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Copper-Mediated Approaches to Selective Modification of Peptides and Proteins
No full textPeptides and proteins have long played crucial roles in diverse applications, including drug development, biomaterials, and diagnostic imaging. However, recent advances in biosynthetic engineering, synthetic methodology, combinatorial screening approaches, and analytical methods have allowed more routine access to diverse peptidic structures that diverge markedly from natural structures, incorporating unnatural amino acids or significantly altering the canonical polypeptide structure. Indeed, the very definition of “peptide” is less clear today, with blurred lines separating peptides from peptoids, peptidomimetics, stapled structures, foldamers, hybrid conjugates, and other structures. Peptides and proteins play increasing roles in drug development, and non-canonical modification is often employed as a tool to improve drug properties, including cellular uptake, in vivo stability, and selective localization. This thesis focuses on the development of selective modification of natural peptides and proteins by transition-metal catalysis.
The first chapter provides a summary of important approaches to side chain modification methods developed in the past two decades, focusing on fundamentally enabling mechanistic, selectivity, or reactivity ideas. The second chapter reviews the synthesis and transformations of sulfines, a class of S-oxides of thiocarbonyl compounds which are widely studied in synthetic chemistry but rarely used in peptide stapling or protein bioconjugation.
Development of selective peptide and protein modification methodologies is discussed in chapters 3-5. Chapter 3 describes a straightforward means of late-stage one-step oxidation of methionine residues within polypeptides to afford NH-sulfoximines. The use of an ex situ gaseous chlorosulfine reagent for peptide macrocyclization and protein bioconjugation is shown in chapter 4. Furthermore, chapter 5 highlights a copper-catalyzed cross-coupling selective for pyroglutamate post-translational modifications (PTMs) that is directed by peptide backbone amides, which serves as a complementary strategy for the histidine-directed pyroglutamate arylation chemistry reported previously.
Based on the rhodium(II)-metallocarbene catalysis developed in the Ball group, the application of rhodium proximity labelling in cell lysates for identifying new drug-protein interactions was described in chapter 6. Taken together, these contributions expand the toolbox for peptide and protein modification, and could provide new opportunities in several areas of chemical biology, such as inhibitor design, cellular imaging, and PTM profiling, etc
Methods and Tools for Risk-informed Resilience Enhancement of Coastal Intermodal Freight Networks
No full textCoastal intermodal freight networks (CIFNs)—comprising maritime, roadway, and railway corridors—are vital to the economies of coastal communities. These networks facilitate efficient cargo transfers, thereby underpinning supply chains. However, they are increasingly vulnerable to disruptions caused by extreme coastal hazards, which are being intensified by climate change and population growth. Such disruptions, as evidenced by past hurricane events, can have devastating effects, with impacts rippling through communities and leading to both short- and long-term socio-economic consequences. Given these challenges, it is essential to model the recovery and resilience of CIFNs to better assess their capacity to restore cargo-transfer functionality and to inform planning efforts aimed at enhancing this capability. Despite the importance of this task, current modeling methods have significant limitations. These include a lack of consideration for multiple commodity types, high computational complexity, limited ability to accommodate stakeholders at various scales, and a failure to effectively incorporate resource-related constraints into the recovery modeling process.
This study aims to address these gaps by proposing a multi-scale probabilistic resilience modeling framework tailored to the intricacies and complexity of CIFNs. Specifically, this framework enables a comprehensive characterization of the intermodal network at the component, link, and network levels. It integrates both roadway and railway corridors with port terminals through specially adapted network flow models, enabling the estimation of network-level functionality while accounting for multiple shipments, diverse commodities, and various stakeholders. In addition to posing the overarching framework for resilience modeling of CIFNs, this study addresses a critical gap in modeling flow-based port functionality under disrupted conditions—a key component in simulating the intermodal recovery of post-disaster satisfied demands between maritime and inland corridors. Specifically, this model incorporates the probabilistic availability of port structural and handling components following a disaster, enabling more detailed, physics-based estimations of flow capacity at the terminal level, extending beyond just the handling capacity of cargo at berth areas. Another critical gap this study aims to bridge is the lack of efficient methods for incorporating resource constraints into the modeling of CIFN recovery following extreme coastal hazards. To address this, the study introduces a resource-aware framework that not only considers the available resources for restoration—both monetary and labor—but also how these resources are allocated by decision-makers under post-disaster strained conditions. Specifically, two allocation algorithms are proposed: an optimization-based approach and a heuristics-based approach. These algorithms are designed to explore the influence of the interplay between different conditions of resource availability and allocation efficiency on network-level resilience outcomes.
