VictorJuiz/thesis huggingface dataset:
Exploring Symmetry and Field-induced Phenomena in Kitaev Materials
Keywords: Kitaev
Magnetic Field
Magnetism
Spin Liquid
Symmetry
Topological Order

A large part of modern condensed matter concerns non-local or global properties of systems under the broad term of topology. Closely intertwined with certain senses of topology are symmetries of the system, which physically constrain our description and offer non-perturbative insights into material properties. The range of possible phases of matter is greatly enriched by quantum mechanics, including certain types of non-local entanglement that cannot be understood in the usual symmetry-breaking paradigm of local order parameters. Beyond weakly interacting topology we find the stronger notion of \textit{topological order} in correlated systems, a prominent example being the $S = \tfrac{1}{2}$ Kitaev honeycomb model in a weak magnetic field.Through a remarkable combination of lattice geometry, strong spin-orbit coupling, and electron interactions, several material candidates have been put forward to realize Kitaev physics, including the $4d$ Mott insulator $\alpha$-RuCl$_{3}$ which offers tantalizing experimental hints of topological order. In this thesis we explore several aspects of Kitaev candidates and related systems under two broad themes. One involves symmetry-informed and constrained observables, including a proposed singularity in a thermodynamic quantity accompanying phase transitions between two Ising topological orders (ITOs). The ITO physics realized by the Kitaev model requires time-reversal symmetry to be broken, and much of the non-trivial physics is found at finite magnetic field. To this end, we study a microscopic spin model appropriate for $\alpha$-RuCl$_{3}$ and show that it exhibits an interesting field-induced paramagnetic state between the low- and high-field magnetic orders, consistent with recent experimental findings. We determine several properties of a lower-dimensional spin-$S$ analogue of the Kitaev model, including a multi-critical point at finite field separating different topological phases. Finally, we derive quantum state purities of entangled photons emitted from a spin-triplet superconducting heterostructure and discuss its use in a new paradigm of entangled spectroscopy.
Versatile Polymer Coatings for Advanced Stability and Bioanalytical Applications of Nanoparticles
Keywords: Click Chemistry
Colloidal Stability
Inorganic Nanoparticles
Upconversion Nanoparticles

One of the challenges in transitioning nanoparticle (NPs) formulations to commercial applications is the limited colloidal stability of these materials in physiologically relevant buffers. Indeed, achieving long-term stability (>3 months) is difficult, particularly for upconversion nanoparticles (UCNPs) which are known for poor stability in buffers like 1×PBS. Versatile surface coatings (surface ligands that bind to many types of NPs) are also difficult to prepare because each type of NP [quantum dots (QDs), iron oxide NPs (IONPs), gold NPs (AuNPs)] has a unique composition and surface chemistry. To address these challenges, nine unique copolymers formulations were prepared and evaluated as NP overcoatings. These polymers were made of a poly(isobutylene-alt-maleic anhydride) (PIMA) backbone functionalized with varying ratios and types of phosphonate anchoring groups (PA) and poly(ethylene glycol) (PEG) moieties. Syntheses of these polymeric ligands was done by the simple, one-pot nucleophilic addition reactions. Copolymers were subsequently coated onto UCNPs, QDs, IONPs, and AuNPs and investigated for colloidal and optical stability in different solutions including water, 1×PBS, and other common aqueous buffers. UCNP colloidal stability improved by up to 4 months when coated with copolymers containing greater proportions of anchoring groups and higher phosphonate valences. Small molecules could also be conjugated to these polymer-coated NPs by use of copper-free click chemistry. Using bio-orthogonal chemistry, folic acid (FA), tripheylphosphonium (TPP) and Cy3 dyes were conjugated to UCNPs (and QDs for Cy3) to demonstrate suitability for biosensor and bio-probe development. Cellular toxicity, uptake, and imaging studies were done to assess the bioanalytical potential of these polymer coatings. Early investigations for the potential theranostic applications of UCNPs was also done along with attempts to unravel the cellular uptake mechanism of these polymer coated NPs.
Room 41, Pictures from
Keywords: Art
Cubism
Orchestra Score
Pattern
Rhythm
Texture

