Understanding the basic mechanisms and dynamics that drive the assembly of molecules into functional structures is critically important in a diverse number of fields, ranging from materials science to drug delivery and biomaterials. In this work, we have focused on examining the self-assembly characteristics, both in solution and at surfaces, of a family of elastin-like peptides (EPs). In addition to directly observing the formation of ordered hexagonally arranged fibrillar EP structures on hydrophobic highly ordered pyrolytic graphite (HOPG), we have studied the dynamics of EP self-assembly process both within physically restricted domains using thermally etched HOPG, and in solution using detergent micelles. We have found that, at surfaces, EP fibril formation occurs via surface stabilization against the hydrophobic surface, while in solution, detergents inhibit EP aggregation at high temperatures and appear to enable the formation of an ordered crystalline structure at low temperatures. These model studies establish a framework for further investigations of peptide self-assembly and the role of hydrophobic interactions in controlling self-assembly.

Understanding the basic mechanisms and dynamics that drive the assembly of molecules into functional structures is critically important in a diverse number of fields, ranging from materials science to drug delivery and biomaterials. In this work, we have focused on examining the self-assembly characteristics, both in solution and at surfaces, of a family of elastin-like peptides (EPs). In addition to directly observing the formation of ordered hexagonally arranged fibrillar EP structures on hydrophobic highly ordered pyrolytic graphite (HOPG), we have studied the dynamics of EP self-assembly process both within physically restricted domains using thermally etched HOPG, and in solution using detergent micelles. We have found that, at surfaces, EP fibril formation occurs via surface stabilization against the hydrophobic surface, while in solution, detergents inhibit EP aggregation at high temperatures and appear to enable the formation of an ordered crystalline structure at low temperatures. These model studies establish a framework for further investigations of peptide self-assembly and the role of hydrophobic interactions in controlling self-assembly.

This thesis investigates the use of density centrifugation with Percoll to separate and enrich the organisms involved in the first step of toluene degradation within a methanogenic toluene degrading consortium. Protocol development resulted in the enrichment of bacteria and archaea in separate layers. However the separation of Eub-1 (an organism suspected to be responsible for the first step in toluene degradation), and bssA (a gene encoding the benzylsuccinate synthase enzyme) using previously developed qPCR primers could not be established. Cloning and sequencing of the toluene degrading consortia were conducted and phylogenetic analysis showed a change in community composition from what had previously been observed, suggesting why previously established primers were not effective. In parallel with these studies, microcosms using soil obtained from a petroleum hydrocarbon-contaminated area in North Carolina were constructed. These microcosms showed benzene degradation in all but one sample over the 444 day period.

Micronutrient deficiency maintains the cycle of poverty. A steady intake of essential nutrients is not available in developing areas due to factors of socioeconomic constraints, limited variety of food sources, and single-carbohydrate based diets. Fortification of a staple food is an effective way of combating micronutrient deficiencies. The food product developed in this study is an extruded, micronutrient-fortified, rice-shaped premix. The target rice premix formulation contains iron, zinc, a B-vitamin complex, and vitamin A and is blended with market rice in a 1:100 ratio. Iron furthers the oxidation of vitamin A, thus various micronutrient encapsulation techniques and antioxidant systems are explored in this study. It is technically and economically feasible to combine the micronutrients in a single formulation by introducing efficient physical and chemical barriers. Optimal formulation designs used coated vitamin A sources and retained >85% vitamin A at 6 months storage with acceptable sensory attributes.

This thesis investigates the use of density centrifugation with Percoll to separate and enrich the organisms involved in the first step of toluene degradation within a methanogenic toluene degrading consortium. Protocol development resulted in the enrichment of bacteria and archaea in separate layers. However the separation of Eub-1 (an organism suspected to be responsible for the first step in toluene degradation), and bssA (a gene encoding the benzylsuccinate synthase enzyme) using previously developed qPCR primers could not be established. Cloning and sequencing of the toluene degrading consortia were conducted and phylogenetic analysis showed a change in community composition from what had previously been observed, suggesting why previously established primers were not effective. In parallel with these studies, microcosms using soil obtained from a petroleum hydrocarbon-contaminated area in North Carolina were constructed. These microcosms showed benzene degradation in all but one sample over the 444 day period.