The proposed models and methodologies are demonstrated through three real-world case studies in Mobile and Baldwin counties, Alabama, involving a multi-commodity port site, a railway network, and a fully integrated CIFN that incorporates these systems along with roadway corridors. These case studies assess post-disaster functionality at both local scales (e.g., recovery of port flow capacity) and regional scales (e.g., restoration of satisfied demands across the intermodal network). These resilience analyses are conducted under various hurricane and resource constraint scenarios. Ultimately, the risk-informed, resource-sensitive resilience assessments developed and demonstrated in this study are aimed at supporting broader community resilience enhancement efforts, which have gained critical importance in light of escalating climate-driven disasters. Notably, this work is part of a multidisciplinary effort supported by the NIST Center for Risk-Based Community Resilience Planning. IN-CORE—a key outcome of this initiative—is an open-source suite of tools for community resilience modeling, which will incorporate the data compiled and methodologies proposed in this work, thereby expanding its potential to contribute towards bolstering community resilience in the face of extreme coastal events
Exploring Pedagogical Research at Rice
No full textThis presentation summarizes the results of a project that involved designing and implementing search and cross-referencing strategies to discover Rice pedagogical research, disseminate this research, and analyze key features of the research. The study was conducted in Fall of 2024, with findings shared in Spring of 2025
Plastic Waste-Derived CO2 Sorbents and Methods for Enhanced Selectivity and Stability
Full text linkCarbon capture will be a key pathway used by heavy carbon dioxide (CO2) emitting industries, such as petroleum refining, electrical power generation, and cement production, to reduce their carbon emissions. Solid sorbent technology has been touted as the most promising method to attain emissions reduction targets; however, many of these sorbents suffer drawbacks related to their cost, performance, or both. Due to these shortcomings, carbon capture solid sorbents have only just now begun to achieve industrial relevance. Chapter 1 will discuss the carbon capture problem and general sorbent performance metrics. At the same time, plastic waste pollution threatens the environment and acts as another significant risk that must be addressed. Current recycling technologies must be improved to limit the buildup of plastic waste. Here, we develop a pyrolytic method producing a highly microporous CO2 sorbent synthesized from plastic waste-salt mixtures. Diverse plastics with applications as packaging, textile, and construction materials were all addressed in this process. Chapters 2 and 3 examine our results regarding plastic-waste sorbents.
