VictorJuiz/thesis huggingface dataset:
Photometric and spectroscopic studies of spider systems

Some millisecond pulsars (MSPs) form a close binary system with a low-mass companion, where the companion is irradiated by the MSP. Such system are broadly known as 'spiders'. In recent years, several of these systems have been discovered through Fermi LAT and targeted follow-ups. The companion of such system has highly complex atmospheres due to extreme pulsar heating on the front side, their surface heating patterns offers a rich and complex view of the physical system, allowing one to indirectly probe these MSPs. Several of such systems are relatively bright and close, allowing detailed optical and x-ray study. In this thesis, we present numerical and analytical analysis of optical and x-ray emissions from these systems. In our study, we explore the possibility that companion atmospheres are altered due to pulsar irradiation as well as magnetic activity, thus the atmosphere might exhibit phenomena like heat circulation, diffusion or local increase in surface temperature through spots generated through magnetic activity. Through this more detailed modeling of optical and x-ray emissions, we estimate important parameters of the system, including the pulsar mass, and find that the spider systems are ideal for search of heavy neutron stars, potentially providing excellent constraint on the neutron star equation-of-state

Keywords: Physics.
Advisor: Romani Roger W. (Roger William)
Blandford Roger D.
Macintosh Bruce
Photonic computing architectures for classical and quantum information processing

As progress in traditional electronic computing systems approaches fundamental physical limits, we must explore alternative approaches for further growth in computing power. Photonics is a promising hardware platform for many emerging computing technologies, including optical neural networks and quantum computation. In this thesis, I will present several novel designs for light-based computing systems. First, I will discuss several advancements we have made in nanophotonic neural networks, including design and experimental realization of electro-optic nonlinear activation functions, and architectures and initialization routines for programmable linear optical devices. Next, I will present two novel schemes for quantum information processing: a programmable photonic gate array which can be dynamically reconfigured to prepare any quantum state, and an architecture for an optical quantum computer which can perform any calculation using only a single directly controllable qubit. Finally, I will discuss a design for a photonic quantum emulator capable of simulating the dynamics of a broad class of Hamiltonians in lattices with arbitrary dimensions and topologies

Keywords: Applied Physics.
Advisor: Fan Shanhui
Safavi-Naeini Amir H.
Solgaard Olav
Phototoxicity of sunscreens to sea anemones and corals

Reports of sunscreen toxicity to corals have raised concerns about the impacts of sunscreens released by ecotourists on corals already weakened by global stressors. This has led to bans on sunscreen ingredients in several jurisdictions with reefs including Hawaii and the US Virgin Islands. However, the toxicity mechanism(s) are not understood, raising questions about the bans, and hindering development of safer sunscreens. This thesis presents research on the phototoxicity of several common sunscreen ingredients to sea anemones and a mushroom coral. Surprisingly, while sunscreens are designed to protect from photo-oxidation by ultraviolet (UV) light, oxybenzone, dioxybenzone, avobenzone and homosalate sunscreens became toxic under UV light, inducing mortality in anemones. Oxybenzone sunscreen, was metabolized in the anemones and corals into glucoside conjugates, which were strong photo-oxidants. Algal symbionts living inside the animals partially protected them by sequestering the sunscreens and their metabolites, suggesting that corals "bleached" by rising seawater temperatures may be at particular risk from sunscreens. These results should help guide research, regulation and design of safer sunscreens, aiding reef conservation efforts

Advisor: Mitch William A. 
Boehm Alexandria
Luthy Richard G.
The physical interactions of magmas and host rock : applications to conduit collapse, transcrustal melt storage, and caldera formation

