VictorJuiz/thesis huggingface dataset:
Hydrolysis and Atmospheric Oxidation Reactions of Perfluorinated Carboxylic Acid Precursors

This dissertation explores a number of different environmentally relevant reactions that lead to the production of perfluorocarboxylic acids (PFCAs), a family of environmental pollutants that does not undergo any further degradation pathways. The compound perfluoro-2-methyl-3-pentanone (PFMP) is a new fire fighting fluid developed by 3M that is designed as a Halon replacement. The environment fate of PFMP with regards to direct photolysis, abiotic hydrolysis and hydration was determined using a combination of laboratory experiments and computational modeling. PFMP was found to undergo direct photolysis giving a lifetime of 4-14 days depending on latitude and time of year. Offline samples confirmed PFCA products and a mechanism was proposed. Polyfluorinated amides (PFAMs) are a class of chemicals produced as byproducts of polyfluorinated sulfonamide synthesis via electrochemical fluorination (ECF). Using synthesized standards of four model compounds, PFAMs were detected and quantified in a variety of legacy commercial materials synthesized by ECF. PFAMs were hypothesized to undergo biological hydrolysis reactions, suggesting their importance as historical PFOA precursors. The PFAMs were also investigated with regards to their environmental fate upon atmospheric oxidation. Using a smog chamber, the kinetics and degradation mechanisms of N-ethylperfluorobutyramide (EtFBA) were elucidated. The lifetime of EtFBA to oxidation by OH was found to be approximately 4 days. Using offline sampling, PFAMs were shown to give PFCAs upon atmospheric oxidation and a plausible mechanism was proposed involving an initial N-dealkylation step followed by loss of isocyanic acid to give a perfluorinated radical. The perfluorinated radical then produces PFCAs by a series of known atmospheric reactions. Finally, the biological hydrolysis of the polyfluoroalkyl phosphate monoesters (monoPAPs) were studied in vitro using a bovine alkaline phosphatase enzyme. Michaelis-Menten kinetic parameters were measured and compared to hexyl phosphate. It was discovered that monoPAPs hydrolyzed on average 100 times faster than hexyl phosphate due to the electron withdrawing fluorine substituents. The results were also used to rationalize the results of a previous in vivo study which suggested monoPAPs were rapidly hydrolyzed in the small intestines of rats following a high dose by oral gavage.

Keywords: environmental
chemistry
analytical
transformation
fluorinated
PFCA
atmospheric
hydrolysis
Advisor: Mabury, Scott A.
Citizen-girls: Girls' Perspectives on Gender, Ciitizenship and Schooling

The voices, perspectives and experiences of girls and young women in history, political and civic education remain rare, and those of girls of color are even rarer still. This dissertation reports on the results of a qualitative study exploring girls’ perspectives on and experiences of citizenship in the Toronto area. Through the use of document analysis, semi-structured interviews; and photovoice, this study suggests that the girls easily identify traditional gendered expectations in their families, schools and in the society at large. At the same time, the girls often make deliberate choices to defy these expectations, carve out their own paths, and serve as advocates for gender equality, social justice and engaged citizenship. This study focuses on the voices of girls and the ways in which concepts of gender enhance, shape and inhibit civic action within schooling. Despite an increased emphasis on education for active citizenship in education more broadly, this study provokes serious questions about what girls are learning about their roles in society and how concepts of gender affect the ways young people understand and enact their citizenship roles. There are new fields of research in the areas of youth civic engagement, citizenship education, feminist and girlhood studies, all of which informed my understanding of these ‘citizen-girls’, however they still often remain separated and inadequately consider the intersections of multiple identity factors as well as the relationship between individual agency and the societal structures that construct dominant values. This study has important implications for educators and policymakers, suggesting a need for more spaces and opportunities both within the classroom, and outside the school, for girls and boys to critically engage with the messaging they receive about gender, democratic participation and citizen engagement. Furthermore, these girls’ experiences also suggest that we must broaden our definition of citizenship and civic participation in order to better reflect the myriad new forms of citizen expression being used by girls and young people in modern societies today.

