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    Structure-Aware Inference from Incomplete Mass Spectra: From De Novo Sequencing to PTM Discovery
    (University of Waterloo, 2026-08-17) Mao, Zeping
    Machine-learning systems are often developed under a convenient assumption: the set of possible answers is known before inference begins. Molecular discovery violates this assumption. A tandem mass spectrum is an incomplete and noisy record of a molecule, while the databases and molecular vocabularies used to train computational models contain only previously described molecules. A model forced to choose among known answers may therefore confuse missing evidence with a negative result or assign an unexpected molecule to the nearest familiar category. This dissertation argues that computational inference should preserve both what a measurement supports and what it leaves unresolved until additional evidence justifies a more specific molecular claim. Rather than treating a database mismatch as the end of analysis, the methods developed here retain informative relationships among measured fragments, use them to formulate explicit hypotheses, and keep the evidence that generates a hypothesis distinct from the evidence used to accept it. Experiments on peptide and glycopeptide inference demonstrate why this distinction matters. When peptide fragments are missing, postponing uncertain local sequence decisions prevents one ambiguous region from corrupting the remainder of the sequence. For branched glycans, relationships between measured fragments and partial molecular compositions recover evidence that cannot be represented by a single linear ordering. The accompanying evaluation work further shows that apparent accuracy and estimated error rates depend on the data distribution, scoring method, and construction of negative controls. Expanding the space of possible molecular explanations must therefore be accompanied by evidence appropriate to the claim being made. These studies culminate in RNovA, which extends de novo sequencing from recognizing predefined modifications to discovering post-translational modifications beyond the training data and reference vocabulary. Without retraining for each new modification, RNovA can detect unexpected mass changes, reconstruct the corresponding modified peptides, and turn computational outputs into experimentally testable molecular hypotheses. Controlled experiments recovered modification types absent from training, while selected discoveries in biological samples were supported using synthetic reference peptides. Together, these results show that artificial intelligence need not treat an existing database as the boundary of molecular discovery. By preserving structural evidence in the measurement and making unresolved information explicit, it can propose and test molecular explanations that were not enumerated in advance.
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    Motion Congruence Outweighs Appearance in Virtual Self-Identification
    (University of Waterloo, 2026-08-17) Al-Bakry, Dara
    The integration of multisensory information in virtual environments (VR) relies heavily on the brain’s ability to resolve cue conflicts between visual appearance and motor feedback. While traditional paradigms often treat visuomotor relationships using binary heuristics, this thesis introduces a novel methodological framework utilizing an exponential moving average (EMA) filter to dynamically quantify and manipulate motion congruence in real time. Across a series of controlled trials, this work investigates the relative influence of visuomotor congruence and avatar appearance on self-identification and subjective experiences of virtual presence and embodiment. The empirical findings demonstrate that motion congruence is a primary driver of avatar self-identification scores, though its efficacy might be modulated by viewing perspective and technological constraints. Specifically, third-person perspectives and hardware limitations (such as restricted fields of view and resolution) impose boundary conditions that alter cue weighting strategies. Furthermore, analyses accounting for sample size constraints and statistical power highlight the necessity of within-participant designs and robust multi-metric evaluation to mitigate subjective response biases. Ultimately, this thesis advances our theoretical understanding of human multisensory integration in virtual settings and provides practical guidelines for the design of interactive systems. By bridging computational innovation in motion filtering with rigorous empirical evaluation, this work establishes foundational principles for optimizing embodiment and fidelity in emerging virtual and augmented reality applications.
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    Control and Stabilization of a Free-Flow Counterflow Gradient Electrophoresis Device for Preparative Protein Purification through Coupled Multiphysics Transport
    (University of Waterloo, 2026-08-17) Carreno-Molina, Oscar Manuel
    Biomolecule purification remains a critical yet resource-demanding component of downstream processing in pharmaceutical and biotechnological applications. Presently, chromatography serves as the gold standard; however, it is constrained by its batch operation, high cost, limited scalability and throughput. Continuous separation techniques, such as Free-Flow Electrophoresis (FFE), offer a promising alternative by enabling gentle, high-throughput separations based on electrophoretic mobility. Despite these advantages, the widespread adoption of FFE has been hindered by challenges related to analyte dispersion, Joule heating, electrochemical instability, and the difficulty of maintaining control over strongly coupled transport variables. Hybrid FFE modalities have been explored to mitigate these limitations. Among them, free-flow Isoelectric Focusing (FF-IEF) has achieved notable success due to its ability to self-focus analytes at their isoelectric points along an imposed pH gradient. However, the pH gradient establishment requires the use of expensive carrier ampholytes – costly reagents that can interact with target biomolecules – introducing complications for downstream processing and limiting practical scalability. This thesis presents the development and stabilization of a preparative-scale Free-Flow Counterflow Gradient Focusing (FF-CGF) system for charge-based biomolecule separation. FF CGF leverages the balance between hydrodynamic counterflow and electrophoretic migration to achieve continuous axial focusing without the need for carrier ampholytes, thereby preserving sample integrity and ensuring compatibility with downstream processes. A theoretical framework is established to describe FFE as a coupled multiphysics system governed by interacting electrical, hydrodynamic, thermal, and chemical fields, providing a unified interpretation of existing FFE modalities as control strategies within a shared parameter space. Guided by this framework, a modular microfluidic platform is designed that integrates optimized flow control, electric field delivery, and ion-exchange membrane interfaces to maximize single analyte focusing and improve voltage efficiency. The system is experimentally validated through the separation of fluorescently labeled monoclonal antibodies, demonstrating stable operation and preparative capability. Overall, this work advances FF-CGF as a viable alternative to chromatographic methods in downstream processing, and establishes a foundation for scalable, continuous biomolecule purification technologies.