Micronutrient deficiency maintains the cycle of poverty. A steady intake of essential nutrients is not available in developing areas due to factors of socioeconomic constraints, limited variety of food sources, and single-carbohydrate based diets. Fortification of a staple food is an effective way of combating micronutrient deficiencies. The food product developed in this study is an extruded, micronutrient-fortified, rice-shaped premix. The target rice premix formulation contains iron, zinc, a B-vitamin complex, and vitamin A and is blended with market rice in a 1:100 ratio. Iron furthers the oxidation of vitamin A, thus various micronutrient encapsulation techniques and antioxidant systems are explored in this study. It is technically and economically feasible to combine the micronutrients in a single formulation by introducing efficient physical and chemical barriers. Optimal formulation designs used coated vitamin A sources and retained >85% vitamin A at 6 months storage with acceptable sensory attributes.

Odour emissions resulting from reduced sulphur compounds in the kraft pulping industry are frequently found in dilute, high flowrate air streams that are costly to treat using incineration and thermal oxidation. Biofiltration, an air treatment method involving passing air through a packed bed of microorganisms, has emerged as a promising treatment strategy for these dilute waste gas streams. However, biodegradation of dimethyl sulphide (DMS) in biofilters is rather poor and is limiting the application of biofiltration to odour streams rich in DMS. Recently, our group has shown that co-treatment of DMS with methanol can increase DMS removal significantly. In this thesis, the effect of methanol on the microbiology of two biofilters treating DMS was explored. Microbial community analysis revealed that the addition of methanol led to a significant increase of up to an order of magnitude in the abundance of Hyphomicrobium spp. in a biofilter co-treating DMS and methanol compared to a biofilter treating DMS alone with no significant difference in the abundance of Thiobacillus spp. between the two biofilters. Further to the biofiltration experiments, the growth kinetics of Hyphomicrobium spp. and Thiobacillus spp. on DMS and methanol in an enrichment culture created from a biofilter co-treating DMS and methanol were studied. A specific growth rate of 0.099 h-1 and 0.11 h-1 was determined for Hyphomicrobium spp. and Thiobacillus spp., respectively, growing on DMS at pH 7, double the highest maximum specific growth rate for bacterial growth on DMS reported to date in the literature. As the pH decreased from pH 7 to pH 5, the specific growth rate of Hyphomicrobium spp. decreased significantly by 85% in the mixed culture while the specific growth rate of Thiobacillus spp. remained similar through the same pH shift. When methanol was used as a substrate, the specific growth rate of Hyphomicrobium spp. declined much less over the same pH range (up to 30%). These results suggest that addition of methanol to biofilters co-treating DMS and methanol can increase DMS removal rates by increasing the abundance of DMS-degrading Hyphomicrobium spp. at pH levels not conducive to high growth rates on DMS alone.

Most stress corrosion cracking (SCC) mechanisms initiate from localised corrosion (pitting, intergranular attack, de-alloying), which provides local stress concentration. Alloys are generally more susceptible to SCC than pure metals because selective dissolution or oxidation is possible. De-alloying involves the selective dissolution of the less noble (LN) component from an alloy. The more noble (MN) component enriches on the surface forming a brittle, metallic, nanoporous layer. In noble metal alloys and brass, SCC shows correlation with the threshold LN content below which de-alloying stops (the parting limit). In Fe-Ni-Cr engineering alloys de-alloying may be responsible for Cl-SCC, although this has not been proven explicitly. Initial indications show that de-alloying causes SCC in hot, caustic environments. In some cases, Ni enrichment and porosity are associated with cracks in stainless steel after long-term service in nuclear high temperature water environments, but it is unclear if this plays a causal role in cracking. Here the de-alloying mechanism (primarily the effect of Ni (MN) content) and its relationship to SCC in Fe-Ni-Cr materials (Fe10Ni, 310SS and Alloy 800) is examined using a hot caustic environment, and compared to classical de-alloying systems. De-alloyed layers formed on all materials, although Alloy 800 required a higher temperature. Increasing Ni content improved de-alloying resistance according to classical theory. Unlike classical systems, de-alloying occurred with concurrent MN dissolution and, at open circuit potential (OCP), the layers retained significant Fe and Cr (LN) instead of being ‘almost pure’ MN. Layers formed with applied anodic potential were friable and highly LN depleted. This behaviour was successfully modelled in Kinetic Monte Carlo simulations. Recently, it has been shown that SCC in noble element alloys depends on the mechanical integrity (quality) of the de-alloyed layer; a finding that was reflected here. At 140 °C at OCP the layer on 310SS was too thin to promote SCC and Alloy 800 did not de-alloy significantly. Layers formed with anodic potential did not result in SCC. In 50% NaOH at 280 °C, severely stressed 310SS cracked where thick de-alloyed layers formed. However, the thin layer formed on Alloy 800 was associated with SCC, even with low residual stress.