Keywords: girls
gender
citizenship
education
civic education
civic engagement
adolescence
youth activism
photovoice
arts-informed methodologies
Canada
schooling
identity
youth civic engagement
Advisor: Joshee, Reva
Fault Tolerant Control of Large Flexible Space Structures under Sensor and Actuator Failures

In this thesis, we study fault tolerant control (FTC) for the decentralized robust servomechanism problem (DRSP) of a colocated large flexible space structure (LFSS) under sensor and actuator failures (SAF). The control objective is to devise a decentralized controller that maintains the stability of the LFSS, tracks a constant reference for healthy outputs, regulates against an unknown constant disturbance for healthy outputs, and is robust against parametric uncertainties, so that ``spillover effects'' do not occur. Two FTC frameworks are considered: An active FTC framework that assumes SAF are known, and a passive FTC framework for which SAF are unknown. The active FTC framework extends existing work on DRSP of a nominal LFSS, and applies a PID controller that has fault-dependent adjustments. Necessary and sufficient conditions for a solution to exist are determined, notably an easy-to-test rank condition. For the passive FTC framework, a PD controller that stabilizes an LFSS under unknown SAF is found. Although perfect tracking and regulation are not attained under the PD controller, by applying high gains, the errors for healthy outputs can be reduced to any desired level. However, outputs with failed sensors and healthy actuators can reach undesirably high magnitude under high gains. To improve performance under low gains, insights on steady-state outputs are applied to develop a feed-forward control that has good performance in tracking, but not regulation. Further analysis on the PD controller reveals a method to diagnose SAF using steady-state outputs. As a result, the PD controller and PID controller are found to have complementary advantages, leading to an 3-stage integrated FTC procedure. First, the PD controller can stabilize the LFSS under unknown SAF (passive FTC). Next, fault diagnosis is performed while the LFSS is stabilized. Finally, a reconfigured PID controller applying diagnosed SAF enables healthy outputs to meet control objectives (active FTC). Three examples, including a benchmark space platform with 200 states obtained by finite-element analysis, are used to illustrate the results throughout this thesis.

Keywords: Fault tolerant systems
Flexible structures
Robust control
Linear systems
Aerospace
Advisor: Davison, Edward J.
Kwong, Raymond H.
Behaviour and Modelling of Reinforced Concrete Slabs and Shells Under Static and Dynamic Loads

A procedure for improved nonlinear analysis of reinforced concrete (RC) slab and shell structures is presented. The finite element program developed employs a layered thick-shell formulation which considers out-of-plane (through-thickness) shear forces, a feature which makes it notably different from most shell analysis programs. Previous versions were of limited use due to their inabilities to accurately capture out-of-plane shear failures, and because analyses were restricted to force-controlled monotonic loading conditions. The research comprising this thesis focuses on addressing these limitations, and implementing new analysis features extending the range of structures and loading conditions that can be considered. Contributions toward the redevelopment of the program include: i) a new solution algorithm for out-of-plane shear, ii) modelling of cracked RC in accordance with the Disturbed Stress Field Model, iii) the addition of fibre-reinforced concrete (FRC) modelling capabilities, and iv) the addition of cyclic and dynamic analysis capabilities. The accuracy of the program was verified using test specimens presented in the literature spanning various member types and loading conditions. The new program features are shown to enhance modelling capabilities and provide accurate assessments of shear-critical structures. An experimental program consisting of RC and FRC slab specimens under dynamic loading conditions was performed. Eight intermediate-scale slabs were constructed and tested to failure under sequential high-mass low-velocity impact. The data from the testing program were used to verify the dynamic and FRC modelling procedures developed, and to contribute to a research area which is currently limited in the database of literature: the global response of RC and FRC elements under impact. Test results showed that the FRC was effective in increasing capacity, reducing crack widths and spacings, and mitigating local damage under impact. Analyses of the slabs showed that high accuracy estimates can be obtained for RC and FRC elements under impact using basic modelling techniques and simple finite element meshes.

