identifier: Islam, Mohammed Fakhrul <https://research.library.mun.ca/view/creator_az/Islam=3AMohammed_Fakhrul=3A=3A.html>   (2009) Performance study of podded propulsors with varied geometry and azimuthing conditions.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: The current research investigates the performance of podded propulsors with varied geometry at different azimuthing conditions for pusher and puller configurations in open water. -- In order to determine the prominent geometric parameters and to establish their effects on the hydrodynamic performance, the first part of the research concentrated on the geometry of pusher- and puller-podded propulsors. This experimental study consisted of investigating five geometrical parameters and their effects on propeller thrust, torque and efficiency, unit thrust and efficiency of podded propulsors. The work used a factorial design (a design of experiment technique) and analysis approach to study these effects. -- The second part of the research focussed on the hydrodynamic properties of the podded propulsors in static and dynamic azimuthing conditions. This study implemented two investigations using two separate experimental apparatus. In the first investigation, two podded propulsors were tested to measure the forces and moments on the propeller and on the unit at different static azimuthing angles within the range of -30° to 30°. In the second investigation, a separate dynamometer system was used to measure forces and moments of a model pod unit at different static and dynamic azimuthing conditions within the range of 0° to 360°. An additional study evaluated the effects of azimuthing rate and propeller shaft speed on the performance parameters under consideration at dynamic azimuthing conditions. -- The study of pods with varied geometry showed that the geometric parameters have noticeable effect on propulsive characteristics of the propulsor. The analysis provided valuable information to the podded propulsor designers. In static azimuthing conditions in the range of +30° to -30°, the propeller and unit performance coefficients changed with the change of propeller loading and azimuthing angles. In the dynamic azimuthing study, the coefficients of the propeller and the pod unit showed a strong dependence on the propeller loading and azimuthing angle. Further, these results can be used as a base for validation of numerical modelling. -- The uncertainty analysis of the measurements provided strong evidence that the presented results revealed the true performance characteristics of the model scale podded propulsors under consideration.


identifier: Fleming, Patrick J. (Patrick James) <https://research.library.mun.ca/view/creator_az/Fleming=3APatrick_J=2E_=28Patrick_James=29=3A=3A.html>   (2009) Retention of specialist physicians in Newfoundland and Labrador.  Masters thesis, Memorial University of Newfoundland.

type: Thesis NonPeerReviewed

abstract: Background: Specialist physicians make up nearly half of the physicians practicing in Newfoundland and Labrador (NL) but very little is known about them. -- Methods: We examined registration data from NL to form cohorts of specialists initially licensed between 2000 and 2004 (cohort I) and between 1993 and 1997 (cohort II) and followed them up to 2007. --  Results: By the end of follow-up, 50.6% of specialists in cohort I were still practicing in the province (median time 66 months) and 15.6% from cohort II were still practicing in the province (median time 35 months). Survival analysis indicated that Memorial University medical graduates (MMGs) were more likely than other groups to remain in NL. Large proportions of specialists in our samples were non-certified and provisionally-licensed. --  Interpretation: Memorial University is a substantial contributor to specialist physician supply in NL. Increased recruitment of MMGs may improve long-term retention.


identifier: Anderson, Mark W. (Mark Willis) <https://research.library.mun.ca/view/creator_az/Anderson=3AMark_W=2E_=28Mark_Willis=29=3A=3A.html>   (2009) Pioneer or invader?: situational metafiction in the settler nations.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: The settler nations of Canada, Australia, New Zealand, and South Africa represent an overlooked area of postcolonial theory. The fact that three of these four countries were among the only four to reject the United Nations Declaration on Aboriginal Rights (September 13, 2007) highlights the unresolved political natures of these "invader-settler nations." Stephen Slemon suggests in his essay "The English Side of the Lawn" that this area of postcolonial theory requires detailed historical and cultural analysis (283). My thesis undertakes this project, by examining the use of historical figures and events in the contemporary fiction of the settler nations, looking at the work of writers from both indigenous and settler traditions. -- My research challenges the applicability of Linda Hutcheon's seminal postmodern work A Poetics of Postmodernism, to the contemporary historiographic novel of the settler nations. These novels are often written in an aesthetic that corresponds to Hutcheon's category of historiographic metafiction. While much of Hutcheon's work is compelling and continues to be useful in defining postmodernism, her overarching definition of historiographic metafiction threatens to subsume much politically driven writing under the apolitical umbrella of postmodernism: "[Historiographic metafiction's| use of history is not a modernist look to the "authorizing past" for legitimation. It is a questioning of any such authority as the basis of knowledge-and power" (Poetics 185). My thesis demonstrates that the application of this construct of postmodern theory to the contemporary historiographic novel of the settler nations is misleading. While clearly and demonstrably partaking of the aesthetic that Hutcheon delineates for the postmodern novel (marked by the conscious use of parody, intertexuality, self-reflexivity, a questioning of the status of the historical referent, and a general scepticism toward meta-narratives) the contemporary historical novel of the settler nations, uses this supposedly apolitical aesthetic in a bifurcated and deeply dialectical fashion, problematizing "public" history and unproblematically asserting a subaltern history. These novels cannot be called postmodern in Hutcheon's terms as they present a clear dialectic. This dialectic (as will be demonstrated) is, in most cases, either settler versus mother country or indigene versus settler. The texts studied in this thesis represent an area of overlap between postmodernism and postcolonialism, an area that is unacknowledged by current theoretical constructs in both fields. This overlap is a rich area of study, which has ramifications for the development of both postmodern and postcolonial theory. -- My work, through literary, historical, and political analysis, elucidates the moral/political vectors of these novels. This new and hybrid form of writing is defined by David Attwell, in his book J. M. Coetzee: South Africa and the Politics of Writing, as situational metafiction: "a mode of fiction that draws attention to the historicity of discourses, to the way subjects are positioned within and by them, and, finally, to the interpretive process, with its acts of contestation and appropriation. Of course, all these things have a regional and temporal specificity” (J. M. Coetzee 20). This thesis applies Attwell's category to the contemporary historiographic novel of the settler nations, where situational metafiction has become a widespread and influential form of political writing.


identifier: Lush, Gail Ruby Shirlene <https://research.library.mun.ca/view/creator_az/Lush=3AGail_Ruby_Shirlene=3A=3A.html>   (2008) Nutrition, health education, and dietary reform: gendering the 'new science' in northern Newfoundland and Labrador, 1893-1928.  Masters thesis, Memorial University of Newfoundland.

abstract: In the early 1900s medical personnel at the Grenfell Mission decided that something should be done to prevent the local fishers of northern Newfoundland and coastal Labrador from developing nutritional deficiencies. Many Mission doctors felt that the local dietary, known for its reliance on fish and starchy foods, caused disabling physical conditions, such as beriberi, night blindness, rickets, and scurvy. Deficiency diseases destroyed the fishers' health, and kept them from participation in the all important seal and cod fisheries. Doctor Wilfred Grenfell, Superintendent and founder of the benevolent organization, urged a staff of teachers, nurses, and doctors to teach prevention by encouraging the local people to obtain a greater variety of food. After a two-decade public education campaign to promote the use of more fruits, vegetables and milk, Mission staff had little success in changing local dietary habits. -- By the 1910s Grenfell observed with great interest new developments in nutrition science and in 1920 learned of two American women who were pioneering career paths in childhood nutrition. Over the following eight years, his interest in their teachings in preventative health and "right living" enticed more than twenty-five nutrition workers to travel to the north-east coast for voluntary service. Nutrition workers, trained in home economics, worked with physicians, dentists, nurses, and educators to improve children's level of health. They conducted social surveys of children's diets and home conditions and tried to advise mothers how to maintain the health of their families. Within three summers, the women nutrition workers acquired a large degree of professional independence in nutrition education and coordinated nutrition clinics and classes for women and their children under the auspices of the Child Welfare Department, an agency which they created. -- Yet shifting professional goals between nutrition workers on the one hand, and nurses and doctors on the other, encouraged the directors of the Mission to dissolve the Child Welfare Department and appoint physicians in charge of child welfare and nutrition work. Elizabeth Criswell, director of the Child Welfare Department, was partially responsible for the demise of the Grenfell nutrition worker. She replaced the nutrition worker with the public health nurse as part other larger, professional strategy to gain cooperation from the established medical community. The aim of this thesis is to explain the goals of women pioneering careers in nutrition work, and the professionalizing strategies they used to slip into the Grenfell Mission medical hierarchy. An examination of professional tensions between them and their medical colleagues will demonstrate how these women fought hard to maintain control of their own Child Welfare Department.


identifier: Humber, Jessica M. (Mary) <https://research.library.mun.ca/view/creator_az/Humber=3AJessica_M=2E_=28Mary=29=3A=3A.html>   (2009) Non-native plant invasion of boreal forest gaps : implications for stand regeneration in a protected area shaped by hyperabundant herbivores.  Masters thesis, Memorial University of Newfoundland.

abstract: While Canada thistle (Cirsium arvense) is notorious as an aggressive, invasive non-native weed in agricultural fields, grasslands, and roadsides throughout North America, it has not typically posed a threat to boreal forests. However, in the balsam fir (Abies balsamea) -dominated lowland boreal forests in Gros Morne National Park (GMNP- Newfoundland, Canada), Canada thistle has recently invaded natural areas on a large landscape scale, occurring in 42% to 55% of anthropogenic and natural forest gaps, respectively, and frequently forming dense monocultures. It is important to determine if and how Canada thistle invasion will affect regeneration of native trees, particularly since regeneration of gaps in GMNP is already threatened by non-native, hyperabundant moose (Alces alces) populations, which exert extreme browsing pressure on forests. This study assessed the condition of forest gaps to support conifer regeneration by describing the current level of balsam fir regeneration, quality of seedbeds, and degree of Canada thistle invasion. Balsam fir seed and seedling addition experiments were performed in gaps to determine the effect of thistle presence on  emergence, growth, and survival of balsam fir. Finally, the potential for allelopathic impacts on native conifers from Canada thistle was assessed in greenhouse experiments. Results revealed that gaps are not regenerating, contain poor seedbeds for conifer recruitment, and are heavily disturbed by moose browsing. Canada thistle invasion further threatens balsam fir emergence and early seedling survival. However, older, transplanted fir seedlings were not negatively affected by thistle, suggesting that seedling planting may be an effective management strategy to encourage fir regeneration in thistle-invaded gaps, and potentially even phase out shade-intolerant thistle plants over time.


