The amount of carbon trapped in hydrates is estimated to be larger than in conventional oil and gas reservoirs, thus methane hydrate is a promising energy resource. The high water pressure and the relatively low temperature needed for hydrate stability restrict the distribution of methane hydrates to continental shelves and permafrost regions. Stability conditions add inherent complexity to coring, sampling, handling, testing and data interpretation, and have profound implications on potential production strategies. New guidelines are identified for sampling equipment and protocols. Then a novel technology is developed for handling, transfering, and testing of natural hydrate bearing sediments without depressurization in order to preserve the sediment structure. Natural samples from the Nankai Trough, Japan, are tested as part of this study. In-situ testing prevents dissociation and the consequences of sampling and handling disturbance. A new multi-sensor in-situ characterization tool is designed and prototyped as part of this research. The tool includes advanced electronics and allows for automated stand-alone operation. Finally, a robust analytical model is developed to estimate the amount of gas that can be recovered from hydrate bearing sediments using depressurization driven dissociation. Results highlight the complexity of gas extraction from deep sediments, and inherent limitations.

This dissertation focuses on structural and electrical characterization of self-organizing discotic molecular materials, specifically alkoxy and thioether side chain modified copper phthalocyanines, both in bulk and at organic/dielectric and organic /metal interfaces. A great deal of effort has been focused on understanding the self-organizing nature in these materials since molecular ordering is believed to control the intrinsic physical as well as electrical properties of these molecular aggregates. It was determined that side chains in these Pcs have a significant impact on the general ordering in these materials: alkoxy side chain modification favors a columnar hexagonal phase with a cofacial intracolumn alignment; thioether side chain modification, however, favors a tilted intracolumn alignment and much rigid columnar packing, driven by sulfur-sulfur interactions among adjacent molecular disks. Incorporation of styrene functionality in the side chain has been shown to enable photopolymerization. An optimal hexagonal columnar packing has been proved to be stabilized via photolysis at the mesophase. It is critical to explore the molecular ordering as well as the charge transport characteristics at interfaces since the organic/dielectric interface controls the charge accumulation in organic field-effect transistors (OFETs) and the metal/organic interface determines the charge injection in devices such as organic photovoltaic cells (OPVs). Two analytical tools have been developed in this dissertation work that successfully address these interfacial issues from a molecular level. 1) Probing interfacial structures at the organic/dielectric interface with X-ray reflectometry (XRR). Surface chemistry has shown a drastic impact on the ordering of the initially deposited materials. Surface engineering strategies, i.e. chemical modification, have been shown to significantly improve the coherence of molecular assemblies thereby optimizing charge transport properties of these molecular materials in an OFET platform. 2) Exploring charge injection and transport characteristics at molecular junctions with conductive-probe AFM (C-AFM). Charge injection processes at the metal/organic molecular junction have shown a strong dependence on the microstructure of these molecular materials. Thermionic emission and field emission were shown to be competing processes at these junctions. One dimensional charge transport is realized only with the appropriate molecular ordering in these discotic materials at metal/organic junctions. 3) Exploring structural and electrical properties of ITO with C-AFM. The ITO surfaces have shown both structural and electrical heterogeneity at the nanometer scale. A tunneling model has been proposed and the presence of thin insulating layers was believed to be the cause of electrically inactive regions of ITO. Aggressive chemical etching protocols have been developed and shown to improve the percentage of surface electrically active area, thereby, enhancing the electrode performance.

A methodology for ligament isolation and specimen preparation for tensile testing of single ligaments from the unit cell of open-cell carbon foams has been successfully developed and implemented. Results are presented for ligaments of three different carbon foam designations. Two of them are reticulated vitreous carbon (RVC) foams of 20 and 45 pores-per- inch (ppi) coated with SiC by chemical vapor deposition (CVD) and the other is a RVC 20 ppi foam without coating. Scanning electron microscopy and digital imaging analysis is used to analyze the fracture surfaces posts tests. The ultimate strength of each ligament evaluated. Weibull statistics is used to describe the strength distribution of ligaments. While the distribution of strengths of the carbon foam ligaments (RVC) could be described with a one-population distribution, it is found that a two-population Weibull distribution is necessary to describe the distribution of strength of the SiC coated ligaments.