This work is scored for orchestra of 3.3.3.3.4.3.3.1, 4 percussionists, piano, and strings. It comprises three movements: I - Hue Superimposed; II - Solids, Strings and Verticals; and III - Endless Rhythm. The durations of the movements are approximately 4’30”, 8’30”, and 11’30”. This composition focuses on the exploration of ideas from the Cubist art movement and in particular, the juxtaposition or combination of different perspective schemas or viewpoints. Each movement centers on musical techniques that aim to represent this idea through the co-existence of musical objects. Common to all movements are three-note pitch cells which serve as the basic object of observation. The first movement’s textualization of the cell creates viewpoints smeared in time and is inspired by Marcel Duchamp’s idea of "a static representation of movement," an idea he explored in paintings such as Sad Young Man on a Train, 1911, and Nude Descending a Staircase No.2, 1912. In the music, this texture is overlaid with versions of itself, at varying transpositions, to create multiple perspective schema. The second movement begins as a powerful release of energy, through solid, block-like, orchestrations of the cell, also combined at changing transpositions. This then moves to contrapuntal representations of the motive that are intimately presented by the string section. The third movement begins by combining the first movement's overlapping textural idea with a version of a rhythmic idea taken from the second. This transforms into repetitive rhythmic motives that change while they explore the pitch cell and build to a dramatic layering of the rhythmic patterns at the climax of the composition. The title of this work is taken from the location, room 41, that featured artworks by the emerging group of ‘salon’ Cubists who presented at the 1911 Salon des Indépendants art exhibition.
The Repertoire of John Beckwith for Solo Voice and Piano: An Interpretive and Pedagogical Guide
Keywords: Art Song
Canadian Music
Grading Rubric
Interpretative Guide
John Beckwith
Voice Pedagogy

This thesis examines the compositions of John Beckwith for solo voice and piano, creating an interpretive and pedagogical guide to these works. Several questions predominate. What aspects of Beckwith’s songs contribute to the overall difficulty level of the pieces? What aspects of Beckwith’s songs should singers and teachers consider in order to give a successful performance and interpretation? What are the key elements of Beckwith’s compositional style for art song and how did these develop over the course of his compositional life? What are the values and pedagogical benefits of disseminating Beckwith songs into the teaching and singing community? This guide is intended to assist voice teachers in assigning repertoire to their students, particularly voice teachers who may not be familiar with John Beckwith’s art song compositions. One of the issues facing voice teachers is determining the level of difficulty of a song. A literature review of various evaluative rubrics for the piano/vocal pairing has revealed a necessity for developing a new grading rubric. Therefore, this guide includes a grading rubric using the Criteria-Specific Rating Scale, which assesses the difficulty level of Beckwith’s forty-six songs for voice and piano, indicating the assigned difficulty rating – Easy, Easy-Moderate, Moderate, Moderate-Difficult, and Difficult. This guide also provides annotations of song cycles, with a deeper focus on select songs. Annotated information includes the date of composition, voicing, vocal ranges, tessitura, song duration, text source and complete texts, publisher information, debut performance, and commissioners. Annotations also include specific statements about the songs from Beckwith and key collaborators, with indications of how performers can interpret each song to create a successful performance. This thesis details the personal and professional history of John Beckwith, focusing on his education and his multi-faceted career, which includes academia, writing, and composition, all of which had a significant impact on the Canadian music scene. Through his song repertoire, this thesis reveals the evolution of his writing style, the timeline of his output, his interactions with poets, performers, and organizations, his compositional processes, his treatment of the text, voice and piano, and ultimately the values and pedagogical benefits of these important works.
Development of Novel Algorithms to Predict Pharmacokinetic Properties of Drug Molecules
Keywords: Ames test
blood-brain barrier
hERG
mutagenicity
pharmacokinetics
qsar

Models of drug pharmacokinetics (PK) and pharmacodynamics (PD) are indispensable in modern drug design. Relatively few in silico models of PK are currently available, especially compared to in silico PD models. Clinically significant PK properties include potentially dangerous food–drug and drug–drug interactions (FDIs and DDIs); mutagenicity, typically measured using the Ames test; and inhibition of the cardiac repolarization channel, human ether-à-go-go related gene (hERG). Virtual screening (VS) of large drug candidate libraries for these properties would facilitate avoidance or prediction of these effects early in drug development. VS methods of predicting another important PK property, blood–brain barrier (BBB) penetrance, are available, but tools for considering this property in de novo drug design are limited.Here, a combination of homology modeling, docking simulations, and quantitative structure–activity relationship (QSAR) analysis was employed in predictive modeling of drug interactions with six membrane transporters known to mediate clinically significant FDIs and DDIs in humans. The accuracy of the homology models varied with availability of foundational data, but, in general, they successfully captured known aspects of the proteins’ structures. No docking simulations accurately reflected literature substrate and inhibitor data for these proteins; further in vitro structural analysis of the proteins’ ligand binding modes is therefore recommended. Machine learning (ML)-assisted binary QSAR analysis successfully yielded predictors for BCRP and P-gp substrate and inhibitor activity, as validated by three established statistical measures of reliability. Using similar methods, a binary QSAR and a “rule of thumb”—simple set of criteria—were developed for predicting hERG inhibition, and two analogous rules were identified for predicting BBB penetrance, with one using only drug structural descriptors that can be readily calculated without computational tools. Finally, a list of structural alerts for positive Ames test results was derived from literature and ML output, and validated using the same methods as for the hERG and BBB rules. Overall, this work has established an approach to detailed, predictive in silico PK modeling based on various levels of availability of structural and fitting data, as well as many example models that can be readily enriched as more such data becomes available.
Experiments on the Formation of Rippled Icicles
Keywords: Dynamic wetting
Ice
Icicle Ripples
Icicles
Morphology
Pattern Formation

