Physical Sciences and Mathematics Commons^™

A New Algorithm For Primer Design, Debanjan Guha Roy

Electronic Thesis and Dissertation Repository

The Polymerase Chain Reaction (PCR) technology is widely used to create DNA copies. It has impacted many diverse fields including genetics, forensics, molecular paleontology, medical applications and environmental microbiology.

The main object in PCR is a primer, a short single strand of DNA, about 18-25 bases long, that serves as the starting point of DNA synthesis. Primers are essential for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA. The PCR starts at the 3’-end of the primer and copies the opposite strand.Designing good primers is essential …

Comparative Assessment Of Downscaling Methods And Application Towards Analysis Of Climate Change Impact On Urban Regions, Markus Eichenbaum

Electronic Thesis and Dissertation Repository

Global climate models (GCM) are sophisticated numerical models used to make long term climate projections. However, the resolution of their output is too coarse for climate change related local impact studies on urban regional scales. Downscaling efforts are taken to address this and increase GCM projection resolution. Physical Scaling (SP) downscaling methodology attempts to incorporate the physical basis of dynamical downscaling efforts with the computational efficiency of statistical methods. In this study, North American Regional Reanalysis surface skin temperature and precipitation data for a 1°x1° region centered on Houston, TX are downscaled to a resolution of 500m via SP and …

Investigations Of The High Pressure Effects On Structural Properties And Co2 Adsorption Performance Of Mofs Using Vibrational Spectroscopy, Shan Jiang

Electronic Thesis and Dissertation Repository

The pre- and post-combustion carbon dioxide capture has drawn much attention in the past few decades owing to the increasing concentration of CO₂ in the atmosphere. Among all the potential solid adsorbents for CO₂ capture, metal-organic frameworks (MOFs) are a promising class of materials due to their large surface areas, high tunability and their high selectivity for gas adsorption applications. It has been widely demonstrated that the application of high external pressure in gigapascal level can substantially tune the structure, pore size and opening of porous material. Consequently, the structural, as well as gas adsorption properties of these …

On The Sparre-Andersen Risk Models, Ruixi Zhang

Electronic Thesis and Dissertation Repository

This thesis develops several strategies for calculating ruin-related quantities for a variety of extended risk models. We focus on the Sparre-Andersen risk model, also known as the renewal risk model. The idea of arbitrary distribution for the waiting time between claim payments arose in the 1950’s from the collective risk theory, and received many extensions and modifications in recent years. Our goal is to tackle model assumptions that are either too relaxed for traditional methods to apply, or so complicated that elaborate algebraic tools are needed to obtain explicit solutions.

In Chapter 2, we consider a Lévy risk process and …

The Synthesis Of Heterocycles And Carbocycles And Work Towards Kainic Acid, Mathew L. Piotrowski

Electronic Thesis and Dissertation Repository

This thesis focuses on the synthesis of a variety of heterocycles and carbocycles such as pyrrolidines, dihydrofurans, dihydropyrroles, cyclopentenes, and 2,5-dihydrooxepines. Traditional synthetic methods are discussed first, followed by the manipulation of donor-acceptor cyclopropanes towards the above-mentioned compounds. This leads to a discussion about an important pyrrolidine-containing natural product known as kainic acid. Kainic acid has been studied in the neuroscience field for its biological properties which have led to a better understanding of common human neurological disorders like epilepsy, Huntington’s disease and the after-effects of strokes.

Chapter two focuses on a common rearrangement of donor-acceptor cyclopropanes known as the …

Functionalization Of Indoles And Donor-Acceptor Cyclopropanes And Their Application Towards The Total Synthesis Of Tronocarpine And Dippinine B, Lauren C. Irwin

Electronic Thesis and Dissertation Repository

The work disclosed in this dissertation outlines novel reactions involving indoles and their applications towards the total synthesis of natural products, tronocarpine and dippinine B.

Showcased in Chapter 2 is a novel mode of activation for donor-acceptor cyclopropanes via an external hydrogen bond. The hydrogen bond increases the cyclopropane’s electrophilicity permitting indole nucleophiles to open the ring. The result is 3-postion functionalized indoles.

