VictorJuiz/thesis huggingface dataset:
Optimization Driven Design and Operation of Foundry Fabricated Silicon Photonics

Motivated by growing capabilities to realize geometrically complex silicon (Si) devices and large scale photonic integrated circuits (PICs), this thesis explores the use of optimization algorithms for design and operation of Si photonics. Optimization procedures are implemented for designing and operating grating couplers, power splitters, and microring optical filters at telecommunication wavelengths. The devices reported in this thesis were fabricated in foundry Si photonics processes at A*STAR Institute of Microelectronics or CEA-Leti using deep ultra-violet lithography on 8" wafers. First, we present an optimization design procedure for bi-layer silicon nitride-on-silicon (SiN-on-Si) grating couplers (GCs). We designed the first SiN-on-Si GCs for the O-band in a new platform. Cross-wafer measurements showed a median peak coupling efficiency of -2.1 dB and a 1-dB bandwidth of 70.8 nm. We also present 3-layer SiN-SiN-Si one-dimensional polarization-independent grating couplers (PI-GCs) designed by optimization methods. The best-performing PI-GC had a peak coupling efficiency of -4.8 dB and a 1-dB polarization-dependent loss bandwidth of >100 nm, setting a record for PI-GCs. The higher than expected loss was likely due to fabrication imperfections in one of the SiN layers. Next, we report the first topology-optimized devices fabricated in a foundry process, a Si photonic 2x2 3-dB splitter within a 4.8 um x 4.8 um footprint. Despite not respecting design rules, the design with the smaller cells had lower insertion losses and broader bandwidth and showed consistent behavior across the wafer. However, results point towards the need to improve consistency between simulation the fabricated devices in future work. Finally, we demonstrate multi-variable tuning control that incorporates optimization algorithms to guide the tuning of multiple phase-shifters simultaneously. Multi-variable control becomes indispensable for PICs with a large (>> 10) number of constituent devices by reducing the number of electrical inputs/outputs and simplifying packaging. Repeatable resonance alignment and wavelength tracking in a 5-ring optical filter and a programmable 2-ring Butterworth filter are demonstrated. An application to switch matrix tuning is also explored. Taken together, this thesis showcases how optimization methods can open up new directions for advancing the field of foundry fabricated Si photonics.

Keywords: Control
Grating Coupler
Integrated Optics
Microring
Optimization
Silicon Photonics
Advisor: Poon, Joyce
Sinfonia, 2018

Sinfonia, 2018 is a three-movement work for wind ensemble, with a combined performance duration of approximately 25 minutes. The instrumentation consists of piccolo, flute 1+2, oboe 1, oboe 2 doubling English horn, clarinet in E flat, clarinet in B flat 1-3, bass clarinet in B flat, bassoon 1+2, soprano saxophone, alto saxophone 1+2, tenor saxophone, baritone saxophone, trumpet in B flat 1-3, horn in F 1-4, tenor trombone 1+2, bass trombone, euphonium, tuba and percussion (minimum 5 players). The compositional style employs a freely chromatic harmonic and melodic language with elements of extended tonality and with rhythms sometimes mimicking those of natural speech. Although open to multiple interpretations and not overtly programmatic, the work was inspired in part by events of the last few years in my native United States, and portions of the music might be heard as evoking by turns a sense of chaos and disorientation and a struggle between hope and despair. Some melodic material is derived from transcriptions of the rhythm and pitch contour of excerpts from recordings of public speeches delivered by Donald Trump and Barack Obama. The well-known American hymn “Amazing Grace” is also quoted in a fragmentary and/or disguised manner throughout the piece, with the most clearly recognizable statement heard near the end of the final movement.

