Generalized atoms in molecules approach (GAIM approach)

This thesis involves two parts. The first is a new-proposed theoretical approach called generalized atoms in molecules (GAIM). The second is a computational study on the deamination reaction of adenine with OH⁻/nH₂O (n=0, 1, 2, 3) and 3H₂O. The GAIM approach aims to solve the energy of each atom variationally in the first step and then to build the energy of a molecule from each atom. Thus the energy of a diatomic molecule (A-B) is formulated as a sum of its atomic energies, EA and EB. Each of these atomic energies is expressed as, EA = Hᴬ + Vₑₑᴬᴬ + 1/2Vₑₑᴬ<>ᴮ EB = Hᴮ + Vₑₑᴮᴮ + 1/2Vₑₑᴬ<>ᴮ where; Hᴬ and Hᴮ are the kinetic and nuclear attraction energy of electrons of atoms A and B, respectively; Vₑₑᴬᴬ and Vₑₑᴮᴮ are the interaction energy between the electrons on atoms A and B, respectively; and Vₑₑᴬ<>ᴮ is the interaction energy between the electrons of atom A with the electrons of atom B. The energy of the molecule is then minimized subject to the following constraint, |ρA(r)dr + |ρB(r)dr = N where ρA(r) and ρB(r) are the electron densities of atoms A and B, respectively, and N is the number of electrons. The initial testing of the performance of GAIM was done through calculating dissociation curves for H₂, LiH, Li₂, BH, HF, HCl, N₂, F₂, and Cl₂. The numerical results show that GAIM performs very well with H₂, LiH, Li₂, BH, HF, and HCl. GAIM shows convergence problems with N₂, F₂, and Cl₂ due to difficulties in reordering the degenerate atomic orbitals Pₓ, Py, and Pz in N, F, and Cl atoms. Further work for the development of GAIM is required. Deamination of adenine results in one of several forms of premutagenic lesions occurring in DNA. In this thesis, mechanisms for the deamination reaction of adenine with OH⁻/nH₂O, (n = 0, 1, 2, 3) and 3H₂O were investigated. HF/6-31G(d), B3LYP/6-31G(d), MP2/6-31G(d), and B3LYP/6-31+G(d) levels of theory were employed to optimize all the geometries. Energies were calculated at the G3MP2B3 and CBS-QB3 levels of theory. The effect of solvent (water) was computed using the polarizable continuum model (PCM). Intrinsic reaction coordinate (IRC) calculations were performed for all transition states. Five pathways were investigated for the deamination reaction of adenine with OH⁻/nH₂O and 3H₂O. The first four pathways (A-D) begin with by deprotonation at the amino group of adenine by OH⁻, while pathway E is initiated by tautomerization of adenine. For all pathways, the next two steps involve the formation of a tetrahedral intermediate followed by dissociation to yield products via a 1,3-hydrogen shift. Deamination with a single OH⁻ has a high activation barrier (190 kJ mol⁻¹ using G3MP2B3 level) for the rate-determining step. Addition of one water molecule reduces this barrier by 68 kJ mol⁻¹ calculated at G3MP2B3 level. Adding more water molecules decreases the overall activation energy of the reaction, but the effect becomes smaller with each additional water molecule. The most plausible mechanism is pathway E, the deamination reaction of adenine with 3H₂O, which has an overall G3MP2B3 activation energy of 139 and 137 kJ mol⁻¹ in the gas phase and PCM, respectively. This barrier is lower than that for the deamination with OH⁻/3H₂O by 6 and 2 kJ mol⁻¹ in the gas phase and PCM, respectively.

Safety in bear country

Safety in Bear Country tells the story of Serena Palmer’s twenty-second year. At a time when she thought she would be making a living in Toronto as an artist and as an independent adult, the economic times and her emotionally fragile state due to the demise of a romantic relationship, prove obstructive. Instead, she lives in the basement of her parents’ home and works for the town’s largest employer, a mental institution. Here she embarks on an internal quest for meaning and a truer understanding of love. Specifically, as the novel’s action shifts through Australia and then to Northern Canada, ending with her near-death and shamanistic spiritual transcendence, Serena explores the contradictions that exist between love and fear: in order to ever fully love, one must make oneself vulnerable at the deepest level. And, in order to ever make oneself vulnerable, one must conquer fear. In this way, fear and love are inextricably connected. Here in lies the irony of the title: Safety in Bear Country.

