VictorJuiz/thesis huggingface dataset:
A Study of Quantum-classical Dynamics in the Mapping Basis

Solving quantum dynamics is an exponentially difficult problem. Thus, an exact numerical solution is inaccessible for any condensed matter system. A promising approach is to divide the system into a quantum subsystem containing degrees of freedom which are of greater interest or those which have more profound quantum character (e.g., have smaller mass) and a classical bath containing the rest of the system. Imposing such a partition and treating the bath classically results in quantum-classical dynamics. The quantum-classical Liouville equation is a general equation in the Hilbert space of quantum degrees of freedom while it resides in the phase space of the classical degrees of freedom. Any numerical solution to this equation requires representation of the quantum subsystem in some basis. Solutions to this equation have been already proposed in the subsystem, adiabatic and force bases, each with its own cons and pros. In this work, the quantum-classical equations of motion are cast in the subsystem basis and subsequently mapped to a number of fictitious harmonic oscillators. The result is quantum-classical dynamics in the mapping basis which treats both quantum and classical degrees of freedom on the same footing, i.e., in phase space. Neglecting a portion of the back reaction of the quantum-subsystem to classical bath results in an expression for the time evolution of an operator (density matrix) equal to its Poisson bracket with the Hamiltonian. This equation can be solved in terms of characteristics to provide a computationally tractable method for calculating quantum-classical dynamical properties. The expressions for expectation values and correlation functions in this formalism are derived. Calculations on spin-boson system, barrier crossing models---the so called Tully models---and the Fenna-Mathews-Olson pigments show very good agreement between the results of this method and numerical solutions to the Schrödinger equation.

Keywords: Quantum-classical
mapping
Advisor: Kapral, Raymond E.
Unequal Citizenship: Being Muslim and Canadian in the Post 9/11 Era

My dissertation is the first empirically based study to closely examine the impacts of 9/11 on Canadian Muslim youth. It develops a critical analysis of how the general public supported by state practices, undermine the citizenship of Canadian Muslims, thereby impacting their identity formation. Conducting qualitative analysis, through the use of 50 in-depth interviews with Canadian Muslim men and women, aged 18 to 30, I have arrived at several important findings. These include findings related to citizenship, the racialization of gender identities and identity formation. First, despite having legal citizenship, Canadian Muslims often do not have access to substantive citizenship (the ability to exercise rights of legal citizenship), revealing the precarious nature of citizenship for minority groups in Canada. My research shows that the citizenship rights of Canadian Muslims may be undermined because they do not have access to allegiance and nationality, important facets of citizenship. Second, young Canadian Muslims are racialized and othered through increasingly stereotypical conceptions about their gender identities. Muslim men are perceived as barbaric and dangerous and Muslim women are imagined as passive and oppressed by their communities. As a result of these dominant conceptions, in their struggle against racism, young Canadian Muslims have to invest a great deal of time establishing themselves as thinking, rational, educated and peaceful persons. Third, to cope with their marginalization, many young Canadian Muslims have asserted their Muslim identities. In order to understand this social process, I extend the work done on ‘reactive ethnicity’ and theorize Muslim identity formation in a post 9/11 context, something not yet been done in academic literature. To do so, I coin the term ‘reactive identity formation,’ and illustrate that the formation of reactive identities is not limited to strengthening ethnic identity and that religious minority groups can experience a similar phenomenon. Furthermore, I find that while claiming their Muslim identity, most of my interviewees also retain their Canadian identity in order to resist the notion that they are not Canadian. By doing so, they attempt to redefine what it means to be Canadian.

Keywords: Muslims
9/11
Advisor: Peng, Ito
Characterization and Prediction of Fracture within Solder Joints and Circuit Boards

Double cantilever beam (DCB) specimens with distinct intermetallic microstructures and different geometries were fractured under different mode ratios of loading, ψ, to obtain critical strain energy release rate, Jc. The strain energy release rate at crack initiation, Jci, increased with phase angle, ψ, but remained unaffected by the joint geometry. However, the steady-state energy release rate, Jcs, increased with the solder layer thickness. Also, both the Jci and Jcs decreased with the thickness of the intermetallic compound layer. Next, mode I and mixed-mode fracture tests were performed on discrete (l=2 mm and l=5 mm) solder joints arranged in a linear array between two copper bars to evaluate the J = Jci (ψ) failure criteria using finite element analysis. Failure loads of both the discrete joints and the joints in commercial electronic assemblies were predicted reasonably well using the Jci from the continuous DCBs. In addition, the mode-I fracture of the discrete joints was simulated with a cohesive zone model which predicted reasonably well not only the fracture loads but also the overall load-displacement behavior of the specimen. Additionally, the Jci calculated from FEA were verified estimated from measured crack opening displacements in both the continuous and discrete joints. Finally, the pad-crater fracture mode of solder joints was characterized in terms of the Jci measured at various mode ratios, ψ. Specimens were prepared from lead-free chip scale package-PCB assemblies and fractured at low and high loading rates in various bending configurations to generate a range of mode ratios. The specimens tested at low loading rates all failed by pad cratering, while the ones tested at higher loading rates fractured in the brittle intermetallic layer of the solder. The Jci of pad cratering increased with the phase angle, ψ, but was independent of surface finish and reflow profile. The generality of the J =Jci(ψ) failure criterion to predict pad cratering fracture was then demonstrated by predicting the fracture loads of single lap-shear specimens made from the same assemblies.