Production of protein and semi-conductor crystals with advanced quality and properties is considered to be possible under microgravity conditions due to the absence of natural convection effects. Such materials have several beneficial properties that can improve the human life. An example is the synthesis of protein crystals with improved structure that can be determined for the production of advanced drugs. In the past experiments conducted aboard several space platforms, however, g-jitter induced convective flow may have resulted in certain effects that reduced the quality of the produced crystals. To investigate the effects of g-jitter on the motion of small particles, experiments were conducted under normal gravity by suspending spherical stainless steel particles of different sizes with a thin wire or synthetic silk thread in a rectangular fluid cell. The fluid viscosities were 350 and 1,000 times higher than water. To produce the g-jitter induced motion in the fluid, the cell was subjected to horizontal sinusoidal vibrations with different frequencies and amplitudes. The focus of the experiments so far has been on vibration-induced force on the particle vibrating parallel to a near wall. Relatively low viscosity fluids such as water have been previously determined to produce a force on the particle which attracts the particle to the nearest fluid cell wall. The present experiments with a more viscous fluid have revealed an interesting change in the force from attraction in low viscosity fluids to repulsion in high viscosity liquids. Moreover, the repulsion force has been observed to increase with an increase in the fluid viscosity and the fluid cell amplitude. A numerical code, Partflow3d, has also been used to predict the vibration effects on the particle. Although, based on the objectives of this study, the numerical simulations were conducted only for a wire-free particle under microgravity, their results were qualitatively in agreement with the experimental results. The numerical simulations also revealed that the physical mechanism of the hydrodynamic attraction-repulsion force on the particle is related to Bernoulli’s principle of reduced pressure in high velocity zones in the fluid surrounding the particle. The results so far have shown new aspects of the g-jitter induced motion of the particle near a fluid cell wall. Better understanding of the forces affecting the particles in a fluid cell subjected to small vibrations, can reveal novel ways to produce new advanced materials and also improve material processing both in microgravity and normal gravity conditions.

Over the past decade, the constraint-based approach to metabolic modeling has become an important tool for understanding and controlling biology. Unfortunately, the application of this novel approach to systems biology in biotechnology has been limited by three significant technical issues: existing metabolic modeling methods cannot completely model the overflow metabolism, cannot model the metabolism of microbial communities, and cannot design strains optimized for productivity and titer. Three computational methods – the Flux Balance Analysis with Membrane Economics (FBAME) method, the Dynamic Multi-species Metabolic Modeling (DyMMM) framework, and the Dynamic Strain Scanning Optimization (DySScO) strategy – have been developed to resolve these issues respectively. First, the FBAME method, which adopts the membrane occupancy limitation hypothesis, was used to explain and predict the phenomenon of overflow metabolism, an important metabolic phenomenon in industrial fermentation, in Escherichia coli. Then, the DyMMM framework was used to investigate the community metabolism during uranium bioremediation, and demonstrated that the simultaneous addition of acetate and Fe(III) may be a theoretically viable uranium bioremediation strategy. Lastly, the DySScO strategy, which combines the DyMMM framework with existing strain design algorithms, was used to design commodity-chemical producing E. coli optimized for a balanced product yield, titer, and volumetric productivity. These novel computational methods allow for broader applications of constraint-based metabolic models in biotechnology settings.