Integrating structured data using property precedence

Data integration systems offer uniform access to a set of autonomous and heterogeneous data sources. One of the main challenges in data integration is reconciling semantic differences among data sources. Approaches that been used to solve this problem can be categorized as schema-based and attribute-based. Schema-based approaches use schema information to identify the semantic similarity in data; furthermore, they focus on reconciling types before reconciling attributes. In contrast, attribute-based approaches use statistical and structural information of attributes to identify the semantic similarity of data in different sources. This research examines an approach to semantic reconciliation based on integrating properties expressed at different levels of abstraction or granularity using the concept of property precedence. Property precedence reconciles the meaning of attributes by identifying similarities between attributes based on what these attributes represent in the real world. In order to use property precedence for semantic integration, we need to identify the precedence of attributes within and across data sources. The goal of this research is to develop and evaluate a method and algorithms that will identify precedence relations among attributes and build property precedence graph (PPG) that can be used to support integration.

Geometric inequalities for initial data with symmetries

We consider a class of initial data sets (Σ,h,K) for the Einstein constraint equations which we define to be generalized Brill (GB) data. This class of data is simply connected, U(1)²-invariant, maximal, and four-dimensional with two asymptotic ends. We study the properties of GB data and in particular the topology of Σ. The GB initial data sets have applications in geometric inequalities in general relativity. We construct a mass functional M for GB initial data sets and we show:(i) the mass of any GB data is greater than or equals M, (ii) it is a non-negative functional for a broad subclass of GB data, (iii) it evaluates to the ADM mass of reduced t − φi symmetric data set, (iv) its critical points are stationary U(1)²-invariant vacuum solutions to the Einstein equations. Then we use this mass functional and prove two geometric inequalities: (1) a positive mass theorem for subclass of GB initial data which includes Myers-Perry black holes, (2) a class of local mass-angular momenta inequalities for U(1)²-invariant black holes. Finally, we construct a one-parameter family of initial data sets which we show can be seen as small deformations of the extreme Myers- Perry black hole which preserve the horizon geometry and angular momenta but have strictly greater energy.

Availability estimation and management for complex processing systems

“Availability” is the terminology used in asset intensive industries such as petrochemical and hydrocarbons processing to describe the readiness of equipment, systems or plants to perform their designed functions. It is a measure to suggest a facility’s capability of meeting targeted production in a safe working environment. Availability is also vital as it encompasses reliability and maintainability, allowing engineers to manage and operate facilities by focusing on one performance indicator. These benefits make availability a very demanding and highly desired area of interest and research for both industry and academia. In this dissertation, new models, approaches and algorithms have been explored to estimate and manage the availability of complex hydrocarbon processing systems. The risk of equipment failure and its effect on availability is vital in the hydrocarbon industry, and is also explored in this research. The importance of availability encouraged companies to invest in this domain by putting efforts and resources to develop novel techniques for system availability enhancement. Most of the work in this area is focused on individual equipment compared to facility or system level availability assessment and management. This research is focused on developing an new systematic methods to estimate system availability. The main focus areas in this research are to address availability estimation and management through physical asset management, risk-based availability estimation strategies, availability and safety using a failure assessment framework, and availability enhancement using early equipment fault detection and maintenance scheduling optimization.

Fall prevention among older adults: a quantitative and qualitative study

The purpose of this study was to investigate the effect of a fall prevention program on older adults as well as to explore the perceptions of older adults have on fall risk and the fall prevention program. This research was completed in Newfoundland and Labrador, Canada with participants above the age of 65. The 10-week fall prevention program focused on balance, strength, and flexibility and was followed by focus groups with the control and intervention groups. Pre and post-test measures (postural sway, TUG test, foam and dome test, ABC Scale, ESE Scale, FES Scale, SAFFE) were completed to determine if the fall prevention program decreased fall risk. The results of the quantitative portion of the study did not produce significant results however the qualitative portion was very informative. Five themes emerged from the focus group data: risk factor awareness, confidence, connectedness, quality of life, and program promotion. This research highlights the importance of fall prevention programs for older adults, not only to keep them healthy, but also for the personal and social benefits they facilitate.

