Physical Sciences and Mathematics Commons^™

Improvements On Seeding Based Protein Sequence Similarity Search, Weiming Li

Electronic Thesis and Dissertation Repository

The primary goal of bioinformatics is to increase an understanding in the biology of organisms. Computational, statistical, and mathematical theories and techniques have been developed on formal and practical problems that assist to achieve this primary goal. For the past three decades, the primary application of bioinformatics has been biological data analysis. The DNA or protein sequence similarity search is perhaps the most common, yet vitally important task for analyzing biological data.

The sequence similarity search is a process of finding optimal sequence alignments. On the theoretical level, the problem of sequence similarity search is complex. On the applicational level, …

Arctic Cold Spring Mineralogy As An Indicator Of Spring Deposits, Water, And Habitable Environments On Mars, Melissa M. Battler

Electronic Thesis and Dissertation Repository

Springs exist in many terrestrial settings and have supported microbial communities throughout Earth’s history. There is mounting evidence for spring deposits on Mars from Noachian age to present, implying that water may be circulating in Mars’ subsurface despite current cold, arid conditions. Current datasets for most of Mars are limited to mineralogy via orbital spectroscopy and geomorphology from visual imagery and laser altimetry. Much is known about terrestrial spring morphology, but few springs exist in Mars analogue settings, and of those, few have been investigated for mineralogy. This study reports on two sets of cold spring sites in the Canadian …

Multi-Sensor Calibration And Validation Of The Uwo-Pcl Water Vapour Lidar, Robin Wing

Electronic Thesis and Dissertation Repository

The Purple Crow Lidar (PCL) has recently participated in a water vapour validation cam- paign with the NASA/GSFC Atmospheric Laboratory for Validation/Interagency Collaboration and Education (ALVICE) Lidar. The purpose of this calibration campaign is to insure that PCL water vapour measurements are of sufficient quality for use in scientific investigations of atmo- spheric change, and to be included in the Network for the Detection of Atmospheric Climate Change (NDACC) data base. The detection of long term changes in water vapour concentra- tion, particularly in the upper troposphere and lower stratosphere (UTLS) is an issue of pressing scientific, ecological and societal …

Simultaneous Radar And Video Meteors, Robert J. Weryk

Electronic Thesis and Dissertation Repository

The goal of this thesis is to better understand the physical and chemical properties of meteoroids by using simultaneous radar and video observations of meteors. The Canadian Meteor Orbit Radar (CMOR) and several Gen-III image-intensified CCD cameras were used to measure common meteors and validate metric errors determined through Monte Carlo modelling and to relate radar electron line density (q) to video photon radiant power (I). By adopting an ionisation coefficient from Jones (1997) and using recorded measurements of q/I, a corresponding estimate of the fraction of meteoroid kinetic energy loss converted into light (luminous efficiency) was found.

It was …

A New Algorithm For De Novo Genome Assembly, Md. Bahlul Haider

Electronic Thesis and Dissertation Repository

The enormous amount of short reads produced by next generation sequencing (NGS) techniques such as Roche/454, Illumina/Solexa and SOLiD sequencing opened the possibility of de novo genome assembly. Some of the de novo genome assemblers (e.g., Edena, SGA) use an overlap graph approach to assemble a genome, while others (e.g., ABySS and SOAPdenovo) use a de Bruijn graph approach. Currently, the approaches based on the de Bruijn graph are the most successful, yet their performance is far from being able to assemble entire genomic sequences. We developed a new overlap graph based genome assembler called Paired-End Genome ASsembly Using Short-sequences …

Strength, Elasticity And Phase Transition Study On Nacl And Mgo-Nacl Mixture To Mantle Pressures, Zhongying Mi

Electronic Thesis and Dissertation Repository

Rheological properties of the Earth control most of the important geological processes, such as mantle convection, plate tectonics, earthquakes and nature of thermal evolution. Most parts of the Earth consist of multi-phase polycrystalline aggregates with various composition and compressibility. Therefore, deformation studies on multi-phase materials are important to understand the rheological properties and convection of the Earth. NaCl and MgO with large contrast in elastic properties are excellent analogue materials for modelling the Earth that is generally made of both strong and weak materials. In addition, NaCl and MgO are widely used as pressure transmitting medium and pressure calibration standard …

Topographic Influences On Trends And Cycles In Nutrient Export From Forested Catchments On The Precambrian Shield, Samson G. Mengistu

