In this study, a genome-scale metabolic model was constructed using published genomic and biochemical data. By employing the flux balance analysis (FBA) framework, the model was able to accurately predict ethanol yields on various carbon substrates, secretion profiles, and key characteristics of central metabolism under various growth conditions. A by-product of the model development was the construction of a pathway genome data-base (PGDB) of the yeast, named PichCyc. The PGDB was constructed using Pathway Tools and the database contains 5,841 genes, 1,457 reactions, 994 gene-associated reactions, and 1,475 metabolites. Pathway Tools also facilitated the annotation of an additional 155 genes through the use of Pathway Hole Filler. Together with the constraint-based model, a platform for model-guided metabolic engineering, high-throughput data contextualization, and a public-access online genomic/biochemical database was created.

The present work focuses on the study of two-phase flow behavior called “Intermittent Buoyancy Induced Flow” (IBIF) resulting from the loss of coolant circulation in a CANDU nuclear reactor core. The main objectives are to study steam bubble formation and migration through the pressure tube and into the feeder tubes and headers, and to study the effect of pressure tube sagging on the two-phase flow behavior during IBIF. Experiments are conducted using air and water flow at atmospheric pressure to qualitatively examine the IBIF phenomena. The test showed oscillating periodic behavior in the void fraction as the air vents. In addition to this, a mathematical model based on a simplified momentum balance for the liquid and gas phases was formulated. The model was further solved and compared to the experimental data. The model predictions showed a reasonable agreement within the investigated range of void fractions.

Petroleum coke (petcoke) has been burned at kraft pulp mills to partially substitute for natural gas and fuel oil used in lime kilns. Due to the high vanadium and sulfur contents in petcoke, there had been concerns over the impact of burning petcoke on kiln and chemical recovery operations. Laboratory studies were performed to examine the fate of vanadium and sulfur in lime kilns and chemical recovery cycle. The results suggest that most of the vanadium in petcoke quickly forms calcium vanadates with lime in the kiln, mostly 3CaO•V2O5. In the causticizers, calcium vanadates react with Na2CO3 in green liquor to form sodium vanadate (NaVO3). Due to its high solubility, NaVO3 dissolves in the liquor circulating around the chemical recovery system. V becomes enriched in the liquor, leading to vanadium build-up in the system. The S in petcoke would stay in the reburned lime, lower the lime availability, increase SO2 emissions from the kiln stack, alter the S balance, increase the liquor sulphidity, and potentially contribute to ring formation in the kiln.

A study is presented on the synthesis and characterization of nanoporous AgPt and AgAu alloys after annealing and dealloying in 5% HClO4. Dealloying removes the less-noble atom from the alloy surface to produce nanoporous, highly-interconnected ligaments. Voltammetry of AgPt and AgAu shows the critical potential, Ec, at various potential scan rates. Potential hold current decay experiments on Ag-23Pt and Ag-23Au further show the intrinsic Ec to be 275 mV and 290 mV, respectively. Ec was governed by thermodynamic clustering in the alloys as opposed to dissolution-diffusion kinetic effects. EDX shows the starting 77Ag-23Pt material changes composition after dealloying to about 12Ag-88Pt. XRD indicates the presence of ordering in AgPt via a superlattice (100)-peak for a specific anneal treatment. EIS measurements done on as-annealed and dealloyed AgPt and AgAu samples show the onset of bulk porosity and show that capacitance increase is equal for both alloys at two different dealloying potentials.

Plasmodium falciparum is the causative agent of malaria, one of the world‟s most prevalent infectious diseases. The emergence of strains resistant to current therapeutics creates the urgent need to identify new classes of antimalarials. Here we present and analyse a constraints-based model (iMPMP427) of P. falciparum metabolism. Consisting of 427 genes, 513 reactions, 457 metabolites, and 5 intracellular compartments, iMPMP427 is relatively streamlined and contains an abundance of transport reactions consistent with P. falciparum’s observed reliance on host nutrients. Flux Balance Analysis simulations reveal the model to be predictive in regards to nutrient transport requirements, amino acid efflux characteristics, and glycolytic flux calculation, which are validated by a wealth of experimental data. Furthermore, enzymes deemed to be essential for parasitic growth by iMPMP427 lend support to several previously computationally hypothesized metabolic drug targets, while discrepancies between essential enzymes and experimentally annotated drug targets highlight areas of malarial metabolism that could benefit from further research.