Many physical models of volcanic processes assume that the host rock is a somewhat passive participant in the volcanic system. For example, conduit flow models often assume the presence of a mechanically stable conduit of unchanging geometry; traditional geodetic models often assume that liquid melt is stored in large reservoirs that can generate elastic deformations of the surrounding crust, but physical models of crustal behavior beyond linear elasticity are generally not considered. In this thesis, I seek to push back on this assumption and explore several ways that the host rock can become an active participant in determining volcanic behavior. In Chapter 1, I show that over the course of an explosive eruption the stress distribution along the conduit wall can evolve, and this changing stress distribution can lead to failure of the conduit wall rock. I further show under which conditions this failure is likely to lead to wholesale failure and slumping of the conduit wall along normal faults, a mechanism which might lead to the termination of an explosive eruption. Chapter 2 considers the failure of host rock during large caldera forming eruptions. I use a modern, mesh-free numerical method, Smoothed Particle Hydrodynamics (SPH), to model the development of caldera ring faults and collapse of the caldera block. This model shows that the development and orientation of ring faults depends in predictable ways on the constitutive model of the host rock, and raises important questions about the validity of sandbox analogue models of caldera collapse. Finally, in Chapter 3, I explore recent ideas about how magmas are stored within the host rock in a ``transcrustal" storage system. I show that proper accounting of a transcrustal magma mush in geodetic models can lead to dramatic effects on predicted surface displacements and calculation of quantities of interest, such as volatile content or inferred chamber volume change

Keywords: Geophysics.
Advisor: Segall Paul
Dunham Eric
Suckale Jenny
Physics-based imaging system simulation : validation and applications

The color technology invented by James Clerk Maxwell in 1855 and implemented by Thomas Sutton in 1861 is the basis of modern color imaging. Maxwell fully appreciated the significance of Thomas Young's trichromatic theory of perception, and he used this knowledge to design an imaging system. The insight of trichromacy remains central to modern imaging, but the specific imaging technologies are unimaginably faster, higher quality, and portable. In the modern age, components in a new imaging system are expected to work smoothly with each other. These advanced imaging systems have a very complex design, and building such systems requires extensive prototyping, which can be time-consuming and costly. Any part of the work that can be done using software simulation can speed the design and optimization process. The "Image Systems Engineering Toolbox" (ISET) is a tool for system simulation. The system simulated the physics of scenes, how the light propagates through optics, and how the irradiance was converted into electrons by sensors. Different post processing algorithms can be applied on the simulated raw image sensor data. The work in this dissertation evaluates the new extensions of the ISET platform and demonstrates the benefits of using the physics-based end-to-end simulation tools that are available in ISET for developing next generation of imaging systems for varies applications

Keywords: Electrical Engineering.
Advisor: Wandell Brian A.
Solgaard Olav
Wetzstein Gordon
The physiological underpinnings of young children's learning and school engagement

This dissertation examines how young children's physiological response to acute and chronic environmental challenges is related to their cognitive skills, self-regulation, and school engagement during the preschool and kindergarten period. I used a three-paper approach. Paper 1 revealed significant interactive effects of hair cortisol concentrations, an index of chronic physiological stress regulation, and family wealth on preschoolers' cognitive skills in rural Pakistan. Paper 2 demonstrated that among kindergartners in the US, highly reactive, subordinate children showed positive change in school engagement, whereas highly reactive dominant children showed negative change in engagement across the school year. Paper 3 illustrated that in the US, kindergartners with lower levels of observed self-regulated behavior showed sudden decreases in parasympathetic activation after a critical feedback task, suggesting that this post-task period was physiologically challenging for them. These findings underscore how physiology can reveal which environments are most optimal for different children's learning

Keywords: Education.
Advisor: Domingue Ben
Obradović Jelena (Education professor)
Reardon Sean F.
Pick your poison : assessing dietary preference & alkaloids in South American poison frogs