The Rodessa Formation is one of the major oil and gas reservoirs in the East Texas Basin. In Van Field, the upper Rodessa Formation consists of interbedded biotic and abiotic mudstones to grainstones. The lower Rodessa is composed of interbedded sandstones, shales, and limestones called the Carlisle Member. Based on core and well log interpretation, the Rodessa Formation was deposited on a broad, restricted, shallow marine platform interpreted to be lagoonal, subtidal, and intertidal. Both Rodessa limestone and sandstone have been altered significantly by diagenetic processes that include micritization, cementation, dissolution, neomorphism and compaction. Dissolution is the main factor that resulted in enhanced porosity and permeability while cementation adversely affected porosity. Diagenesis is interpreted to have begun in the marine phreatic environment and continued through the freshwater phreatic and shallow burial environments. Two reservoir units have been identified from core and well log interpretations. The potential reservoir within the Rodessa Formation occurs in the Carlisle Member which is composed mainly of medium to coarse grained sandstone with porosities and permeabilities in ranges of 8 to 11 percent and 46 to 896 millidarcies, respectively. The water saturation analysis has also shown the reservoir to be hydrocarbon bearing, having water saturation below 46 percent.

The Spraberry Formation is traditionally thought of as deep-water turbidites in the central Midland Basin. At Happy Spraberry field, Garza County, Texas, however, production is from a carbonate interval about 100 feet thick that has been correlated on seismic sections with the Leonardian aged, Lower Clear Fork Formation. The "Happy field" carbonates were deposited on the Eastern Shelf of the Midland Basin and consist of oolitic skeletal grainstones and packstones, rudstones and floatstones, in situ Tubiphytes bindstones, and laminated to rippled, very-fine grained siltstones and sandstones. The highest reservoir "quality" facies are in the oolitic grainstones and packstones where grain-moldic and solution-enhanced intergranular porosity dominate. Other pore types present include incomplete grain moldic, vuggy, and solution-enhanced intramatrix. The purpose of this study was to relate pore geometry measured by digital petrographic image analysis to petrophysical characteristics, and finally, to reservoir quality. Image analysis was utilized to obtain size, shape, frequency, and total abundance of pore categories. Pore geometry and percent porosity were obtained by capturing digital images from thin sections viewed under a petrographic microscope. The images were transferred to computer storage for processing with a commercial image analysis program trademarked as Image Pro Plus (Version 4.0). A classification scheme was derived from the image processing enabling "pore facies" to be established. Pore facies were then compared to measured porosity and permeability from core analyses to determine relative "quality" of reservoir zones with different pore facies. Pore facies are defined on pore types, sizes, shapes, and abundances that occur in reproducible associations or patterns. These patterns were compared with porosity and permeability values from core analyses. Four pore facies were identified in the Happy field carbonates; they were examined for evidence of diagenetic change, depositional signatures, and fractures. Once the genetic categories were established for the four pore facies, the pore groups could be reexamined in stratigraphic context and placed in the stratigraphic section across Happy field. Finally, the combined porosity and permeability values characteristic of each pore facies were used to identify and rank good, intermediate, and poor flow units at field scale.

Microstructural characterization and mechanical properties of Excel (Zr-3.5%Sn-0.8%Mo-0.8%Nb), a dual phase αZr-hcp and βZr-bcc pressure tube material, is discussed in the current study which is presented in manuscript format. Chapter 3 discusses phase transformation temperatures using different techniques such as quantitative metallography, differential scanning calorimetry (DSC), and electrical resistivity. It was found that the αZr → αZr+βZr and αZr+βZr → βZr transformation temperatures are in the range of 600-690°C and 960-970°C respectively. Also it was observed that upon quenching from temperatures below ~860°C the martensitic transformation of βZr to –hcp is halted and instead the microstructure transforms into retained βZr with ω hexagonal precipitates inside βZr grains. Chapter 4 deals with aging response of Excel alloy. Precipitation hardening was observed in samples water-quenched from high in the αZr+βZr or βZr regions followed by aging. The optimum aging conditions were found to be 450°C for 1 hour. Transmission electron microscopy (TEM) showed dispersion of fine precipitates (~10nm) inside the martensitic phase. Energy dispersive X-ray spectroscopy (EDS) showed the chemical composition of precipitates to be Zr-30wt%Mo-25wt%Nb-2wt%Fe. Electron crystallography using whole pattern symmetry of the convergent beam electron diffraction (CBED) patterns together with selected area diffraction (SAD) polycrystalline ring patterns, suggests the -6m2 point group for the precipitates belonging to hexagonal crystal structure, with a= 2.936 Å and c=4.481 Å, i.e. c/a =1.526. Crystallographic texture and high temperature tensile properties as well as creep-rupture properties of different microstructures are discussed in Chapter 5. Texture analysis showed that solution treatment high in the αZr+βZr or βZr regions followed by water quenching or air cooling results in a more random texture compared to typical pressure tube texture. Variant selection was observed upon water quenching while partial memory effect and some transformation texture with variant selection was observed in the air-cooled sample. The results of creep-rupture tests suggest that fully martensitic and aged microstructure has better creep properties at high stress levels (>700 MPa) while the microstructure from air cooling from high in the αZr+βZr region is less sensitive to stress and shows better creep properties compared to the as-received annealed microstructure at lower stresses (<560 MPa). / Thesis (Ph.D, Mechanical and Materials Engineering) -- Queen's University, 2012-08-23 16:22:45.395