An external hydrogen-bond donor, HFIP (1,1,1,3,3,3-hexafluoroisopropanol), is used as a solvent to provide the medium necessary for favourable hydrogen-bond interaction with donor-acceptor cyclopropanes. Hydrogen bond activation of donor-acceptor cyclopropanes was successful in generating a multitude of functional …

Novel Avenues Toward Controlling The Photophysical Properties Of Ultra-Small Silicon Quantum Dots, Mohammed Abdelhameed

Electronic Thesis and Dissertation Repository

Quantum dots (QDs) have attracted an increasing attention in the last decade over many conventional organic dyes. This is due to their unique optical properties including broad absorption spectra, high photostability, and size-tunable photoluminescence (PL). However, some toxicity concerns associated with traditional quantum dots have hindered their wide applicability. Interestingly, silicon quantum dots (SQDs) have been shown to be more advantageous than most of QDs thanks to their excellent biocompatibility and biodegradability, low cytotoxicity, and versatile surface functionalization capability. Thus, SQDs are promising candidates for various biological and biomedical applications such as bioimaging, biosensing, and photodynamic therapy. Unfortunately, only a …

Progress Toward Durable Icephobic Materials, Matthew J. Coady

Electronic Thesis and Dissertation Repository

Ice accumulation is a major engineering challenge in many fields including aerospace, power generation, transportation, and infrastructure. A variety of solutions are being researched to address this challenge. Perhaps the most promising method of combating ice accumulation is by applying coatings with low values of interfacial ice adhesion strength, τ_ice. Icephobic materials are those with ice adhesion below 100 kPa, and it has been shown that passive delamination can occur on surfaces with τ_ice below 20 kPa. While various low adhesion surfaces have been prepared, durability concerns pervade applications where surfaces experience repeated icing or freeze-thaw cycles, …

Zinc–Phosphorus Clusters For Solution Synthesis Of Zinc Phosphide Nanoparticles, Kyungseop Lee

Electronic Thesis and Dissertation Repository

Synthesis of zinc phosphide (Zn₃P₂) nanoparticles is an emerging topic of investigation as Zn₃P₂ is a candidate material for the next generation solar cells. Despite the early discovery of its favorable electronic properties that are well-suited for photovoltaic applications, a major focus of synthetic strategy was with vapor/chemical deposition methods. Solution methods with greater control over size, crystal structure and composition at a lower production cost, has been underdeveloped in comparison. In this context, this thesis describes the synthesis, characterization and reactivity of zinc phosphido clusters: [Zn₂(μ-PPh₂)₂(PPh …

Statistical Modeling And Characterization Of Induced Seismicity Within The Western Canada Sedimentary Basin, Sid Kothari

Electronic Thesis and Dissertation Repository

In western Canada, there has been an increase in seismic activity linked to anthropogenic energy-related operations including conventional hydrocarbon production, wastewater fluid injection and more recently hydraulic fracturing (HF). Statistical modeling and characterization of the space, time and magnitude distributions of the seismicity clusters is vital for a better understanding of induced earthquake processes and development of predictive models. In this work, a statistical analysis of the seismicity in the Western Canada Sedimentary Basin was performed across past and present time periods by utilizing a compiled earthquake catalogue for Alberta and eastern British Columbia. Specifically, the frequency-magnitude statistics were analyzed …

Methodologies For Metal Functionalization Of Phosphorus Based Photopolymer Networks, Vanessa Béland

Electronic Thesis and Dissertation Repository

Photopolymer networks with phosphonium cation, alkyl phosphine and olefin functionality were designed, synthesized and functionalized with metals by metathesis, coordination and hydrometallation reactions, respectively. The materials were strategically designed so that the metal functionalization step could be monitored and quantified. In some cases, this involved characterization by IR, NMR, or X-ray spectroscopic techniques, or by comparison to molecular analogues. It was found that by using a bi-functional photopolymer network, the material could be bi-metallized by orthogonal mechanisms. All metallized polymer networks were tested for their suitability as precursors to metal-containing ceramics. The polymers were pyrolyzed, and on analysis it was …

The Stability Of Temperate Lakes Under The Changing Climate, Aleksey Paltsev

Electronic Thesis and Dissertation Repository

There is a collective prediction among ecologists that climate change will enhance phytoplankton biomass in temperate lakes. Yet there is noteworthy variation in the structure and regulating functions of lakes to make this statement challengeable and, perhaps, inaccurate. To generate a common understanding on the trophic transition of lakes, I examined the interactive effects of climate change and landscape properties on phytoplankton biomass in 12,644 lakes located in relatively intact forested landscapes. Chlorophyll-a (Chl-a) concentration was used as a proxy for phytoplankton biomass. Chl-a concentration was obtained via analyzing Landsat satellite imagery data over a 28-year period (1984-2011) and using …

Shock Effects Recorded By The U-Pb Radiometric System In Zircons Of Apollo 17 Impact Breccias And By Raman Spectroscopy In Enstatite Meteorites, Bidong Zhang

Electronic Thesis and Dissertation Repository

Impact cratering processes and formations are ubiquitous on the rocky planets within the Solar System. The Earth-Moon system was formed by a massive planetary impact, and numerous impacts afterwards significantly reshaped the topography and lithology of the Moon surface. This dissertation focuses on studying some specific geochemical, geochronological, and geophysical signatures of impact processes preserved in lunar rocks and asteroidal meteorites.