Keywords: shell structures
nonlinear analysis
impact testing
reinforced concrete
shear
fibre-reinforced concrete
Advisor: Vecchio, Frank J.
Electronic Energy Transfer in Light-harvesting Antenna Complexes

The studies presented in this thesis explore electronic energy transfer (EET) in light-harvesting antenna complexes and investigate the role of quantum coherence in EET. The dynamics of energy transfer are investigated in three distinct length scales and a different formulation of the exciton transport problem is applied at each scale. These scales include: the scale of a molecular dimer, the scale of a single protein and the scale of a molecular aggregate. The antenna protein phycoerythrin 545 (PE545) isolated from the photosynthetic cryptophyte algae Rhodomonas CS4 is specifically studied in two chapters of this thesis. It is found that formation of small aggregates delocalizes the excitation across chromophores of adjacent proteins, and that this delocalization has a dramatic effect in enhancing the rate of energy transfer between pigments. Furthermore, we investigate EET from a donor to an acceptor via an intermediate site and observe that interference of coherent pathways gives a finite correction to the transfer rate that is sensitively dependent on the nature of the vibrational interactions in the system. The statistical fluctuations of a system exhibiting EET are investigated in the final chapter. The techniques of non-equilibrium statistical mechanics are applied to investigate the steady-state of a typical system exhibiting EET that is perturbed out of equilibrium due to its interaction with a fluctuating bath.

Keywords: Electronic energy transfer
photosynthesis
light-harvesting
antenna proteins
Advisor: Scholes, Gregory D.
CMOS Contact Imagers for Spectrally-multiplexed Fluorescence DNA Biosensing

Within the realm of biosensing, DNA analysis has become an indispensable research tool in medicine, enabling the investigation of relationships among genes, proteins, and drugs. Conventional DNA microarray technology uses multiple lasers and complex optics, resulting in expensive and bulky systems which are not suitable for point-of-care medical diagnostics. The immobilization of DNA probes across the microarray substrate also results in substantial spatial variation. To mitigate the above shortcomings, this thesis presents a set of techniques developed for the CMOS image sensor for point-of-care spectrally-multiplexed fluorescent DNA sensing and other fluorescence biosensing applications. First, a CMOS tunable-wavelength multi-color photogate (CPG) sensor is presented. The CPG exploits the absorption property of a polysilicon gate to form an optical filter, thus the sensor does not require an external color filter. A prototype has been fabricated in a standard 0.35μm digital CMOS technology and demonstrates intensity measurements of blue (450nm), green (520nm), and red (620nm) illumination. Second, a wide dynamic range CMOS multi-color image sensor is presented. An analysis is performed for the wide dynamic-range, asynchronous self-reset with residue readout architecture where photon shot noise is taken into consideration. A prototype was fabricated in a standard 0.35μm CMOS process and is validated in color light sensing. The readout circuit achieves a measured dynamic range of 82dB with a peak SNR of 46.2dB. Third, a low-power CMOS image sensor VLSI architecture for use with comparator based ADCs is presented. By eliminating the in-pixel source follower, power consumption is reduced, compared to the conventional active pixel sensor. A 64×64 prototype with a 10μm pixel pitch has been fabricated in a 0.35μm standard CMOS technology and validated experimentally. Fourth, a spectrally-multiplexed fluorescence contact imaging microsystem for DNA analysis is presented. The microsystem has been quantitatively modeled and validated in the detection of marker gene sequences for spinal muscular atropy disease and the E. coli bacteria. Spectral multiplexing enables the two DNA targets to be simultaneously detected with a measured detection limit of 240nM and 210nM of target concentration at a sample volume of 10μL for the green and red transduction channels, respectively.