Icicles are a common sight during winter, hanging from rooftops and otherstructures from which water drips. The long slender shape of an icicle develops through a highly non-equilibrium process in which water flows down its surface, partially freezing along the way. This is an example of ``wet ice growth.'' Many icicles exhibit rippled pattern along their length with a near universal9~mm wavelength. While measurements of icicle ripples date back to at least 1933, the mechanism through which they form has eluded physicists. The existence and amplitude of ripples was previously shown to depend on the presence of impurities in the source water, but no existing model for icicle ripples includes impurities. The problem of how icicles form in the presence of impurities is the focus of this thesis. A pre-existing model for the rippling instability was extended to includephysical effects of impurities. A linear stability analysis performed on this model showed that it did not predict ripples. The stability of the model is not sensitive to concentration, so such a model will likely never agree with experiment. A set of 120 icicles were grown using various chemical species as the impurity.The changes in morphology from impurities were only affected by the molar concentration, showing that icicle ripples only depend on the number of dissolved molecules. One of the impurities used was a dye that only fluoresces when dissolved inwater. The liquid flowing down the surface of icicles was observed directly using this dye. Contrary to previous models, we find that the ice is incompletely and intermittently wetted by the liquid phase, and the concentration of impurities modifies the wetting properties of ice. The location of impurities trapped inside of icicles was also observed. All ofthe impurities were found inside small spherical inclusions. The inclusions are organized into chevron patterns aligned with the peaks of ripples, with a layered substructure, suggestive of cyclic wetting and freezing. These observations must inform any successful model of an impurity-drivenrippling instability. Our results have general implications for the evolution of many gravity-driven wet ice growth processes.
Stress, Strain, and Failure in Heterogeneous and Anisotropic Rock
Keywords: Geomechanics
Grain based model
Hydrulic Fracturing
Laboratory Testing
Rock Mechanics
True Triaxial Tests

Strain evaluation of various testing frames/devices indicated that they have significant impacts, lowering the expected E by up to 50%, leading to a correction factor, termed “system-compliance”, that is unique to the test systems and setups. Also introduced, is a novel approach for sub-core extraction relying on CNC milling, which has proven a success rate of about 85% in any direction to the bedding plane. This technique was used to plug and assess the mechanical anisotropy of heterogeneous, anisotropic, water sensitive shale. The mechanical test results varied with change in the bedding plane with the exception of the E when the bedding planes were perpendicular to the test direction.Numerically, models should be able to capture the heterogeneity of the rock sample being simulated. The grain based modelling (GBM) within the combined finite-discrete element method (FDEM) demonstrated its ability to predict more realistic microscopic and macroscopic response of rocks than conventional FDEM models. The explicit modelling of crack boundaries captured microscopic failure transition from along grain boundaries to coalescence along shear bands, dominated by intraphase cracks. GBM can also represent pre-existing cracks by specifically assigning friction and cohesion values along the grain-grain interfaces. The results of the simulation indicated that for rough fractures, the effect of fracture intensity was minor and was more predominant on both stress-strain curves and macroscopic strength properties for smoother fractures. Hydro-mechanical response ranges from the mechanical response due to the in-situ stress condition and how the rock fabric reacts to the additional stresses imposed by the injection fluid. In the true-triaxial experiments, the hydraulic fracture occurred perpendicular to the intermediate stress in a strike-slip fault regime along the plane of weakness. A new conceptual model is proposed to explain the failure processes, based on which the shut-in pressure corresponds to the magnitude of the principal stress perpendicular to the fracture plane. Other values of shut-in pressure are indicative of a complex fracture network. The resulting fracture network is greatly impacted by the fluid viscosity, with lower viscosity promoting the interaction with bedding planes and existing discontinuities.
A Hetorogeneous Stack for a Re-configurable Data Centre
Keywords: Artificial Intelligence
Big Data
Computer Hardware
Data Centers
FPGAs
Networking