Anomaly detection from time-changing environmental sensor data streams

This thesis stems from the project with real-time environmental monitoring company EMSAT Corporation. They were looking for methods to automatically ag spikes and other anomalies in their environmental sensor data streams. The problem presents several challenges: near real-time anomaly detection, absence of labeled data and time-changing data streams. Here, we address this problem using both a statistical parametric approach as well as a non-parametric approach like Kernel Density Estimation (KDE). The main contribution of this thesis is extending the KDE to work more effectively for evolving data streams, particularly in presence of concept drift. To address that, we have developed a framework for integrating Adaptive Windowing (ADWIN) change detection algorithm with KDE. We have tested this approach on several real world data sets and received positive feedback from our industry collaborator. Some results appearing in this thesis have been presented at ECML PKDD 2015 Doctoral Consortium.

Cooperative routing for collision minimization in wireless sensor networks

Cooperative communication has gained much interest due to its ability to exploit the broadcasting nature of the wireless medium to mitigate multipath fading. There has been considerable amount of research on how cooperative transmission can improve the performance of the network by focusing on the physical layer issues. During the past few years, the researchers have started to take into consideration cooperative transmission in routing and there has been a growing interest in designing and evaluating cooperative routing protocols. Most of the existing cooperative routing algorithms are designed to reduce the energy consumption; however, packet collision minimization using cooperative routing has not been addressed yet. This dissertation presents an optimization framework to minimize collision probability using cooperative routing in wireless sensor networks. More specifically, we develop a mathematical model and formulate the problem as a large-scale Mixed Integer Non-Linear Programming problem. We also propose a solution based on the branch and bound algorithm augmented with reducing the search space (branch and bound space reduction). The proposed strategy builds up the optimal routes from each source to the sink node by providing the best set of hops in each route, the best set of relays, and the optimal power allocation for the cooperative transmission links. To reduce the computational complexity, we propose two near optimal cooperative routing algorithms. In the first near optimal algorithm, we solve the problem by decoupling the optimal power allocation scheme from optimal route selection. Therefore, the problem is formulated by an Integer Non-Linear Programming, which is solved using a branch and bound space reduced method. In the second near optimal algorithm, the cooperative routing problem is solved by decoupling the transmission power and the relay node se- lection from the route selection. After solving the routing problems, the power allocation is applied in the selected route. Simulation results show the algorithms can significantly reduce the collision probability compared with existing cooperative routing schemes.

Meating the social: sharing atiku-euiash in Sheshatshiu, Labrador

This work examines atiku-euiash (caribou meat) sharing practices in Sheshatshiu, Newfoundland and Labrador, and aims to elucidate an overarching question: how do sharing practices participate in the co-constitution of the Innu ‘social’? The ‘social’ is understood in this work as a descriptor that refers to the emergent properties of the Innu collective. The thesis is that sharing practices participate in the co-constitution of the Innu social and enact its boundaries. Inside these boundaries, atiku-euiash is more than simply a food resource: by realizing Innu values of generosity, respect and autonomy, sharing implicates the associations of human, animal, and animal masters that constitute the Innu world. Sharing is connected with the enskilment of the younger generations by their el-ders, and thus with the reproduction of Innu values through time. The ways of sharing are relevant because changes in such practices affect the constitution of the Innu social. Giv-en Euro-Canadian colonization, the Innu are in a fraught social space in which sharing is interrupted by colonization practices and values. Understanding sharing is necessary to develop policies that do not interrupt the reproduction of the Innu world This work uses several research methods: participant observation, sharing surveys, and interviews. It also uses network analysis as sharing practices leave traces of giving and receiving actions and these traces can be represented as a network of givers, receivers and circulating caribou meat. There are two main ways in which caribou is hunted and shared: household-based hunts and community-based hunts. The household-based hunts are organized by the hunters themselves, who are able and willing to hunt. Community-based hunts are completely organized and funded by the SIFN or the Innu Nation. In or-der to understand the differences in the distribution of the two hunt types, the categories of centrality and clustering are used to show how the flow of atiku-eiuash and its associ-ated realization of values and enskilment correlate with different degrees of centralization inside the sharing clusters.