Keywords: Wind Ensemble
Advisor: Kulesha, Gary
The Role of Instructional Coaching for Teacher Learning in Elementary Mathematics: A Multi-case Study

This study examines how instructional coaching shapes teacher learning in elementary/intermediate mathematics education. Coaching is an initiative that is currently being implemented in a large Ontario Board of Education to address the teaching and learning needs in mathematics education. This multi-case study, with a cross-case analysis examines the perceptions of five elementary and intermediate teachers and four instructional coaches who have participated in instructional coaching specific to mathematics. The overall impression of instructional coaching from the participants’ perspectives was a positive one. Instructional coaching as a form of professional learning adhered to many of the components that are deemed to be important for effective professional learning environments of taking place over time, embedded in the teachers’ practice, self-directed, and relevant (Desimone, 2009). The teachers took an active role in their learning by choosing and determining the focus of the coaching sessions, and at the end of the study, commented about how they were incorporating aspects of the instructional coaching learning into their mathematics practice. The instructional coaches also commented about the work having impact, emphasizing the importance of choice and working with teachers who had elected to participate in the instructional coaching initiative. The major findings from the study are: (1) perceptions of the instructional coaching vary amongst the superintendents, administrators and teachers; (2) instructional coaching is an effective means of professional learning; (3) it is evident that the teachers perceived that their mathematics program was positively impacted by the work that took place with their instructional coach; (4) instructional coaching has a transient nature to it because there were many changes in personnel, which meant that some schools were working with various instructional coaches since the program was first introduced; and (5) instructional coaching has the ability to make school-wide change, through the work done with collaborative inquiry groups, as well as individual teachers. Findings from the study may inform how instructional coaching is implemented in school districts. The hiring practices of how coaches are selected and assigned to various schools need to be considered.

Keywords: Instructional Coaching
Mathematics Education
Professional Learning
Advisor: McDougall, Douglas
Elegy at Dawn: For Orchestra

Elegy at Dawn is a twenty-minute composition for orchestra with the following instrumentation: solo violin, two flutes (piccolo), two oboes, two clarinets in B-flat, two bassoons, four horns in F, two trumpets in C, two tenor trombones, one bass trombone, one tuba, one timpani, two percussion, one piano, and strings. The title refers to the composer’s mother (Dawn Judith Marwood) who passed away from cancer in 2011. The work is a tribute to her memory, as well as an exploration and musical interpretation of the different emotions that accompany deep loss. The featured solo violin part embodies much of the emotional grief, and may be imagined as representing the memory or voice of the departed parent. The work comprises six sections which alternate static and dense string chords with sections of different textures and instrumental colours. The solo violin is prominent in several sections throughout the composition, while in others it quietly soars above the rest of the ensemble. Notable moments in the work include a quasi-cadenza by the solo violin emerging from the low, dark string chords of the beginning; a brass chorale – composed as if set to the text of Psalm 23 “The Lord is my Shepherd” – in section four that begins in the background and gradually gains prominence; and a duet between the solo violin and piano in section five. This section uses free notation, where each instrument is given an approximate timing for their parts. The strings are gradually added, with the conductor giving cues for chord changes and entrances only. The work ends in a high register with all instruments fading out, leaving only the solo violin and piano to conclude the composition.

Keywords: composition
elegy
grief
orchestra
solo
violin
Advisor: Palej, Norbert
Angiogenic Patterning By STEEL, An Endothelial-enriched Long Noncoding RNA

Endothelial cell (EC)-enriched protein coding genes, such as endothelial nitric oxide synthase (eNOS), define quintessential EC-specific physiologic functions. It is not clear whether long noncoding RNAs (lncRNAs) also define cardiovascular cell-type specific phenotypes, especially in the vascular endothelium. Here, we report the existence of a set of EC-enriched lncRNAs and define a role for STEEL (spliced transcript – endothelial enriched lncRNA) in angiogenic potential, macrovascular/microvascular identity and shear stress responsiveness. STEEL is expressed from the terminus of the HOXD locus and is transcribed antisense to HOXD transcription factors. STEEL RNA increases the number and integrity of de novo perfused microvessels in an in vivo model and augments angiogenesis in vitro. The STEEL RNA is polyadenylated, nuclear-enriched and has microvascular predominance. Functionally, STEEL regulates a number of genes in diverse endothelial cells. Of interest, STEEL upregulates both eNOS and the transcription factor Kruppel-like factor 2 (KLF2), and is subject to feedback inhibition by both eNOS and shear-augmented KLF2. Mechanistically, STEEL upregulation of eNOS and KLF2 is transcriptionally mediated, in part, via interaction of chromatin-associated STEEL with the poly-ADP ribosylase, PARP-1. For instance, STEEL recruits PARP-1 to the KLF2 promoter. This work identifies a role for EC-enriched lncRNAs in the phenotypic adaptation of ECs to both body position and hemodynamic forces, and establishes a newer role for lncRNAs in the transcriptional regulation of EC identity.