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Peroxisomes are virtually found in all eukaryotic cells, but unlike mitochondria and chloroplasts, they do not contain DNA or a protein secretory apparatus. Therefore, all of their proteins must be imported by a process called peroxisomal biogenesis. This requires a group of protein factors referred to as peroxins which are encoded by the pex genes. Currently, there are approximately thirty-two known peroxisomal proteins. Among all the peroxisomal proteins, two enzymes namely GPD1, LYS1 and a peroxin, PEX7 were selected for the research. GPD1 is a NAD+ -dependent glycerol 3-phosphate dehydrogenase1 that catalyzes the conversion of dihydroxyacetone phosphate (DHAP) to glycerol 3-phosphate which is crucial for growth under osmotic stress. Its purification was achieved using ion exchange chromatography and the pure protein was crystallized for structure determination. Diffraction data sets were obtained to a resolution of 2.2 Å which were used to solve the C-terminal portion of the structure. Unfortunately, the N-terminal portion remained disordered. LYS1 is the terminal enzyme of α-aminoadipate pathway and catalyzes the reversible NAD-dependent oxidative cleavage of saccharopine to yield L-lysine and α-ketoglutarate. The purification of LYS1 was carried out using affinity chromatography. Another protein, PEX7 is responsible for peroxisome biogenesis by importing newly synthesized proteins bearing PTS2 (peroxisome targeting signal sequence2) into peroxisomes. PEX7 presented the greatest challenge among the three proteins at both the expression stage and the purification stage. Its soluble fraction was purified using ion exchange and affinity chromatographies, although the final yield was too low for crystallization trials. A much large proportion of the protein was found in the insoluble cell debris and attempts were made to purify this fraction after denaturation. An alternative, protocol involving the formation of a GPD1-PEX7 complex proved to be effective route to co-purification of the two proteins and crystallization trials are proceeding. Having known the structures of peroxisomal proteins, it would be helpful for studying the development and maintenance of the organelle related to its metabolic diseases in the eukaryotic cells.

Peroxisomes are virtually found in all eukaryotic cells, but unlike mitochondria and chloroplasts, they do not contain DNA or a protein secretory apparatus. Therefore, all of their proteins must be imported by a process called peroxisomal biogenesis. This requires a group of protein factors referred to as peroxins which are encoded by the pex genes. Currently, there are approximately thirty-two known peroxisomal proteins. Among all the peroxisomal proteins, two enzymes namely GPD1, LYS1 and a peroxin, PEX7 were selected for the research. GPD1 is a NAD+ -dependent glycerol 3-phosphate dehydrogenase1 that catalyzes the conversion of dihydroxyacetone phosphate (DHAP) to glycerol 3-phosphate which is crucial for growth under osmotic stress. Its purification was achieved using ion exchange chromatography and the pure protein was crystallized for structure determination. Diffraction data sets were obtained to a resolution of 2.2 Å which were used to solve the C-terminal portion of the structure. Unfortunately, the N-terminal portion remained disordered. LYS1 is the terminal enzyme of α-aminoadipate pathway and catalyzes the reversible NAD-dependent oxidative cleavage of saccharopine to yield L-lysine and α-ketoglutarate. The purification of LYS1 was carried out using affinity chromatography. Another protein, PEX7 is responsible for peroxisome biogenesis by importing newly synthesized proteins bearing PTS2 (peroxisome targeting signal sequence2) into peroxisomes. PEX7 presented the greatest challenge among the three proteins at both the expression stage and the purification stage. Its soluble fraction was purified using ion exchange and affinity chromatographies, although the final yield was too low for crystallization trials. A much large proportion of the protein was found in the insoluble cell debris and attempts were made to purify this fraction after denaturation. An alternative, protocol involving the formation of a GPD1-PEX7 complex proved to be effective route to co-purification of the two proteins and crystallization trials are proceeding. Having known the structures of peroxisomal proteins, it would be helpful for studying the development and maintenance of the organelle related to its metabolic diseases in the eukaryotic cells.

Continuous accumulation of Mature Fine Tailings (MFT) is a major challenge to oil sands industry. To reduce the inventory of MFT through development of novel tailings treatment technologies, it is essential to understand the stabilization mechanism of fine solids in MFT. This project aims at characterizing fine solids of MFT. A novel method is developed in this study to understand characteristics of fine solids in MFT by studying their response to the changes in water chemistry and chemical treatment. Settling and rheological response of MFT to chemical additives is determined. Combined with solids characterization of the different layers of settled MFT, an enhanced understanding of stabilization of fine solids in MFT is gained. The knowledge generated through this study will provide a scientific basis for technology development of MFT treatment. / Chemical Engineering