The zircon U-Pb radiometric system is one of the most reliable geochronometers in measuring geological time. Recently, unsupported radiogenic Pb enrichment has been reported to compromise the accuracy and precision of zircon U-Pb geochronometer in terrestrial rocks. In Chapter …

Strategies For The Preparation Of Functional Pendant Group Polymer Materials Via Click Chemistry, Rajeshwar Vasdev

Electronic Thesis and Dissertation Repository

This thesis describes the development of a polymer via a unique masking-unmasking strategy allowing for physical and chemical modification as desired. Modifiable polymers may lead to improved applications in drug delivery, photo-patterning and emissive materials design. In recent years, these potential traits have motivated the search for efficient protocols for the synthetic modification of polymers. Accordingly, click chemistry, characterized by fast, clean and high yielding reactions represents an effective tool for the modification of polymers. To achieve this goal, an efficient methodology is created to incorporate a highly reactive strained alkyne functional group as a modification site to expand the …

Vertical Ionization Energies From The Average Local Electron Energy Function, Amer Marwan El-Samman

Electronic Thesis and Dissertation Repository

It is a non-intuitive but well-established fact that the first and higher vertical ionization energies (VIE) of any N-electron system are encoded in the system's ground-state electronic wave function. This makes it possible to compute VIEs of any atom or molecule from its ground-state wave function directly, without performing calculations on the (N-1)-electron states. In practice, VIEs can be extracted from the wave function by using the (extended) Koopmans' theorem or by taking the asymptotic limit of certain wave-function-based quantities such as the ratio of kinetic energy density to the electron density. However, when the wave function is expanded in …

Sm-Nd, Lu-Hf, And Mn-Cr Isotope Geochemistry Of Achondrite Meteorites: Implications For The Formation Reservoirs Of Differentiated Planetesimals, Zhiguo Guo

Electronic Thesis and Dissertation Repository

Accretion and differentiation of planetesimals are critical steps of planetary formation. By studying achondrite meteorites, we can bring further geochemical and chronological constraints on the source and composition of materials and their evolution throughout the protoplanetary disk. Major and trace element analyses for mineral and whole-rock compositions and high-precision isotopic compositions for the short- and long-lived radiochronometers ⁵³Mn-⁵³Cr, ^147,146Sm-^143,142Nd and ¹⁷⁶Lu-¹⁷⁶Hf are reported for two eucrites, two diogenites, and three ungrouped achondrites. Of these, NWA 12338 is a newly classified ungrouped achondrite with an anomalously higher Δ¹⁷O than mean …

The Ghrelin Receptor And Its Appetite For Highly Potent Ghrelin Analogues, Tyler J. Lalonde

Electronic Thesis and Dissertation Repository

The growth hormone secretagogue receptor-1a (GHS-R1a) is expressed in many human tissues, most notably the hypothalamus, and causes an increase in appetite upon activation by its endogenous ligand, ghrelin. GHS-R1a is differentially expressed in malignant compared to benign tumours. Therefore, there is an interest in developing GHS-R1a-targeted peptides as novel drugs to modulate signaling for diseases such as cancer cachexia and obesity and to image the receptor for disease diagnosis and following progression.