Keywords: Angiogenesis
Chromatin
Endothelium
Hemodynamics
long noncoding RNA
Advisor: Marsden, Philip A.
“A Battle for the Soul of the Climate Movement”: The Expansion of the Intersectional Climate Justice Frame Among Young Activists in Canada

In this dissertation, I argue that the climate justice movement in Canada is conceptually aligned with tenets of feminist political ecology and demonstrates intersectional and decolonial approaches to activism and organizing. Such a framework did not emerge spontaneously but was developed through intellectual work and communication of climate justice activists, a contentious process tantamount to what one activist identified as a “battle for the soul of the climate movement”. Climate justice seeks to address the underlying conditions that generate and perpetuate climate change, understood to be caused by inequities, oppressions, and systems of domination inherent in the colonial-capitalist pursuit of endless growth. Intersectional climate justice further understands that groups and individuals experience and contribute to climate change differentially, based on contextual power relations, privilege, and identity, and thus seeks to incorporate recognition, (re)distributive, and participatory justice in climate change mitigation and adaption. My findings suggest that young Canadian activists began articulating climate justice between 2006 and 2015, in response to a Conservative-led federal government that attempted to (re)create Canada as a global ‘energy superpower’ while simultaneously weakening domestic environmental protection, vilifying activists, and contesting territorial rights of Indigenous peoples. I suggest that this intersectional climate justice movement inhabits the ‘glocal’ scale (e.g., Swyngedouw Kaika, 2003; Harcourt, 2015), constituted by interrelated, multi-scalar processes as well as actors that contest and co-create global narratives that generate and respond to locally-specific conditions. In this case, activist organizing appears to be structured differently than other environmental and social movements that promote allegiance to a group. Instead, principles of intersectional climate justice are disseminated through youth training networks which connect ‘free agents’ (activists without traditional organizational affiliations) from across the country into new linkages for mobilization. Many of the activists interviewed have engaged in processes of relational reflexivity, grappling with their own complicity and advantage in a society that continues to contribute to climate change. Their approaches to enacting intersectional analysis and decolonial solidarity are, arguably, empirical demonstrations of how to “stay with the trouble” (Haraway, 2016), and provide alternatives to hegemonic climate governance approaches that rely on technological interventions or market mechanisms.

Keywords: Canada
climate justice
environmental politics
youth activism
Advisor: Bunce, Susannah
Ruddick, Susan
Kinetic Consequences of Surface Oxygen Species during Catalytic C3H6-O2, CO-O2, and COx-H2 Reactions on Transition Metal and Alloy Clusters