Keywords: Lead-free solder
Mixed-mode fracture
Microstructure
Mode ratio
Critical energy release rate
J-integral
Elastic-plastic finite element analysis
Crack tip opening displacement
Cohesive zone modeling
Pad cratering
Epoxy cracking
Printed circuit board
Chip scale package
Bending
Advisor: Spelt, Jan K.
The Role of the Principal in the Micropolitical Context of Secondary Schools in Establishing and Maintaining School Community Partnerships

Principals as agents in secondary schools shape the meaning of what goes on in the school. To some extent, what happens in the school is a reflection of their beliefs, values and the dominant societal norms. School-community partnerships are a result of competing values, beliefs and visions of what can contribute to the success of the school from the perspective of the principal, the policy of the district school board and the teachers’ interests. School-community partnerships are therefore generally a compromise between the values of the principal and the teachers in the school through nurturing relationships and interpersonal leadership style. This study focused on the role of principals in establishing and maintaining school-community partnerships in an urban district school board in southern Ontario. The study employed qualitative research methods, drawing on two case studies in secondary schools. Data for the study was collected over a period of eight months through in-depth interviews of two principals and sixteen teachers. I used a micropolitical conceptual framework to analyze the principal’s role in school-community partnerships. The conceptual framework contributes to revealing the role of agency in organizations. The study revealed that principals initiate, support, coordinate, approve, allocate resources and evaluate school community partnerships. Through these roles, principals influence how partnerships unfold in the school. Principals’ roles in school-community partnerships are a reflection of the leadership style they enact in schools. The role is indicative of her/his values, beliefs and preference. This insight is important as a variable to how policies are implemented at different levels on the chain of implementation. It confirms other research that have strongly suggested that policies can be implemented best if the principals’ and teachers’values and beliefs are consistent. The implementation of policies are negotiated on daily basis between the principal and the teachers and principals have upper hand in determining their outcome. The result from this study illustrates how the roles of individuals in an organization mirror their values and beliefs and in turn affect how policies are implemented. The presence of school-community partnerships in secondary schools, although mandated by the district school board policy are the result of the role played by principals rather than merely policy provision. The role of the principal that was not clear was evaluating partnerships. There is need for further study to examine the criteria of evaluating partnerships in schools in order to ascertain the total contribution of the same to the success of schools.

Keywords: Education policy High schools principal micropolitics scool community partnerships leadership
Advisor: Bascia, Nina
Computational Prediction of Gene Function From High-throughput Data Sources

A large number and variety of genome-wide genomics and proteomics datasets are now available for model organisms. Each dataset on its own presents a distinct but noisy view of cellular state. However, collectively, these datasets embody a more comprehensive view of cell function. This motivates the prediction of function for uncharacterized genes by combining multiple datasets, in order to exploit the associations between such genes and genes of known function--all in a query-specific fashion. Commonly, heterogeneous datasets are represented as networks in order to facilitate their combination. Here, I show that it is possible to accurately predict gene function in seconds by combining multiple large-scale networks. This facilitates function prediction on-demand, allowing users to take advantage of the persistent improvement and proliferation of genomics and proteomics datasets and continuously make up-to-date predictions for large genomes such as humans. Our algorithm, GeneMANIA, uses constrained linear regression to combine multiple association networks and uses label propagation to make predictions from the combined network. I introduce extensions that result in improved predictions when the number of labeled examples for training is limited, or when an ontological structure describing a hierarchy of gene function categorization scheme is available. Further, motivated by our empirical observations on predicting node labels for general networks, I propose a new label propagation algorithm that exploits common properties of real-world networks to increase both the speed and accuracy of our predictions.