Chapter 2 discusses a fluorescently labelled ghrelin analogue for imaging GHS-R1a in ex vivo biopsy analysis and in vivo distribution studies. The analogue was created through side-chain …

A Programming Model For Internetworked Things, Hao Jiang

Electronic Thesis and Dissertation Repository

The Internet of Things (IoT) emerges as a system paradigm that encompasses a wide spectrum of technologies and protocols related to Internetworking, services computing, and device connectivity. The main objective is to achieve an environment whereby physical devices and everyday objects can communicate and interact with each other over the Internet. The Internet of Things is heralded as the next generation Internet, and introduces significant opportunities for novel applications in many different domains. What is missing right now is a programming model whereby developers as well as end-users can specify any addressable resource at a higher level of abstraction, and …

Ni And Fe Isotope Fractionation During Weathering And The Formation Of Ni Laterite Ore Deposits In The Philippines, Congxi Zhu

Electronic Thesis and Dissertation Repository

Weathering processes on Ni-rich ultramafic rocks in tropical areas produce laterites that become exploitable for Ni mining. To better understand these processes, samples were collected stratigraphically with water samples from several Ni mines in the Philippines and studied for Ni and Fe isotope compositions. This study found that Ni isotope fractionation takes place during the formation of Ni-enriched minerals (goethite), when light Ni isotopes are preferentially incorporated into new minerals formed, leaving heavy Ni isotopes in groundwater. The Δ⁶⁰Ni_{Limonite-Bedrock} is up to -0.19 ± 0.32‰. Even though Fe is partitioned with redox state change during these reactions, …

Climate Change And Dissolved Organic Matter In Subarctic Lakes: Relevance To Methylmercury Bioavailability, Kyra Lyn Simone

Electronic Thesis and Dissertation Repository

One of the first steps of methylmercury (MeHg) bioaccumulation, uptake by phytoplankton, is regulated by dissolved organic matter (DOM). Methylmercury binds strongly with DOM, especially high-molecular weight (HMW) compounds containing reduced sulphur; this binding decreases MeHg bioavailability. Climate-induced changes were measured at the landscape level using ArcGIS; land-cover changes between 2005-2010 were assessed around lakes in Mackenzie Valley, NWT. The observed changes, a 10% increase in forest-classified area and up to 15% decrease in wetland area, will likely increase delivery of HMW DOM and MeHg to lakes. Partitioning experiments were conducted to examine effects of DOM ligand quality on MeHg …

High Multiplicity Strip Packing, Andrew Bloch-Hansen

Electronic Thesis and Dissertation Repository

In the two-dimensional high multiplicity strip packing problem (HMSPP), we are given k distinct rectangle types, where each rectangle type T_i has n_i rectangles each with width 0 < w_i and height 0 < h_i The goal is to pack these rectangles into a strip of width 1, without rotating or overlapping the rectangles, such that the total height of the packing is minimized.

Let OPT(I) be the optimal height of HMSPP on input I. In this thesis, we consider HMSPP for the case when k = 3 and present an OPT(I) + 5/3 polynomial time approximation algorithm for …

Shape-Controlled Nanoparticles As Effective Catalysts For Proton Exchange Membrane (Pem) Fuel Cells, Ali Feizabadi

Electronic Thesis and Dissertation Repository

Polymer electrolyte membrane fuel cell (PEMFC), is considered a promising candidate for the next generation power sources in transportation, stationary and portable applications. However, oxygen reduction reaction (ORR), one of the key reactions occurring on PEMFC is kinetically slow; this has limited performance and further advancement in this kind of fuel cells. Thus, improving the PEMFC efficiency requires a thorough understanding of the ORR mechanism on the desired catalyst. To address the above-mentioned demands, the scope of this thesis is focused on the fundamental understanding of facet-controlled nanoparticles, metal-support interactions, and bimetallic platinum catalysts, utilizing synchrotron-based X-ray absorption, X-ray photoelectron …

Synthesis Of Crosslinkable Poly(Ester Amide)S For Cell Encapsulation And Delivery, Yu Ting (Natalie) Liang

Electronic Thesis and Dissertation Repository

Tissue engineering using adipose-derived stromal cells (ASCs) shows promise for soft tissue regeneration. Biodegradable polymers are potential biomaterials as they support the growth and delivery of cells. Specifically, poly(ester amide)s (PEAs) are a class of biodegradable polymers with tunable structures that have been shown to exhibit low cytotoxicity and support the growth of various cell types. This thesis involved the development of new water soluble amino acid-based PEAs with crosslinkable moieties to enable formation of hydrogel scaffolds for ASC encapsulation. These hydrophilic phenylalanine-based and alanine-based PEAs were synthesized by solution polycondensation and photo-crosslinked into a series of hydrogels with and …

The Effect Of Stiffness Anisotropy Of A Glacial Clay On The Behaviour Of A Shallow Wind Turbine Foundation, Jesús A. González-Hurtado

