Theses

Permanent URI for this collectionhttps://uwspace.uwaterloo.ca/handle/10012/6

The theses in UWSpace are publicly accessible unless restricted due to publication or patent pending.

This collection includes a subset of theses submitted by graduates of the University of Waterloo as a partial requirement of a degree program at the Master's or PhD level. It includes all electronically submitted theses. (Electronic submission was optional from 1996 through 2006. Electronic submission became the default submission format in October 2006.)

This collection also includes a subset of UW theses that were scanned through the Theses Canada program. (The subset includes UW PhD theses from 1998 - 2002.)

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A proof-technique-independent framework for detector imperfections in QKD
(University of Waterloo, 2026-01-14) Nahar, Shlok
The security of Quantum Key Distribution (QKD) protocols is theoretically established using idealised device models. However, the physical implementations upon which practical security relies inevitably deviate from these ideals. This thesis develops a rigorous and versatile framework to address a subclass of such deviations: detector imperfections. This framework, termed ’noise channels’, is independent of security proof technique. This approach recasts imperfections as a quantum channel preceding an idealised measurement process. By granting the eavesdropper control over this channel, the security analysis is simplified to an ideal scenario, with the effects of the imperfections mathematically contained within a well-defined parameter. The utility and versatility of the framework are demonstrated through applying it to the postselection technique, and for phase error estimation. The application to phase error estimation is an improvement over past analyses which either assumed qubit detection setups, IID attacks, or required hardware modifications. We observe a remarkably high tolerance to imperfections when using the postselection technique. Finally, we extend the framework to address cross-round correlations, providing a methodology to prove security against detector memory effects such as afterpulsing and dead times. This work thus establishes a structured and powerful toolkit for analysing detector imperfections in practical QKD systems, unifying their treatment across different security proof techniques and advancing the development of robust implementation security.
Detection and Characterization of Viruses in the Environment Using Established and Novel Sequencing Approaches
(University of Waterloo, 2026-01-14) Nash, Delaney
Viruses play critical roles in both the environment and public health systems. This thesis integrates genomic sequencing methodologies to detect, characterize, and monitor viral diversity, advancing both fundamental ecological research and applied pathogen surveillance. Through three focused research projects, this work demonstrates how targeted and metagenomic sequencing strategies can address key knowledge gaps in environmental virology, plant pathology, and viral public health surveillance. The first objective (Chapter 2) was to develop and apply novel tiled-amplicon sequencing assays for Influenza A virus (IAV) H3N2 and respiratory syncytial virus (RSV) A in wastewater-based surveillance. These assays successfully recovered near-complete viral genomes from wastewater samples collected during the peak of the 2023/2024 respiratory virus season. Genomic coverage trends mirrored clinical case data within the associated public health region, validating the approach as a complementary tool to traditional clinical surveillance. Variant deconvolution analyses revealed distinct spatiotemporal patterns in variant distribution, demonstrating the capacity of these assays and bioinformatic tools to resolve community-level transmission dynamics and emerging viral lineages. The second objective (Chapter 3) extended this surveillance framework to the agriculturally significant Tomato brown rugose fruit virus (ToBRFV). A multiplexed tiled-amplicon assay was developed, achieving significant improvements in viral genome recovery compared to metagenomic RNA shotgun sequencing while reducing sequencing costs and resource requirements. ToBRFV clades circulating in Ontario wastewater were identified, including variants later recognized through global surveillance initiatives, underscoring the assay’s potential for early detection and the value of wastewater systems as environmental reservoirs for plant viruses. The third objective (Chapter 4) involved the assembly and characterization of the complete genome of a novel freshwater algal virus, Chrysochromulina parva virus BQ1 (CpV-BQ1). Using a hybrid Nanopore and Illumina sequencing strategy, a high-quality 165,454 bp genome was assembled and annotated, revealing hallmark nucleocytoplasmic large DNA virus (NCLDV) genes and diverse functional categories associated with viral replication, host manipulation, and capsid formation. This work offers important insights into viral infection of the ecologically important freshwater algal species C. parva. Moreover, it establishes a methodological framework for the complete sequencing, assembly, and annotation of algal virus genomes. Collectively, this thesis advances environmental virology and viral surveillance systems by developing scalable, sensitive, and cost-effective genomic workflows for virus detection and characterization in freshwater environments. By integrating virus ecology with applied public health and agricultural surveillance within a One Health framework, this work underscores the interconnectedness of environmental, human, and agricultural systems and provides practical guidance for future viral genomics research and pathogen monitoring programs.
The Forces Behind the Flux: Methane, Carbon Dioxide, and Nitrous Oxide Dynamics and Their Environmental Drivers in Restored Agricultural Wetlands
(University of Waterloo, 2026-01-14) Meinzinger, Shayna
Wetlands provide vital ecosystem services such as water filtration and flood mitigation but are also significant natural sources of greenhouse gases (GHGs), particularly methane (CH₄). This study examined seasonal and spatial patterns of CH₄, carbon dioxide (CO₂), and nitrous oxide (N₂O) emissions from seven restored agricultural wetlands in the Ontario portion of the Lake Erie Basin, focusing on diffusive and ebullitive flux pathways. Emissions were measured across four seasons, alongside water quality parameters used to identify key environmental drivers. Dissolved oxygen (DO) emerged as a strong driver of GHG fluxes, with lower DO concentrations consistently promoting higher CH₄, CO₂, and N₂O emissions. Duckweed cover also enhanced CH₄ production by creating anoxic conditions. GHG emissions peaked during summer months with heightened biological activity, while winter fluxes, though reduced, remained detectable, emphasizing the contribution of cold-season processes. N₂O emissions remained consistently low throughout the year. Across sites, methane emissions were generally low relative to natural temperate wetlands, except at one nutrient-enriched outlier (Site MA). Spatial variation within wetlands was minimal, suggesting that sampling from a single representative location may be sufficient for long-term monitoring. These findings show that restored agricultural wetlands can act as both carbon sinks and GHG sources depending on local biogeochemical conditions. By identifying major environmental controls on emissions, this study advances understanding of GHG dynamics in restored wetlands, informs efficient monitoring and modelling considerations, and strengthens national inventory and restoration policy development.