C3H6 epoxidation, CO oxidation, and COx methanation reactions are important for emission abatement and value-added compound production. They occur on transition metal/alloy clusters via the kinetic coupling of steps that involve activation of carbon containing reactants (C3H6, COx) with co-reactants. The reaction mechanisms for each of these processes involve partial or total oxidations of reactants with distinct reactive oxidants. Kinetic and isotopic measurements, micro-kinetic modelling, and titration experiments reveal the mechanistic similarities between these seemingly different reaction systems, despite their distinctly different operating conditions and types of surface reactive oxygen species. For the first case of C3H6-O2 reactions, competitive epoxidation and combustion reactions occur on Ag clusters predominantly covered by O*. The desired epoxidation occurs via reactions between O* and C3H6. Contrarily, the undesired combustion to COx and H2O involves C-H bond cleavage by OOH*, which forms auto-catalytically from O2 and H2O. For the second case of CO oxidation, which is a step within C3H6 combustion, reactions between O2* and CO* take place on Ag and Group VIII metal cluster surfaces saturated with reactive O* or CO*. Here, the reactant ratios, reaction temperature, and the O* and CO* heats of adsorption on surfaces determine the O* and CO* coverages. While O* is much more abundant, O2* is the more reactive oxidant for CO oxidation. For the third case of COx methanation, a hydrogenation, the reaction occurs via the transfer of hydrogen from OH* to CH3* on Co and Ni-Co clusters partially covered with O* and via transfer of hydrogen from H* to CH3* on Ni and Ni-Co clusters partially covered with C*. The reaction conditions and metal affinities to O* and C* determine the competing adsorbate coverages. The competing coverages of reactive species lead to complex rate expressions that depend on the reaction temperature and inlet gas compositions. Simultaneously, the catalyst metal identity and average cluster diameters alter the heats of adsorption of the surface species and vary their reactivities and coverages. This study connects these kinetic and thermodynamic consequences across three catalytic processes and derives the expressions for these trends, allowing for reactor designs that optimize desired product yields.

Keywords: Catalysis
DFT
Kinetics
Methanation
Oxidation
Thermodynamics
Advisor: Chin, Ya-Huei C
Output Reach Control Problem with Applications to Motion Planning for Robotic Systems

As electronic devices become more embedded into everyday products, an increasing number of consumer devices are being equipped with control systems. These control systems are sometimes required to achieve complex specifications such as safety constraints or switching between distinct tasks. Among a wide range of techniques to deal with the control design of complex systems, one is to partition the state space into polytopic regions, and solve a control problem on each region such that the collective behaviour of the hybrid system solves the original complex control specification. In this dissertation we consider such a methodology where the control problem on each polytopic region is called the {\em Reach Control Problem} (RCP). The RCP is to find a state feedback to make the closed-loop trajectories of an affine control system defined on a polytope reach and exit a prescribed facet of the polytope in finite time. There is already an extensive literature on the RCP. This dissertation extends this literature by considering the {\em Output Reach Control Problem} (ORCP). The ORCP is to control the output trajectory of the control system on a simplex in the output space, in contrast to control the entire state trajectory. We also extend the applications of the RCP by developing a unified framework for control with complex specifications. This dissertation contains four distinct contributions. The first contribution provides an extension of classical linear regulator theory to affine systems and exosystems. This extension then provides the basis to develop a framework for the output reach control problem with disturbances. The second contribution leverages existing literature on viability theory to convert the ORCP in the output space on a simplex to a RCP in the full state space on a polytope. The third contribution is to propose a unified framework for solving control problems with complex specifications. Our framework is targeted at robotic systems. Finally, our fourth contribution is a set of so called {\em motion primitives} which comprise one of the layers of our aforementioned framework. These motion primitives are based on our approach to the ORCP.

Keywords: Integrator Systems
Motion Planning
Motion Primitives
Output Reach Control
Reach Control Problem
Advisor: Broucke, Mireille E
Effect of Nozzle-nozzle Interaction on Lean Flame Transitions in a Multi-swirler Combustor

