This thesis is missing pages 68, 118, 129 and 189 and these pages are not in any other copies of the thesis. -Digitization Centre / This thesis is a design of a three-dimensional plotting routine for the computer facilities at McMaster University with a subroutine to adopt the package for use on other computer systems and is divided into four sections. Section A is a review of the necessity of computerized plotting in science and engineering design with particular emphasis on software sophistication, which is the subject of this work. Section B describes the principles employed and the basic logic of the software package. The method by which a three-dimensional solid is mapped is also explained. Section C is a complete user's guide to the package. Section D deals with some applications for the package such as the solution of design optimization problems, visual analysis of data sets, an aid to teaching and combined interpolation and display of experimental results. / Thesis / Master of Engineering (ME)

Organoboron derivatives represent an important class of compounds due to the versatility of the carbon-boron bond in a variety of chemical reactions. Boron-containing compounds have garnered increasing attention as synthetic intermediates and medicinal agents. Therefore, the introduction of carbon-boron bonds to organic molecules continues to be an important field of study. This dissertation describes novel methodology for the regio- and stereo-selective introduction of carbon-boron bonds to generate β-borylacrylonitrile and 1-boryl-1,3-enyne products. Propiolonitriles are intriguing research targets due to the electron-withdrawing nature of the cyano group on the adjacent alkyne. In this dissertation, we developed a phosphine-catalyzed regio- and stereo-selective hydroboration of propiolonitriles to generate novel β-borylacrylonitriles in up to 89% yield and 97:3 (E)-selectivity. These products were converted to the corresponding postassium 1,2-vinylcyanotrifluoroborate salts and demonstrated applications in oxidation and Suzuki-Miyaura cross-coupling reactions. Interestingly, 31P and 13C NMR studies suggest that this hydroboration reaction proceeds in a 1,2-phosphine addition pathway instead of a canonical 1,4-conjugate addition pathway. We also developed a transition metal-free cis hydroboration of 1,3-diyne substrates. In the presence of catalytic amounts of tri-n-butylphosphie and the unsymmetric diboron reagent pinBBdan, 1-boryl-1,3-enyne products were generated in up to 63% and >99:1 (Z)-selectivity. These 1,8-diaminonaphthalene products can be converted to the corresponding pinacolboranes or trifluoroborate salts. They also demonstrated applications in protodeboronation and Suzuki-Miyaura cross-coupling reactions. We propose that this hydroboration occurs via a nucleophilic boron addition mechanism. / Doctor of Philosophy / Incorporating boron into organic molecules provides access to a variety of otherwise difficult chemical reactions. Therefore, our laboratory seeks to develop new methods for synthesizing organoboron compounds. A major goal of our work is to develop transition metal-free reactions due to the expense and environmental impact of transition-metal mediated methodology. This dissertation reports two new methods for installing boron to organic molecules without the use of transition metals. The reported reactions utilize mild conditions to selectively generate functionalized products, and applications of these products are demonstrated. Chapter 1 describes a hydroboration reaction of propiolonitrile derivatives to afford (E)-β-borylacrylonitrile products. Notably, this reaction proceeds via a unique mechanism, contrasting that of similar reported reactions. Chapter 2 reports a transition metal-free hydroboration of 1,3-diynes to afford (Z)-1-boryl-1,3-enyne products. These products are structurally similar to relevant molecules in medicinal, polymer, and synthetic chemistry.

The genus Phytophthora contains a large number of species that are known plant pathogens of a variety of important crops. Phytophthora sojae, a hemibiotroph, causes approximately 1-2 billion dollars (US) of lost soybean world-wide each year. P. infestans, the causative agent of the Irish potato famine, is responsible for over 5 billion dollars (US) worth of lost potato each year. These destructive plant pathogens facilitate pathogenesis through the use of small secreted proteins known as effector proteins. A large subset of effector proteins is able to translocate into host cells and target plant defense pathways. P. sojae Avr1b is able to suppress cell death triggered by BAX and hydrogen peroxide. The W-domain of Avr1b is responsible for this functionality, and is recognized by the Rps1b gene product to induce effector triggered immunity. These oomycete effector proteins translocate into host cells via a highly conserved N-terminal motif known as RXLR-dEER without the use of any pathogen encoded machinery. In fungi an RXLR-like motif exists, [R,K,H] X [L,F,Y,M,~I] X, that is able to facilitate translocation without pathogen encoded machinery. Both functional RXLR and RXLR-like motifs are able to bind phosphatidylinositol-3-phosphate (PtdIns- 3-P) to mediate entry into host cells. The use of novel inhibitory mechanisms has shown effector entry can be blocked either by sequestering PtdIns-3-P on the outer leaflet of plant and animal cells or by competitive inhibition of the binding pocket of the RXLR or RXLR-like motifs. / Ph. D.