Microbial fuel cells (MFCs) are alternative energy resources that generate electricity from organic matter, where microorganisms such as the Geobacter species oxidize organic waste and transfer electrons to an electrode. Mathematical models are used to study biofilm processes, in hopes of developing MFCs into commercial applications. Existing biofilm models are based on Nernst-Monod type expressions, and are restricted to studying extracellular electrochemical/microbiological components, separated from the metabolic behavior of microorganisms. In this thesis, a model was developed combining extracellular biofilm conditions, with the intracellular metabolic fluxes of microorganisms under spatial heterogeneities (electron donor/acceptor levels) across the biofilm. This model predicts biofilm processes under varying extracellular conditions (presence/absence of NH4+, shear stress in continuous mode MFCs), and intracellular conditions (ATP maintenance fluxes); and also provides a preliminary evaluation of the pH changes across the biofilm. A sensitivity analysis based on the cell density and the biofilm conductivity was also conducted.

Neurotrophin-3 (NT-3) and anti-NogoA have shown promise in regenerative strategies after spinal cord injury; however, conventional methods for localized release to the injured spinal cord are either prone to infection or not suitable for sustained release. To address these issues, we have designed a composite drug delivery system that is comprised of poly(lactic-co-glycolic acid) (PLGA) nanoparticles dispersed in an injectable hydrogel of hyaluronan and methyl cellulose (HAMC). Achieving sustained and bioactive protein release from PLGA particles is a known challenge; consequently, we studied the effects of processing parameters and excipient selection on protein release, stability, and bioactivity. We found that embedding PLGA nanoparticles in HAMC results in more linear drug release due to the formation of a diffusion-limiting layer of methyl cellulose on the particle surface. Co-encapsulated MgCO3 was able to significantly improve NT-3 bioactivity, while trehalose + hyaluronan was able to improve anti-NogoA bioactivity and release.

An air cathode, membrane-less microbial fuel cell (MFC) containing a co-culture of Geobacter sulfurreducens and Escherichia coli was constructed and compared to pure culture MFCs of both organisms. The E. coli containing MFCs were unsparged and relied on E. coli for oxygen removal. The pure G. sulfurreducens MFC had a power output of 128 mW/m2, compared to 63 mW/m2 for the co-culture at an early stage and 56 mW/m2 for the late stage co-culture. The limiting current density is 404 mA/m2 for the pure G. sulfurreducens culture, 184 mA/m2 for the early co-culture, and 282 mA/m2 for the late co-culture, despite an increase in internal resistance between the early and late co-culture cells. Analysis of metabolites has shown that succinate production is likely to have negatively affected current production by G. sulfurreducens, and the removal of succinate is responsible for the increased current density in the late co-culture cell.

In this study, a genome-scale metabolic model was constructed using published genomic and biochemical data. By employing the flux balance analysis (FBA) framework, the model was able to accurately predict ethanol yields on various carbon substrates, secretion profiles, and key characteristics of central metabolism under various growth conditions. A by-product of the model development was the construction of a pathway genome data-base (PGDB) of the yeast, named PichCyc. The PGDB was constructed using Pathway Tools and the database contains 5,841 genes, 1,457 reactions, 994 gene-associated reactions, and 1,475 metabolites. Pathway Tools also facilitated the annotation of an additional 155 genes through the use of Pathway Hole Filler. Together with the constraint-based model, a platform for model-guided metabolic engineering, high-throughput data contextualization, and a public-access online genomic/biochemical database was created.

The effects of crosslinking on EVA foaming are studied in this thesis. A fundamental approach was applied to describe the influences of crosslinking on EVA/gas viscosities, gas solubility and diffusivity in EVA, EVA foaming nucleation and early stage of bubble growth, which leads to a better understanding of the plastic foaming mechanism. Although crosslinked polyolefin foaming technology has been well applied in industry, more fundamental and thorough studies are demanded to understand the mechanism, which can serve to improve the present technology. The shear and extensional viscosities have been measured for the chemically crosslinked EVA with dissolved gas which could not be found from literature. Furthermore, by controlling the crosslinking agent amount, the polymer melt strength/viscosity can be controlled, so as to obtain optimum foam morphology. The crosslinking also has effects on the diffusivity and solubility of a blowing agent inside EVA. The solubility and the diffusivity of the blowing agent in the EVA decrease with the crosslinking degree increases. The diffusivity decrease makes more gas is utilized for the foaming rather than leak out of the polymer matrix quickly. This thesis also presents the fundamental studies on the effects of crosslinking on cell nucleation and early bubble growth. Theoretical work and in-situ visualization experimental results indicate that partial crosslinking leads to higher cell nucleation density and slower bubble growth, both of which benefit a fine-cell foam morphology generation. Last but not least, an optimized foaming process was conducted to produce chemically crosslinked EVA foams with large expansion ratios in a batch system, using a chemical blowing agent. The results determine that an optimal crosslinking degree is critical for the crosslinked EVA foaming with maximum expansion ratio. Furthermore, all research results not only benefit the foaming of crosslinked EVA, but also serve the better production of other crosslinked polyolefin foams.