Negotiating Restoration through Representation: The role of visualization in the public process of Riverside Dam
(University of Waterloo, 2026-01-14) Polera, Jordana
As climate change intensifies ecological uncertainty and infrastructure risk, low-head dam removals have become sites where environmental, cultural, and political tensions converge. This thesis examines the case of Riverside Dam in Cambridge, Ontario (2008-2019), to explore how visualization acts not only as a tool of communication but as an active agent in shaping negotiations over the whether to remove, rebuild Riverside Dam. The Municipal Class Environmental Assessment (EA) for Riverside Dam including consultant drawings, City reports, and community responses based on eight “preferred alternative” designs for the dam. Visual materials play a decisive role in how potential futures are understood, aiding in understanding, participation, and decision-making. Drawings are political tools that can include or exclude voices, clarify or obscure impacts, and build or erode public trust. By closely studying the Municipal EA process for Riverside Dam, this thesis examines how values, trade-offs, and potential designs are communicated through visualizations and contested. Drawing from literature on landscape architecture visualization studies, Indigenous knowledge systems, and environmental design, the thesis proposes a framework for negotiated design to better support engagement with the community. Negotiated design in this thesis is an approach to environmental planning and restoration that prioritizes structured dialogue and collaboration among diverse stakeholders with often competing interests. This framework is a call for transparency, accessibility, and legibility in architectural drawings in so that the public is aware of what is at stake with each “preferred alternative” within the Environmental Assessment process. Within the proposed framework, this thesis lays out four visualization principles including: 1) contextual clarity, 2) embodied perspectives, 3) temporal layering, and 4) making conflict visible. Engagement principles also emphasize the use of physical space, co-creation, and writeable, decision-oriented drawings. Rather than producing an original design proposal, this thesis reinterprets three existing shortlisted design options (or “preferred alternatives”) for the Riverside dam: rebuilding, removing and naturalizing, and building an offline dam and naturalizing the river. Through different forms of visualization, the framework developed in the thesis are applied to visualize trade-offs, reveal biases, and imagine the realities of each design to best engage and educate the public. These River drawings are not final answers but rather invitations for further negotiation. By centering legibility over resolution, this work positions visualizing ecological projects as a collaborative and evolving act. It contributes to broader conversations on climate resilience and adaptation, decolonial landscape practice, and the role of design in environmental governance.
Beyond the Reason-Emotion Divide: Philosophical Theories of Autonomy from a Neuroscience Perspective
(University of Waterloo, 2026-01-14) Drecun, Darlene
This dissertation explores how recent neuroscience research might bear on philosophical theories of personal autonomy, with a special focus on the work of Christine Korsgaard and Harry Frankfurt. A central question within the personal autonomy literature is what gives our actions self-governing authority? Many approaches have answered this question with requirements about how we ought to reason or feel about our desires. One prominent way of dealing with this question of authority is a requirement of reason being “in control” of our emotions, presenting the relationship between reason and emotion as competitive processes fighting for control over our decisions. However, by examining recent neuroscience research related to the concept of autonomy, I argue that this research paints a different picture, where reason and emotion function cooperatively rather than antagonistically. Furthermore, the research suggests a prominent role for emotion in many different autonomy-related processes. In order to widely capture the many processes that underlie autonomy, I discuss the neuroscience of decision-making, self-control, voluntary action, and the conscious feelings related to agency and ownership over our actions. I examine some of the emerging trends in cognitive neuroscience that suggests that complex behaviours like decision-making and self-control emerge from large-scale neural networks located across widely distributed areas of the brain, where cognitive, emotional, and motivational information are deeply integrated at the neural level. I argue that this new notion of cognitive, emotional and motivational information as integrated in various processes, such as decision-making and control, has a direct impact on the concept of personal autonomy. First, this integration suggests that cognitive, emotional and motivational information all cooperatively contribute to autonomy processes, rather than competing. Second, the research suggests a larger role for emotion and motivation in processes like decision-making and self-control than is commonly assumed in philosophical theories of autonomy. Therefore, I argue that this integrated neuroscientific perspective highlights some important tensions between the neuroscience research on autonomy processes and philosophical theories of personal autonomy, like those of Korsgaard and Frankfurt. I examine the possible implications that the neuroscience of decision-making, self-control, voluntary action, and conscious feelings of agency may have on the autonomy theories of Korsgaard and Frankfurt. I point out several key tensions between the neuroscience research and how these theories of autonomy understand desires as motivating our actions, the role of emotion in decision-making and self-control, and whether we ought to rely on our conscious feelings of agency and control over our actions when determining whether our actions are autonomous. I suggest overall that an integrated neuroscientific understanding of the processes that support autonomy-related behaviours can provide a novel approach to understanding the concept of personal autonomy.
Learning to Reach Goals from Suboptimal Demonstrations via World Models
(University of Waterloo, 2026-01-14) Ali, Qasim
A central challenge for training autonomous agents is the scarcity of high-quality and long-horizon demonstrations. Unlike fields such as natural language or computer vision—where abundant internet data exists—many robotics and decision-making domains lack large, diverse, and high-quality datasets. One underutilized resource is leveraging suboptimal demonstrations, which are easier to collect and potentially more abundant. This limitation is particularly pronounced in goal-conditioned reinforcement learning (GCRL), where agents must learn to reach diverse goal states from limited demonstrations. While methods such as contrastive reinforcement learning (CRL) show promising scaling behavior when given access to abundant and high-quality training demonstrations, they struggle when demonstrations are suboptimal. In particular, when training demonstrations are short or exploratory, CRL struggles to generalize beyond the training demonstrations, and the resulting policy exhibits lower success rates. To overcome this, we explore the use of self-supervised representation learning to extract general-purpose representations from demonstrations. The intuition is that if an agent can first learn robust representations of environment dynamics—without relying on demonstration optimality—it can then use these representations to guide reinforcement learning more effectively. Such representations can serve as a bridge between noisy demonstrations and goal-directed control, allowing policies to learn faster. In this thesis, we propose World Model Contrastive Reinforcement Learning (WM-CRL), which augments CRL with representations from a world model (WM). The world model is trained to anticipate future state embeddings from past state–action pairs, thereby encoding the dynamics of the environment. As the world model aims to only learn environment dynamics, it can leverage both high and low quality demonstrations. By integrating these world model embeddings into CRL’s framework, it can help CRL more easily comprehend the environment dynamics and select actions that more effectively achieve its goals. We evaluate WM-CRL on tasks from the OGBench benchmark. We explore performance on multiple locomotion and manipulation environments and multiple datasets varying in quality. Our results show that WM-CRL can substantially improve performance over CRL in suboptimal-data settings, such as stitching short trajectories or learning from exploratory behavior. However, we find our method offers limited benefit when abundant expert demonstrations are available. Ablation studies further reveal that success depends critically on the stability of world model training and on how its embeddings are integrated into the agent’s architecture.