Despite being a low fat fish and consequently a low omega-3 fish, tilapia have widespread consumer acceptability due to its mild taste, cheap price and low mercury content. However some sources claim that farmed tilapia can be detrimental to human health due to high omega-6:3 ratios and low omega-3 content specifically eicosapentaenoic acid, docosapentaenoic acid, and docosahexaenoic acid. The objective of this study was to create an omega-3 enriching feed that would increase omega-3 content in tilapia and subsequently decrease the omega-6:3 ratio. An 8 week feeding trial was conducted. Tilapia were cultured in a recirculating aquaculture system on one of eight diets (control, commercial, 1, 3, 5% fish oil or 1.75, 5.26, 8.77% ALL-G-Rich (algae). Water quality, selected fish biometrics and growth performance were recorded. Fillet and rib meat tissues were collected at weeks 4 and 8, and liver and mesenteric fat tissues were collected at week 8. Fat was extracted, trans-methylated and identified as fatty acid methyl esters using gas chromatography-mass spectrometry. Docosahexaenoic acid increased in concentration in all tissues as percent fish oil and ALL-G-Rich increased in the diets with 8.77% ALL-G-Rich resulting in significantly (P<0.0001) greater concentrations in the fillet and mesenteric fat compared to all other diets after 8 weeks. The 8.77% ALL-G-Rich diet resulted in significantly (P=0.003) greater cumulative accumulation of EPA, DPA and DHA on a mg/4oz fillet basis after 4 weeks compared to control. The results of this study suggest that an ALL-G-Rich finishing feed could be produced that would result in a value added farmed tilapia fillet. / Master of Science in Life Sciences

Cryptographic hash functions are used extensively in information security, most notably in digital authentication and data integrity verification. Their performance is an important factor of the overall performance of a secure system. In 2005, some groups of cryptanalysts were making increasingly successful attacks and exploits on the cryptographic hash function, SHA-1, the most widely used hash function of the secure hashing algorithm family. Although these attacks do not work on SHA-2, the next in the series of the secure hashing algorithm family, the National Institute of Standards and Technology still believes that it is necessary to hold a competition to select a new algorithm to be added to the current secure hashing algorithm family. The new algorithm will be chosen through a public competition. The entries will be evaluated with different kinds of criteria, such as security, performance and implementation characteristics. These criteria will not only cover the domain of software, but the domain of hardware as well. This is the motivation of this thesis. This thesis will describe the experiments and measurements done to evaluate the SHA-3 cryptographic hash function candidates' performance on both ASIC and FPGA devices. The methodology, metrics, implementation details, and the framework of the experiments will be described. The results on both hardware devices will be shown and possible future directions will be discussed. / Master of Science

This project aims to design a safe and healthy space for orphan girls in Iraq, considering their needs and culture. Moreover, to set a foundation for girls to grow and become confident young individuals. My approach to this project was working both in plan and perspective. From the first days of the project, I started drawing the qualities that I was looking for in the design in perspective. Moreover, this is an extensive project, on a 1400 square meter site, so one of the important aspects of the project was to have a language through the design that makes the project coherent. In this book final renders are presented along with the initial ideas and sketches. Iraq is chosen because "there are 11,000 children addicted to drugs in Baghdad, that many girls aged 12 to 16 years old have been victims of abuse, and that many girls aged 12 years and above have endured harassment." This project shows that a well-thought design can improve the lives of orphaned girls, and hopefully, the outcome will raise awareness for the education and well-being of orphaned girls in Iraq. / Master of Architecture / Life is not easy, even when you live in a healthy family. Now, imagine what it looks like when you are traumatized as a kid. Kids who lost their parents in the war or are traumatized by their own family have a blurry glass on their eyes; they are confused about their feelings and experiences and often have difficulties trusting others and making meaningful connections. Moreover, orphan kids who had observed severe scenes may have panic attacks. Traumatized kids have very specific needs that the architectural design of their environment should address.