identifier: Johansen, Brian R. <https://research.library.mun.ca/view/creator_az/Johansen=3ABrian_R=2E=3A=3A.html>   (2008) Numerical investigations of the Korteweg-de Vries (KdV) equation.  Masters thesis, Memorial University of Newfoundland.

abstract: This thesis will develop material regarding the Korteweg-de Vries (KdV) equation, a nonlinear partial differential equation which has soliton solutions. We introduce the equation with its history and establish some preliminaries in §1. In §2, we will examine the soliton solutions and the uniqueness of such. We will also speak of the construction of multiple soliton solutions, as well as other solutions. Next, the conservation properties of the KdV equation will be visited, then the properties of interacting solitons. In §3 we will discuss the historical numerical schemes for the KdV equation, including finite difference methods, pseudospectral methods, collocation, and finite element methods. We will comment on their accuracy and efficiency. Contained within §4 is a selection of numerical schemes which were implemented (and in one case, improved!) by the author.


identifier: Zhang, Liang <https://research.library.mun.ca/view/creator_az/Zhang=3ALiang=3A=3A.html>   (2008) New methods for the implementation of statistical cipher feedback mode.  Masters thesis, Memorial University of Newfoundland.

abstract: In this thesis, we investigate a recently proposed mode of operation for block ciphers, referred to as statistical cipher feedback (SCFB) mode. SCFB mode is designed for high speed stream-oriented transmission where it is necessary to recover from any number of bit slips or insertions in the communication channel, that is, SCFB has the capability of self-synchronization. SCFB mode is a hybrid of CFB mode and OFB mode, and hence, it has a higher throughput than CFB mode and can obtain self-synchronization while OFB mode cannot. As a result, SCFB mode can be applied physical layer security for applications such as SONET/SDH. -- In this thesis, SCFB mode using both serial transfer and parallel transfer is implemented in hardware. Additionally, we have implemented pipelined SCFB mode based on parallel transfer in hardware as well. The hardware implementation of these SCFB structures is thoroughly investigated. Throughout this research, VHDL and ModelSim SE 6.0 are used in the process of hardware design and verification. Further these SCFB modes which have been implemented are synthesized by using Synopsys tool (version 2002 and 2004) targeting to ASICs! based on 0.18 micron CMOS technology based on the TSMC (Taiwan Semiconductor Manufacturing Company) process supported by Canadian Microelectronics Corporation (CMC). -- As an outcome of our result, we have created a new modified version of SCFB mode, which we refer to as pipelined SCFB mode. Pipelined SCFB mode applies a block cipher, which has pipelined architecture, and Counter(CTR) mode instead of OFB mode which is used in conventional SCFB mode. --  Based on the synthesis results, the throughput of the SCFB using serial transfer and parallel transfer (block transfer size equal to 4 bits) can reach 100 Mbps and 222 Mbps, respectively. The total number of gates of these two SCFB systems are 41600 and 43697, respectively. For the pipelined SCFB mode, the throughput and area complexity are 333 Mbps and 189963 gates. -- The performance analysis of pipelined SCFB mode is also provided with respect to characteristics such as synchronization recovery delay (SRD) and error propagation factor (EPF). Moreover, the analysis of system queues such as the number of bits in the plaintext queue, the queue size requirements and probability of queue overflow is also provided. -- Among these different implementations, the pipelined SCFB mode based on parallel transfer mode can obtain the highest throughput and the SCFB mode using serial transfer mode has the lowest area complexity. Hence, the pipelined SCFB mode using parallel transfer is more suitable for high speed physical layer security.


identifier: Knickle, David Craig <https://research.library.mun.ca/view/creator_az/Knickle=3ADavid_Craig=3A=3A.html>   (2009) Spawning patterns and retention and dispersal of early life stages of Atlantic cod (Gadus morhua) in a Newfoundland fjord.  Masters thesis, Memorial University of Newfoundland.

abstract: Ichthyoplankton and hydroacoustic surveys were used to examine Atlantic cod (Gadus morhua) distribution and behaviour as well as cod egg abundance and distribution during spring and summer 2006 and 2007 to infer on cod spawning activity in Smith Sound, a known overwintering area on Newfoundland's northeast coast. In the first section of the thesis, estimated spawning times from egg abundance and distribution patterns and environmental data suggested a prolonged spawning period with spring and summer spawning peaks. Spring egg distribution indicated dispersal of eggs out of the Sound. In summer, egg and larval densities were highest within the innermost portion of the Sound, suggesting significant retention and local development. In the second part of the thesis, acoustic measurements of cod behaviour were closely linked with egg production times adding further support that vertical shoaling behaviour is associated with reproduction of cod in the wild.


identifier: Talukder, Mohammad Kamruzzaman <https://research.library.mun.ca/view/creator_az/Talukder=3AMohammad_Kamruzzaman=3A=3A.html>   (2009) Seismic response of pile foundation in saturated sand using Beam on Nonlinear Winkler Foundation approach.  Masters thesis, Memorial University of Newfoundland.

abstract: Evaluating the interaction of soil-pile systems to earthquake ground motions is an important step in the seismic design of piles. Three Dimensional Finite Element Models have been developed by a number of researchers. But these models are computationally expensive, complicated and not readily used in design offices. In this study, a Beam on Nonlinear Winkler Foundation (BNWF) approach consisting of simple nonlinear springs, dashpots and pile elements is used to account for nonlinearity of soil-pile relative movement, energy dissipation through radiation damping of soil and material damping of pile. The p-y curves within the framework of two dimensional Winkler foundation approach are widely used in design offices to calibrate soil springs where p is the unit soil reaction and y is the pile lateral deflection. The p-y curves proposed by American Petroleum Institute (2000) are used to estimate the lateral response of single flexible pile that is embedded in saturated sand. An effective stress based ground response analysis is performed to predict input motions to soil springs at various depths of soil. Performance of the BNWF model when compared with centrifuge test results is shown to be an inexpensive procedure and compatible with readily available structural analysis software, ABAQUS, for prediction of dynamic response of pile foundations in design offices. Pile peak response curves are given by comparing maximum computed and experimental pile peak responses (pile peak head accelerations, pile peak superstructure acceleration and pile peak bending moments) for a range of peak ground input accelerations, and pile material damping parameter, so the designer can choose peak pile response quantities within the resulting range based on conservativeness of the design.


identifier: Abu Alrub, Tayseer Rafe <https://research.library.mun.ca/view/creator_az/Abu_Alrub=3ATayseer_Rafe=3A=3A.html>   (2008) Superconductivity in the heavy fermion system PrOs₄Sb₁₂.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: Superconductivity was observed in the Pr-filled skutterudite heavy fermion system PrOs₄Sb₁₂in 2002. Symmetry considerations, based on the Landau theory of second order phase transitions, were used to derive all possible superconducting states in this material. It was found that a three-component order parameter that belongs to the Tu irreducible representation of the tetrahedral point group Th best describes superconductivity in PrOs₄Sb₁₂. Two different superconducting phases have been observed in PrOs₄Sb₁₂; the lower temperature B phase occupies the bulk of the phase diagram, while the higher temperature A phase is found in a narrow region below Hc2 , and possibly does not exist at all. The proposed gap function in the A phase is unitary and has two point nodes in the [00 ± 1] directions. In the B phase, the proposed gap function is nonunitary and the lower branch has four point nodes in the [±α,0,±β] directions. Hence, thermodynamic and transport properties of a nonunitary superconducting state are analyzed. It is shown that the conductivity tensor has inequivalent diagonal components due to the off-axis nodal positions of the B phase. Moreover, nonuniversal conductivities (impurity scattering dependent) have been obtained. A semi-classical approach based on the Doppler shift of the quasiparticle energy is used to calculate the oscillatory past of the magnetic field-angle dependent density of states and thermal conductivity. All possible point node configurations for superconducting phases of a tetrahedral superconductor are considered.