Sanctuaries of the Heart: Perception, Phenomenology and the Architecture of Salutogenic Healing
(University of Waterloo, 2026-01-13) Ahsan, Rabbiya
The thesis investigates the role of architecture as an active agent of healing by redefining salutogenic design through the lens of spatial phenomenology. It draws from the author’s own lived experience with mood disorders as well as extensive interdisciplinary research. The paper critiques historic, as well as modern healthcare approaches and treatment methods for mental health, with case studies such as Bethlem Royal Hospital and more sterile hospitals of today. In contrast, it studies the ancient healing methods that integrate the mind, body and spirit through spatial symbolism and rituals. Additionally, the project incorporates Maggie Keswick Jencks’ diaries through the lens of Critical Discourse Analysis, to understand a patient’s perspective when they navigate healthcare facilities. The thesis further studies the impact of the diaries in the form of a detailed case study of the Maggie Centre. Other case studies also contribute to understanding nature, materiality and sensory experience which combine under the umbrella term of spatial phenomenology and often nurtures positive recovery. Central to this research is salutogenesis, an idea that can be reframed to fit in the architectural narrative. This results in a proposed design of a mental wellness facility, located on the banks of the Grand River, a site with rich history and ecological vitality. The design serves as a manifesto for salutogenic design, choreographing light, sound, scent, texture and time, it dissolves the Cartesian split between mind and body and creates a space which contributes actively in the healing process.
A Proteomic Analysis of Biological Sex and Health in Gurat, France
(University of Waterloo, 2026-01-13) Sellers, Cassidy
Paleoproteomics, the study of ancient proteins, uses mass spectrometry to identify and characterize proteins by their amino acid sequences. This thesis explores the potential of paleoproteomics to inform bioarchaeological interpretations of biological sex and health in a small medieval population from Gurat, France. Ten milligram enamel samples from six individuals excavated from a rock-cut cave church were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify proteins in enamel and evaluate their interpretive potential. The primary aim of this project was to test a modified method to investigate its ability to successfully identify amelogenin (amelogenin-X and amelogenin-Y) and immune proteins (C-reactive protein and immunoglobulin-gamma). This method was intentionally modified to reduce analytical costs and resource requirements, while remaining applicable to very small quantities of dental enamel, thereby increasing its feasibility for archaeological and ethically sensitive sampling contexts. The enamel-specific protein amelogenin was successfully identified in all six samples, allowing for proteomic estimations of biological sex to be made. In contrast, one non-enamel-specific immune protein (C-reactive protein) was identified in only one sample, reflecting uncertainty regarding the abundance and preservation of immune proteins in enamel, the immune histories of the Gurat individuals, and the sensitivity of the modified method for immune protein detection. These results highlight both the strengths and limitations of paleoproteomics, offering avenues of exploration in future directions. Above all, this thesis finds that proteomic analyses can complement osteological analyses to offer valuable insight into archaeological populations.
Balancing female basketball players’ career progression with family planning decisions
(University of Waterloo, 2026-01-13) Miscione, Alliasen
Abstract Background: Female professional athletes face unique challenges, including lack of funding for league improvements or player salaries, fewer opportunities in terms of exposure to or abundance of professional leagues, and gender norms that limit their engagement in professional sport careers. These limitations are exacerbated when childbearing during the peak years of their career comes into consideration. The goal of this research is to better understand the impact of family planning and pregnancy on career progression of professional female basketball players. Research Questions: This thesis examined: What impact, if any, do female basketball players believe pregnancy, giving birth, and parenting may have on their career progression? Specifically, I explored (a) What potential implications on physical performance exist because of pregnancy? (b) What financial changes do athletes anticipate pregnancy, childbirth, and the postpartum period could bring to a career in sport? (c) What supports are necessary to help female athletes balance pregnancy and motherhood with a career in sport? Methods: This study employs a qualitative research design. Narrative inquiry was used to examine how athletes navigate decisions regarding pregnancy, childbearing, and the career progression. The study population included nine professional athletes who are considering or who have experienced childbearing, and who have or had a basketball career. Participants were recruited through personal social media accounts. Individuals were eligible for this study if they self-identified as a professional basketball player and felt they could speak on pregnancy or motherhood in sport through personal experiences. Semi-structured, individual interviews lasting approximately 45-60 minutes explored participants’ accounts regarding the factors influencing their pregnancy decisions and the effects childbearing may have on their careers. Narrative thematic analysis was used to capture common themes across interviews. Findings: Three stories were created from a compilation of participants’ accounts at three stages of the decision-making process to have children. Five participants did not have children at the time of interviews, and four participants were mothers of one or more children. First, a professional basketball player before pregnancy and motherhood, a professional basketball player after pregnancy while still competing, and lastly, a retired professional basketball player who waited until after their career was over to have children. These three stories demonstrate multiple stages of this decision and how the participants navigate the decision-making experience. These three stories also highlight four main themes within the analysis. The themes highlighted are financial insecurity and structural constraints that exist within professional women’s basketball, global mobility in sport, the body as a site of uncertainty because of pregnancy, and lastly, the stigma surrounding pregnancy and motherhood in professional sport. Many participants experienced difficulty or conflict in making decisions about pregnancy and childbearing and participants often found balancing motherhood and professional basketball challenging. Lastly, their perspectives on pregnancy and motherhood in sport was largely influenced by their personal situations and experiences and therefore is different for every athlete. Conclusions: The findings from this study contribute to understanding the unique challenges female athletes might face when making decisions about pregnancy and childbearing. The findings can also be leveraged to advocate for improved support systems and practices in professional sports to ensure female athletes who choose to become pregnant and give birth are supported in maintaining their athletic career. Ultimately, this research highlights the need for further exploration into the intersection of gender, sport, and reproductive choices.
