Life cycle assessment is an important tool to evaluate the impact of 2nd generation lignocellulosic ethanol, and its potential greenhouse gas (GHG) emissions benefits relative to gasoline. The choice of feedstock, process technology, and co-products may affect GHG emissions and energy metrics. Co-products may improve both the financial and environmental performance of the biorefinery. 26 well-to-wheel models of future lignocellulose-to-ethanol pathways were constructed, considering corn stover, switchgrass, and poplar feedstocks, three pre-treatment technologies, four co-product options, and the use of ethanol in a light-duty vehicle. Model results showed that all pathways with lignin pellet co-production had significantly lower net GHG emissions relative to gasoline and corresponding pathways producing only electricity. Pathways co-producing xylitol had at least 66% greater GHG emission reductions relative to pathways co-producing only lignin pellets. All feedstock/pretreatment/co-product combinations led to GHG reductions of at least 60%, meeting the threshold stipulated under the Energy Independence and Security Act.

Spinal cord injury and stroke are two devastating neurological events that lack effective clinical treatments. Recent neuroregenerative approaches involving the delivery of cells or drugs to the injured tissue have shown promise, but face critical challenges to clinical translation. Herein, hyaluronan-methylcellulose (HAMC) hydrogels were investigated as a versatile means of overcoming the challenges facing central nervous system cell and drug delivery. HAMC was shown to support the viability of encapsulated human umbilical tissue-derived cells, demonstrating utility as a scaffold for therapeutic cell delivery to the injured spinal cord. In a drug delivery context, release of the neuroregenerative drug cyclosporin A from the hydrogel was tunable over 2-28 days and the drug diffused to the stem cell niche in the brain and persisted for up to 24 days at a stable concentration when the HAMC-based system was implanted epi-cortically. HAMC is thus a promising tool for emerging neuroregenerative therapies.

Large-scale production of plant secondary metabolites is of interest because of their application in production of many valuable products. Recent advances in the area of DNA recombinant technology has made it possible to produce these valuable compounds using microbial routes. The objective of this work was, to design a platform strain of Saccharomyces cerevisiae with improved intracellular tyrosine pools using computational modeling. This engineered yeast could be used as a host for producing important plant secondary metabolites on an industrial-scale. In this study, a combination of steady-state and dynamic modeling methods were used for strain design. Initial strain design was performed using steady-state modeling, and the predictions from steady-state modeling were prioritized for experimental validation using dynamic modeling. The final strategy proposed included deletion of PDC1, ZWF1, ARO10; over-expression of ALD6, and alleviation of tyrosine feedback resistance in shikimate pathway. Initial experiments for validation of this strategy showed promising results.

As the plastics sector moves towards sustainable growth and development, natural fibres start to play an important role as constituents in composite materials in several industries including automotives. However, drawbacks such as fibre-matrix incompatibility and poor fibre dispersion still exist. In this thesis, Kraft pulp fibre (KF)-Polylactic Acid (PLA) composites were prepared using thermal compounding and aqueous blending to study fibre-matrix interactions. Fibre surfaces were also modified to improve fibre dispersion and water absorption properties. A biorefinery lignin was added to PLA and high density polyethylene (HDPE) as a biofiller and potential interface modifier. Aqueous blended composites showed better mechanical and dynamic mechanical performance than the thermally compounded materials. The fibre surface modification improved dispersion and material properties at higher fibre content. Furthermore, the addition of lignin to polymers resulted in improved mechanical properties in both PLA and HDPE; however, lignin failed to improve interface bonding between KF and PLA.

Across Canada, and around the world, very large amounts of pesticides are produced and applied to agricultural crops each year. Although pesticide usage is declining, they are still a necessary part of industrial agriculture. Numerous pesticides have been quantified in the atmosphere, at high levels near regions of use and at lower, but still significant levels in remote regions. Some of the most persistent pesticides have been banned, but others continue to be used despite their persistence and potential for long-range transport (LRT). We have applied and refined an XAD-2 resin-based passive air sampler (PAS) to study the concentrations of pesticides in the atmosphere. A set of laboratory experiments measured the equilibria sorption coefficients for chemicals on XAD-2 resin, allowing the determination of a new predictive equation for equilibria sorption coefficients, and thus interpretation of the range of applicability of both XAD-based PAS and active air samplers (AAS). A set of field experiments were performed to compare the data obtained by both PAS and AAS, and to study the temporal trends of a wide range of pesticides in an agricultural area of southern Ontario. Because it is now apparent that XAD-PAS sampling rates can vary between compounds and with temperature, we also determined new compound-specific sampling rates for pesticides in the XAD-PAS. The XAD-PAS were deployed in two transects across Canada, one from the Great Lakes region to the Canadian Arctic, and one across southern British Columbia in four different mountain regions and at different elevations. The air concentrations of current-use pesticides were correlated with regions of their use in both transects. The variation of air concentration with elevation was correlated with local, ground-level sources in British Columbia. The LRT of pesticides was determined from the north-south transect, and correlated to their atmospheric half-lives. Historic-use pesticides such as hexachlorobenzene and hexachlorocyclohexane were found to have relatively uniform distributions in the Canadian atmosphere, while further evidence of α-hexachlorocyclohexane evaporation from oceans was observed in both transects.