Electronic Thesis and Dissertation Repository

This dissertation explored topographic controls on spatial and temporal patterns in water yield and nutrient (carbon, nitrogen and phosphorus) export from forested headwater catchments in the Turkey Lakes Watershed in central Ontario, where other factors contributing to differences in water yield and nutrient export, including climate, geology, forest, and soils, are relatively constant. Topographic characteristics, including (a) hydrological flushing potential (expansion of water table into nitrate-N producing areas); (b) hydrological storage potential (area of wetlands, which can alternatively allow water and nutrients to bypass wetlands when storage capacity is filled with water or to trap them when not filled); and …

The Reasonable Effectiveness Of Mathematics In The Natural Sciences, Nicolas Fillion

Electronic Thesis and Dissertation Repository

One of the most unsettling problems in the history of philosophy examines how mathematics can be used to adequately represent the world. An influential thesis, stated by Eugene Wigner in his paper entitled "The Unreasonable Effectiveness of Mathematics in the Natural Sciences," claims that "the miracle of the appropriateness of the language of mathematics for the formulation of the laws of physics is a wonderful gift which we neither understand nor deserve." Contrary to this view, this thesis delineates and implements a strategy to show that the applicability of mathematics is very reasonable indeed.

I distinguish three forms of the …

Optimization Of Chiral Separation Of Nadolol By Simulated Moving Bed Technology, Nesma Nehad Hashem

Electronic Thesis and Dissertation Repository

Simulated Moving Bed (SMB) technology has gained increasing attention as one of the most powerful techniques for chromatographic separations due to its cost-effectiveness and efficiency. Application of SMB technology is especially important in the pharmaceutical industry for production of enantiopure drugs, as required under strict FDA regulations, to avoid possible adverse effects of racemic drugs. In this study, the performance of the SMB process in separation of racemic nadolol on a perphenyl carbamoylated beta cyclodextrin (β-CD) stationary phase was investigated. The equilibrium dispersive model coupled with bi-Langmuir adsorption isotherm and lumped kinetic approximation, constitute the mathematical model used to simulate …

Incomplete Market Models Of Carbon Emissions Markets, Walid Mnif

Electronic Thesis and Dissertation Repository

New regulatory frameworks have been developed with the aim of decreasing global greenhouse gas emissions over both short and long time periods. Incentives must be established to encourage the transition to a clean energy economy. Emissions taxes represent a "price" incentive for this transition, but economists agree this approach is suboptimal. Instead, the "quantity" instrument provided by cap-and-trade markets are superior from an economic point of view. This thesis focuses on the cap-and-trade instrument. Carbon emissions markets have recently been implemented in different countries. We summarize the state of world cap-and-trade schemes. We also provide a literature review of existing …

Studies On Molecular Sieve Crystallization And Heteroatomic Substitution, Adam R. Macintosh

Electronic Thesis and Dissertation Repository

Molecular sieves have been scientifically and industrially important materials since their inception. These porous, crystalline networks of tetrahedrally coordinated atoms bridged by oxygen are known for their extremely high surface area and low density, making them excellent systems for catalysis. The framework of the AlPO₄ family of molecular sieves is itself non-catalytic, but through heteroatomic substitution these materials can diversify into the catalytically active silicoaluminophosphate (SAPO) and metalloaluminophosphate (MAPO) families of heterogeneous acid and redox catalysts. Research into the methods by which these substitutions occur, and the effects therein on the crystallization of the sieves, is of great importance, …

Characterization Of Novel Ichnofossils In Meteorite Impact Glass From The Ries Impact Structure, Germany, Haley M. Sapers

Electronic Thesis and Dissertation Repository

The initial catastrophic biological effects of hypervelocity impacts are well established. However, a growing body of evidence suggests that meteorite impact events have beneficial effects for microbial life. This, in turn, has led many to suggest that impact craters may have been important habitats for life on early Earth. Any large meteorite impact into a water-rich target on a solid planetary body has the potential to generate hydrothermal systems. Impact-generated hydrothermal systems expand the potential environments for microbial colonization to environments without endogenous volcanic heat sources to drive hydrothermal activity. Examination of impact glass from the Ries impact structure, Germany, …

On The Distribution Of Quadratic Expressions In Various Types Of Random Vectors, Ali Akbar Mohsenipour