Investigating Isotropy in Atmospheric Turbulence Using Large Eddy Simulations
(University of Waterloo, 2026-01-12) Mohammadifar, Mohammad
Turbulence plays a key role in many atmospheric and engineering flows, but understanding how it becomes isotropic under different conditions is still a challenge. In this thesis, we use the WRF model in idealized mode to explore how turbulence evolves in four setups: two driven by buoyancy (convective boundary layer and plume) and two by shear (random and bubble-perturbed Shear). We analyze anisotropy of the eddy dissipation using eddy-viscosity-based metrics, comparing how different forcing mechanisms and spatial resolutions affect the development and isotropization of turbulence. Buoyancy-driven cases showed smoother, more gradual transitions to isotropy, while shear-driven cases featured stronger bursts, persistent anisotropy, and slower convergence in time, especially at low resolution. It can also be understood that vertical velocity is more anisotropic in buoyancy-driven cases, while vertical shear dominates in shear-driven cases. These results highlight how both physical forcing and resolution shape the anisotropy of turbulence and point to important considerations for model setup in future turbulence studies.
Influence of Boundary Conditions on the Sheared Edge Fracture Limits of a 3rd Generation Advanced High Strength Steel.
(University of Waterloo, 2026-01-12) Advaith Narayanan, .
A fundamental trade-off between strength and ductility exists in advanced high strength steels (AHSS), particularly for sheared edge splitting in automotive forming operations. The widely used ISO16630 conical hole expansion test for edge stretchability is known to be a poor representation of the in-plane deformation modes that are the primary source of edge splitting in stamping, leading to an overestimation of formability in virtual tryouts. Additionally, virtual experiments rely upon the input of a single fracture strain value to predict edge cracking in stamped parts, disregarding the effects of deformation mode and element size. An efficient and reliable modeling approach for edge failure is required without having to simulate the shear cutting process. The present work addresses some of these challenges through four interrelated tasks aimed at developing guidelines to efficiently characterize the anisotropic plasticity behavior and edge fracture limits, to support reliable experimental assessment and finite-element modelling of sheared edge fracture in practical forming applications. There is a need to develop efficient strategies for anisotropic plasticity characterization of sheet materials to be able to accurately simulate the various tensile edge stretching modes ranging from splitting without necking to potential localization before fracture. To this end, the baseline plasticity characterization of four approximately pressure-independent aluminum alloys (AA) and steels with varying ductilities and anisotropy levels: AA5182-O, AA7075-T6, DC04, and 980GEN3 steels were performed using uniaxial tensile tests in multiple orientations. Using digital image correlation (DIC), the area strain at the neck center was monitored to measure the flow stress response to strain levels more than twice the uniform elongation, with the added advantage of probing anisotropic hardening effects. A hybrid inverse analysis procedure was further developed and applied to notch tensile tests to obtain the major stress under plane strain tension while constraining the minor-to-major principal stress ratio to remain near 1:2. Anisotropic yield functions were subsequently calibrated using data from a range of stress states with emphasis on plane strain tension. The calibrated yield functions and hardening responses were shown to accurately reproduce both the local and global behavior in flat punch hole expansion tests, which activate a wide range of tensile-dominated stress states. Flat punch hole expansion simulations using yield functions calibrated without plane strain data consistently deviated from the DIC in-plane strain magnitudes with absolute differences of up to 15% for DC04 steel. The proposed methods provide general guidelines for efficient calibration of anisotropic constitutive models for approximately pressure-independent materials that are accurate to large deformation levels. Next, the mechanics of the conical hole expansion test were examined to assess the role of necking and anisotropy and to develop methodologies for fracture strain estimation. Finite-element (FE) models of the test were created in LS-DYNA software for two AHSS grades with differing plastic strain anisotropies using hexahedral solid elements. An analysis of through-thickness stress and strain gradients from the numerical models revealed that localization is suppressed until a hole expansion ratio of 200%, with the outer hole edge exhibiting a proportional uniaxial tensile stress state. Any non-uniformity in hole shape or thickness around the circumference of the extruded hole was found to be a manifestation of the tensile plastic strain anisotropy distribution and not necking. The hole expansion ratio was found to be suboptimal for quantifying edge stretchability since the inner hole edge undergoes a non-linear strain path transitioning from compression to uniaxial tension. Furthermore, when using the HER as a fracture metric, the local outer hole edge element strains from FE simulations were underpredicted with absolute differences of up to 10%. An analytical technique was proposed to obtain the local major fracture strain from conical hole expansion using the outer hole diameter measured at the crack location, with the equivalent failure strain then obtained using plastic work equivalence. The strains obtained using the proposed method were in excellent agreement with the elemental strains from numerical models with a maximum difference of 4% for the highly anisotropic CP800, confirming its suitability for fracture strain measurement from the test. Subsequently, a novel four-point fixture and specimen geometry that promotes failure under the deformation mode of in-plane bending was developed to characterize the uniaxial fracture limits of moderate ductility materials. The in-plane bending mode is also representative of edge splitting at peripheral regions of stamped parts. Techniques to detect the onset of fracture and accurately measure the edge strains from the in-plane bend tests were proposed that is applicable to a wide range of material ductilities. The uniaxial fracture strain measured in the in-plane bend test conducted with a machined edge was found to agree closely with the conical hole expansion true fracture strain of 0.68 for a 3rd generation 980GEN3 advanced high strength steel. The in-plane bend test also showed promise for plastic strain anisotropy characterization under uniaxial tension and compression to strain levels much larger than the material uniform elongation. A gauge height-to-thickness