state simulations. We devote additional study to the development of the new overlapping modified jackknifed Durbin--Watson estimator and demonstrate some of its useful properties. Next, we consider the problem of finding the best simulated system under a primary performance measure, while also satisfying stochastic constraints on secondary performance measures, known as constrained ranking and selection. We first present a new framework that allows certain systems to become dormant, halting sampling for those systems as the procedure continues. We also develop general procedures for constrained R&S that guarantee a nominal probability of correct selection, under any number of constraints and correlation across systems. In addition, we address new topics critical to efficiency of the these procedures, namely the allocation of error between feasibility check and selection, the use of common random numbers, and the cost of switching between simulated systems.

All computer simulation models require some form of initialization before their outputs can be considered meaningful. Simulation models are typically initialized in a particular, often "empty" state and therefore must be "warmed-up" for an unknown amount of simulation time before reaching a "quasi-steady-state" representative of the systems' performance. The portion of the output series that is influenced by the arbitrary initialization is referred to as the initial transient and is a widely recognized problem in simulation analysis. Although several methods exist for removing the initial transient, there are no methods that perform well in all applications. This research evaluates the effectiveness of several techniques for reducing initialization bias from simulations using the commercial transportation simulation model VISSIM®. The three methods ultimately selected for evaluation are Welch's Method, the Marginal Standard Error Rule (MSER) and the Volume Balancing Method currently being used by the CORSIM model. Three model instances - a single intersection, a corridor, and a large network - were created to analyze the length of the initial transient for varying scenarios, under high and low demand scenarios. After presenting the results of each initialization method, advantages and criticisms of each are discussed as well as issues that arose during the implementation. The results for estimation of the extent of the initial transient are compared across each method and across the varying model sizes and volume levels. Based on the results of this study, Welch's Method is recommended based on is consistency and ease of implementation.

Most modern systems are equipped with very complex, expensive, and high technology components whose maintenance costs have become an increasingly large portion of the total operating cost of these systems. Thus, the efficacy of the maintenance policy for these and related systems has become a major concern to both manufacturing and design engineers. Different kinds of maintenance strategies have been proposed to solve the problem. While some of these have proven effective, there is yet no definitive approach that has been found that support the maintainability requirements of transient systems or systems that exhibit transient behavior. Transient behavior is the notion of non-steady state operation, which is the characteristic of system operation during its useful life. For designing convenience most of the maintenance strategies have assumed negligible maintenance or repair time which is not practical.In this research an opportunistic maintenance (OM) approach is implemented on a multi-unit system that exhibits transient behavior. Under OM policy, if a maintenance event has been scheduled for certain components and in the process of implementing the scheduled maintenance of these targeted components, the maintenance of other components whose maintenance times are in close proximity is also implemented at the same time. As a result, the time and cost of marshalling and staging maintenance resources are reduced. As part of the system effectiveness measure, the instantaneous system availability based on the transient nature of the system, is estimated using the renewal theory approach.

Spray cooling is a high heat removal technique which has been used widely in many industries, especially metallurgical, where the control of the temperatures of metals is an important factor to obtain the desired microstructure; and also in microelectronics where is very important to obtain high heat fluxes at relatively low surface temperatures. In this study, an open loop spray cooling system has been fabricated to provide an upward-facing spray over a 12 mm diameter test surface. A full cone spray nozzle was used to deliver deionized water to the test surface at five pressures (10, 15, 20, 25 and 30 psi), and at three different distances to the test surface (3, 7 and 12 mm). The volumetric flow rate at the surface used in the experiments depended on both the pressures and the distances. For a distance of 3 mm and 7 mm, the volumetric flow rate range from 336.6 to 627 ml/min while for 12 mm, the range was from 336.6 to 484.28 ml/min. Heat fluxes of 1.92 to 451 W/cm2, 2.1 to 417.3 W/cm2 and 1.9 to 409.5 W/cm2 for distances of 3, 7 and 12 mm respectively were registered at different input power levels. For all the three distances, the volumetric flow rate affects the heat flux, especially for 3 mm; and this effect decreases for higher distances. However, the distance between the nozzle and the test surface has little effect on the heat flux at low pressures but at higher pressures, the difference in heat flux is mainly due to the fact that part of the spray does not impinge the test surface.

The human mitochondrial DNA (mtDNA) genome must be faithfully maintained by the mitochondrial DNA replication machinery. Deficiencies in mtDNA maintenance result in the accumulation of mutations and deletions, which have been associated with a number of neuromuscular degenerative disorders including, mtDNA depletion syndrome, Alpers syndrome, progressive external opthalmoplegia (PEO), and sensory ataxic neuropathy, dysarthria, and opthalmoparesis (SANDO). The mtDNA replication machinery is comprised of a nuclearly-encoded DNA polymerase gamma (Pol γ), single-stranded DNA binding protein (mtSSB), and a hexameric mtDNA helicase. In this work, we employed quantitative pre-steady state kinetic techniques to establish the mechanisms responsible for the replication of the human mitochondrial DNA by Pol γ and explored the effects of point mutations that are observed in heritable diseases. With our biochemical characterization of mutants of Pol γ, we have shown unique characteristics that would lead to profound physiological consequences over time. Additionally, we have made significant progress towards reconstitution of the mitochondrial DNA replisome by monitoring DNA polymerization that is dependent on helicase unwinding of double stranded DNA. Overall, this work provides a better understanding of the mechanism of mtDNA replication and has important implications toward understanding the role of mitochondrial DNA replication in mitochondrial disease, ageing and cancer. In addition to the work on the mtDNA replisome, we have applied pre-steady state kinetic techniques to better understand the mechanism of RNA-dependent DNA polymerization by HIV reverse transcriptase (HIV-RT). This enzyme is responsible for the replication of the viral genome in HIV and is a common target for anti-HIV drugs. We have characterized the role of enzyme conformational changes in the kinetics of incorporation of correct nucleotide and the Nucleotide Reverse Transcriptase Inhibitor (NRTI) AZT by wild-type enzyme, as well as a mutant with clinical resistance to AZT. This work provides a better understanding of the complete mechanism of RNA-dependent DNA polymerization, the changes in the mechanism in the presence of inhibitor and the development of resistance to this nucleoside analog; and thereby this work contributes to the long-term goal of designing more effective drugs that can possibly deter resistance and be used successfully for treatment of HIV. / text