Bibliography: leaves 117-124 / 124 leaves,[31] leaves : ill ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Physics, 1984

Includes bibliographical references / 119 leaves, [67] leaves : ill., maps ; 31 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--Dept. of physics, University of Adelaide, 1983

Computational and mathematical models of cellular processes promise great benets in important elds such as molecular biology and medicine. Increasingly, researchers are incorporating the fundamentally discrete and stochastic nature of biochemical processes into the mathematical models that are intended to represent them. This has led to the formulation of models for genetic networks as continuous-time, discrete state, Markov processes, giving rise to the so-called Chemical Master Equation (CME), which is a discrete, partial dierential equation, that governs the evolution of the associated probability distribution function (PDF). While promising many insights, the CME is computationally challenging, especially as the dimension of the model grows. In this thesis, novel methods are developed for computing the PDF of the Master Equation. The problems associated with the high-dimensional nature of the Chemical Master Equation are addressed by adapting Krylov methods, in combination with Finite State Projection methods, to derive algorithms well-suited to the Master Equation. Variations of the approach that incorporate the Strang splitting and a stochastic analogue of the total quasi-steady-state approximation are also derived for chemical systems with disparate rates. Monte Carlo approaches, such as the Stochastic Simulation Algorithm, that simulate trajectories of the process governed by the CME have been a very popular approach and we compare these with the PDF approaches developed in this thesis. The thesis concludes with a discussion of various implementation issues along with numerical results for important applications in systems biology, including the gene toggle, the Goldbeter-Koshland switch and the Mitogen-Activated Protein Kinase Cascade.

Computational and mathematical models of cellular processes promise great benets in important elds such as molecular biology and medicine. Increasingly, researchers are incorporating the fundamentally discrete and stochastic nature of biochemical processes into the mathematical models that are intended to represent them. This has led to the formulation of models for genetic networks as continuous-time, discrete state, Markov processes, giving rise to the so-called Chemical Master Equation (CME), which is a discrete, partial dierential equation, that governs the evolution of the associated probability distribution function (PDF). While promising many insights, the CME is computationally challenging, especially as the dimension of the model grows. In this thesis, novel methods are developed for computing the PDF of the Master Equation. The problems associated with the high-dimensional nature of the Chemical Master Equation are addressed by adapting Krylov methods, in combination with Finite State Projection methods, to derive algorithms well-suited to the Master Equation. Variations of the approach that incorporate the Strang splitting and a stochastic analogue of the total quasi-steady-state approximation are also derived for chemical systems with disparate rates. Monte Carlo approaches, such as the Stochastic Simulation Algorithm, that simulate trajectories of the process governed by the CME have been a very popular approach and we compare these with the PDF approaches developed in this thesis. The thesis concludes with a discussion of various implementation issues along with numerical results for important applications in systems biology, including the gene toggle, the Goldbeter-Koshland switch and the Mitogen-Activated Protein Kinase Cascade.

Thesis (M. Sc.)--University of Canterbury, 2007. / Typescript (photocopy). Includes bibliographical references (p. 62-63). Also available via the World Wide Web.

Thesis (M. Sc.)--University of Canterbury, 2009. / Typescript (photocopy). "July 15, 2009." Includes bibliographical references (p. 71-73). Also available via the World Wide Web.

University, Diss., 2004--Kiel.

University, Diss., 2004--Kiel.