To enhance the CO2 selectivity performance of plastic-derived sorbents, an amine-containing polymer, polyethylenimine (PEI), was added to the carbon sorbent in Chapter 4. To do this, we first modulated the pore structure of the sorbent to become more mesoporous through a liquid-salt templating mechanism. More mesoporosity allowed better accommodation of PEI into the carbon pore network. The PEI-carbon sorbent, although having better uptake and selectivity performance, showed poor stability especially in the presence of oxygen. Oxidative degradation pathways of PEI lead to imine formation and ammonia evolution; these end-products greatly reduce the sorbent’s CO2 uptake capacity. While strategies to reduce oxidative degradation exist through polymer modification, we show here that oxygen-related PEI destruction could be improved by maintaining some adsorbed CO2 during cycling. This adsorbed CO2 acts as a carbamate-protecting group to the amines and prevents continual polymer degradation. In this regard, the formed carbamates prolong PEI-based sorbent lifetimes
6.7 NGL Entreaty on Access and Equity
Full text linkThis entreaty was created as part of The Spirit of Asilomar and the Future of Biotechnology summit (February 23-26, 2025) in Pacific Grove, CA.At the Spirit of Asilomar Summit, conversations about biotechnology’s future took center stage. One of the most important discussions was on Access and Equity, under the "Framing Biotechnology’s Future" theme - focusing on the barriers, needs, and opportunities for making science more accessible, especially for researchers from resource limited or low and middle-income countries. The original Asilomar Conference balanced innovation with responsibility, but failed to address equity. The 'Spirit of Asilomar' organizers were able to address that and position entreaties as a corrective to that oversight. As young leaders in biotech, we wanted to bring our experiences to the table - sharing the initiatives we’ve worked on, the challenges we’ve faced, and the opportunities we see to build a more inclusive and equitable field
The Blue Hour
Full text linkThe Blue Hour is the second movement of Symphony No. 1, a work that explores memory, change, and renewal. Inspired by my experiences in the Gabriela Lena Frank Creative Academy of Music’s Composing Earth Cohort, the symphony reflects on environmental shifts and personal transformation. Growing up in Korea, I was surrounded by vibrant blue skies, but upon returning as an adult, I witnessed the effects of air pollution, with children now coloring the sky in shades of gray. This realization, contrasted with the vivid blue skies I encountered in southern France, became a central theme in the symphony. The work unfolds across four movements, each depicting stages of nostalgia, tension, and resolution.
In The Blue Hour, the symphony’s central melody intensifies, embodying the contrast between cherished memories and present realities. Influenced by Berlioz’s use of recurring themes in Symphonie Fantastique, this movement captures a pivotal moment of reckoning and transformation. Symphony No. 1 as a whole serves as a meditation on the passage of time, illustrating how personal and collective experiences shape our perception of the world. Through its evolving themes, the work ultimately seeks to convey a sense of hope and renewal
Biofabrication technologies enabling vascularization of organ- scale engineered tissues for clinical translation
No full textTransplantable engineered organs could one day offer life-saving treatments for patients with end-stage organ failure. However, producing hierarchical vascular networks that sustain the viability and function of cells within human-scale organs after implantation remains a major challenge. Sacrificial templating has emerged as a promising strategy that could overcome this challenge by confining fabrication stressors to a temporary scaffold that is later removed, leaving behind perfusable channels for convective transport of nutrients, gases, and waste. However, current sacrificial approaches remain restricted by tradeoffs between tissue size, channel resolution, architectural complexity, and biocompatibility. In this thesis, we use biomaterial and three-dimensional (3D) printing strategies to begin dismantling these tradeoffs, advancing sacrificial templating towards organ-scale engineered tissue vascularization. First, we address biocompatibility and scalability challenges by embedding microparticles within sacrificial templates to enable controlled, rapid template evacuation while preserving cellular viability in the tissue parenchyma. We next address resolution and architecture limitations by combining patterned and self-assembled vascularization approaches. In this combinatorial strategy, we additionally improved in vivo host integration by patterning collagen and endothelial cell “tracks” within cell-laden biological matrices, achieving vascular assemblies that were seamlessly connected with host circulation and were perfused with host red blood cells (RBCs). Notably, we demonstrate that tuning biomaterial and cellular compositions modulate the vascularization response once implanted, enabling volumetric vascularization of centimeter-scale tissues. Finally, we develop an injection molding technique that combines the advanced 3D architectural capabilities of high-resolution stereolithography with the enhanced biocompatibility of sacrificial templating. We additionally demonstrate pipelines for fluid flow analyses and 3D characterizations of vascular networks, supporting iterative design improvements towards organ-specific optimal tissue architectures. Collectively, these contributions advance the field of tissue engineering and regenerative medicine closer to the realization of clinically viable, organ-scale engineered tissues
Essays on Education Markets
No full textThis dissertation investigates educational disparities in the matching markets of high school choice and college admissions.