identifier: Zhou, Ningzhang <https://research.library.mun.ca/view/creator_az/Zhou=3ANingzhang=3A=3A.html>   (2008) Study of new functional organic materials based on pi-conjugated oligomers and [60]fullerene.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: In recent years, monodisperse and structurally defined π-conjugated oligomers have attracted great attention of materials chemists, owing to their fascinating applications as novel nanoscale building blocks for various molecular based electronic, photonic, and optoelectronic devices. To date, the molecular architectures of functional π-oligomers have evolved beyond the realm of simple one-dimensional (1D) linear conjugation and started to enlist some unique two-dimensional (2D) and three-dimensional (3D) structures. Such progress has opened a new avenue to develop and explore esoteric molecular materials with appealing and unprecedented molecular properties and functions, which can be of great use in various device fabrications, for instance, highly efficient organic light-emitting diodes (OLEDs), field- effect transistors (FETs), photovoltaic (PV) or solar cells, chemical and biological sensors, and so on. -- The work of this thesis is primarily dedicated to exploring a class of new hybrid organic materials based on π-conjugated oligomers and Buckminster[60]fullerene (C₆₀), and the detailed studies of which are divided into three major projects. The first project investigates a series of dumbbell shaped C₆₀-π-C₆₀ triads, in which the π units are designed to be linear or cruciform shaped OPE/OPV co-oligomers. The second project deals with a series of bifullerene endcapped oligoynes, and the third project embarks on a group of novel H-shaped OPE/OPV co-oligomers. The chemical synthesis of these conjugated oligomers and C₆₀ derivatives has been implemented on the basis of various classical and modern organic synthetic methodologies, such as Arbuzov reaction, Horner-Wittig reaction, Sonogashira coupling and Hay coupling. In particular, an in situ ethynylation protocol has been extensively employed in the synthesis of numerous C₆₀ derivatives throughout this thesis work. Subsequent to the synthesis, the compounds obtained are subjected to comprehensive property characterizations using UV-Vis absorption and fluorescence spectroscopy to disclose their π-electronic characteristic, cyclic voltammetry (CV) to probe their redox behavior, differential scanning calorimetry (DSC) to probe their solid-state reactivity, and atomic force microscopy (AFM) to reveal their surface morphologic features at the microscopic level. -- In this thesis, a number of efficient synthetic strategies for novel 1D and 2D conjugated OPE/OPV co-oligomers, linear and star-shaped phenylene-oligoynes, and related multiple C₆₀ adducts have been successfully established. Insight into the essential structure-property relationships of these novel π-conjugated molecular systems has been gained by comparative studies. Finally, some of the molecules are found to display appealing molecular properties and functions that portend practical uses in organic photovoltaic and nonlinear optical materials as well as molecular sensing devices.


identifier: Tricco, Terrence S. (Terrence Stansilaus) <https://research.library.mun.ca/view/creator_az/Tricco=3ATerrence_S=2E_=28Terrence_Stansilaus=29=3A=3A.html>   (2010) Simulation and visualisation of astrophysical plasmas with smoothed particle magnetohydrodynamics.  Masters thesis, Memorial University of Newfoundland.

abstract: A numerical implementation of the equations of magnetohydrodynamics has been developed using the Smoothed Particle Hydrodynamics (SPH) method. Self gravitational forces have been included using the Barnes-Hut octree algorithm. A nearest neighbour search algorithm has been devised which links adjacent, spatially exclusive nodes from a spatial decomposition tree to create a mesh facilitating efficient searching. Visualisations of SPH fluids were created using Delaunay triangulation with particles serving as triangle vertices.


identifier: Churchill, Stephen <https://research.library.mun.ca/view/creator_az/Churchill=3AStephen=3A=3A.html>   (2009) Sensor and data fusion of remotely sensed wide-area geospatial targets.  Masters thesis, Memorial University of Newfoundland.

abstract: This thesis consists of the examination of methodologies for sensor fusion and data fusion of remotely sensed, sparse geospatial targets. Methods for attaining an increased awareness of targets in both tactical and strategic roles are proposed and examined. The example methodologies are demonstrated, and areas for further research noted. Discussions of the proposed methods are carried forth in the context of iceberg detection. -- Amongst the difficulties associated with the combination of sensor parameters and sensor data are the wide variety of technologies, performance ability, coverage, and reliability that are available to those users of remote sensing technology. Typical sensors include airborne search radars, marine search radars, surface wave radar, and satellite synthetic aperture radar. The ability to mitigate the related parametric variances is the test of an appropriate sensor or data fusion algorithm. -- Documented herein are the efforts to find such an algorithm using various statistical methods.   Primary among these is Bayes Theorem combined with tracking systems such as the multiple hypothesis tracker. This and other methodologies are explored and evaluated, where appropriate. It will be demonstrated that such a methodology can combine sensor data returns to provide high performance, wide-area, situational awareness with sensors considered to have poor performance.


identifier: Mercer, Robert C. C. <https://research.library.mun.ca/view/creator_az/Mercer=3ARobert_C=2E_C=2E=3A=3A.html>   (2010) Slow skeletal muscle actin: confirmation and further insights.  Masters thesis, Memorial University of Newfoundland.

abstract: 1) The 1° structures of three sarcomeric actin isoforms were inferred from cDNA sequences: Atlantic herring (Clupea harengus) fast skeletal muscle actin, Acc# GQ455648; Atlantic herring slow skeletal muscle actin, Acc# EF495203; and Atlantic Mackerel (Scomber scombrus) fast skeletal muscle actin, Acc# EF607093. The two herring skeletal muscle actin cDNAs possess different non-coding regions and are concluded to arise from different genes. -- 2) Sequence comparisons demonstrate that actin from a given type of skeletal muscle has been conserved across teleost evolution. Herring slow muscle actin and salmonid slow muscle actin (Salmo trutta; Acc# AF267426 [Mudalige et.al. 2007]) share a single substitution, Gin 354 Ala (herr:sal), while, in addition to this substitution the fast skeletal muscle actins from Atlantic herring and atlantic salmon (Salmo salar; Acc# AF304406 [Mudalige et.al. 2007]) contain Ser 160 Thr for a total of two substitutions. -- 3) There are thirteen inferred substitutions between fast and slow skeletal muscle actins isolated from Atlantic herring, six that are non-conservative in nature. This is a record for two vertebrate sarcomeric actins. The replacements (non-conservative underlined) are: residues: 2, 3, 103, 155, 160, 165, 278, 281, 310, 329, 358, 360 and 363. Most of the heterogeneity occurs after residue 100. Also of note is the exchange of Gin (fast actin) for Asp (slow actin) at position 360, which endows the slow type isoform with a greater negative charge in the neutral pH range. Comparison with the actin found in the skeletal muscles of the rabbit demonstrates 11 replacements (five non-conservative) with herring slow skeletal muscle actin and four (one non-conservative) when compared to herring fast skeletal muscle. -- 4) Two skeletal muscle actins of non-identical net-charge were detected by alkaline urea PAGE in the slow skeletal muscle of the following species - mackerel and smelt - but not in other teleosts (halibut and tiliapia), primitive fish (hagfish and lamprey), birds or amphibians. --  5) Herring slow skeletal muscle G-actin (CaATP) is less resistant to thermal, and chemical, -induced denaturation (as monitored by electronic circular dichroism) than its fast muscle counterpart. Thermal melting temperatures (Tms) and [urea] unfolding midpoints, respectively, are: 50°C and 55°C; 3.5 M and 4.0 M. A rate of unfolding for slow skeletal muscle actin was determined, in the presence of 0.1 mM EDTA, to be 6.5x10⁴ sec⁻¹. The fast skeletal muscle isolated from Atlantic mackerel has a Tm of 55°C and a midpoint of unfolding in the presence of urea of 4.0 M. --  6) Fast skeletal muscle G-actin from Atlantic mackerel contains a non-conservative substitution in common with slow skeletal muscle actin: Ser 155 Ala (herr fast: mack fast/herr slow). This finding rules out the identity of this residue as a contributor to the observed instability. -- 7) Herring slow skeletal muscle G-actin (CaATP) is less resistant to cleavage by subtilisin and thrombin than the fast muscle counterpart. Subtilisin cleavage between residues 48 and 49 was confirmed by Edman sequencing of Western blotted peptides. Of the two actin isoforms, only slow skeletal muscle actin could be cleaved by thrombin. The fast skeletal muscle actin isolated from mackerel, in spite of the present substitutions, behaves as the other fast skeletal muscle actins when subjected to subtilisin and thrombin exposure. -- 8) Fluorescence spectra of all G-actins (Ca - 2'-deoxy 3' O- (N'- Methylanthraniloyl) ATP) studied is characterized by emission maxima at 430 nm; demonstrating a virtual identity of the nucleotide binding pockets of the three isoforms. Emission intensity was reduced in the case of the slow muscle actin, consistent with it having a weaker affinity for the nucleotide.


identifier: Strong, Grant <https://research.library.mun.ca/view/creator_az/Strong=3AGrant=3A=3A.html>   (2009) Similarity-based image organization and browsing.  Masters thesis, Memorial University of Newfoundland.

abstract: Users do not always know what they want, in which case traditional query-based image retrieval approaches fail. This thesis serves to amend this shortcoming with a novel approach to organize and browse large image collections based on visual similarities in a way that extends the user's natural search sense. Starting with an unordered set of images, salient color and gradient information are extracted into feature vectors. A self organizing map (SOM) then projects these high-dimensional vectors onto a 2D canvas so that similar ones are grouped together. When browsing around on the canvas through intuitive operations like pan and zoom, a dynamic collage is generated that shows the most pertinent images. To make organizing larger image collections practical, a parallel SOM training algorithm is designed that runs on graphics processing units. The results of using a variety feature vectors are also evaluated.