Keywords: fluorescence
spectral-multiplexing
contact imaging
CMOS
image sensor
imager
microsystem
lab-on-a-chip
quantum dot
wide dynamic range
high dynamic range
self-reset
subranging ADC
microfluidics
DNA detection
DNA analysis
point-of-care
medical diagnostics
Advisor: Genov, Roman
Gulak, P. Glenn
Ancient Egyptian Cubits &ndash; Origin and Evolution

This thesis suggests that prior to Ptolemaic and Roman times, ancient Egypt had two distinct and parallel linear systems: the royal system limited to official architectural projects and land measurements, and a great (aA) system used for everyday measurements. A key 1/3 ratio explains ancient Egyptian linear measurements and their agricultural origin. Emmer is 1/3 lighter than barley, consequently, for an equal weight, a container filled with emmer will be 1/3 greater than a container filled with barley. The lengths derived from both containers share the same 1/3 ratio. The second chapter, Previous Studies, lists the work of scholars involved directly or indirectly with ancient Egyptian metrology. The third chapter, The Royal Cubit as a Converter and the Scribe’s Palette as a Measuring Device, capitalizes on the colour scheme (black and white on the reproduction of Appendix A) appearing on the Amenemope cubit artifact to show the presence of two cubits and two systems: the black (royal system) and the white (great [aA] system) materialized by the scribe's palette of 30, 40, and 50 cm. The royal cubit artifacts provide a conversion bridge between the royal and the great systems. The information derived from the visual clues on the Amememope cubit artifact are tested against a database of artifacts scattered in museums around the world. The fourth chapter, The Origin and Evolution of Ancient Egyptian Cubits, historically relates the ancient Egyptian linear systems to the closed metrological systems they belong to. A closed metrological system is a system in which units of length, volume, and weight are related to each other. The conclusion is that the ancient Egyptian metrological system is backward compatible as it is possible - using a hin as a closing volumetric unit and emmer, barley, wheat (triticum durum) and water as commodities - to re-construct the linear metrological systems of all ancient Egyptian periods.

Keywords: Metrology
Cubits
Advisor: Leprohon, Ronald
Interplay between Electron Correlations and Quantum Orders in the Hubbard Model

We discuss the appearance of quantum orders in the Hubbard model for interacting electrons, at half-filling. Such phases do not have local order parameters and need to be characterized by the quantum mechanical properties of their ground state. On one hand, we study the Mott transition from a metal to a spin liquid insulator in two dimensions, of potential relevance to some layered organic compounds. The correlation-driven transition occurs at fixed filling and involves fractionalization of the electron: upon entering the insulator, a Fermi surface of neutral spinons coupled to an internal gauge field emerges. We focus on the transport properties near the quantum critical point and find that the emergent gauge fluctuations play a key role in determining the universal scaling. Second, motivated by a class of three-dimensional transition metal oxides, the pyrochlore iridates, we study the interplay of non-trivial band topology and correlations. Building on the strong spin orbit coupling in these compounds, we construct a general microscopic Hubbard model and determine its mean-field phase diagram, which contains topological insulators, Weyl semimetals, axion insulators and various antiferromagnets. We also discuss the effects many-body correlations on theses phases. We close by examining a fractionalized topological insulator that combines the two main themes of the thesis: fractionalization and non-trivial band topology. Specifically, we study how the two-dimensional protected surface states of a topological Mott insulator interact with a three-dimensional emergent gauge field. Various correlation effects on observables are identified.

Keywords: strongly correlated
Hubbard model
topological insulators
Mott insulator
quantum orders
spin liquids
pyrochlore iridates
Weyl semi-metal
slave-rotors
emergent gauge fields
Advisor: Kim, Yong Baek
Late Pliocene–Early Pleistocene North Atlantic Circulation: Integrating Dinocyst Assemblages and Foraminiferal Geochemistry