Electronic Thesis and Dissertation Repository

Several approximations to the distribution of indefinite quadratic expressions in possibly singular Gaussian random vectors and ratios thereof are obtained in this dissertation. It is established that such quadratic expressions can be represented in their most general form as the difference of two positive definite quadratic forms plus a linear combination of Gaussian random variables. New advances on the distribution of quadratic expressions in elliptically contoured vectors, which are expressed as scalar mixtures of Gaussian vectors, are proposed as well. Certain distributional aspects of Hermitian quadratic expressions in complex Gaussian vectors are also investigated. Additionally, approximations to the distributions of …

Strategies For Visco-Acoustic Waveform Inversion In The Laplace-Fourier Domain, With Application To The Nankai Subduction Zone, Rie Kamei

Electronic Thesis and Dissertation Repository

Waveform inversion is a non-linear and ill-posed inverse problem, with the objective of utilizing the full information content of recorded seismic waveforms. A Laplace-Fourier domain implementation allows a natural `multiscale' approach that mitigates the non-linearity and ill-posedness by inverting low-frequency, early arrival data in the initial stages of inversion. High-frequency components, and late arrivals are incorporated at a later stage. This allows the development of robust inversion strategies capable of handling large wide-angle crustal surveys, leading to reliable, high-resolution velocity and attenuation models of crustal structures. I apply waveform inversion to extract a P-wave velocity model of the active megasplay …

Controlled Degradation Of Poly(Ester Amide)S Via Cyclization Of Pendant Functional Groups, Jose Samuel Mejia

Electronic Thesis and Dissertation Repository

Polyesters have been used for many biomedical applications ranging from sutures to drug delivery vehicles. However, their bulk degradation results in an accumulation of acidic byproducts, which is detrimental to the human body. In order to circumvent this problem, as well as to impart new properties and functions to polymers for biomedical applications, poly(ester amide)s (PEAs) have been proposed as a different class of biodegradable polymers. However, up to date, there exists no way to stimulate the degradation of these polymers.

The Gillies research group has previously incorporated self-immolative spacers into polymers and has been able to stimulate their degradation …

The Behavior Of A Falling Particle In A Funnel, Tahani Hassn Aldahri

Electronic Thesis and Dissertation Repository

Recent theoretical work has suggested that a frictional, inelastic, spherical particle falling under gravity through a symmetric funnel will display interesting behavior as a function of the angle of the funnel walls. We have studied this system experimentally, using high-speed video to record the particle trajectories. By analyzing the video images, we have analyzed the time the ball spends in the funnel and its energy loss as functions of the angle of the walls with respect to the horizontal. The coefficient of restitution was also varied by using different balls and funnel materials. We found some similarities and differences between …

Evaluation Of Jarosite As A Biosignature: A Comparison Of Biogenic And Synthetic Jarosites, Liane Loiselle

Electronic Thesis and Dissertation Repository

The detection of jarosite (K)Fe₃(SO₄)₂OH₆ on Mars has been interpreted as mineralogical evidence of acid-sulfate aqueous processes, including putative evidence of biological activity. Terrestrial habitats where acidic conditions occur are environments where microbiota thrive and generate biological signatures. A biotic and synthetic jarosite were produced to evaluate the ability and effectiveness of existing analytical methods to identify biosignatures in targeted geological materials. Using a comprehensive suite of microscopic (light microscopy, SEM and TEM), mineralogical (XRD), spectroscopic (IR, LIBS, Mössbauer, UV-Vis-NIR, and Raman) and mass spectrometry (ToF-SIMS) techniques, the two jarosites were found to …

Geography, News Media Discourse, And Water Management: A Case Study Of The Devils Lake Outlet, Daniel J. Bednar

Electronic Thesis and Dissertation Repository

This thesis explores the print news media discourse surrounding the dispute between Manitoba and North Dakota over a flood mitigation plan in Devils Lake North Dakota. In order to do so, critical discourse analysis was applied to news media from a seventeen year period during the dispute. Findings were compared between media sources as well as to pertinent policy documents. The thesis finds that the political arena provided by local newspapers as well as the discourses of scale, confrontation, history, and economics had the largest effect on the dispute’s public face. A total of nine findings within these areas are …

Diatoms In Castor Lake (North-Central Washington, Usa) – Proxies Of Climate And Hydrologic Variation, Kelly D. Hollingshead

Electronic Thesis and Dissertation Repository

This research provides a high temporal resolution (1 sample / 2-3 years) record of hydrologic variation for the last 2,000 years using a lake sediment record from Castor Lake, a closed-basin system in Washington, USA. The core was dated using ¹³⁷Cs, ¹⁴C, and tephrochronology. Approximately 600 diatoms were identified and enumerated in 198 samples from a Castor Lake freeze core and Livingstone-piston core. A diatom-inference model for salinity was applied to reconstruct fossil diatom salinity. Diatom-inferred salinity for the last century tracked Palmer Drought Severity Index, indicating diatom community composition tracks effective moisture and can be used to …