Trophic interactions within aquatic ecosystems are complex, with many different pathways facilitating transfer of energy and nutrients among trophic levels and many different mechanisms that influence energy and nutrient transfer. This is illustrated in the “top down” and “bottom up” regulatory effects on aquatic food webs, through which primary producer biomass and, therefore, herbivore and carnivore densities, are influenced by both nutrient availability (bottom up) and densities of consumers at higher trophic levels (top down). In an aquatic food web, planktivore presence can directly alter zooplankton density via consumption, while indirectly shaping phytoplankton biomass via reduced herbivore abundance and the release of nutrients due to excretion, egestion, and decomposition. Novel species introduced into an established food web may have important consequences. An invasive species may impact an invaded food web through competition, predation, alteration of nutrient cycling, or, potentially, through facilitation of native species or other invasives. For example, an invasive planktivore may shift zooplankton density or community composition, thereby facilitating phytoplankton blooms. Such a planktivore may also compete with and, potentially, replace native species. Moreover, an invasive species that reaches high densities within its invaded range may serve as an important nutrient sink as it consumes a high biomass of native species or a nutrient source via excretion or decomposition. Two such invasive species with the capacity to dramatically alter native food web dynamics are bighead (Hypophthalmichthys nobilis) and silver carp (H. molitrix; collectively, bigheaded carp). Bigheaded carp are large-bodied, planktivorous fishes that were introduced into the United States in the 1970s and have since spread throughout much of the Mississippi River and its tributaries. These species currently threaten the Great Lakes, where they may constitute a threat to native planktivores such as gizzard shad (Dorosoma cepedianum) and commercially important species such as walleye (Sander vitreus), although there remains a great deal of uncertainty surrounding their potential ecosystem impacts. Consumption of both zooplankton and phytoplankton has been observed in bigheaded carp, although their impact on primary producer biomass is not well understood. Although field observations suggest that condition and abundance of native planktivores, including gizzard shad and bigmouth buffalo (Ictiobus cyprinellus), as well as zooplankton density, have declined following the bigheaded carp invasion, there is little direct, experimental evidence of bigheaded carp food web impacts. Therefore, I sought to examine the effects of bigheaded carp on native ecosystems through a series of mesocosm experiments at the Southern Illinois University pond facility. My primary objectives were to 1) observe potential competition between bigheaded carp and the native gizzard shad, 2) evaluate effects of bigheaded carp predation on zooplankton and phytoplankton communities, 3) assess impacts of bigheaded carp decomposition on nitrogen and phosphorus availability, and 4) measure the rate at which bigheaded carp excrete nitrogen and phosphorus. In order to elucidate the impacts of bigheaded carp on gizzard shad growth and survival, zooplankton and phytoplankton densities, and nitrogen and phosphorus availability in the pelagic and benthic pools and to determine whether gizzard shad experience a diet shift in response to bigheaded carp presence, I performed two mesocosm experiments with three treatments: gizzard shad only, gizzard shad, bigheaded carp, and fishless control (Chapter 1). I predicted that bigheaded carp would reduce zooplankton densities but that gizzard shad, which are both detritivorous and planktivorous, would be unaffected due to their ability to use detritus as an alternative food source. Additionally, both predator release via zooplankton consumption and increased nutrient availability from bigheaded carp excretion would stimulate phytoplankton. I found that gizzard shad survival was reduced by bigheaded carp presence but that surviving gizzard shad did not experience a decline in growth in the bigheaded carp plus gizzard shad treatments. This may have been due to the ability of gizzard shad to consume detritus, as foreguts of sampled gizzard shad in Experiment 2 contained mostly detritus. Moreover, phytoplankton density declined in the presence of silver carp in Experiment 2, suggesting silver carp herbivory. In addition, nitrogen and phosphorus availability in either the pelagic or benthic pools did not appear to be impacted by bigheaded carp presence. After demonstrating experimentally the overall negative impact of bigheaded planktivory on native food webs, I focused my remaining two chapters on the effects of silver carp on nutrient availability. In Chapter 2, I outline a decomposition experiment testing for potential changes in pelagic and benthic nitrogen and phosphorus availability and, in turn, phytoplankton, zooplankton, and macroinvertebrate densities in response to silver carp decomposition. Although silver carp die offs have been reported throughout the Midwest, little is known about the magnitude of those die offs and their consequences for the ecosystem. In this study, silver carp decomposition did not appear to alter nutrient availability or densities of phytoplankton or invertebrates. However, in comparison to northern streams in which salmon spawning and decomposition provide an important nutrient subsidy, the mesocosms used in this study have relatively higher background nutrient concentrations. Thus, silver carp decomposition, at least at the densities studied, may have little importance to in-stream nutrient availability. Lastly, because I am interested in how bigheaded carp, particularly silver carp, alter nutrient dynamics in invaded food webs, it is necessary to calculate silver carp nitrogen and phosphorus excretion rates, as well as body nitrogen and phosphorus content (Chapter 3). Nutrient stoichiometry theory predicts a balance between the relative consumption of nutrients by an organism and the extent to which the organism retains nutrients in its tissues or excretes them. Thus, it is a useful tool in determining how an invasive species may alter nutrient availability via consumption and excretion. In Chapter 3, I describe the body and excretion N:P ratios for silver carp, which exhibit a lower body N:P ratio than excretion N:P, suggesting that these organisms may serve as a sink for phosphorus. Moreover, silver carp body excretion N:P ratios were higher than those reported for gizzard shad, suggesting that, in regions where silver carp may replace gizzard shad or lower gizzard shad population density via competition (Chapter 1), silver carp may alter nutrient cycling processes in aquatic ecosystems by shifting the overall available N:P ratio. Bigheaded carp may pose a significant threat to invaded ecosystems through their potential to compete with native species, reduce plankton densities, and alter nutrient availability. However, although bigheaded carp are expanding in range and approaching the Great Lakes, the full extent of their ecosystem impacts remain uncertain. Through my work on bigheaded carp food web impacts, particularly the influence of silver carp on native species and nutrient cycling processes, I have found that bigheaded carp have the capacity to negatively impact invaded ecosystems overall by reducing zooplankton, phytoplankton, and forage fish densities. Moreover, as bigheaded carp in particular continue to reach high densities as they expand in range, their capacity to alter relative nitrogen and phosphorus availabilities must be monitored to understand the extent of their influence. Due to their ability to disrupt top down and bottom up processes in freshwater ecosystems, bigheaded carp constitute a critical environmental issue in the Great Lakes area and throughout the Midwest and, thus, it is imperative to continue to experimentally assess how bigheaded carp interact with native species to the detriment or benefit of U.S. freshwater communities.

This work presents a model of the fouling mechanism and the evaluation of compressor washing on line. The results of this research were obtained from experimental and computational models. The experimental model analyzed the localization of the particle deposition on the blade surface and the change of the surface roughness condition. The design of the test rig was based on the cascade blade arrangement and blade aerodynamics. The results of the experiment demonstrated that fouling occurred on both surfaces of the blade. This mechanism mainly affected the leading edge region of the blade. The increment of the surface roughness on this region was 1.0 μm. This result was used to create the CFD model (FLUENT). According to the results of the CFD, fouling reduced the thickness of the boundary layer region and increased the drag force of the blade. The model of fouling was created based on the experiment and CFD results and was used to calculate the engine performance in the simulation code (TURBOMATCH). The engine performance results demonstrated that in five days fouling can affect the overall efficiency by 3.5%. The evaluation of the compressor washing on line was based on the experimental tests and simulation of the engine performance. This system demonstrated that it could recover 99% of the original blade surface. In addition, this system was evaluated in a study case of a Power Plant, where it proved itself to be a techno-economic way to recover the power of the engine due to fouling. The model of the fouling mechanism presented in this work was validated by experimental tests, CFD models and information from real engines. However, for further applications of the model, it would be necessary to consider the specific conditions of fouling in each new environment.