identifier: Chakrabortty, Pradipta <https://research.library.mun.ca/view/creator_az/Chakrabortty=3APradipta=3A=3A.html>   (2008) Seismic liquefaction of heterogeneous soil: mechanism and effects on structural response.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: In the current practice of liquefaction prediction analysis, horizontally layered soil (with uniform properties within distinct soil layers) is usually assumed to estimate the liquefaction susceptibility of a soil deposit. However most of the soil properties of a natural deposit not only vary in the vertical direction but they could also vary in the horizontal direction, even within the so-called 'uniform' soil layers. This soil variability can be broadly classified into two main groups. They are the lithological heterogeneity (variability due to geological layers) and the small scale spatial variability. The first source of variability (variability due to layers) is considered properly in the current practice. But the second source of soil variability (small scale spatial variability), which is the subject of this research, is not properly addressed in general. -- From recent numerical research it was observed in the case of seismically induced excess pore water pressure (EPWP) generation that more EPWP is generated during an earthquake in a heterogeneous soil deposit than in a homogeneous soil with equivalent average soil relative density. EPWP is generated in the loose sand pockets first and then the water migrates into the neighbouring dense soil, and softens the dense soil by reducing the effective stress. However, to date, a limited amount of experimental verifications are available to the practicing engineering community to help in recognizing, quantifying and accepting the above-mentioned behaviour of heterogeneous soils. Therefore the first major objective of the present study is to investigate, quantify, and explain the effects of small scale soil heterogeneity on seismically induced liquefaction using both numerical modelling and centrifuge experiments. The second major objective of this research is to provide recommendations for seismic design of structures on heterogeneous soil. -- A series of three centrifuge tests were performed in this study: one on homogeneous soil and two on heterogeneous soil. The test on uniform soil was performed on a soil deposit with the soil relative density lower than the average soil relative density of heterogeneous soil. The results, such as EPWP, accelerations, and settlements were monitored and measured throughout the test duration. However, it is very difficult and expensive to monitor all this responses everywhere in the model. Therefore, a numerical model was calibrated and validated from the centrifuge test results on uniform soil first. Then, the liquefaction mechanism in heterogeneous soil was studied in more details using the numerical simulations. Experimental results support the conclusion of previous research that more EPWP is generated in a heterogeneous soil than in the corresponding homogeneous soil. From this study it is concluded that although the average soil relative density of heterogeneous soil deposit (test2 and test3) was larger than that of the uniform soil (test1), the liquefaction resistance of the heterogeneous soil was lower than that of the uniform soil due to water migration from loose to dense soil pockets in heterogeneous soil deposit. --  In the last part of this research, a parametric study was performed for finding the effects of soil heterogeneity on the structural response. The numerical model validated based on the results from the centrifuge experiments with heterogeneous soil was used in this study. Dynamic analyses were performed for various types of structures situated on heterogeneous soil. Based on the type of structure, this segment of the research is divided into two parts. The performance of a tower structure (where total settlements and base rotations were of primary interest) was studied in the first part. In the second part, the performance of a frame structure (where total and differential settlements were of primary interest) was studied. Quantitative and qualitative recommendations for geotechnical design practice are provided for structures on liquefiable heterogeneous soil deposits for a wide range of soil relative densities. The results of reliability analysis for the structure situated on heterogeneous soil are presented in the form of fragility curves and combined damage curves. -- Current design guidelines for spectral amplification of seismic motion were also verified for a range of soil properties, and updated guidelines were also provided after considering the effect of soil heterogeneity. The effect of soil variability was found to be not very significant in the studied ranges for calculating the values of spectral amplification factors. There is a less than 10% change in the values of Fₐ and Fᵥ for heterogeneous soil compared to that in equivalent homogeneous soil.


identifier: Quaile, Meredith Leigh <https://research.library.mun.ca/view/creator_az/Quaile=3AMeredith_Leigh=3A=3A.html>   (2010) Sisters in toil: the progressive devaluation and defeminization of Ontario dairywomen's work and tools 1813-1914.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: In nineteenth and early-twentieth century Ontario, dairywomen toiled daily with cows and manure, sour milk and greasy butter, yet without improved apparatus, agricultural education, or male support. On the provincial family farm, milking, cream-separating, and butter-making chores included various time-consuming steps, physical labour, and an array of task-specific objects. This thesis analyses agriculture, and dairying in specific, as it began the transition from traditional to industrial, and consequently from female to male. -- This dissertation touches on particular topics relevant to farmwomen's labour, including: agricultural education and improvement through science; public debate and perception surrounding gendered work; the government's role in promoting industrialization and thus defeminization; the concept of the dairyqueen in technological advertising; and, in particular, real farmwomen. These dairying 'sisters' include the well known, like Susanna Moodie and Catharine Parr Traill, Laura Rose, and Eliza Jones, and the unknown, such as Mary Newsam and the Hallen sisters, while focusing on Lamira Billings and her daughters Sabra and Sally. --  This qualitative study reveals that by employing common dairy tools as a dominant, primary source, there are alternative perspectives from which to consider rural women's experiences. Analysis of material culture objects, like milking stools and pails, butter bowls and scotch hands, shallow separating pans and tin creamer cans, also allows for exploration of the tensions between projected male ideals and tangible female work - a question central to understanding gender and labour within a social history context. In addition to technologies, sources like The Farmer's Advocate, the photographs of Reuben Sallows, and early dairy advertisements, add to our understanding of the concerns surrounding dairywomen's labour during the period discussed. -- Historians have suggested that dairy work was removed from the female sphere before the turn of the twentieth century in Ontario. Male agriculture authorities, scientific experts, and government officials, indeed initiated a conscious devaluation of farmwomen's work, oriented toward the defeminization of dairying. Rather than being removed from dairy work, however, Ontario's farmwomen continued separating cream and making butter between 1813 and 1914, habitually and simply equipped with their two hands, their mother's knowledge, and their grandmother's tools.


identifier: Meade, Steven R. (Steven Roy) <https://research.library.mun.ca/view/creator_az/Meade=3ASteven_R=2E_=28Steven_Roy=29=3A=3A.html>   (2008) Structure of the Spruce Brook thrust stack at the base of the Humber Arm Allochthon, Western Newfoundland Appalachians.  Masters thesis, Memorial University of Newfoundland.

abstract: Spruce Brook drains a low-lying area east of the Lewis Hills and south of Blow-Me-Down Mountain in Western Newfoundland. The area is underlain by a dismembered succession of Cambrian-Ordovician platform carbonate and a succession of siliciclastic rocks assigned to the Taconic syn-tectonic flysch deposits of the Goose Tickle Group. Structurally juxtaposed against these strata are rocks of the Humber Arm Allochthon including altered ultramafic rocks and metamorphic rocks of the Bay of Islands Complex, as well as continental shelf and slope sedimentary rocks of the Humber Arm Supergroup. -- The occurrences of platform carbonate constitute thin, planar, structural slices that are bounded by thrust faults. The thrust slices are overall moderately east-dipping and imbricated from west to east. Their internal structural architecture is characterized by west-verging asymmetrical fold forms that are attributed to a combination of buckle folding and ramp-related bending. Contact relationships at the leading edge of the carbonate thrust stack indicate that strata of the Goose Tickle Group are structurally interleaved with the carbonate thrust sheets. Furthermore, the eastern trailing edge of the carbonate thrust stack is structurally overlain by the basal strata of the Humber Arm Supergroup, suggesting that the carbonate thrust stack lies as a duplex within the deformed Taconic foreland flysch succession and carries on its roof thrust the Humber Arm Allochthon. -- The thrust stack is cut by a major out-of-sequence thrust array that truncates and re-imbricates pre-existing structures related to the initial emplacement in the thrust stack. The out-of-sequence array includes a steep fault zone that carries a duplex of serpentinite and amphibolite of the Bay of Islands Complex suggesting that the emplacement and subsequent deformation of the Spruce Brook Thrust Stack is indicative of the structural interaction between the basal portion of the allochthon and the upper portion of the par-autochthonous succession during the Taconic Orogeny.


identifier: Talukder, Waheduzzaman Md. <https://research.library.mun.ca/view/creator_az/Talukder=3AWaheduzzaman_Md=2E=3A=3A.html>   (2008) Seismic attenuation analysis of vertical seismic profiles for gas-bearing sedimentary reservoirs.  Masters thesis, Memorial University of Newfoundland.

abstract: Quality factor (Q) estimation of vertical seismic profiles requires precise computation of seismic energy or amplitude over a certain frequency band width of a propagating wave field through the earth media. It is a big challenge to have the correct amplitude spectra over a frequency band for reliable estimation of anelastic attenuation factor in seismic data. Q is a very useful petrophysical parameter in the characterization of different layered earth media. Estimation of Q in this study is for both numerically generated zero-offset vertical seismic profiles and field VSP. A finite difference technique has been applied to model wave propagation in elastic isotropic layered media. In finite difference modeling a staggered grid scheme is implemented in second-order in time and second-order in space that provides a convenient way to define model boundaries. For forward 2D Q analysis of model VSP and field VSP data, spectral ratio (SR) and centroid frequency down shift (CFD) methods have been used in this study. Validity and sensitivity studies of SR and CFD methods, has been done on synthetically generated model VSP data prior to attenuation analysis of field VSP data. The use of two different methods (SR and CFD methods) provides an opportunity to validate attenuation measurements. The results of the synthetic modeling studies with and without intrinsic attenuation in different models shows very close agreement with model values and validates these methods. The Q analysis of total field VSP over the 30m depth interval, illustrates that the Q estimation is satisfactory, however a few shows a physically unrealizable phenomenon of negative values. The formation wise average Q analysis result of the field VSP indicates that the Bhuban formation is more attenuative than Tipam and Bokabil formations and the gas bearing zone (2420-2460m) has a low Q value (SR=28 and CFD=23). This highly attenuative thin gas bearing layer alters the seismic signal both in shape and size. The spectral analysis and estimated Q values of the total VSP section indicates that amplitude spectra drastically losses energy when the signal passes through the gas bearing zone.


identifier: Haghighi, Mohammad <https://research.library.mun.ca/view/creator_az/Haghighi=3AMohammad=3A=3A.html>   (2010) Supersonic separators : a gas dehydration device.  Masters thesis, Memorial University of Newfoundland.

abstract: The ever growing demand for natural gas has led to the discovery and development of reservoirs in the most unreachable off-shore locations. Formation of hydrate is one of the most problematic issues involved in the production and transportation of natural gas. Gas dehydration is an effective and efficient method of preventing this difficulty. One of the main challenges in designing a dehydration unit for off-shore locations is its size. Supersonic separator is a device that combines the principles of Joule-Thompson expansion and cyclonic separation to efficiently remove the water content of natural gas produced from reservoir as a means of hydrate prevention. This device is small enough to suit the limitations of an off-shore location. This thesis is investigates the performance of supersonic separators in various operating conditions. A variety of design parameters are identified and analyzed through CFD techniques and a novel configuration is proposed for the supersonic separators. A lab test is set up for the validation of CFD results and extensive discussions are presented.