Evolution Of The Late Ordovician Plaesiomyid Brachiopod Lineage In Laurentia, Colin D. Sproat

Electronic Thesis and Dissertation Repository

During the Late Ordovician, a transgression flooded much of Laurentia. The fauna of these intracratonic basins became differentiated from the fauna of the pericratonic shelves and platforms, typically displaying gigantism and coarser shell ornamentation. In this study, 509 specimens from 11 species of the Plaesiomyidae brachiopod family from the Katian and Hirnantian were measured, of which 198 included in principal component analysis to quantify morphological changes over this interval. Three trends were revealed: 1) increasing globosity and dorsal convexity from the early to late Katian, 2) coarser, but fewer ribs on species from the paleoequatorial intracratonic seas compared to species …

Stratigraphy And Sedimentology Of The Late Cretaceous (Coniacian) Muskiki And Marshybank Members, Southern Alberta And Northwestern Montana, Meriem Grifi

Electronic Thesis and Dissertation Repository

A high-resolution allostratigraphic study of the Coniacian Muskiki and Marshybank members of the Wapiabi Formation in southern Alberta revealed a southwest thickening wedge of mudstone-dominated strata that was deposited on a shallow storm-dominated shelf. Well-log correlations and biostratigraphy show that the Muskiki Member forms the bulk of the succession; the Marshybank Member is thin or absent in the subsurface. The lower and middle units of the Muskiki Member display regional subsidence patterns consistent with thrust sheet loading in the Cordillera. The upper unit comprises a linear trough filled by southeastward-accreting clinothems. The northeast boundary of the clinoform package corresponds with …

Investigation Of Hydrothermal Alteration Processes In The Troodos Ophiolite And The Abitibi Greenstone Belt, Tamara P. Sredojevic

Electronic Thesis and Dissertation Repository

Hydrothermal alteration is an important and ubiquitous process between rocks in the Earth’s crust and seawater. To gain more understanding of such processes, two localities are investigated here: the Troodos Ophiolite Complex of Cyprus and the syenitic rocks associated with gold mineralization at the Upper Canada property, Kirkland Lake, Ontario. This thesis reports unique effects of hydrothermal activity. The Troodos Ophiolite samples consist of sheeted diabase dykes, gabbroic and ultramafic rocks in the CY-4 drill hole. The oxygen isotopic signature of these rocks indicates that alteration temperatures increased downhole and channeling of low-temperature fluids occurs at the dyke – gabbro …

Technique Design To Increase In-Situ Electrical Connections In A Cubic Anvil Press, Marie April Burford

Electronic Thesis and Dissertation Repository

An experimental technique designed to increase in-situ electrical connections in a cubic anvil press has been developed. Two encompassing cell designs (extruded gasket and pre-formed gasket) were tested with several electrical barrier methods: PVD coatings, G-10/FR-4 and Canvas Electrical (C. E.) phenolic, Teflon and Al ceramic tubing.

Many variations of techniques were attempted and each (n)^th attempt was founded on the experience from/observation of the results obtained with the (n-1)^thtechnique variation. Eighteen pressure cell configurations were designed and tested. The cells with self-extruded gaskets were unsuccessful due to the destructive nature of the extruding gaskets on the …

Studies Of Microscopic Scale Strains In Nickel Alloys Resulting From Mechanical And Chemical Forces, Jing Chao

Electronic Thesis and Dissertation Repository

The nickel-based Alloy 600, also known as Inconel 600 has been found to be susceptible to stress corrosion cracking (SCC) in high temperature aqueous environments. Despite extensive research, the mechanisms by which this process occurs remain in question. It is known that SCC results from the simultaneous effects of a chemically corrosive environment and a tensile stress. Many studies have been conducted on the microscopic chemical changes associated with SCC. There have been fewer studies of the microscopic stress/strain process. The main objective of this thesis is to use the new x-ray based diffraction technique – polychromatic x-ray microdiffraction (PXM) …

In-Capillary Reduction And Digestion Of Proteins At Nano-Liter Volume Using Capillary Electrophoresis, Thasneen Naina Nazeema