ratio of 4.0 or lower is recommended as a specimen design guideline to mitigate buckling based on a comprehensive experimental study conducted on multiple materials and thicknesses. Finally, the influence of loading conditions on the sheared edge fracture limits of 980GEN3 steel punched with a 5.0 mm hole and 12% clearance was investigated using five different test methods that imposed different stress and strain gradients in the vicinity of the sheared edge. A convergent fracture strain value of approximately 0.30 was observed across the in-plane edge fracture tests, with the conical hole expansion test exhibiting a higher strain of 0.45 due to out-of-plane deformation and fracture being defined at through-thickness cracking. Differences in fracture strains between the in-plane tests were also magnified by the choice of DIC lengthscale or virtual strain gauge length, reflecting each test’s varying sensitivity to DIC strain averaging. Global stretchability metrics were proposed for each deformation mode, enabling edge crack assessment in industrial applications without the need for DIC. The global edge stretch metrics were also found to inform the appropriate choice of DIC lengthscale for design and FE modelling. Finally, FE simulations of the edge fracture tests were conducted using multiple mesh sizes, revealing that a boundary condition dependence can also manifest in simulations with the added influence of lengthscale sensitivity. The predicted major strains at the experimental fracture instant varied with mesh size, suggesting that a single strain value may be insufficient to describe edge fracture. The elemental thinning strain showed reduced dependence on mesh size, making it a more reliable parameter for assessment of edge fracture in simulations. Importantly, the simulations indicated that the edge fracture strain cannot be represented by a unique value but is rather a function of the imposed loading condition. The in-plane stretching mode exhibited the lowest engineering thinning strain limit of 8.8%, making it the critical deformation mode for edge crack initiation in 980GEN3 steel. A key outcome of this work is the quantitative understanding of the effect of boundary conditions and lengthscale on the edge fracture limits. Prediction of sheared edge fracture must account for both the imposed loading and numerical lengthscale, with thinning strain offering a more robust metric for use in simulations. The developed methodologies provide practical and efficient guidelines that can be implemented in industrial environments for edge crack assessment and prediction in stamping simulations.
Systems and Control Protocols for Neutral-Atom-Array Quantum Processors
(University of Waterloo, 2026-01-12) Zhutov, Artem
Neutral atom arrays are a leading platform for programmable quantum processors, offering individual qubit addressability, long-lived hyperfine ground states, and strong Rydberg interactions. Recent progress has demonstrated coherent control over thousands of atoms. However, achieving scalable control requires precise mitigation of environmental and hardware imperfections that degrade gate performance. This thesis presents an integrated neutral-atom array platform built from the ground up that incorporates quantum sensing directly into the processor. Each atom functions both as a qubit and a local magnetometer. We design, build, and characterize from first principles three subsystems: 1) a microwave control system for driving hyperfine transitions in ground-state rubidium atoms; 2) a Raman laser system for site-selective single-qubit gates; and 3) a Rydberg laser system with quantum optimal control for robust two-qubit gates. This work provides a universal gate set and quantifies which error sources limit performance. First, we develop an in-situ magnetic field imaging technique using the atom array as a quantum sensor. Through site-resolved Ramsey spectroscopy, we image magnetic fields across a 260 μm × 160 μm region with 3 μm spatial resolution. We then apply computed corrections that compensate for the bias magnetic fields, producing uniform global microwave single-qubit rotations. Second, we introduce a hardware-aware simulation framework to evaluate Raman laser systems for hyperfine qubit manipulation. Simulations predict a single-qubit gate infidelity of 4.4 × 10⁻⁴ using BB1 composite pulses to mitigate thermal motion errors. We validate the Raman laser system by building and characterizing its phase noise. Third, we develop a Rydberg laser system for high-fidelity entangling gates. We apply linear response theory to map laser phase noise to single-atom Rydberg excitation fidelity. We then demonstrate fast phase-noise engineering by optimizing laser servo parameters. We employ hardware-aware quantum optimal control to design both Rydberg excitation and two-qubit gate pulses with built-in robustness against physical and control parameter fluctuations, outperforming analytical benchmarks. This integrated platform demonstrates high-fidelity universal control of neutral-atom registers with hundreds of qubits. By systematically addressing environmental inhomogeneities through integrated sensing and hardware-aware control design, this work provides a validated path for scaling quantum processors while maintaining gate fidelity.
Ja, goed idee! Arranging joint future activities as a 'Big Package' in Dutch phone conversations
(University of Waterloo, 2026-01-12) de Rooij, Geertruida
Arrangement-making is an important part of daily life and even a simple get-together may require a longer stretch of such preparatory talk. Using the method of conversation analysis and building on Heritage and Clayman's (2024) work on arrangement-making packages in English, this thesis analyzes the way arrangements are made in spontaneous Dutch telephone conversations. This research places itself in the context of work on longer stretches of talk, also known as long sequences (Sacks, 1995) or big packages (Jefferson, 1988). The analysis first takes a broad perspective of the arrangement-making package as a whole, concentrating on the boundaries that set it apart from the conversation in which it is embedded. For the beginning of the arrangement-making process, some of the ways in which participants signal shared knowledge, for example through discourse particles, are explored, while at the end of the package, some practices for confirming the agreed upon plan or for postponing the final arrangements to a later time are addressed. Subsequently, the analysis zooms in on a specific linguistic resource, 'anders dan' (otherwise), and its role in the body of the package. I show that this adverbial expression is found both in extended turns and at the beginning of a new turn. In the latter position, it can serve to propose an alternative to an arrangement solution being pursued, allowing for closure of the arrangement-making segment or package. Data are from the Corpus Gesproken Nederlands (Corpus of Spoken Dutch).