The first chapter, joint with Ph.D. students Victor Delgado and Rui Zeng, studies the spatial inequality issue in high school choice within the context of the centralized system of public high school admissions in Mexico City's metropolitan area (COMIPEMS). The uneven spatial distribution of elite high schools, combined with students' sensitivity to commuting distance when making applications, results in high-achieving students from distant areas being significantly underrepresented in elite schools. By assuming the observed matching is stable in the equilibrium, we estimate student preferences via a parametric Bayesian approach with a Gibbs sampler, allowing for track heterogeneity. Our preference estimates show that students face a quality-proximity tradeoff, which is more salient for the academic track (versus the non-academic track). Counterfactual distance-based subsidies would significantly increase high-achieving students' admission to elite school programs, especially of the academic track. In contrast, prioritization policies alone have negligible effects on assignment outcomes without addressing the demand side or the locations of supply. Our findings call for increasing the supply of elite high schools in distant areas within this centralized assignment system.
The second chapter, coauthored with Professor YingHua He and Professor Jin-Tan Liu, examines the STEM gender gap in Taiwan's university admissions. Leveraging economy-wide data on Taiwan's centralized university admissions and a matching model, this paper decomposes the STEM gender gap into factors of both demand and supply sides. We find that either the demand factors, i.e., gendered preferences, or the supply factors, i.e., gender-specific labor market outcomes after graduation, contribute to a relatively small fraction of the overall STEM gender gap. Most of this gap results from the disproportionately low participation of female applicants in university entrance exams for STEM-related subjects, which are critical for admission to STEM majors. Counterfactual simulations show that some commonly proposed policies can be effective to improve female representation in STEM majors, particularly for the applicants who have taken STEM subject exams. Our findings underscore the importance of earlier-stage interventions, such as encouraging female students to build more STEM-related readiness before applying to university.
The third chapter, collaborated with a group of researchers, uses data from centralized application and admissions systems in ten economies to document differences in gender representation among talented students applying to STEM majors. These ten settings are very different in size, economic development, culture, gender norms, and geographic location. We focus on students scoring in the top 10% of the university admission exams. While we find some significant variation in female representation among top 10% scorers, the gender gap in applications to STEM majors is remarkably stable across settings. The results indicate that closing gaps in academic performance is not enough to eliminate inequality in college trajectories between genders
Engineered probiotics to sense and respond to inflammation
No full textEngineered probiotics represent a powerful new frontier in diagnostics and immunotherapy, with the potential to detect and treat disease directly at the site of pathology. However, practical deployment remains constrained by the need for biosensors responsive to physiologically relevant biomarkers, strategies for controllable therapeutic delivery, and consistent performance within complex host environments. In the first part of this work, we develop a platform for sensing and responding to intestinal inflammation in situ using the probiotic strain Escherichia coli Nissle 1917 (EcN). We establish the transcriptional regulator KynR as a dual-ligand biosensor that detects the inflammation-associated metabolite kynurenine and is selectively inhibited by tryptophan. Structural modeling, biochemical binding assays, and genetic knockout studies reveal the molecular basis of this dual-ligand regulation. Localized cytokine delivery offers a strategy to resolve inflammation at its source while avoiding the systemic side effects that limit conventional immunotherapies. To this end, we integrate a YebF-based protein secretion system into EcN and construct a closed-loop genetic circuit that links biosensing to therapeutic cytokine release, advancing the development of autonomous microbial theranostics.