Understanding the assembly of monomeric components into specific molecular motifs is a central theme in materials and surface engineering. Motif designs, specifically using a controllable template, can yield materials with desired optical or electronic properties. The objective of this thesis is to understand the aggregate size, packing, and monomer orientation for the cationic dye, pseudoisocyanine. These organic molecules assemble into crystals in solution, on planar bilayer templates, and on the membranes of living cells. Pseudoisocyanine J-aggregates were found to form on top of the heterogeneous lipid domains in a phospholipid bilayer. This behaviour is limited to a few headgroup chemistries and lateral packing motifs, allowing one to control aggregation via a combination of these two factors. These aggregates are low-dimensional and display polymorphism. Using atomic force microscopy and visible-light spectroscopy, distinct optical characteristics can be correlated to different bilayer templated J-aggregate morphologies. The molecular packing of a similar J-aggregate crystal was resolved using both atomic force microscopy and selected area electron diffraction. The infrared absorption spectra of different polymorphs also displayed distinct differences. These separate examinations enabled a perspective that clarifies the geometry, packing, orientation, and size of templated J-aggregates. Insights into the templating of J-aggregates on the molecular scale reveals that they are sensitive reporters of membrane phase in adherent cells, and are compatible with established cell biology techniques. Lipid domains in live mammalian cells were visualized using fluorescent J-aggregates in combination with endogenous marker proteins of the endocytic process. Analysis of live cell images and additional biophysical work revealed that pseudoisocyanine J-aggregates formed on domains of the anionic lipid bis(monoacylglycerol)phosphate. Only by using J-aggregates can this lipid be shown to form well-ordered domains during endosomal maturation, leading to multivesicular body formation. These data demonstrate that a correlated optical and topographical approach is necessary to understand the structure of fluorescent molecular assemblies, and form the basis for utilizing such aggregates in a biological context.

The viscous oil-water hydrodynamics in a microchannel and phase equilibria of heavy oil and carbon dioxide gas have been investigated in connection with the enhanced recovery of heavy oil from petroleum reservoirs. The oil-water flow was studied in a circular microchannel made of fused silica with an I.D. of 250 µm. The viscosity of the silicone oil (863 mPa.sec) was close to that of the gas-saturated heavy oil in reservoirs. The channel was always initially filled with the oil. Two different sets of experiments were conducted: continuous oil-water flow and immiscible displacement of oil by water. For the case of continuous water and oil injection, different types of liquid-liquid flow patterns were identified and a flow pattern map was developed based on Reynolds, Capillary and Weber numbers. Also, a simple correlation for pressure drop of the two phase system was developed. In the immiscible displacement experiments, the water initially formed a core-annular flow pattern, i.e. a water core surrounded by a viscous oil film. The initially symmetric flow became asymmetric with time as the water core shifted off centre and also the waves at the oil-water interface became asymmetric. A linear stability analysis for core-annular flow was also performed. A characteristic equation which predicts the growth rate of perturbations as a function of the core radius, Reynolds number, and viscosity and density ratios of the two phases was developed. Also, two micro cells for gas solubility measurements in oils were designed and constructed. The blind cell had an internal volume of less than 2 ml and the micro glass cell had a volume less than 100 µl. By minimizing the cell volume, measurements could be made more quickly. The CO2 solubility was determined in bitumen and ashphaltene-free bitumen samples to show that ashphaltene has a negligible effect on CO2 solubility.