identifier: Kolypetri, Panayota <https://research.library.mun.ca/view/creator_az/Kolypetri=3APanayota=3A=3A.html>   (2009) Studies on iodine-accelerated spontaneous autoimmune thyroiditis in NOD.H2h⁴ mice.  Masters thesis, Memorial University of Newfoundland.

abstract: This thesis has no abstract


identifier: Rizk, Emad Raouf <https://research.library.mun.ca/view/creator_az/Rizk=3AEmad_Raouf=3A=3A.html>   (2010) Structural behaviour of thick concrete plates.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: Most concrete codes have empirical equations to estimate the minimum steel reinforcement requirements for flexural members. High-strength thick concrete plates are used as structural component in offshore and containment structures for nuclear power generation. An accurate estimate of the minimum steel flexural reinforcement ratio can result in saving millions of dollars for a single project. The recommended concept utilizes the fracture mechanics principles to modify the sandwich panel model and to account for slab thickness. In summary, the two new main contributions in this research includes consideration of the size effect through fracture mechanics and consideration of the torsional moment for thick plates in calculating the minimum reinforcement of thick plates. -- Different design codes have different formulae to calculate crack spacing and crack width developed in flexural members. Most of these formulae are based on the analysis of results on beams or one-way slabs. Crack control equations for beams underestimate the crack width developed in plates and two-way slabs due to loading and constraint effects. It seems that little attention has been paid in determining the crack spacing and width in reinforced concrete plates. The behavior of reinforced concrete plates is different from beams or one-way slabs; therefore, the methods developed for beams cannot be directly applied to plates and two-way slabs. In this research investigation, a two-way numerical model is proposed for calculating the crack spacing for plates. A special focus is given to thick concrete plates used for offshore and nuclear containment structures. The proposed equation takes into account the effect of steel reinforcement in the transverse direction through the splitting bond stress. The equation provides good estimates for crack spacing and crack width in plates and two-way slabs with different concrete covers. -- Concrete slabs without shear reinforcement usually exhibit brittle shear failure under a concentric force transferred between the column and the slab. Conventional design methods consider potential shear failures of a slab as a wide beam as well as punching failures in the vicinity of concentrated loads. Most of design codes try to avoid minimum shear reinforcement requirements for slabs by limiting nominal shear stresses at well-defined critical sections to guard against such failure modes. With the extensive use of thick plates of more than 250 mm thick, made of high strength concrete (HSC) for offshore structures, different guidelines must be used to provide minimum shear reinforcement requirements for thick concrete plates. The current research provides procedure for dimensioning of the plate shear core that is the main interest of this work. The proposed models to calculate minimum shear reinforcement for thick plates account for member size effect through fracture mechanics concepts. -- The experimental phase of this research work includes testing of two groups of specimens. The first group (Group A) is designed to investigate the effect of small reinforcement ratios and slab thickness on the behaviour of two-way slabs. The second group (Group B) is designed to investigate the effect of slab thickness, reinforcement ratio and shear reinforcement on the structural behavior of thick concrete plates. -- The strut-and-tie method is a rational approach to structural concrete design that results in a uniform and consistent design philosophy. A strut-and-tie model is developed to model the punching shear behaviour of thick concrete plates. This model provides a quick and simple approach to evaluate the punching shear capacity of concrete slabs.


identifier: Sarker, Muzaddid <https://research.library.mun.ca/view/creator_az/Sarker=3AMuzaddid=3A=3A.html>   (2010) Structures and interactions of lung surfactant protein B (SP-B) peptides.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: Lung surfactant is a complex mixture of lipids and proteins that enables normal breathing by  reducing the surface tension at the alveolar air-water interface, and additionally provides the first line of defense against inhaled microbes in the lungs. Surfactant protein B (SP-B) is an indispensable component of lung surfactant system and absolutely essential for the survival of mammals. SP-B is thought to function by facilitating large-scale rearrangements of lipid structures at various stages of the breathing cycle. However, neither the structural mechanisms for this ability nor the physiological ramifications of the lipid rearrangements are yet understood, in part because a high-resolution structure of SP-B has not been determined. As is generally the case for membrane and other lipid-associated hydrophobic proteins, the production of an SP-B sample for structural studies has been very challenging and unsuccessful to date. Interestingly, synthetic fragments of SP-B retain substantial biological activity when compared to the full-length protein. This Ph.D. research has applied solution nuclear magnetic resonance (NMR) methods to three SP-B-based peptides to reveal at least some of the critical structural features and lipid/protein interactions that presumably underlie the functional mechanisms of SP-B in physiological conditions. --  The high-resolution structure of Mini-B, an N-terminal - C-terminal construct of SP-B that exhibits even better performance than the full-length protein in rat models, is determined in the presence of surfactant lipid-mitnetic sodiumdodecylsulfate (SDS) micelles. Mini-B consists of two a-helices with a projecting tryptophan anchor and displays a strikingly amphipathic surface. The structure of Mini-B appears very well-suited for making strong interactions with surfactant phospholipid analogues. Indeed, Mini-B binds both anionic and zwitterionic micelles composed of SDS, dodecylphosphocholine (DPC), lysomyristoylphosphatidylcholine (LMPC), lysomyristoylphosphatidylglycerol (LMPG) and mixed LMPC/LMPG, and induces substantial rearrangements of the micelle structures. To prepare a foundation for directly probing the interaction between Mini-B and surfactant protein A (SP-A),  the conformation and lipid interactions of SP-A are investigated separately in the presence of micelles composed from the same model surfactant lipids. SP-A also binds both zwitterionic and anionic micelles. Surprisingly, in the presence of micelles, SP-A exists predominantly as smaller oligomers, in sharp contrast to the octadecamers observed when in an aqueous environment, and the form in which SP-A has long been presumed to function. Mini-B appears to interact with SP-A in all micelle systems, although the interaction is indirect and the degree of the interaction is dependent on the type of detergent/lipid headgroup. Next investigated are the changes to SP-B's structure and lipid interactions brought about by tryptophan oxidation, a modification which is thought to be a major contributor to acute  respiratory distress syndrome (ARDS). Replacement of tryptophan by one of its oxidized forms, kynurenine, substantially disrupts the helical structure of SP-B8-25, an N-terminal fragment of SP-B, and also affects its interactions with the micelles. Lastly, as a step towards the determination of the structure of full-length SP-B, the overall conformation of Maxi-Bcr, the C-terminal half of SP-B, has been investigated in the organic solvent hexafluoroisopropanol (HFIP) and SDS micelles. --  SP-B is indispensable for life, but the molecular basis for its activity is not yet understood. The findings of this Ph.D. research contribute to the ongoing endeavor in characterizing SP-B's structure-function relationships and its mechanisms of lipid/protein interactions that are crucial for lung surfactant function. This work also provides a strong foundation for future studies on the conformation and interactions of full-length SP-B.


identifier: Hancock, Stephanie D. <https://research.library.mun.ca/view/creator_az/Hancock=3AStephanie_D=2E=3A=3A.html>   (2009) Stress and the development of disordered eating in rats.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: Development of an eating disorder involves an interplay of factors, which may be environmental, biological, developmental, genetic, and/or psychological. All eating disorders are more prevalent in females, have an increased propensity for adolescent onset, and are, in most instances, precipitated by stressful life events. The value inherent in using an animal model to investigate the etiology of disordered eating lies in the real-life validity of such a model. Despite clinical evidence that early-life stress and heightened anxiety frequently precede the onset of pathological eating, animal models of eating disorders have not incorporated these findings to any great extent. Nor do most models take into account that the largest population of eating-disordered individuals is comprised of adolescent females and young women. The goals of this thesis were: (i) to present an overview of the physiological mechanisms that underlie stress-induced alterations in feeding systems and eating behaviours; and (ii) to examine potential factors that influence susceptibility to develop binge eating and anorexia using the most well-established animal models of these disorders. The research presented demonstrates that low levels of maternal care in early life are associated with greater vulnerability to the later development of stress-induced binge eating of highly-palatable food and, further, that this heightened vulnerability manifests in females during adolescence. In an activity-based animal model of anorexia nervosa (ABA), young adult animals that experienced early-life maternal separation lost weight faster, ate less, ran more, and required fewer days to reach removal criterion compared to their handled counterparts, with females, in particular, showing increased vulnerability. Finally, using a milder version of the ABA paradigm, early-life maternal separation increased females' susceptibility to ABA during adolescence, but not in adulthood, whereas males' susceptibility to ABA was increased only in adulthood. Together, these findings highlight the interplay between environmental, biological, and developmental factors in the etiology of binge eating and ABA.


identifier: Johnson, Albert Noel <https://research.library.mun.ca/view/creator_az/Johnson=3AAlbert_Noel=3A=3A.html>   (2009) Students' perceptions of effective teaching in higher education.  Masters thesis, Memorial University of Newfoundland.

abstract: Using a unique online approach to data gathering, students were asked to isolate the  characteristics they believe are essential to effective teaching. An open-ended online survey  was made available to over 17,000 graduate and undergraduate students at Memorial University of Newfoundland during the winter semester of 2008. Derived from this rich data is a set of student definitions that describe nine characteristics and identify instructor behaviours that demonstrate effectiveness in teaching. The survey also takes into account the opinions of students studying both on-campus and at a distance via the web, with the intention of  determining if the characteristics of effective teaching in an online environment are different from those in the traditional face-to-face setting. Students identified nine behaviours that are characteristic of effective teaching in both on-campus and distance courses. Instructors who are effective teachers are respectful of students, knowledgeable, approachable, engaging, communicative, organized, responsive, professional, and humorous. Students indicated that the nine characteristics were consistent across modes of delivery. Respondents to the distance portion of the survey, however, did place different emphasis from the on-campus responses on the significance of each characteristic.