Electronic Thesis and Dissertation Repository

Shallow wind turbine foundations are designed based on investigations of the ultimate, serviceability and fatigue limit states. The serviceability limit state design approaches in particular are based on simple isotropic elastic half-space analyses that ignore coupling between loading directions, and soil non-linearity and elastic anisotropy. Many of the wind farms in Ontario are constructed around the Great Lakes basin and a number of these areas are characterized as stiff clayey glacial tills. It is recognized that many of these glacial materials exhibit some degree of strength, stiffness and fabric anisotropy. This research aimed to characterize the anisotropic geotechnical properties of …

New Algorithms For Computing Field Of Vision Over 2d Grids, Evan Debenham

Electronic Thesis and Dissertation Repository

In many computer games checking whether one object is visible from another is very important. Field of Vision (FOV) refers to the set of locations that are visible from a specific position in a scene of a computer game. Once computed, an FOV can be used to quickly determine the visibility of multiple objects from a given position.

This thesis summarizes existing algorithms for FOV computation, describes their limitations, and presents new algorithms which aim to address these limitations. We first present an algorithm which makes use of spatial data structures in a way which is new for FOV calculation. …

Synthesis And Characterization Of Peptide Nucleic Acids Incorporating Modified Nucleobases, Ali Heidari

Electronic Thesis and Dissertation Repository

Peptide Nucleic Acid (PNA), is a mimic of natural nucleic acids with exceptional binding properties. As such, numerous applications in biochemistry, medicine and biotechnology for PNA exist or have been proposed so far. Pseudo-complementary PNAs containing diaminopurine and thiouracil base pairs have been prepared and are shown to bind with high specificity and efficiency to complementary targets in double-stranded DNA by a mechanism termed ‘‘double duplex invasion’’ in which the duplex is unwound and both DNA strands are targeted simultaneously, each by one of the two pseudo-complementary PNAs. Chapter 2 describes a method for the preparation of modified nucleic acids …

The Effect Of Spatial Averaging On Db/Dt Exposure Values For Implanted Medical Devices, Christopher Ap Brown

Electronic Thesis and Dissertation Repository

Magnetic resonance imaging (MRI) is a medical imaging modality that has seen continuous growth in the decades since its introduction. In conjunction with this increase in the use of MRI, there has also been a growth in the number of patients having implanted medical devices, such as pacemakers. These devices can have undesirable interactions with the MR system. The safety of these interactions must be guaranteed while ensuring that safety limits are not so conservative that they would preclude too many patients from benefiting from MRI. One factor that could make limits less restrictive is spatial averaging of the fields …

A New Approach To Sequence Local Alignment: Normalization With Concave Functions, Qiang Zhou

Electronic Thesis and Dissertation Repository

Sequence local alignment is to find two subsequences from the input two sequences respectively, which can produce the highest similarity degree among all other pairs of subsequences. The Smith-Waterman algorithm is one of the most important technique in sequence local alignment, especially in computational molecular biology. This algorithm can guarantee that the optimal local alignment can be found with respect to the distance or similarity metric. However, the optimal solution obtained by Smith-Waterman is not biologically meaningful, since it may contain small pieces of irrelevant segments, but as long as they are not strong enough, the algorithm still take them …

Algebraic Companions And Linearizations, Eunice Y. S. Chan

Electronic Thesis and Dissertation Repository

In this thesis, we look at a novel way of finding roots of a scalar polynomial using eigenvalue techniques. We extended this novel method to the polynomial eigenvalue problem (PEP). PEP have been used in many science and engineering applications such vibrations of structures, computer-aided geometric design, robotics, and machine learning. This thesis explains this idea in the order of which we discovered it.

In Chapter 2, a new kind of companion matrix is introduced for scalar polynomials of the form $c(\lambda) = \lambda a(\lambda)b(\lambda)+c_0$, where upper Hessenberg companions are known for the polynomials $a(\lambda)$ and $b(\lambda)$. This construction can …

Towards Using Model Averaging To Construct Confidence Intervals In Logistic Regression Models, Artem Uvarov

Electronic Thesis and Dissertation Repository

Regression analyses in epidemiological and medical research typically begin with a model selection process, followed by inference assuming the selected model has generated the data at hand. It is well-known that this two-step procedure can yield biased estimates and invalid confidence intervals for model coefficients due to the uncertainty associated with the model selection. To account for this uncertainty, multiple models may be selected as a basis for inference. This method, commonly referred to as model-averaging, is increasingly becoming a viable approach in practice.

Previous research has demonstrated the advantage of model-averaging in reducing bias of parameter estimates. However, there …