With the increase of heterogeneity in data centres, the scalability of such devices, from the perspective of both ease of development and performance has been more difficult. The work in this thesis introduces a heterogeneous development and deployment stack at scale, particularly in integrating FPGAs and CPUs. This stack is a series of abstraction layers, where these layers can be swapped for different devices at the lowest level (we demonstrate this with CPUs and FPGAs), and different application domains at a higher level. End-to-end we present the translation of an application into hardware IP cores, to partitioning across devices, down to implementing on multiple FPGAs and CPUs. We also present the applicability of this heterogeneous stack for large scale applications through a large machine learning application. Through the use of multiple abstraction layers we have increased productivity and increased performance by unrolling our application across more devices at scale.
Structuring Horizontal Accountability in Ontario’s Health Care System
Keywords: Accountability
Healthcare
Horizontal accountability
Inter-organizational network
Organizational accountability

Background: In health systems comprised of independent health care organizations, the structuring of integrated delivery systems relies on organizations structuring horizontal accountability (HA) with one another. Despite this requirement, we know very little about how this is achieved. While scholars acknowledge that HA should exist as complementary to an organization’s vertical accountabilities, research has found that the structuring of HA can be disrupted by strong vertical accountabilities. This research seeks to understand: how can HA be structured within a system historically reliant on vertical accountabilities?Methods: This was an embedded, multi-case, case study research design, utilizing two Ontario-based cases. I utilized multiple qualitative methods with semi-structured interviews with administrators and governors as a primary source of data collection. Drawing on definitions of accountability in the public administration literature and Bovens (2010) and Dubnick and Frederickson’s (2010) concepts of accountability as a mechanism and as a virtue, I developed a preliminary conceptual framework that would guide this research. The focus was exploratory with goals of analytic applicability, generalization, and the expansion of theory. Results: Where organizations are compelled to structure HA, they will structure HA with contingencies that maintain their independence. For HA to be successful, it must be structured in a way that maintains its virtues while also institutionalizing aspects of HA that codify the interdependence of the partners. Actions and behaviours from the principal and governors, and participant willingness to tackle various tensions resulting from the historical environment, will all be core to establishing a facilitative environment for HA. Democratic, political, clinical, and community dimensions of accountability are well suited to HA whereas high degrees of funding, performance, and bureaucratic forms of accountability may determine whether HA will be replaced by a hierarchical scenario. Conclusion: This research adds to the literature by considering necessary processes, mechanisms, and environments for structuring HA and presents conceptual and analytic frameworks that can be utilized by administrators, policy makers, and researchers. This comprehensive approach is important as the presence of mechanisms alone have proven to be insufficient to the successful structuring of HA relationships (Addicott & Shortell, 2014; Andersson & Wikström, 2014).
The Role of Oxygen and Oxygen-Dependent Enzymes in Protein Folding, Metabolism, and Redox Homeostasis
Keywords: ADO
Hypoxia
Oxygen Dependent Enzymes
PRODH
Protein Folding
Tumour Microenvironment

Low levels of oxygen (hypoxia) in solid tumors contributes to therapy resistance and poor patient prognosis. How the cells in the tumor microenvironment (TME) adapt to hypoxia at a transcriptional, epigenetic, and translational level has been extensively explored. Here, we provide a comprehensive review on how molecular signaling in hypoxia represents an intricate, coordinated response triggered by oxygen dependent enzymes. Our work also highlights the lack of understanding of the requirement for oxygen in protein folding and the biological roles of an oxygen dependent enzyme, 2-aminoethanethiol dioxygenase (ADO). Secreted proteins contribute to aggressive cancer phenotypes in the TME. These secreted proteins are thought to utilize an oxygen dependent mechanism for disulfide bond formation required for proper folding, which represents a paradox when they are expressed under hypoxic conditions. Here we confirm the existence of oxygen independent pathways for disulfide bond formation. For the first time we demonstrate that key hypoxia-induced proteins such as vascular endothelial growth factor (VEGF-A) and carbonic anhydrase 9 (CA9) remain fully competent at disulfide bond formation in the absence of oxygen, supporting their efficient expression in hypoxia. This work highlights that the ability of individual proteins to undergo protein folding in the absence of oxygen ultimately determines their expression in the extracellular space in hypoxia. In parallel, we explored the cellular and physiological roles of a relatively uncharacterized oxygen sensing enzyme, ADO. ADO synthesizes hypotaurine and directly regulates protein stability through catalyzing a post translational modification in an oxygen dependent manner. Here we show that ADO is essential for the growth and survival of cancer cells and promotes tumor xenograft growth. ADO mitigates reactive oxygen species (ROS) through regulating proline metabolism. These data provide novel insights into how depletion of an oxygen dependent enzyme may elicit a metabolic imbalance leading to loss of redox homeostasis. Taken together, this thesis explores the role and the importance of oxygen and oxygen dependent enzymes that drive acute responses such as affecting the disulfide bond formation of protein folding and deregulation of the cancer metabolome.