Lake Ice Thickness Retrieval from SWOT and Legacy Spaceborne SAR Altimetry
(University of Waterloo, 2026-01-08) Fatt, Jennifer
Lakes play a critical role as climate change proxies and cover a significant portion of the northern latitude landscape. Lake ice phenology offers valuable insight into changing climate patterns, yet in-situ observations of lake ice have declined substantially in recent decades. This observational gap underscores the growing importance of remote sensing as a tool for understanding and monitoring lake ice. Northern and remote communities particularly rely on lake ice quality, quantity, and thickness for transportation on ice roads, subsistence activities, and recreational use. There has been limited research exploring the use of satellite altimetry for the retrieval of lake ice thickness (LIT); however, its efficacy and utility have been highlighted in recent studies. The Ku-band SWOT (Surface Water and Ocean Topography) nadir altimeter (NAlt) provides an opportunity to retrieve ice properties and directly measure ice thickness. This study assesses the retrieval of LIT from SAR altimeters aboard the legacy Sentinel-3 and Sentinel-6 sensors over the winter seasons 2019 to 2025 on Lhù’ààn Mân (Kluane Lake), Yukon, and compares it with the estimated LIT derived from the SWOT altimeter analysis. LIT can be determined using Ku-band altimetry through the analysis of double-peaked waveforms characteristic of lake ice formed by the interaction of the radar signal with the ice interfaces. The utilization of SWOT altimetry has the potential to advance understanding of lake ice processes and to provide valuable datasets for d hydrological models, as well as overall resource management. This thesis discusses the potential applications of SWOT altimetry in lake ice thickness retrieval, emphasizing its capacity to fill critical data gaps. This study implements a dual-peak waveform methodology to estimate LIT using SWOT NAlt and reports an overall RMSE of <0.15m for the SWOT scientific period 2024-2025.
Development of a 7-item Dietary Screener Questionnaire for Determining Intakes of Eicosapentaenoic and Docosahexaenoic Acid in Canadians
(University of Waterloo, 2026-01-08) Liu, Ming Rong
The intakes of the omega-3 polyunsaturated acids, eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic acid (DHA, 22:6n-3) are associated with various health benefits. The main dietary sources of EPA and DHA are seafood, but there are non-seafood sources that contain significant amounts of EPA and DHA. Determining the dietary intake of EPA and DHA can be challenging due to the sporadic nature of seafood intake. An online 7-item dietary screener has been used to estimate the DHA intake of pregnant women from both seafood and non-seafood sources in the United States. Using this screener as a template, a Canadian screener for estimating EPA and DHA intakes was developed. In Project 1, EPA values were added and DHA values revised to match those in the Canadian Nutrient File, the questions were reordered to focus on seafood commonly consumed, questions about eggs were expanded to include options for size and omega-3 enrichment, and a French version of the screener was developed. In Project 2, fatty acid quantitation analyses were completed on screener items when the Canadian Nutrient File EPA and DHA data was either missing or not consistent with literature. This included eggs (medium, large, extra-large, omega-3, and omega-3 plus), liver (beef, pork, and chicken), and chicken (regular and organic). For Project 3, the “Canadianized” screener was evaluated for errors using mock. To do this, intake information from the 24-hour dietary recalls in the 2015 Canadian Community Health Survey (CCHS) were extrapolated to bimonthly intakes and entered into the screener. The EPA and DHA intakes estimates from the screener agreed with those from the CCHS 2015 Nutrition, indicating that the Canadian screener is ready for a proper validation study in the future. Once validated, this online tool should be able to improve our ability to estimate the intakes of EPA and DHA by Canadians. In addition, the process that was used to “Canadianize” the screener can be used as a template top adapt the screener for different countries.
Label-free optical microscopy: Photon Absorption Remote Sensing (PARS) and other methods for label-free histopathological imaging of tissues
(University of Waterloo, 2026-01-08) Ecclestone, Benjamin
Emerging label-free microscopy methods offer promising new avenues to view cells and tissues in their native environment, minimizing external influences. These label-free techniques are an exciting departure from gold standard methods for visualizing microscopic cellular and tissue structures, which rely on centuries-old chemical staining processes. In current practice, chemical labelling can unavoidably interfere with specimens’ physical and biochemical integrity. As a result, samples are effectively consumed by staining with only a single stain set normally applied to each sample. This limitation is especially impactful in applications such as clinical oncology and medical histopathology. In these settings, irreversible staining processes can severely limit the diagnostic utility of samples; especially when there is limited sample volume (e.g., brain tumor biopsies). As an alternative, label-free imaging techniques offer a potential avenue to visualize subcellular tissue anatomy while preserving samples in their entirety. Subsequently label-free microscopy methods have significant potential to greatly increase the diagnostic utility of each specimen, thereby enhancing patient outcomes. This thesis focuses on developing new methods for label-free microscopy, specifically emphasizing techniques for label-free histopathology. As a starting point the targeted objective is to develop a label-free analog to chemical hematoxylin and eosin (H&E) staining. This objective is chosen as H&E represents the gold standard contrast applied in effectively every clinical diagnostic case. Subsequent developments in this thesis can be broken into three major sections, which focus on (1) developing label-free microscopy methods for H&E-like imaging, (2) exploring the biomolecular specificity of developed methods to validate the label-free H&E-like contrast, and (3) producing a label-free microscopy architecture capable of meeting the imaging requirements necessary for clinical adoption. The first collection of works explores the development of a range of label-free microscopy methods. These studies establish new variations and combinations of optical absorption and scattering microscopes to visualize microscopic tissue anatomy label-free. These efforts ultimately resulted in the development of a new optical absorption microscopy modality, Photon Absorption Remote Sensing (PARS). This comprehensive technique provides biomolecule-specific visualizations