Electronic Thesis and Dissertation Repository

To analyze the proteins present in biological samples several major steps are involved. One of the crucial steps in proteomics has been sample preparation. Prior to mass spectral analysis proteins containing disulfide bonds must be reduced which is followed by digestion. In this work, a novel way of performing protein reduction and digestion at nano-liter volume using capillary electrophoresis is presented. In this work, zone passing CE technique was utilized to analyze the reduction products in CE. After the successful in-capillary reduction, digestion of protein was also performed. A pH mediated stacking was used to bring the reduced protein and …

Influence Of Quantum Dot Structure On The Optical Properties Of Group Iv Materials Fabricated By Ion Implantation, Eric G. Barbagiovanni

Electronic Thesis and Dissertation Repository

In nanostructures (NSs), to acquire a fundamental understanding of the electronic states by studying the optical properties is inherently complicated. A widely used simplification to this problem comes about by developing a model for a small scale representation of types of NSs and applying it to a hierarchy of fabrication methods. However, this methodology fails to account for structural differences incurred by the fabrication method that lead to differences in the optical properties. Proper modelling is realized by first considering the proper range of experimental parameters individually as inputs to a theoretical model and applying the correct parameters to the …

Fundamental Studies And Bioanalytical Applications Of Nanostructured-Initiator Mass Spectrometry (Nims), Jin Li

Electronic Thesis and Dissertation Repository

Nanostructured-Initiator Mass Spectrometry (NIMS), which uses ‘initiator’ molecules trapped within a nanostructured material to assist the release and ionization of intact molecules adsorbed on that material's surface upon laser or ion irradiation, is a new soft desorption/ ionization technique with several positive attributes including extraordinarily high detection sensitivities, relatively simple sample preparation protocols, and can be initiated using photon or ion irradiation sources. As result NIMS has a great deal of potential for the ready detection of small molecules from complex biofluids including metabolites, and for tissue imaging.

In the thesis, a variety of nanostructured materials including porous silicon (pSi), …

Interactive Augmented Reality As A Support Tool For Parkinson’S Disease Rehabilitation Programs, Andrés Ayala García

Electronic Thesis and Dissertation Repository

In this thesis, an augmented reality system is proposed as an alternative to create multiple interactive virtual environments that might later be used in Parkinson’s Disease rehabilitation programs. The main objective of this thesis is to develop a Wearable Tangible Augmented Reality Environment focused on providing the sense of presence required to effectively immerse patients so that they are able to perform different tasks in context–specific scenarios. By using our system, patients are able to freely navigate different virtual environments. Moreover, by segmenting and then overlaying users’ hands and objects of interest above the 3D environment, patients have the ability …

Examining Atmospheric Dust Deposition And Its Effects On Alpine Lakes In The Uinta Mountains, Utah, Oliver J. Squire

Electronic Thesis and Dissertation Repository

The composition and effects of atmospheric dust on remote alpine lakes were investigated using geological and paleolimnolgical techniques. Short cores (< 50 cm long) were retrieved from five lakes on the eastern side of the Uinta Mountains, Utah. Sediment core chronologies are based on 210 Pb and 14C dates. Dust and lake sediment core samples were analyzed for their particle size distribution, mineralogy, and chemistry. Dust was fine grained (< 10 μm) and was enriched (i.e., 50X greater concentrations) in 31 major, minor and trace elements relative to local bedrock material. In lake sediments, changes in the concentrations of key dust elements were recorded beginning in ~ AD 1900. Elements that increased in all five lakes included metals (Bi, Pb, Sb, Sn) and the nutrient P. The metals Cu and Cd also increased in four lakes. These changes are coincident with European settlement, the onset of mining, and the intensification of agriculture. The findings of this thesis show that atmospheric deposition in the Uinta Mountains is unique in composition relative to the last several hundred years. Percentage organics also increased during this period indicating increased productivity. Cladocera community composition recorded changes potentially caused by variations in atmospheric deposition of Ca in this region, although results were inconclusive.

Topics In Field Theory, Alexander Patrushev

Electronic Thesis and Dissertation Repository

This thesis consists of different projects in classical and quantum field theory on a curved background which are connected by a common usage of theoretical ideas as well as cal- culation techniques. The introduction clarifies such connections. In the second chapter we apply the Dirac constraint formalism to the second and first order 1 + 1 dimensional gravitational action coupled to a scalar field. The third chapter is devoted to a calculation of the one loop effective action for a spinor field coupled to a constant background chiral vector field. In the fourth chapter we find a new expression for …