Identifying the major spilled oil constituents and fate in harsh offshore environments

The behaviour and fate of spilled oil in harsh marine environments, such as the North Atlantic and the Arctic Ocean are complex due to environmental factors and the composition of the crude. In order to develop appropriate oil spill prevention and management methods, we must first understand how the oil behaves in these harsh environmental conditions. This study focuses on determining the fate of oil in harsh marine environments by first identifying target compounds in the oil that can be used to determine the fate of a spill. This thesis presents the partitioning behaviour of six polycyclic aromatic hydrocarbons (PAHs), which represent different groups, and phenols in cold conditions. The smallest PAH, naphthalene, dominated in terms of concentration in water accommodated fraction (WAF) of oil, while the larger ringed PAHs presented at lower concentrations. The smallest oil-water partition coefficient was recorded by phenol which partitioned into the seawater more quickly than PAHs. The partitioning of larger PAHs was slower and they indicated high partition coefficients. The oil partitioning increased slightly as temperature increased from 4ᴼC to 15ᴼC. The oil loading (0.1 g/L to 10 g/L) also contributed in deciding the concentrations in water. The use of chemical dispersants is a common response to spills. This study identified that chemical dispersants can change the fate of an oil spill by increasing the availability of oil in seawater. The concentration of larger PAHs such as pyrene and chrysene increased significantly with the application of dispersants. The information obtained are used in developing a molecular imprinted polymer (MIP) sensor to identify oil spills in the North Atlantic Ocean.

Quantifying confinement effects in ice impact loads

Ships and offshore structures, that encounter ice floes, tend to experience loads with varying pressure distributions within the contact patch. The effect of the surrounding ice adjacent to that which is involved in the contact zone has an influence on the effective strength. This effect has come to be called confinement. A methodology for quantifying ice sample confinement is developed, and the confinement is defined using two non-dimensional terms; a ratio of geometries and an angle. Together these terms are used to modify force predictions that account for increased fracturing and spalling at lower confinement levels. Data developed through laboratory experimentation is studied using dimensional analysis. The characteristics of dimensional analysis allow for easy comparison between many different load cases; provided the impact scenario is consistent. In all, a methodology is developed for analyzing ice impact testing considering confinement effects on force levels, with the potential for extrapolating these tests to full size collision events.

Attachment, psychological functioning, and resilience within the street involved youth populations: describing youth who access community agency support

Youth homelessness is defined within the literature as youth who have left their homes and are living independent of parental figures and/or caregivers, have no stable residence or source of income, and lack access to the supports needed to make the challenging transition into adulthood (Canadian Observatory on Homelessness, 2015). Previous research studying homeless (or street-involved) youth has primarily focused on risk factors hindering the development of this population, and has largely ignored resilience, coping, and help-seeking behaviours. The current study examined the attachment styles (both categorically and dimensionally), psychological functioning, resilience, and help-seeking behaviours in street-involved youth of St. John’s, Newfoundland. Face-to face interviews were completed over a four-month period with 63 youth (42 males, 21 females) aged 15-29 (Mage = 20.00), recruited from a local community organization providing outreach services to street-involved youth. Results revealed the disproportionate struggles of the street-involved youth population, and highlighted higher levels of attachment insecurity, psychological distress and lower resilience compared to normative peers. Findings also showed a significant difference in psychological functioning, overall resilience, and emotional reactivity based on individual attachment style. In an exploratory model of help-seeking, a positive relationship was found between overall resilience (defined as a sense of mastery and sense of relatedness) and frequency of community service access. However, contrary to predictions, no relationships were found between frequency of community service access and attachment, psychological functioning, or emotional reactivity. Implications of the present findings in development of interventions for street-involved youth are discussed, in addition to strengths and limitations of the present research, and suggested areas of future inquiry.