Keywords: Computational Biology
Machine Learning
Predicting Gene Function
Biological Networks
Combining High-Throughput Data Sources
Advisor: Morris, Quaid
Shape Estimation under General Reflectance and Transparency

In recent years there has been significant progress in increasing the scope, accuracy and flexibility of 3D photography methods. However there are still significant open problems where complex optical properties of mirroring or transparent objects cause many assumptions of traditional algorithms to break down. In this work we present three approaches that attempt to deal with some of these challenges using a few camera views and simple illumination. First, we consider the problem of reconstructing the 3D position and surface normal of points on a time-varying refractive surface. We show that two viewpoints are sufficient to solve this problem in the general case, even if the refractive index is unknown. We introduce a novel ``stereo matching'' criterion called refractive disparity, appropriate for refractive scenes, and develop an optimization-based algorithm for individually reconstructing the position and normal of each point projecting to a pixel in the input views. Second, we present a new method for reconstructing the exterior surface of a complex transparent scene with inhomogeneous interior. We capture images from each viewpoint while moving a proximal light source to a 2D or 3D set of positions giving a 2D (or 3D) dataset per pixel, called the scatter-trace. The key is that while light transport within a transparent scene's interior can be exceedingly complex, a pixel's scatter trace has a highly-constrained geometry that reveals the direct surface reflection, and leads to a simple ``Scatter-trace stereo'' algorithm for computing the exterior surface geometry. Finally, we develop a reconstruction system for scenes with reflectance properties ranging from diffuse to specular. We capture images of the scene as it is illuminated by a planar, spatially non-uniform light source. Then we show that if the source is translated to a parallel position away from the scene, a particular scene point integrates a magnified region of light from the plane. We observe this magnification at each pixel and show how it relates to the source-relative depth of the surface. Next we show how calibration relating the camera and source planes allows for robustness to specular objects and recovery of 3D surface points.

Keywords: Computer Vision
3D reconstruction
Transparency
Stereo
Multi-view
Dynamic
Specular
Advisor: Kutulakos, Kiriakos Neoklis
Chipping and Wear of Glass Edges by the Low VelocityIimpact of Spherical Particles

The edge rounding of brittle materials by vibratory finishing, VF, was investigated. Borosilicate glass and silicon nitride specimens were processed in two typical VF setups. In all cases, the processed specimens exhibited wear and chipping at their edges, whereas their flat surfaces remained intact. Edge chipping was strongly affected by the edge geometry and process parameters such as the media size and vibration amplitude of the finisher. Therefore, to achieve smooth chip-less edge, samples were processed in several steps, starting with the least energetic conditions, followed by more energetic ones as the edge became progressively blunter. The analysis of edge wear by VF revealed a new mechanism of wear, not previously reported in the literature. A stochastic numerical model was subsequently developed to model this mechanism of wear. To confirm the validity of the model, the model predictions were compared to the experimental observations of wear in the vibratory finisher. The model was used to investigate the effect of various VF process parameters on the edge wear of brittle materials. A VF simulator was used to investigate wear and chipping under more controlled conditions. The VF simulator launched particles against the specimens at adjustable velocities and impact angles. The effect of particles’ shape, and impact velocity and angle, on the wear of glass edges was investigated. Fundamental differences were observed between wear by abrasive and smooth particles. These differences were attributed to the mechanisms of material removal by abrasive iii and smooth balls. Abrasive balls remove material by the sharp indentation of their surface asperities, whereas smooth particles lack such sharp peaks and hence apply blunt indentation on the edges. To identify the fundamental differences between material removal by sharp and blunt indenters, a series of indentation experiments were carried out on glass edges. Subsequently, these differences were discussed in terms of their implications on wear by abrasive and smooth particles.

Keywords: edge chipping
glass
erosion
impact
Advisor: Spelt, Jan K.
East Meets West: The Cultural-relativity of Emotional Intelligence

My dissertation examines a fundamental but poorly understood aspect of emotional intelligence: its potential cultural-relativity. Significant differences in emotional intelligence test scores have been found between different cultural groups. To explain these past findings, I develop a theory of how and why different cultural groups—specifically, Westerners and East Asians—hold different conceptions of emotional intelligence. In effect, I argue that what is considered emotionally intelligent behaviour by members of one ethnic group may not be considered emotionally intelligent behaviour by members of another group due to contrasting cultural values and beliefs. Empirically, I test this theory through a two-part investigation. In Study 1, I measure cultural values and show that they mediate the relation between ethnicity and emotional intelligence test scores. In Study 2, I experimentally manipulate (prime) cultural beliefs to test whether they cause different judgments of what is considered emotionally intelligent behaviour. Some evidence for the hypothesis that culture helps account for ethnic differences in emotional intelligence was found through Study 1’s measurement-of-mediation design, however, not through Study 2’s experimental-causal-chain design. Theoretically, my dissertation helps challenge the implicit assumption that emotional intelligence is universal by explaining how and why it is culturally-relative. Practically, my dissertation provides some evidence that current tests of emotional intelligence may be culturally-biased and hence adversely impact non-Western candidates when used as part of selection and promotion decisions.