identifier: Blokhina, Marina <https://research.library.mun.ca/view/creator_az/Blokhina=3AMarina=3A=3A.html>   (2009) Shoaling internal solitary waves.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

title: Shoaling internal solitary waves

abstract: Internal solitary waves are encountered throughout the ocean and are a key part of coastal water dynamics. With the theoretical basis developed for infinitesimally small weakly-nonlinear waves several decades ago and a fully nonlinear theory still under development, internal waves remain on the front edge of ocean science. -- In the present study, properties of high-frequency internal solitary waves propagating in a shallow water environment are studied using both field observations and numerical simulations. An array of bottom moorings and shipboard instruments are used to track internal wave packets propagating towards the flank of the Ile-aux-Lievres Island (St. Lawrence Estuary). The transformation leading to dissipation of a wave of depression into a number of waves of elevation is documented. The observed spatio-temporal wave characteristics are compared to the first-order Korteveg-de Vries theory and a fully nonlinear two-layer theory. --  High resolution two-dimensional nonhydrostatic numerical simulations are performed to supplement the field observations. The focus is on the properties of internal waves of elevation (often referred to as boluses) resulting from the shoaling of the wave of depression onto a linear slope. A hypothesis that boluses play a significant role in mass transport is tested. -- This work contributes to better understanding of the mechanisms of internal wave shoaling over linear slopes. The formation of the trapped cores inside waves of elevation is demonstrated using nonhydrostatic numerical simulations. To our knowledge this is a novel result which helps to explain field and laboratory observations of trapped cores. The detailed study of the transport properties of waves of elevation is also done. A simple parametrization of the mass transport caused by waves of elevation is proposed.


identifier: Bari, Wasimul <https://research.library.mun.ca/view/creator_az/Bari=3AWasimul=3A=3A.html>   (2007) Robust estimation in familial and longitudinal models.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: There exists many studies on the robust estimation of the regression effects in a linear model set up for continuous such as Gaussian data possibly containing one or more outliers. The robust estimation of the regression effects in a generalized linear model (GLM) set up for the count and binary data in the presence of outliers is, however, relatively difficult. In this thesis, we deal with this difficult estimation issue and develop the robust estimation procedures under three scenarios. First, a fully standardized Mallows-type quasi-likelihood (FSMQL) estimation technique is developed to obtain consistent regression estimates in the GLM set up for both independent count and binary data. Secondly, we develop a robust generalized quasi-likelihood (RGQL) estimation procedure to deal with the outliers in the generalized linear mixed model (GLMM) set up for both count and binary data. Finally, we also develop the RGQL estimation procedure to deal with possible outliers in the GLM set up for the longitudinal count and binary data. The performances of the proposed robust estimators are examined through extensive simulation studies under all three set up: the GLM for the independent count and binary data; the GLMM for the familial count and binary data; and the GLM for the longitudinal count and binary data.


identifier: Coulter, Stephen Edwin <https://research.library.mun.ca/view/creator_az/Coulter=3AStephen_Edwin=3A=3A.html>   (2008) Seismic initiation of submarine slope failures using physical modelling in a geotechnical centrifuge.  Masters thesis, Memorial University of Newfoundland.

abstract: The stability of offshore slopes is a major consideration in the development of both offshore and nearshore areas. The consequences of such slope failures can include the destruction of adjacent facilities, as well as the production of dangerous tsunamis. This phenomenon poses a unique and evident threat to human populations as well as valuable infrastructure. Most of these types of failures have occurred in prehistoric times and for the most part the initiation mechanisms behind them remain unobserved. One such triggering mechanism of these failures is seismic movement or in more common terms, an earthquake. -- This thesis presents a research program into the physical centrifuge modelling of the seismic initiation of submarine slope failures. The effects of impermeable layer presence, earthquake magnitude, and a phenomenon known as "seismic strengthening" are investigated. Properly scaled centrifuge modelling has been proven to be a useful tool in observing geotechnical engineering situations that would otherwise be costly or impractical to investigate due to financial and time constraints. --  A series of five centrifuge tests were performed on idealized slope geometries at a scale of 1:70. These tests were designed for ease of comparison with finite element analyses, with some associated compromises compared to field conditions. Generally, the test geometries consisted of a 2:1 slope constructed using Fraser River sand in a strongbox with a rectangular inner plan area. Models were either tested with the presence of a buried and draped silt layer, an inclined silt layer featuring an approximate 5.5:1 profile, or with no silt layer present at all. Much of the equipment and procedures required for this testing at the C-CORE Centrifuge Centre were developed by the author based on the experiences from other centrifuge centres. Models were air pluviated to obtain a target relative density of 40% and then saturated with a viscous pore fluid to achieve similitude of both static and dynamic scaling laws. Following construction procedure, models were tested in the Earthquake Simulator that is situated upon the C-CORE centrifuge and spun to a test level of 70 g. The response of the models to various earthquake loadings was observed with a high-speed data acquisition system. These responses primarily consisted of short-term and long-term data collected from installed accelerometers and pore pressure transducers, as well as other instruments used to observe the vertical and horizontal displacements of the model. -- Analysis consisted of examining the test data, as well as comparing analogous model tests to determine the effects mentioned above. The presence of a relatively impermeable silt layer in an appropriate orientation was found to increase the possibility of instability. A dilative response, characterized by observed upslope acceleration spikes coupled with negative spikes in pore pressure was observed in models that featured a silt layer as well as in the model that did not feature a silt layer. Seismic strengthening, through the process of densification due to the application of small seismic movements, was also observed to occur.   Increased dilative response also occurred with increased earthquake magnitude, but the increase in failure resistance caused by this dilative response was overcome by the delayed dissipation of generated excess pore pressure underneath the relatively impermeable silt layer. Slope failure was characterized by long-term horizontal and vertical slope movements that continued, and sometimes recommenced, after the cessation of earthquake shaking, short-term slope face surface heave, and the evidence of silt layer movement in post-test observations.


identifier: Lee, Jon D. <https://research.library.mun.ca/view/creator_az/Lee=3AJon_D=2E=3A=3A.html>   (2008) SARS and illness narratives: an examination of an epidemic.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: One of the largest recent disease outbreaks began in November of 2002, when the first cases of a disease that would soon be known as SARS began spreading in China. Since then, the SARS coronavirus has achieved infamy seldom seen among diseases, sweeping through media and Internet sources to create a panic that left thousands of people halfway around the world wearing surgical masks in attempts to protect themselves from perceived harm. -- The goal of this dissertation is to examine and understand the narratives that people told about the SARS outbreak-the rumors, gossip, legends, jokes, and other forms of oral communication. Examining these narratives will provide insights into why people believe the things they do about diseases, and why narratives both shape and are shaped by disease. -- A key concept included in this examination involves the reasons behind the exaggerated, and in many cases disproportionate reactions exhibited by the public. Tied up in these reactions were issues of race and ethnicity, personal and familial protection, and fear, all of which were directly influenced by oral narratives, as well as by information gathered from media sources. Ultimately, sources such as newspapers and news broadcasts can be blamed for the larger part of the hysteria that surrounded the outbreak. But oral narratives were also culpable, and so a second thrust of this work will be to examine what steps can be taken to counteract, or possibly preempt these sources of information. -- Ultimately, it is the goal of this work to demonstrate that the types of narratives that circulated during the SARS outbreak closely resembled narratives associated with other diseases, thereby establishing a template or typology of disease narratives. The existence of such a typology would mean that medical and health personnel, responding to future disease outbreaks, would be able to better predict the forms of narrative that would arise, and would thus be better able to respond to the panic and xenophobia that so often accompany epidemics.


identifier: Rankin, Sherri L. (Sherri Lynn) <https://research.library.mun.ca/view/creator_az/Rankin=3ASherri_L=2E_=28Sherri_Lynn=29=3A=3A.html>   (2008) Signalling pathways involved in the inhibition and promotion of axonal regeneration.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: Axonal regeneration following nerve injury requires the complex orchestration of various molecular events. Neurite outgrowth can be initiated by a variety of cues from the extracellular environment, including neurotrophins (e.g. nerve growth factor; NGF) and the extracellular matrix (ECM). Biological responses to neurotrophins are mediated by two distinct receptors: Trks, which initiate distinct signalling for the promotion of growth and survival, and p75NTR. Signalling pathways initiated by p75NTR exhibit considerable complexity and can elicit a variety of paradoxical physiological responses depending upon cellular context. Biological responses to ECM components, including laminin (LN), are mediated by a group of receptors known as integrins, which facilitate signal transmission to regulate cellular behaviour. Signalling pathways initiated by NGF and LN, have been previously reported to synergize resulting in optimized axonal regeneration of sensory neurons. The present series of studies sought to explore the molecular mechanisms underlying the enhanced growth initiated by stimulation with neurotrophins and LN, with a particular focus on the roles of the NGF receptors; specifically, TrkA phosphorylation-induced signalling cascades, and events associated with p75NTR ligand-dependent and independent signalling. --  My initial studies utilized a series of PC 12 cell derivatives expressing TrkA phosphorylation mutants, to investigate the potential role of TrkA in the regulation of p75NTR expression. I determined that TrkA played a role in the regulation of constitutive p75NTR expression, and further, controlled the upregulation of p75NTR in response to neurotrophin stimulation. In a subsequent study, I demonstrated that this occurred via a Phospholipase C γ-Protein Kinase C δ-dependent mechanism, and confirmed the existence of this regulatory pathway in cerebellar granule neurons (CGN). I further investigated the contribution of the ECM to regenerative growth, in both its capacity to signal synergistically with the TrkA receptor for the enhancement of early signalling intermediates, and its ability to elicit growth in a neurotrophin-independent scenario. Strikingly, integrin activation in the absence of neurotrophins was responsible for the promotion of neurite outgrowth via a rapid and potent Egr-1-dependent increase in the expression of the phosphatase PTEN, which relocalized to the nucleus where it dephosphorylated transcription factor Spl, thereby decreasing its ability to bind to the p75NTR promoter, resulting in the subsequent downregulation of p75NTR and depression of Rho activity. This novel ECM-induced signalling paradigm was also determined to occur in CGNs, and following the development of a unique motility assay, I demonstrated that interference with this cascade impaired motility, suggesting that this signalling cascade may contribute to the developmental migration of CGNs. -- p75NTR is a unique and flexible pleiotropic receptor which may promote or inhibit cell growth depending upon the presence or absence of neurotrophins. Taken together, the results of these studies detail the mechanisms involved in the upregulation of p75NTR expression in the presence of neurotrophins, but additionally present a novel signalling paradigm initiated by the ECM for the downregulation of the p75NTR in the absence of neurotrophin stimulation. Interestingly, both scenarios result in the promotion of neurite outgrowth and cellular motility as a result of the flexible signalling interactions of p75NTR, particularly those involving Rho, which can directly influence cytoskeletal dynamics.