This work investigates the transition between different flame stabilization modes in a gas turbine model combustor consisting of a linear array of five interacting nozzles, which is representative of advanced designs for next generation engines. Simultaneous multi-kHz repetition rate OH planar laser induced fluorescence and stereoscopic particle image velocimetry were used to examine the hydrodynamics and nozzle-nozzle interactions during the transient flame blowoff and reattachment processes. Two different reactants feeding configurations were designed to isolate the effects of different operating and geometric parameters on the combustor's fuel lean performance. In the first configuration, reactants to each nozzle were fed through a common plenum; while reactants to each nozzle were controlled separately in the second configuration. The lean blowoff point was tested for different inter-nozzle spacings, by changing the nozzles receiving reactants. The combustor's lean operability was optimized when only two nozzles were operated, as a result of the complex interaction between the cross-nozzle flame transport, fluid dynamic strain field, and the recirculation strength. Nevertheless, blowoff occurred at a relatively constant Damkӧhler number. The blowoff/reattachment process for an individual flame was initiated in a similar manner to isolated bluff-body stabilized flames, though with cross-nozzle flame interactions providing additional means of re-stabilizing a partially extinguished flame. In the connected plenum configuration, blowoff/reattachment dynamics of the three central nozzles were coupled to each other. Blowoff transitions were preferentially initiated in one of the off-center nozzles, with the transition of subsequent nozzles occurring in a random order. Similarly, the center nozzle tended to be the last nozzle to reattach. However, such temporal coincidence of the blowoff/reattachment transitions were not observed in the individual plenum configuration, suggesting the upstream coupling is significant in the combustor dynamics. A statistical analysis demonstrated that changes in downstream conditions would lead to flow re-distribution inside the connected plenum. Both in-chamber and upstream cross-nozzle interactions are equally important in flame blowoff transitions inside a practical combustor, while the in-chamber cross-nozzle interaction plays a more important role in reattachment transitions.

Keywords: Blowoff
Cross-Nozzle Flame Transport
Laser Diagnostics
Multi-Nozzle Combustor
Nozzle-Nozzle Interaction
Advisor: Steinberg, Adam M
Mononuclear Phagocyte Modulation of the Tumor Microenvironment and Control of Anti-tumor Immunity

Tumors are heterogeneously comprised of various cell types that make up a complex tissue-like structure, where cancer cells interact with various non-malignant cells. Immune cells represent one of these non-malignant cell types, and are particularly suitable as targets for anti-cancer therapeutics. Therapeutics that target the immune system (Immunotherapeutics), which are currently in clinical application, aim to restore immune responses to cancer cells by inhibiting the immune checkpoints that dampen lymphocyte responses. The efficacy of these immunotherapeutics results in good prognosis for some patients. Unfortunately, there are many non-responders, and we are only now just starting to discern the mechanisms that govern response efficacy. Targeting these immune checkpoints, with αPD-1 and αCTLA-4 monoclonal antibodies, restores anti-tumor effector function to dysfunctional tumor infiltrating lymphocytes, and facilitates the reduction of regulatory T cells. However, there are other aspects of tumor immunology that are unaffected by these drugs. Combinatorial treatment strategies that amplify the effects of current immune modulating drugs are thus predicted to enhance response efficacy. It is well established that myeloid cells contribute to oncogenesis, but how the constellation of receptors they express regulates their functions within the tumor microenvironment is less clear. Furthermore, cells of the mononuclear phagocytic system have the potential to function in a pro-tumoral capacity, or to promote anti-tumor immunity for cancer cell elimination. Here we demonstrate that autocrine and paracrine EGFR signaling between intratumoral macrophages and cancer cells facilitates tumorigenesis through macrophage mediated trophic support. Specifically, we show a novel AhR-AREG axis facilitates maintenance of the tumor microenvironment in BRCA1-associated breast cancer. Alternatively, in a syngeneic melanoma model we illustrate that Toso (FCMR), the putative receptor for soluble IgM, modulates myeloid cell responses to cancer to inhibit anti-tumor immunity. Furthermore, Toso negatively regulated the activation and migratory capacity of skin-associated myeloid cells in vivo, and bone-marrow derived dendritic cell-dependent T cell activation in vitro. Importantly, preliminary data indicates therapeutically targeting Ahr in BRCA1-associated cancers, or Toso in melanoma, may improve patient prognosis. Overall, these results suggest that targeting myeloid cell function within the TME represents a potential therapeutic avenue for bolstering current checkpoint immunotherapeutics.

Advisor: Mak, Tak W