During the Late Pliocene, between 3.3 Ma and 2.6 Ma, tectonic events changed ocean basin interactions against a background of shifting orbital forcing mechanisms and a global cooling trend. A climate system that had been locked in a stable, warm state gradually transformed into one typified by the high-amplitude glacial–interglacial fluctuations characteristic of the later Quaternary. The onset of Northern Hemisphere glaciations in the Late Pliocene marks an important step in this transition, due to the role of feedback mechanisms including ice albedo. A crucial factor in this Northern Hemisphere ice sheet expansion is the North Atlantic surface ocean circulation. To evaluate how they are linked, a ca. 200-kyr time slab spanning 2782-2520 ka (Late Pliocene–Early Pleistocene) was analyzed at millennial scale resolution from eastern North Atlantic Deep Sea Drilling Project (DSDP) Site 610 and Integrated Ocean Drilling Program (IODP) Site U1313. The causes of the Plio-Pleistocene climatic turnover are compared to that of the well-documented Marine Isotope Stage (MIS) M2 occurring in the Late Pliocene (3.3 Ma). MIS M2, a severe glacial event seen as a precursor to later Quaternary-style glaciations, was investigated from western North Atlantic DSDP Site 603. Utilizing a same-sample methodology, two paleoceanographic proxies were used: (1) dinocyst assemblages, and (2) foraminiferal geochemistry (δ18O and Mg/Ca). Dinocysts are proven tracers of sea-surface temperature (SST), salinity, nutrient supply, and sea ice cover, and are analyzed here to characterize the overlying water masses at the studied sites. Strong dinocyst assemblage fluctuations attest to variations in the influence of the North Atlantic Current (NAC). Using Mg/Ca ratios for the planktonic foraminifer Globigerina bulloides to determine absolute SSTs allows salinity changes to be reconstructed when combined with stable oxygen isotopes. This study shows a persistent Gulf Stream–NAC in the western North Atlantic during MIS M2, favoring a southern shift of the NAC over a shutdown of the thermohaline circulation. At the newly established Plio-Pleistocene boundary, a profound turnover in dinoflagellate cyst assemblages reveals a shift in ocean mode during MIS 104 (2.6 Ma). Three distinct dinocyst ecozones demonstrate this fundamental reorganization of the North Atlantic circulation.

Keywords: Dinoflagellate cysts
North Atlantic
Pliocene
Pleistocene
Northern Hemisphere Glaciation
Foraminifera
Stable Isotopes
Mg/Ca
Advisor: Head, Martin
Displaced Spaces, Shocks, Negations: A Musical and Gestural Analysis of Stefan Wolpe's Studies for Piano, Part I (1946-48) and its Implications for Performance

The core project of this dissertation is a musical and gestural analysis of Studies, Part I: Displaced Spaces, Shocks, Negations, A New Sort of Relationship in Space, Pattern, Tempo, Diversity of Actions, Interactions and Intensities (1946-48) by post-tonal composer Stefan Wolpe (1902-72). The analytical methods consist of Set Class analysis (Allen Forte), the Effort Shape analysis of gesture (Rudolf von Laban), and the Time and Tone analysis of accordion performance (Joseph Macerollo). Wolpe played a leading role in the emergence of abstract expressionism among the painters, poets, dancers and composers of New York in the mid to late 1940s.Wolpe’s oeuvre reveals a unique way of composing in the post-tonal era. Chapter 1 provides the historical and stylistic contextualization of this particular study Displaced Spaces. Chapter 2 is concerned with the musical analysis, presented as pitch class and shape analysis. By nature, Wolpe’s pieces are best described as very physical, which explains the rationalization for the application of the gestural analysis in chapter 3. The Effort Shape graphic notation method by Rudolf von Laban (1879-1958) widely used in dance is applied to the musical gestures in Wolpe’s score. Wolpe’s overall title for the series of studies, Music for Any Instrument (1944-49), leaves the choice of instrument to the performer; as these studies require a polyphonic instrument, the classical accordion seems an appropriate choice. Laban’s principles as applied to Wolpe are compared to Macerollo’s Time and Tone analysis to implement gesture on one specific instrument. Battle Piece, a composition for piano solo which he began in 1943 is central to a change in Wolpe’s development: After finishing the first three movements of the piece, Wolpe explored new ideas in the study Displaced Spaces. The degree of coherence between the later parts of Battle Piece and Displaced Spaces is presented in chapter 4 focussing on new techniques that Wolpe was able to formulate through this “detour”. Chapter 5 as a conclusion brings together results from the set theory and the gestural analysis of this particular work in order to bridge the gap between the disciplines of music theory, performance and dance.

Keywords: classical accordion
displaced spaces
The Eight Basic Efforts
Rudolf von Laban
Stefan Wolpe
Advisor: Walter, Cameron