identifier: McHugh, Sherry L.  <https://research.library.mun.ca/view/creator_az/McHugh=3ASherry_L=2E_=3A=3A.html> and McHugh-Warren, Sherry L. <https://research.library.mun.ca/view/creator_az/McHugh-Warren=3ASherry_L=2E=3A=3A.html>   (2009) Satellite synthetic aperture radar in the prosecution of illegal oil discharges.  Masters thesis, Memorial University of Newfoundland.

creator:
McHugh, Sherry L.
McHugh-Warren, Sherry L.

abstract: Illegal oil discharges from ships are a problem that affects the world's oceans. Aircraft has been the main surveillance method since the 1960s; however, the advent of earth observation satellites offers many advantages over this traditional technique. In the past, oblique aerial photographs and optical satellite imagery have been used as evidence to prosecute illegal discharges; but satellite Synthetic Aperture Radar (SAR) imagery has not been used as frequently. During this thesis research, the legal challenges of using remote sensing as evidence in the prosecution of illegal oil discharges were investigated. A review of the legal literature revealed two limitations on the use of remote sensing within a legal context, which included the admissibility and authentication of evidence. The admissibility and authentication of satellite SAR imagery and oblique photographs as evidence in the prosecution of illegal oil discharges were the focus of this research. Expert witness qualifications and the reliability of the two methods were outlined to address admissibility. All of the elements of the image interpretation used in the identification of oil slicks using oblique aerial photographs and SAR imagery were compiled to address the legal requirement of authentication. In addition, standards were shown to be used within each remote sensing method. A case study using a RADARSAT-1 SAR image and oblique aerial photographs from an oil pollution incident off the coast of Newfoundland, Canada, was used to illustrate the legal chain of custody and how these data can be presented as evidence. The results from this analysis revealed that there are no technological barriers to satellite SAR images as evidence in court for illegal ship discharges when used in conjunction with oblique aerial photographs.


identifier: Adibi-Asl, Reza <https://research.library.mun.ca/view/creator_az/Adibi-Asl=3AReza=3A=3A.html>   (2008) Simplified limit load determination for integrity assessment.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: The codes and standards in the pressure vessels and piping areas of the energy, petrochemical and related industries are based on the identification of potential modes of failures and a strategy for their avoidance. Instantaneous failures, specifically limit state and fast fracture, in the components and structures, can lead to catastrophic events. Therefore, integrity assessment of components and structures is required. --  Inelastic finite element method is widely used to conduct failure analysis. However, it can often be complicated, time consuming and expensive. As well, accurate results are dependent on the specification of adequate mesh density and an assurance of numerically stable solutions. Independent verification methods that are alternatives to inelastic finite element methods are often required for engineering designs. The methods discussed in this thesis, based on elastic modulus adjustment procedures (EMAP), provide rapid and stable solutions at a relatively lower cost. -- The elastic modulus adjustment methods rely on the convergence of the specific moduli adjustment procedure. A criterion for assessing the degree of convergence of EMAP is developed, and a procedure for achieving improved convergence is studied in this thesis. Also, simplified methods are developed in order to estimate the limit load in components and structures using iterative linear elastic methods. One of these procedures is the concept of reference volume that can be used to identify the kinematically active volume and dead zones in the components or structures. The reference volume method is shown to give a more accurate prediction of limit loads comparing to available traditional methods based on total volume. Furthermore, by invoking the concept of reference volume the systematic procedures are proposed to estimate the lower bound limit load solutions with high accuracy. This is very helpful for limit load analysis of the components/structures with stress razors such as notches and cracks. --  The concept of equivalence of "static indeterminacy" that relates a multidimensional component configuration to a "reference two-bar structure" is introduced for rapid estimation of the limit loads in components or structures. The procedures and methods discussed in this thesis are applied to some practical components (including cracks and notches) in order to verify their effectiveness in analyzing different geometries. Based on the proposed methods, integrity assessment analysis of different crack configurations, including multiple cracks and three dimensional effects, are studied in this thesis.


identifier: Wideman, Gail <https://research.library.mun.ca/view/creator_az/Wideman=3AGail=3A=3A.html>   (2010) Strengthening rural social work practice with older persons - the relevance of intermediate resources in one Newfoundland community.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: The capacity for older residents to age in place in rural Newfoundland and Labrador has been profoundly affected by out-migration and the resultant dismantling of traditional networks of support. Using a case study design, this qualitative research project asked what we can learn from residents in one rural community that will strengthen rural social work practice and policy with older persons. More specifically, the research asked about the intermediate resources needed to age in place, their maintenance in the context of depopulation, and about the role of social work policy and practice with older persons in supporting intermediate resources. -- Described as an emerging construct, intermediate resources are defined as non-intimate, non-professional helping encounters that assist older persons to maintain or restore their capacity to remain in their homes and communities despite health or mobility restrictions. Intermediate resources are operationalized as activities that are provided by local organizations, that are user-driven, and that provide assistance with Instrumental or Advanced Activities of Daily Living. --  The theoretical framework links key principles of community development and critical gerontology - the support and strengthening of existing resources, the creation and facilitation of associations among resources, and the empowerment of individuals and communities to identify their own needs and to define solutions. The data from Leary Harbour demonstrate the relevance of these theoretical constructs, and the corresponding concepts of partnership, participation and self-organization, to the development and maintenance of intermediate resources. --  The study contributes to strengthening social work practice and policy with older persons by providing a framework for assessing the availability and effectiveness of intermediate resources and by bringing forward information about the benefits of, and challenges to, the provision of intermediate resources. The study also identifies social work practices relevant to the development and maintenance of this level of support in rural communities. The practices themselves are not new but are foundational principles of community development in general, and of locality development theory in particular. This research highlights the need to return these considerations to the forefront of professional social work education and practice.


identifier: Smith, Caryn Y. <https://research.library.mun.ca/view/creator_az/Smith=3ACaryn_Y=2E=3A=3A.html>   (2008) Snag longevity and availability for cavity-nesters in post-harvest landscapes in western Newfoundland.  Masters thesis, Memorial University of Newfoundland.

abstract: Standing dead trees (hereafter snags) are a valuable component of forest systems, comprising habitat for wildlife, nursery sites for forest regeneration, and as stores of biomass, nutrients, and carbon. I examined populations of snags present following harvest in a chronosequence of balsam fir (Abies balsamea) dominated boreal forests in western Newfoundland to assess: (1) snag density, longevity and biomass in a post-harvest landscape, and (2) the availability and quality of snags for cavity-nesting birds and other wildlife. Average snag longevity was indicated by a sharp decline in snag numbers 10 to 15 years after harvest, followed by low snag densities until the regenerating forest reached senescence. A smaller but more immediate snag density decline was observed 1 to 4 years after harvest when residual snags and live trees were prone to windfall and domestic harvesting. Snag longevity was positively correlated with stem diameter at breast height (dbh). A large portion (55%) of 1260 snags encountered were balsam fir which have a small average dbh. These small-diameter snags were short-lived, contributing low biomass and a long period of low snag abundance. White birch (Betula papyrifera) produced the largest diameter and longest standing snags. -- Cavity nesters used snag species based on availability with 41% of the 81 cavities identified being in balsam fir. Cavity presence was most strongly positively correlated to snag diameter at breast height (dbh), followed by decay class, time since harvest and height. Less than 40% of snags available throughout the chronosequence had large enough dbh for cavity nesters. Downy Woodpeckers (Picoides pubescens) were responsible for 47% of all cavities identified, excavating balsam fir ~50% of the time. Two larger cavity nesters present, Northern Flickers (Colaptes auratus) and Three-toed Woodpeckers (P. tridactylus), were preferentially using large-diameter white birch snags. Northern Flickers excavated the largest cavities, potentially providing habitat for the greatest variety of secondary cavity-nesters. Managing for snags with >30 cm dbh, which flickers target for excavation, has the greatest potential to enhance the broader snag cavity-based community in western Newfoundland.


identifier: Mahmoud, Nahla. <https://research.library.mun.ca/view/creator_az/Mahmoud=3ANahla=2E=3A=3A.html>   (2009) Study of ecological risk assessment of PAHs and phenols in produced water after partitioning in the water phase.  Masters thesis, Memorial University of Newfoundland.