characterizing the dominant photophysical effects caused when photons are absorbed by a biomolecule. As a direct result, novel PARS specific contrasts are developed as the total absorption (TA) and quantum efficiency ratio (QER). These PARS measurements may provide unique views into biomolecules’ excited state dynamics, accessing characteristics related to the quantum yield. By specifically probing specimens’ response to the absorption of deep ultraviolet light, PARS is shown to provide label-free contrast directly reminiscent of gold standard chemical H&E staining methods. As a proof of concept, the initial PARS architecture is applied to capture submicron resolution images of key H&E-like diagnostic markers across a variety of human and animal tissue specimens. The second section of this thesis expands the basis for PARS histopathology by validating PARS capacity to produce H&E-like visualizations. Two main avenues of exploration are pursued in this effort. The first endeavor explores the underlying biomolecular contrast of the PARS measurements. Established statistical methods are applied to develop characteristic PARS profiles for biomolecules. These PARS signatures are then applied to map the abundance of molecules label-free inside complex specimens. As a proof of concept, key diagnostic features including nuclei, red blood cells, and connective tissues are directly characterized and unmixed label-free. Resulting statistical abundance mappings are directly validated against chemically stained ground truth counterparts. The second endeavor introduces an end-to-end pipeline which uses deep learning-based image-to-image transforms to emulate chemical H&E visualizations from label-free PARS data. Resulting PARS emulated H&E-like visualizations are validated against chemical H&E staining through a clinical concordance study. In this diagnostic validation study, statistical analysis is applied to determine if pathologists produce the same diagnoses on both PARS and chemical H&E images. In this preliminary test, the PARS-based virtual staining method achieves > 90% concordance with very high statistical confidence (Kappa > 0.7) across all measured diagnostic tests. The final thesis section develops a new PARS architecture which achieves pragmatic imaging performance, nearing the requirements for clinical diagnostic settings. The presented system features a hybrid opto-mechanical scanning architecture which allows for high-speed MHz rate imaging. This results in imaging speeds which are more than an order of magnitude faster than earlier PARS embodiments developed in the PhotoMedicine Labs (at the University of Waterloo). This work simultaneously develops an end-to-end control system and imaging workflow which enables fully automated PARS imaging of whole specimens. Deep learning methods are applied to the resulting PARS images to produce virtual H&E-like visualizations. Qualitative and quantitative methods are applied to validate the imaging performance across a range of human and animal tissue samples. Results indicate the PARS virtual H&E images are largely indistinguishable from chemically H&E-stained ground truth images. Notably, the presented system forms the basis for a commercially available clinically ready prototype for label-free PARS histopathology imaging. In total, the findings presented across this thesis encompass the development of a new variation of microscopy technique (PARS). This method provides unique views into the absorption and scattering characteristics of specimens opening a new avenue of label-free contrast. For the presented histopathology application, PARS can provide powerful H&E-like images which may circumvent key challenges of chemical staining. In clinical histopathology, this method could enhance the diagnostic utility of tissue specimens directly improving patient outcomes. Beyond histopathology, the principles of PARS may be directly applicable to a wide range of imaging applications spanning material science, biological research, and clinical diagnostics. Overall, the methods developed in this thesis lays the groundwork for new label-free optical absorption microscopy techniques, which are already achieving real-world commercial and clinical success in histopathology applications.
Advancing Semi-Supervised Domain Adaptive Semantic Segmentation Through Effective Source Integration Strategies
(University of Waterloo, 2026-01-08) Kurien, Joshua
Semantic segmentation is a highly valuable visual recognition task with applications across fields such as medical imaging, remote sensing, and manufacturing. However, training segmentation models is challenging because it requires large-scale, densely labeled data specific to the target. Semi-supervised learning (SSL) addresses this challenge by leveraging unlabeled data alongside limited labeled data, reducing the reliance on fully labeled datasets. Semi-supervised domain adaptation (SSDA) further mitigates this issue by incorporating labeled data from a source domain alongside minimally labeled target data. While existing SSDA methods often underperform compared to fully supervised approaches, recent SSL methods that utilize foundation models achieve near fully supervised performance. Given the strength of current SSL methods using foundation models, this thesis investigates effective strategies for integrating source-domain data from a different distribution into existing pipelines to improve segmentation performance. First, we explore a simple source transfer mechanism that merges target and source data into a single unified labeled set for SSL pipelines. Our analysis demonstrates the accuracy benefits of this setup while also highlighting some downsides, particularly in terms of training efficiency. We also examine the use of ensembling SSL and SSDA models to enhance target-domain performance. This ensemble combines a model trained solely on target data with a source-transferred SSDA model. We find that ensembling can improve performance in certain cases but is less effective in others, and training efficiency remains suboptimal due to the need to train two models. Given the training inefficiencies of simple source transfer and ensembling, we propose a dual-curriculum source integration strategy to address and improve these limitations. This approach consists of two complementary learning strategies: curriculum retrieval, which progressively samples source examples from easy to hard, and curriculum pasting, which increases the diversity of target-labeled data. Across our experiments, we compare against and outperform state-of-the-art SSL and SSDA methods on a variety of benchmarks, including synthetic-to-real and real-to-real scenarios. Our findings highlight the benefits of effective source data integration into modern SSL pipelines for boosting segmentation performance, opening a new avenue for label-efficient semantic segmentation.