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    Investigating Pulse-Type Glaciers in the Canadian Arctic: A Case Study of the Characteristics of Dobbin Bay Glacier, Parrish Glacier, and Eugenie Glacier within the Agassiz Ice Cap
    (University of Waterloo, 2026-08-14) Nowitsky, Owen
    Characterizing irregular glacier dynamics is crucial for understanding the drivers of variations in ice motion, improving glacier dynamic modelling, and projecting future contributions to sea-level rise. The majority of glaciers exhibiting irregular dynamics have been classified as ‘surge-type’ glaciers, even though some glaciers display dynamic behaviour that falls outside the classical definition of surging. One such category is ‘pulse-type’ glaciers, which have been identified as a subset type of glacier surging within the Canadian Arctic. Similar to surge-type glaciers, ‘pulsing glaciers’ experience quiescent and active phases but experience variations of ice motion on shorter timescales, with fluctuations in glacier flow restricted to the terminus region where the bed lies below sea level. Due to the recency of this identification (i.e., first reported in Van Wychen et al., 2016), few studies of ‘pulse-type’ glaciers have been conducted, leaving a gap in the understanding their processes and characteristics. In this study, three previously identified pulse-type glaciers, Dobbin Bay Glacier, Parrish Glacier and Eugenie Glacier, located on Agassiz Ice Cap within the Canadian High Arctic, are studied using measurements of surface elevation, ice flow, terminus position and subglacial topography and are used to investigate and distinguish pulse characteristics from other forms of dynamic instability. Pulse events were identified on Dobbin Bay Glacier from 2004 to 2008, Parrish Glacier from 2004 to 2010, and Eugenie Glacier from before 2000 to 2008. Across all three glaciers, a surface elevation rise of 2-5 m a-1 was observed at regions where subglacial sills or sharp valley turns were present, while downglacier regions experienced surface elevation loss of 2- 4 m a-1. During pulse events, velocities within the pulse region ranged from 500 to 1100 m a-1, compared to upglacier regions, which experienced velocities from 50 - 110 m a-1 during both quiescence and pulse events. These findings refine the current definitions of pulse-type glaciers and provide further insight into irregular glacier dynamics within the Canadian Arctic Archipelago.
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    Sense of belonging and well-being among Indigenous Peoples of Canada: The role of community involvement
    (University of Waterloo, 2026-08-14) Cantafio, Alexis
    Well-being is a multidimensional construct whose conceptualizations vary across disciplines, cultures, and contexts. Belonging is a fundamental human need that plays a key role in fostering well-being with extensive research showing that stronger sense of belonging is linked to better mental and physical health. Indigenous conceptualizations of well-being and belonging reflect a holistic, relational understanding of health as balance among mental, physical, emotional, and spiritual domains, that are cultivated through reciprocal relationships with family, community, natural world, ancestors, and culture. Community involvement represents an avenue through which belonging and well-being are cultivated. While there is extensive research exploring the association between well-being, belonging, and community involvement there remains a lack of research exploring these associations within Indigenous populations in Canada. The present study used data from the 2017 Aboriginal Peoples Survey (N = 18,679) to examine whether two types of community involvement (organizational volunteering and helping others) moderated the association between belonging and well-being among Indigenous Peoples living off reserve in Canada. By running two separate moderation regression analysis, we hypothesized that belonging (H1) and both forms of community involvement (H2) would be positively associated with well-being, and that both types of community involvement would moderate this association (H3). In Model 1 (organizational volunteering), did not reveal a main effect for belonging. Community involvement significantly predicted well-being (b = .05, p < .001), and no significant interaction was found. In Model 2 (helping others), we found a significant main effect for both belonging (b = .03, p = .006), and community involvement in (b = .01, p = .028) Model 2 also revealed a significant interaction between belonging and helping others (b = .02, p = .028), indicating that the positive association between belonging and well-being was stronger at higher levels of helping others. Our findings highlight that different forms of community involvement may have unique impacts on the belonging-well-being relationship, and that informal participation in community may be meaningful target of focus to promote well-being among Indigenous Peoples.