abstract: The impact of produced water from oil and gas operations is not only a function of its chemical composition but also of the receiving environment (e.g. marine versus freshwater organisms, high energy versus low energy water etc.). The resulting toxicity of produced waters is related to chemical compositions, and varies widely from nontoxic (LC₅₀>100% whole effluent) to moderately toxic (LC₅₀<l% whole effluent). The impact of produced water tends to be chronic rather than acute and therefore determining the agents in the produced water with the greatest impact has proved difficult, particularly in offshore operations where dilution is rapid. However, the polycyclic aromatic hydrocarbon (PAH) fraction in the oil present in the produced water has been proposed as toxic agent. -- In general, regulations prohibit the discharge of produced water containing more than 40 mg/L of oil. The purpose of this paper is to determine the effect of PAHs and phenols in produced water that tend to partition in the water phase once discharged to the ocean, as these compounds will be more readily bioavailable and therefore toxic. Experiments with produced waters from the Hibernia offshore platform and Terra Nova offshore platforms have been performed at Memorial University. The produced water contains dissolved and dispersed oil. In these experiments, the relative amount of PAH and phenol which partition into the water phase after the dispersed oil was separated, and was measured. The results were then used to determine what the hazard quotient (HQ) is for each of the identified PAHs and phenols in the water phase. A hazard index (HI) for PAHs and phenols, which is the summation of all hazard quotients, was then calculated. The HI gives an overview of the worst-case estimated hazard of PAHs and phenols to the marine environment. It was found that there was a strong relation between dispersed oil and the amount of naphthalenes and 4-6 rings PAHs as well as phenols but there was no relation between the amount of dispersed oil in produced water and 2-3 rings PAHs. According to the results of risk assessment for PAHs and phenols, there is no significant hazard from either PAHs or phenols on marine organisms. Also, this study showed the importance of dilution in reducing hazards of produced water in marine organisms. However, it was found there was no significant cancer risk from 4-6 ring PAHs in human.


identifier: Adsool, Shubhangi V. <https://research.library.mun.ca/view/creator_az/Adsool=3AShubhangi_V=2E=3A=3A.html>   (2010) Studies on an organocatalytic synthesis of functionalized nitrocyclohexanones and (+)-lycoperdic acid.  Masters thesis, Memorial University of Newfoundland.

abstract: A strategy for enantioselective double Michael addition reactions of acetone to nitroalkene 1 has been investigated. The feasibility of employing an enamine-mediated, organocatalytic route to functionalized cyclohexanones 2 was examined in this study (Scheme 1). -- [special characters omitted] -- Scheme 1: Synthesis of functionalized nitrocyclohexanones. -- Simultaneously, in continuation with the Pansare group's interest in organocatalytic conjugate addition reactions, an organocatalytic, conjugate addition based synthesis of (+)-lycoperdic acid (10) was examined. Lycoperdic acid is an unusual amino acid isolated from a mushroom (lycoperdon perlatum ). Its unique structure and potential glutamate receptor activity, makes it a challenging synthetic target. Our approach to lycoperdic acid is based on the enantioselective organocatalytic Mukaiyama-Michael addition of furan 5 to acrolein, mediated by catalysts 11 and 12 to provide the key butyrolactone 6 (Scheme 2). It is noteworthy that only a few examples of enantioselective organocatalytic Mukaiyama-Michael conjugate additions of furans related to 5 and β-substituted α,β-unsaturated aldehydes are known, and the use of acrolein as a Michael acceptor in these reactions has not previously been reported. Conversion of 6 to (S)-homocitric acid lactone (8) not only provided a new synthesis of this natural product enantiomer, and also established the stereochemistry of the Michael addition of 5 to 6. An organocatalytic α-amination of 6 using catalyst 12 provided 9 which is an advanced intermediate to lycoperdic acid. -- [special characters omitted] -- Scheme 2: Organocatalytic synthesis of (+) lycoperdic acid.


identifier: Ostrander, John Francis <https://research.library.mun.ca/view/creator_az/Ostrander=3AJohn_Francis=3A=3A.html>   (2009) Self-determination meanings in concurrent disorders treatment and recovery experiences: a qualitative study.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: Growing attention is being paid to co-occurring mental health and substance use disorders or concurrent disorders (CDs) in relation to treatment services and supports. A related theme is the mental health self-advocate vision of recovery that includes respecting peoples' subjective self-determination (SD) in treatment. Client SD is an important social work concept but its meaning and purpose remains unclear and it is typically defined from the professional perspective. Understanding SD meanings of people with CDs in relation to recovery may help social workers better assist people with CDs to achieve their recovery goals. This study explored the meanings of SD in CDs treatment and recovery experiences among five female and three male participants. Interview transcripts were analyzed using a qualitative grounded theory approach. -- SD meanings hinged on the subjective “sense of self” of participants within their ecosystem. Three interrelated SD meaning components were identified: key standpoint elements (beliefs and values, attitudes towards self and ecosystem, sense of control, and aspirations), a power or force (associated with being determined) and determining processes (knowledge building and decision making). A primary sense of self and a later more “nuanced” sense of self in CDs recovery were distinguishable within participants' descriptions and meanings. The more nuanced sense of self reflected more situationally relative, compatible, and discerning meanings of the self, SD, the ecosystem, mental health, addiction, and CDs recovery. Hermeneutic knowledge building is interpreted as facilitating the trend towards a more nuanced sense of self over time. One practice implication involves the role and importance of SD in relation to regulating the relative stability of the sense of self simultaneously with growth and change associated with CDs recovery.


identifier: Rajabi, Khadijeh <https://research.library.mun.ca/view/creator_az/Rajabi=3AKhadijeh=3A=3A.html>   (2010) Structures of gaseous ions by infrared multiple photon dissociation (IRMPD) spectroscopy.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: The technique of infrared multiple photon dissociation (IRMPD) spectroscopy has shown its ability to determine the 3D (dimensional) structure of gaseous ions. Using this technique, the structures of small biologically relevant ions such as amino acids and nucleic acid bases bound with a proton or metal cations in the gas-phase were determined. The necessity of employing computational methods to analyze and interpret the experimental data has been demonstrated. However, the computational results must be analyzed with extreme caution to prevent any incorrect conclusions. Among the parameters one has to consider when dealing with the computational results is the experimental method used to obtain the data. For example, the simulated IR spectra for only two of the four lowest-energy protonated adenine dimer isomers were similar to the experimental IRMPD while, based on gas-phase calculations, the four lowest-energy structures were almost isoenergetic. Since the ions were produced by electrospray ionization (ESI) from the solution phase, the effect of water as a solvent was considered by applying two independent computational approaches to take solvation effects into account. Polarizable continuum model (PCM) calculations as well as microsolvation with five explicit water molecules calculations showed that water only preferentially stabilizes these two observed isomers, consistent with the interpretation of the IRMPD spectra. The results suggest great caution is required when using gas-phase calculations to predict the structures of gaseous ions borne in solution by ESI. -- To investigate the influence of solvent on the structure of ions, an experimental method was developed to produce solvated ions in the gas-phase. These solvated ions then were investigated by IRMPD spectroscopy and blackbody infrared radiative dissociation (BIRD) to obtain kinetic and thermodynamic data. The solvation of electrosprayed ions occurs in the accumulation/collision hexapole of a hybrid quadrupole-Fourier transform mass spectrometer (Q-FTMS) by introducing the solvent into the collision cell. The most sensitive parameters based on our experience were the collision energy in the hexapole, the pressure of both collision gas and solvent in the hexapole, ion accumulation time, and the chemical nature of the species. This method was successfully applied to adenine and thymine cluster ions to produce multiply hydrated ions. The structures of singly hydrated ions were determined by IRMPD spectroscopy. -- Due to the importance of m-DNA (metalated-DNA), an attempt to investigate the structure of singly hydrated thymine zinc ion-bound dimer was initiated. It was found that thymine loses one proton in the presence of zinc. Therefore, the [(Thy₂-H)-Zn-(H₂O)]+ cluster was singly charged. Solely comparing the IRMPD spectrum in the 3100-3850 cm⁻¹ and simulated IR spectra was not sufficient to assign only one structure to the observed spectrum. Based on thermodynamical values, the two lowest energy structures were assigned as possible structures under the experimental conditions. In the most stable structure, the water is directly attached to the zinc in the zinc ion-bound dimer in which the Zn²⁺ is shared between the two atheneums at N3O4 sites. Furthermore, computational data suggested that recording an IRMPD spectrum in the 1800-2800 cm⁻¹ region might be useful to distinguish between the two lowest energy structures. Therefore, recording the spectrum for the [(Thy₂-H)-Zn-(H₂O)]+ cluster in this lower energy region is part of the future work.


identifier: Mohamad, Zakaria <https://research.library.mun.ca/view/creator_az/Mohamad=3AZakaria=3A=3A.html>   (2008) Stability and bifurcation analysis of a nutrient-phytoplankton model.  Masters thesis, Memorial University of Newfoundland.

abstract: This Master thesis consists of six chapters, which are mainly concerned with the stability and bifurcation analysis of a Nutrient (N), Phytoplankton (A) model. -- In chapter 1, some existing Nutrient-Phytoplankton models and the motivation for this work are presented.  -- In chapter 2, we introduce a two dimensional (N, A) model to describe the nutrient-phytoplankton interactions, and investigate the dynamical properties of this model. We show the existence of a boundary equilibrium point, and use geometerical and analytical methods to find conditions for the existence of none, one, or at most two positive equilibrium points. We then analyze the stability of each equilibrium point. -- In chapter 3, we modify the previous model by introducing a time delay γ, and discuss its effect on the stability of each equilibrium point, by investigating the distribution of the roots in the corresponding characteristic equation. -- In chapter 4, we discuss the bifurcations. By using the projection method, we prove the existence of a saddle-node bifurcation for the system without delay. And by using the center manifold theory and normal form method, we study the direction of Hopf bifurcation and the stability of the periodic solutions for both systems, and we prove the existence of Hopf-Zero bifurcation for the system with delay. -- In chapter 5, we provide numerical simulations to verify our theoretical predictions in the previous chapters, and biological interpretations based on these simulations. In the last chapter, we summarize the results obtained in the previous chapters and provide suggestions to improve the model.