REMind: A Robot Role-Playing Game To Promote Bystander Intervention
(University of Waterloo, 2026-01-07) Sanoubari, Elaheh
Peer bullying is a pervasive social problem, with bystanders' inaction being a critical challenge despite widespread disapproval of bullying. Effective intervention strategies must move beyond explanation-based instruction to facilitate embodied situated learning. This dissertation explores how social robots can serve as mediators for applied drama to foster prosocial bystander intervention in the context of peer bullying. It introduces Robot-Mediated Applied Drama (RMAD): an innovative framework that integrates drama-based pedagogy with social robotics to create safe, reflective, and embodied learning experiences. Using a Research through Design (RtD) methodology, this work advances through an iterative sequence of design studies that culminate in the development and evaluation of REMind (short for Robots Empowering Minds): a mixed-reality role-playing game where children engage in dramatized bullying scenarios performed by social robots. In REMind, three robots enact a conflict involving a bully, a victim, and a passive bystander. Players are invited to assume control of robotic avatar, reflect on the unfolding narrative, and improvise an intervention by using the robot as a proxy in order to change the story’s outcome. Through this structure, children rehearse bystander intervention strategies within a psychologically safe, yet emotionally engaging environment. The iterative design process of REMind unfolded across complementary empirical inquiries. A crowdsourced feasibility study first established that observers perceive aggression toward robots as morally wrong, validating the viability of using robots in the intervention. A narrative co-design study with children revealed storytelling patterns such as preferences for emotionally expressive and customizable robot characters. Interviews with teachers grounded the design in classroom realities, identifying gaps in existing programs. A game design focus group study further examined what makes educational robot role-play games pleasurable for children, leading to identifying concrete design elements that informed REMind’s interactive components such as core mechanics, use of tangible props, world aesthetics and narrative structure. This dissertation presents the resulting artifact, REMind, as a system consisting of five interconnected components: Learning Goals, Mechanics, Narrative, Technology, and Aesthetics. The learning goals were defined through consultation with subject-matter experts to ensure grounding in evidence-based best practices. By deliberate aligning the game pleasures identified in prior studies with the learning objectives, REMind introduces a suite of game mechanics that scaffold socio-emotional skills (such as robot-mediated spect-actorship or "puppet mode" for moral intervention, interpretation of immersive affective displays for empathy-training and perspective taking, and custom-made logic-gate puzzles for moral reasoning). Narrative design is scaffolded by borrowing a five-step cognitive model of bystander intervention from social psychology. The technical implementation is realized through StorySync, a novel spreadsheet-based scripting toolkit developed to synchronize multimodal cues (including multiple robots, graphical interfaces, ambient lighting, and sound) and manage narrative branching for live interactive robot drama. Finally, the aesthetic elements leverages emotional design, ambient cues, and digital scenography to create an emotionally resonant learning experience. This concrete high-fidelity prototype serves as a proof of concept for RMAD. This research contributes a theoretical and practical foundation for designing robot-mediated experiential learning systems, offering RMAD as a new direction for social robotics and educational technology. It further illustrates how embodied storytelling and interactive systems design might cultivate reflective, prosocial action in a complex domain of social-emotional learning. More broadly, it advocates for a shift in Human-Robot Interaction (HRI) research toward systems thinking, positioning game design as a powerful systems lens for creating and analyzing holistic user experiences.
Two-sample Inference, Order Determination, and Data Integration for Functional Data
(University of Waterloo, 2026-01-07) Zhang, Chi
Functional data analysis has gained increasing prominence in modern statistics, largely due to advancements in data collection technologies. It provides a nonparametric framework for analyzing discrete observations obtained from realizations of a continuous random function, often defined over time or space. In this thesis, we focus on three distinct problems, each reflecting a different aspect of functional data analysis. In Chapter 2, we address the problem of comparing mean functions between two groups of sparse functional data within the framework of a reproducing kernel Hilbert space. The proposed method is well-suited for sparsely and irregularly sampled functional data. Traditional approaches often assume homogeneous covariance structures across groups, an assumption that is difficult to justify in practice. To circumvent this limitation, we first develop a novel linear approximation for the mean estimator, which naturally leads to its desirable pointwise limiting distributions. Furthermore, we establish the weak convergence of the mean estimator, enabling the construction of a test statistic for the mean differences. The finite-sample performance of our method is demonstrated through extensive simulations and two real-world applications. In Chapter 3, we study the problem of determining the number of eigenpairs to retain in functional principal component analysis---a problem commonly referred to as order determination. When a covariance function admits a finite representation, the challenge becomes estimating the rank of the corresponding covariance operator. While this problem is straightforward when the full trajectories of functional data are available, in practice, functional data are typically collected discretely and are subject to measurement error contamination. Such contamination introduces a ridge in the empirical covariance function, obscuring the true rank. We develop a novel procedure to identify the true rank of the covariance operator by leveraging the information of eigenvalues and eigenfunctions. By incorporating smoothing techniques to accommodate the nonparametric nature of functional data, the method is applicable to functional data collected at random, subject-specific points. Extensive simulation studies demonstrate the excellent performance of our approach across a wide range of settings, outperforming commonly used information-criterion-based methods and maintaining effectiveness even in high-noise scenarios. We further illustrate our method with two real-world data examples. In Chapter 4, we investigate the integration of multi-source functional data to extract a subspace that captures the variation shared across sources. In practice, data collection procedures often follow source-specific protocols. Directly averaging sample covariance operators across sources implicitly assumes homogeneity, which may lead to biased recovery of both shared and source-specific variation structures. To address this issue, we propose a projection-based data integration method that explicitly separates the shared and source-specific subspaces. The method first estimates source-specific projection operators via smoothing to accommodate the nonparametric nature of functional data. The shared subspace is then isolated by examining the eigenvalues of the averaged projection operator across all sources. If a source-specific subspace is of interest, we re-project the associated source-specific covariance estimator onto the subspace orthogonal to the estimated shared subspace, and estimate the source-specific subspace from the resulting projection. We further establish the asymptotic properties of both the shared and source-specific subspace estimators. Extensive simulation studies demonstrate the effectiveness of the proposed method across a wide range of settings. Finally, we illustrate its practical utility with an example of air pollutants data.
Pretending Architecture: The Journey Towards Verne Station
(University of Waterloo, 2026-01-07) Ferreira, Jamie Verdell
This is a record of pretend architecture, a journey of fabricating fantasy in the form of a virtual environment that is an authentic fake. This is an exploration inspired by the many fictional stories that I have encountered in order to create an interpretation of a space station. Framed by the harsh reality of space and contrasted by idealistic viewpoints in film, literature and video games, the end result presented is a far cry from initial expectations. It is a means to an end; a way to explore architecture in outer space with the use of constructs. Verne Station exists as fragments of experiences; attempts to understand and discover the intoxicating ideals of a limitless frontier ruled by the harshest of living conditions. By use of the machine, one has the ability to create complex virtual environments to simulate and visualize space architecture concepts; a field that has historically been inaccessible to many. By simulating different scales of artificial gravity design, the real-time exploration of designed spaces can facilitate a clearer understanding and more effective visual feedback of potential space architecture designs. This is a thesis about coming to terms with not arriving at your original destination, the one you imagine and expect to reach, but instead, the real one which you never quite anticipated.

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