Classically 13% Cr is required for stable passivity of steel in acidic and neutral solutions. Some authors (Mansfeld, Fujimoto) have published potential cycling procedures that generate thick Cr-rich films. Fujimoto cycles right to the transpassivity potential and back in H2SO4 solution. Our idea is to work close to the reactivation potential where the passive film (Fe2O3) is reductively dissolved to Fe2+. While using an equimolar acetate buffer (pH 4.7), we have obtained new insights into the reactivation process. It is under a kind of thermodynamic control, in that the film cannot be reduced, and the metal cannot be dissolved, faster than would exceed the equilibrium concentration of Fe2+ at the electrode surface. Reductive dissolution leads to gel-like Cr-rich film, but Fe dissolution occurs through it, if formed in a single step. However alternating formation and reductive dissolution of a Fe-rich film assist the formation of a more robust Cr-rich film

In this study, novel bio-inks formulated with horseradish peroxidase, HRP, and some additives were successfully developed for piezoelectric inkjet application. The optimized bio-ink formulation had a reliable jetting performance and maintained the biofunctionality before and after printing. The bio-ink also demonstrated a good storage life for up to 40 days at 4 oC with a negligible loss of biofunctionality. However, it was observed that some additives used in the bio-ink for obtaining necessary operational characteristics had detrimental effects on the enzyme activity. Especially, it was found that various viscosity modifiers typically used in commercial inkjet inks significantly impaired HRP activity prior to printing. Sodium Carboxymethyl Cellulose was shown to be an effective viscosity modifier that had no adverse effect on the biological activity of the HRP enzyme. Using a confocal scanning fluorescent microscope, a method for characterizing the spatial distribution of the active enzyme within the cellulosic paper substrates after inkjet printing was developed. Interestingly, it was found that the active printed HRP enzyme was mostly located in the cell walls of the cellulosic fibers instead of near the pigments or fillers. In an effort to better understand the fundamental interactions between the enzyme and the immobilization substrates, HRP adsorption isotherms on various substrate surfaces were obtained using the depletion method. The substrates included not only pulp fibers with varying degree of hydrophobicity and pigment and latex (the key materials used in papermaking), but also other types of cellulosic fibers of different morphologies, crystallinities, porosities, or surface charge densities. The influence on enzyme adsorption and inactivation behaviour of these substrates was compared with that of polystyrene beads (dialysed), which has been well studied in the literature. Results from this thesis indicated that hydrophobic interactions between the enzyme and the substrate surfaces had a major impact on the HRP adsorption behavior, while electrostatic interactions played a minor role. However, strong hydrophobic interactions could lead to enzyme inactivation. Research findings from this study suggested that cellulosic pulp fibers could be tailor-made into excellent enzyme immobilization supports by using existing fiber surface modification techniques.

Biofilm systems such as the moving bed biofilm reactor (MBBR) are finding increased application in wastewater treatment. One important process that governs MBBRs and yet is poorly understood is the rate of biofilm detachment. The detachment of cells from biofilm surfaces controls both the accumulation of biofilm and the quantity of biomass that is suspended in the bulk liquid phase. This changing balance of attached and suspended cells, in this thesis named the biosolids dynamics, can impact the efficacy of MBBRs. The goal of this research was to investigate how the biosolids dynamics are influenced by process changes relevant to applied wastewater treatment systems and suggest new routes to reactor design and optimization. To achieve this goal, the work addresses three separate but interconnected lines of inquiry. First, multivariate analysis (Principal Component Analysis, Partial Least Squares) was used to examine 2 years of historical data from an MBBR operating at a Canadian pulp mill in order to identify key process variables, perform process diagnostics, and act as a predictive tool. Secondly, the effect of calcium concentration on biofilm structure, microbiology and reactor performance was investigated in four laboratory-scale MBBRs operated at a range of calcium concentrations (1 to 300 mg/L Ca2+). It was found that above a threshold calcium concentration between 1-50 mg/L, MBBR biofilms were observed to be thicker with greater density, contain larger anoxic regions adjacent to the carrier substratum, have more proteinaceous EPS, and have altered microbial community structure. The results suggest an important role for calcium that should be considered in the design and operation of MBBRs. In the final line of inquiry, a diffusion-reaction biofilm model was adapted to represent the key processes of the MBBR. The model was found to simulate average trends observed in the lab-scale experiments allowing for quantification of the detachment rate. Transient periods of reactor starvation were also simulated by introducing a novel metabolic state function to account for down-regulation of metabolism as a result of starvation. This approach was found to accurately simulate starvation response when coupled with detachment expressions that were growth-dependant.