Keywords: Culture
Emotion
Advisor: té, S
Shi‘ite Higher Learning and the Role of the Madrasa-yi Sulṭānī in Late Safavid Iran

This dissertation explores the ways in which religious knowledge was produced and transmitted in Safavid madrasas, particularly in Isfahan, during the later Safavid period—from the reign of Shāh Abbās II (1642–66) to the end of Shāh Sulṭān Ḥusayn’s reign (1694–1722). It argues that Safavid madrasas functioned as multifaceted cultural centres that disseminated religious knowledge, preserved the Shi‘ite intellectual heritage, and played an important role in reconstructing, re-articulating, and contextualizing or contemporizing the past. Safavid madrasas, which were established thanks largely to the largesse and piety of the Safavid shahs, very often acted on behalf of the established political power. However, due to the flexible, inclusive, and personal character of Islamic pedagogy, Shi‘ite learning, like that of the wider Muslim community, could occur in a wide variety of places, from the houses of scholars to any mosque or shrine. After surveying Shi‘ite scholarship and its institutions from the early decades of Islamic history until the mid-seventeenth century, this study contextualizes the Madrasa-yi Sulṭānī, or Royal Madrasa, of late Safavid Isfahan within its political, social, and religious setting. This particular madrasa exemplifies the ways in which religious knowledge was transmitted in early modern Iran. By analyzing the deeds of endowment (waqfiyyas) of the Madrasa-yi Sulṭānī and other madrasa-mosque institutions built by Shāh Sulṭān Ḥusayn and members of the Safavid elite, this study sheds light on the organizing mechanisms and structures for such educational and charitable foundations. Based on the large number of extant ijāzas that were issued by Safavid scholars, and other primary sources, including waqfiyyas and autobiographies, this study reconstructs the curriculum of the Safavid madrasa and describes the pedagogical methods that Safavid scholars employed to transmit religious knowledge to their students. It also discusses the major problems facing Shi‘ite higher learning by examining the critiques of such scholars as Mullā Ṣadrā (d. 1635 or 1640), the Safavid philosopher, Muḥsin-i Fayḍ Kāshānī (d. 1679), a renowned traditionalist, and Muḥammad Bāqir Khurāsānī, known as Muḥaqqiq-i Sabzawārī (d. 1679), the Shaykh al-Islam of Isfahan and a prominent mujtahid. Finally it examines the life and career of Sayyid Mīr Muḥammad Bāqir Khātūnābādī (d. 1715), the first Safavid mullā-bāshī (head of religious scholars) and the first rector and professor of the Madrasa-yi Sulṭānī.

Keywords: Islamic/Persian Studies
Shi'ite Higher Learning
Advisor: Subtelny, Maria Eva
Structure and Application of Photosensitive Self-assembled Pseudoisocyanine J-aggregates on Membrane Surfaces

Understanding the assembly of monomeric components into specific molecular motifs is a central theme in materials and surface engineering. Motif designs, specifically using a controllable template, can yield materials with desired optical or electronic properties. The objective of this thesis is to understand the aggregate size, packing, and monomer orientation for the cationic dye, pseudoisocyanine. These organic molecules assemble into crystals in solution, on planar bilayer templates, and on the membranes of living cells. Pseudoisocyanine J-aggregates were found to form on top of the heterogeneous lipid domains in a phospholipid bilayer. This behaviour is limited to a few headgroup chemistries and lateral packing motifs, allowing one to control aggregation via a combination of these two factors. These aggregates are low-dimensional and display polymorphism. Using atomic force microscopy and visible-light spectroscopy, distinct optical characteristics can be correlated to different bilayer templated J-aggregate morphologies. The molecular packing of a similar J-aggregate crystal was resolved using both atomic force microscopy and selected area electron diffraction. The infrared absorption spectra of different polymorphs also displayed distinct differences. These separate examinations enabled a perspective that clarifies the geometry, packing, orientation, and size of templated J-aggregates. Insights into the templating of J-aggregates on the molecular scale reveals that they are sensitive reporters of membrane phase in adherent cells, and are compatible with established cell biology techniques. Lipid domains in live mammalian cells were visualized using fluorescent J-aggregates in combination with endogenous marker proteins of the endocytic process. Analysis of live cell images and additional biophysical work revealed that pseudoisocyanine J-aggregates formed on domains of the anionic lipid bis(monoacylglycerol)phosphate. Only by using J-aggregates can this lipid be shown to form well-ordered domains during endosomal maturation, leading to multivesicular body formation. These data demonstrate that a correlated optical and topographical approach is necessary to understand the structure of fluorescent molecular assemblies, and form the basis for utilizing such aggregates in a biological context.

Keywords: Membrane bilayers
J-aggregates
Lipid rafts
AFM
Advisor: Yip, Christopher M.