In the second part of this work, we engineer a hydrogel encapsulation platform to enhance oral delivery and in vivo performance of probiotic biosensors. This system preserves bacterial viability, limits off-target dispersal, and enables robust diagnostic function in the gastrointestinal tract. We validate the approach by combining it with a previously characterized bacterial biosensor of intestinal inflammation in a rat model of colitis. Encapsulated bacteria remain viable post-transit and report disease severity with high fidelity. To improve safety, we embed UV-absorbing nanoparticles within the hydrogel matrix to enable targeted sterilization of the capsule surface without compromising internal bacterial viability. We further reinforce the hydrogel with a polymer network that improves biocontainment. Together, these technologies establish a foundation for safe, programmable, and responsive living therapeutics with diagnostic and therapeutic capabilities suited to complex host environments
Enslaved Images: Gregory of Nyssa and the Discourse of Slavery, Mastery, and Liberation
No full textIn the context of late ancient Roman slave society, Gregory of Nyssa stands apart because of his rejection of the practice of owning slaves in his Fourth Homily on Ecclesiastes. He argues that owning slaves is fundamentally immoral because it upsets the natural order of creation, where human beings are only subject to God and not each other. For Gregory, human beings are the rational image of God and are entitled to rule over creation under the supervision of God. Therefore, in the eyes of Gregory, the practice of owning of slaves is a prideful challenge to the sovereignty of God and the freedom of humanity as images of God.
While Gregory articulates a wholesale rejection of slavery in his Fourth Homily on Ecclesiastes, the situation he presents in his hagiographical texts is more nuanced. In The Life of Macrina, his elder sister establishes a monastic community made up of her former slaves. Gregory’s literary depiction of Macrina illustrates a tension between Gregory’s anthropologically motivated rejection of the practice of ownings slaves, and his depiction of Macrina as a social exemplar who perpetuates aspects of the Roman slave-master relationship in her monastic community.
My central argument is that we can only understand this tension between Gregory’s rejection of slave owning practice and his idealized social model’s interface with the slave-master relationship dynamics of late ancient Roman society through a careful textual analysis of his theological anthropology, his idealized social models, and his relationship to Care of the Self as articulated by Michel Foucault.
Informed by Gregory’s rejection of the practice of owning slaves in his Fourth Homily on Ecclesiastes, I take the position that theological anthropology is the focus of Gregory’s argument against the practice of owning slaves. For Gregory, humans are beyond enslavement because they are made in the image of God.
In Chapter One I examine the text of Gregory’s Fourth Homily on Ecclesiastes, alongside his anthropologically oriented texts, On the Human Image of God and On the Soul and the Resurrection. I establish a detailed understanding of Gregory’s theological anthropology, the human image of God. This forms the foundation of Chapter Two’s examination of The Life of Macrina, in which Gregory’s depiction of Macrina’s formation of a monastic community is still governed by the logics of the Roman slave-master relationship. The social ideal presented in The Life of Macrina fails to create the conditions which afford all individuals the autonomy which Gregory defends in his Fourth Homily on Ecclesiastes.
From here I move into a study of The Life of Moses, which Gregory uses to articulate his beliefs that the telos the human being is an infinite eschatological approximation to God. In Chapter Three, an analysis of this text helps us to understand the central tension between Gregory’s claims in his Fourth Homily on Ecclesiastes and The Life of Macrina by highlighting the ways by which the structure of the literary Macrina’s ascetic community inhibits Macrina’s former slaves from reaching that telos.
I then turn to the reception of Gregory’s writings on the practice of holy virginity in the works of Michel Foucault as Foucault theorizes Gregory as part of a transhistorical lineage of thinkers who advocate for the practice of Care of the Self. In Chapter Four, I discuss how Gregory of Nyssa and Michel Foucault’s theoretical models serve as a cautionary tale for contemporary scholars. Both thinkers do not sufficiently account for the limited conditions of agency in their systems that bar enslaved persons from taking up the practices of self-formation by their own volition. It is here that the tension between Gregory’s theology of freedom and his social context becomes clear. Although Gregory argues that all humans are inherently free, the social conditions under which his hagiographical role models achieve perfection are unattainable for enslaved persons. On the one hand, Gregory advocates that all humans, as images of God, are meant to be free and able to shape their lives in relation to God. On the other hand, Gregory is bound by the slave-owning logics of his time and does not articulate social ideals that escape the model of the Roman slave-master relationship