Integrated sensitivity analysis, calibration, and uncertainty propagation analysis approaches for supporting hydrological modeling

The successful performance of a hydrological model is usually challenged by the quality of the sensitivity analysis, calibration and uncertainty analysis carried out in the modeling exercise and subsequent simulation results. This is especially important under changing climatic conditions where there are more uncertainties associated with climate models and downscaling processes that increase the complexities of the hydrological modeling system. In response to these challenges and to improve the performance of the hydrological models under changing climatic conditions, this research proposed five new methods for supporting hydrological modeling. First, a design of experiment aided sensitivity analysis and parameterization (DOE-SAP) method was proposed to investigate the significant parameters and provide more reliable sensitivity analysis for improving parameterization during hydrological modeling. The better calibration results along with the advanced sensitivity analysis for significant parameters and their interactions were achieved in the case study. Second, a comprehensive uncertainty evaluation scheme was developed to evaluate three uncertainty analysis methods, the sequential uncertainty fitting version 2 (SUFI-2), generalized likelihood uncertainty estimation (GLUE) and Parameter solution (ParaSol) methods. The results showed that the SUFI-2 performed better than the other two methods based on calibration and uncertainty analysis results. The proposed evaluation scheme demonstrated that it is capable of selecting the most suitable uncertainty method for case studies. Third, a novel sequential multi-criteria based calibration and uncertainty analysis (SMC-CUA) method was proposed to improve the efficiency of calibration and uncertainty analysis and control the phenomenon of equifinality. The results showed that the SMC-CUA method was able to provide better uncertainty analysis results with high computational efficiency compared to the SUFI-2 and GLUE methods and control parameter uncertainty and the equifinality effect without sacrificing simulation performance. Fourth, an innovative response based statistical evaluation method (RESEM) was proposed for estimating the uncertainty propagated effects and providing long-term prediction for hydrological responses under changing climatic conditions. By using RESEM, the uncertainty propagated from statistical downscaling to hydrological modeling can be evaluated. Fifth, an integrated simulation-based evaluation system for uncertainty propagation analysis (ISES-UPA) was proposed for investigating the effects and contributions of different uncertainty components to the total propagated uncertainty from statistical downscaling. Using ISES-UPA, the uncertainty from statistical downscaling, uncertainty from hydrological modeling, and the total uncertainty from two uncertainty sources can be compared and quantified. The feasibility of all the methods has been tested using hypothetical and real-world case studies. The proposed methods can also be integrated as a hydrological modeling system to better support hydrological studies under changing climatic conditions. The results from the proposed integrated hydrological modeling system can be used as scientific references for decision makers to reduce the potential risk of damages caused by extreme events for long-term water resource management and planning.

Labeling large scale social media data using budget-driven One-class SVM classification

The social media classification problems draw more and more attention in the past few years. With the rapid development of Internet and the popularity of computers, there is astronomical amount of information in the social network (social media platforms). The datasets are generally large scale and are often corrupted by noise. The presence of noise in training set has strong impact on the performance of supervised learning (classification) techniques. A budget-driven One-class SVM approach is presented in this thesis that is suitable for large scale social media data classification. Our approach is based on an existing online One-class SVM learning algorithm, referred as STOCS (Self-Tuning One-Class SVM) algorithm. To justify our choice, we first analyze the noise-resilient ability of STOCS using synthetic data. The experiments suggest that STOCS is more robust against label noise than several other existing approaches. Next, to handle big data classification problem for social media data, we introduce several budget driven features, which allow the algorithm to be trained within limited time and under limited memory requirement. Besides, the resulting algorithm can be easily adapted to changes in dynamic data with minimal computational cost. Compared with two state-of-the-art approaches, Lib-Linear and kNN, our approach is shown to be competitive with lower requirements of memory and time.

Numerical simulation for dynamic positioning in pack ice

This thesis investigates the numerical modelling of Dynamic Position (DP) in pack ice. A two-dimensional numerical model for ship-ice interaction was developed using the Discrete Element Method (DEM). A viscous-elastic ice rheology was adopted to model the dynamic behaviour of the ice floes. Both the ship-ice and the ice-ice contacts were considered in the interaction force. The environment forces and the hydrodynamic forces were calculated by empirical formulas. After the current position and external forces were calculated, a Proportional-Integral-Derivative (PID) control and thrust allocation algorithms were applied on the vessel to control its motion and heading. The numerical model was coded in Fortran 90 and validated by comparing computation results to published data. Validation work was first carried out for the ship-ice interaction calculation, and former researchers’ simulation and model test results were used for the comparison. With confidence in the interaction model, case studies were conducted to predict the DP capability of a sample Arctic DP vessel.