A holographic recording method using an optical heterodyne 2-D scanning technique for 3-D imaging of fluorescent objects in turbid media is described and experimentally demonstrated. For the first time, 3-D imaging of fluorescentobjects in turbid media by a holographic method is achieved, and the diffused photon rejecting process through a heterodyne technique is analyzed. We also propose and realize a multiplexing and a digital decoding method for removing twin-image noise in optical scanning holography. The holographic method studied can be applied to 3-D biomedical imaging of fluorescent objects in turbid media as well as diffusely reflecting objects. / Master of Science

Increased consumer interest in omega-3 fatty acids (FA) has led to novel foods with added omega-3 FA. Additional information regarding omega-3 FA fate within foods is needed for improving quality and stability. This research modeled DHA, an omega-3 FA, fate and explored means of preventing degradation and oxidation of FA in algal oil and mozzarella cheese. In algal oil, TBHQ (synthetic antioxidant) at 0.0175g/g algal oil prevented DHA degradation for at least 6 weeks, and mixed tocopherols (natural antioxidant) at 400ppm prevented DHA degradation and oxidation for about 4 weeks. DHA degradation in algal oil was modeled by an autocatalytic equation. The fate of DHA from algal oil in mozzarella cheese was also modeled by an autocatalytic equation. In an effort to prevent DHA degradation and oxidation, mixed tocopherols were added. The optimum combination of those tested was found, using a response surface design, to be 3% algal oil with 110ppm mixed tocopherols for maximum DHA and minimum oxidation over 2 weeks. This algal oil/antioxidant combination in mozzarella cheese successfully prevented oxidation and DHA degradation over 3 weeks of storage. Approximately 0.1g DHA may be consumed from a 28g serving of this cheese. Approximately 0.5-18 servings of this cheese are equivalent to DHA consumed from a 3oz serving of fish, depending on fish type. Sensory evaluation tests found consumers could distinguish between mozzarella cheese with/without algal oil. Results from this study improve understanding of omega-3 FA behavior in mozzarella cheese and provide a means for preserving quality and nutrition. / Master of Science

No / A transition-metal-free efficient method for the preparation of 1,2,3-trisubstituted benzenes from bispropargyl alcohols and 1,3-dicarbonyl compounds has been developed. The reaction of bispropargyl alcohol with 1,3-dicarbonyl compound proceeds through [3,3]-rearrangement, 6π-electrocyclization, and unexpected Csp3−Csp2 regioselective σ-bond cleavage processes.

No / Investigations of structural reactivity, molecular interactions and vibrational characterization of pharmaceutical drugs are helpful in understanding their behaviour. The aim of this study is to determine the molecular, electronic and chemical properties of the antibiotic drug nitrofurantoin (NF), after cocrystallisation with 3-aminobenzoic acid (3ABA) and to understand how those changes lead to variation of properties in the cocrystal NF–3ABA. NF–3ABA formation is explained by stabilization via the hydrogen-bond network between NF and 3ABA molecules. It is thoroughly characterized by IR, Raman and CP-MAS solid-state 13C NMR techniques, along with quantum chemical calculations. The results of IR, Raman, and 13C NMR analyses showed that imide N–H23 and C12[double bond, length as m-dash]O of NF interact with the acid C[double bond, length as m-dash]O and –OH groups in 3-ABA, respectively. Therefore the IR, Raman, and 13C NMR spectra verified the formation of N–H⋯O and O–H⋯O hydrogen bonds. To study hydrogen bonding interactions theoretically in NF–3ABA, two functionals B3LYP and wB97X-D have been used. A comparison is made between the results obtained by B3LYP and those predicted at the wB97X-D level. It is found that wB97X-D is best applied density functional theory (DFT) functional to describe the hydrogen bonding interactions. The strength and nature of hydrogen bonding in NF–3ABA have been analysed by quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. To validate the results obtained by QTAIM theory and to study the long-range forces, such as van der Waals interactions, the steric effects in NF–3ABA, the reduced density gradient (RDG) and the isosurface have been plotted using Multiwfn software. QTAIM and isosurface analysis suggested that the hydrogen bonding interactions present in NF–3ABA are moderate in nature. The calculated HOMO–LUMO energy gap shows that NF–3ABA is more active than NF and 3ABA. Chemical reactivity descriptors are calculated to understand the various aspects of pharmacological sciences. Chemical reactivity parameters show that NF–3ABA is softer and chemically more reactive than NF. The results suggest that cocrystals can be a feasible alternative for positively changing the targeted physicochemical properties of an active pharmaceutical ingredient (API). / Royal Society of Chemistry for the mobility grant (2015/17); DST (New Delhi) under the DST purse programme; UGC under the BSR meritorious fellowship scheme; DST, India under the Indo-Brazil project