Poison frogs (Family Dendrobatidae) are native to Central and South America, and many carry small molecule alkaloids in their skin for defense against predation. These chemical defenses are acquired through their diets, but dietary prey availability and consumption have never been directly compared. In order to fill this gap, my dissertation work takes an integrative approach to understand which arthropods dendrobatids consume and what motivates them to do so. We found that leaf litter of forest and pasture habitats differed significantly in ant community structure and that forest and pasture frogs (Oophaga sylvatica) differed significantly in diet and alkaloid profiles.. Finally, ant species composition of frog diets resembled the surrounding leaf litter, but diets were less variable, which suggests that frogs tend to consume particular ant species within each habitat. Our next study's results validated our previous study's findings, as frog alkaloid content and ant consumption and availability all differed between the five localities. Further, we compared the diets of a sympatric and non defended, cryptic Dendrobatid species, Hyloxalus infraguttatus, to those of Oophaga sylvatica and found that defended O. sylvatica eats more ants and mites. Overall, our findings suggest that poison frogs have dietary preferences for certain ants. Finally, supplemented our field-based chapters with lab-based Chapter 4, where we conducted dietary preference assays in a controlled laboratory setting, along with nutritional evaluations of ecologically relevant prey items (ants, beetles, flies, larvae). We used Dyeing Poison frog (Dendrobates tinctorius) to test how prior alkaloid consumption and prey traits (size, taxon) would influence dietary preferences, and found that frogs preferred interacting with small prey items. Taxonomic prey preferences were further tested as we experimentally increased their chemical defense load by feeding frogs decahydroquinoline (DHQ), an alkaloid compound similar to those naturally found in their diet. Contrary to our expectations, overall preferences did not change during alkaloid consumption. Finally, we assessed the protein and lipid content of the prey items used in our assays, and found that small ants have the highest lipid content while large larvae have the highest protein content. Our mutually informative studies provide insights into the evolutionary history of diet-acquired defenses by combining manipulative, individual-level behavioral data with ecologically relevant field studies. More generally, these studies have broader implications for our general understanding of community ecology and the evolution of adaptive traits

Keywords: Biology.
Advisor: O'Connell Lauren A.
Dirzo Rodolfo
Gordon Deborah (Deborah M.)
Peay Kabir
Planning and control for multi-robot manipulation and assembly in unstructured environments

While humans and other social animals (such as ants) can easily form teams to move heavy or bulky objects, robots struggle in collaborative manipulation tasks, especially under partial information about the environment or the object being transported. This thesis looks to enable flexible, scalable coordination in robot teams, looking toward a future where robots not only move objects together, but also work together to perform autonomous assembly of structures and manufactured goods. In Part I of this thesis, we investigate methods for collaborative manipulation and grasp synthesis under considerable uncertainty about the object's size and physical properties. Using tools from nonlinear control, we present a novel decentralized adaptive controller for collaborative manipulation that allows a team of robots to asymptotically track a desired trajectory in SE$(3)$. We also study the problem of synthesizing robust grasps of objects using only RGB images; we present a method which leverages a novel learned object representation to generate risk-sensitive grasps which can reason about the ambiguity inherent in the object shape. In Part II of this thesis, we turn our attention to the problem of multi-robot assembly planning. We show this problem can be posed as a mixed-integer linear program, which can be solved to global optimality using commercial solvers, and present effective heuristic strategies which can be computed quickly. Further, we present a method that uses supervised learning to accelerate the online solution of general mixed-integer convex programs using offline data. We show our method provides significant speedups over commercial solvers in a variety of robotics problems, including grasp selection and task allocation

Keywords: Mechanical Engineering.
Advisor: Gerdes J. Christian
Schwager Mac
Bohg Jeannette
Platform design in educational contexts

Educational platforms have grown increasingly important as learning occurs in digitally mediated environments, and this growth has only been accelerated by the COVID-19 pandemic. My dissertation explores three domains of platform design in education research. I frame my work with the conceptual tools of operations research and industrial engineering. In the first paper I cast online learning as a blending/mixture problem. I explore the relationship between video playback speed and student learning outcomes in massive open online courses. Using an experimental design, I present the results of a pre-registered study that assigns users to watch videos embedded in courses at either 1.0x or 1.25x speed. I find that students who consume temporally accelerated content are more likely to get better grades in a course, attempt more content, and obtain more certificates. I also find that when videos are sped up, students spend less time consuming videos and are marginally more likely to complete more video content. In the second paper I examine postsecondary degree completion as a production scheduling problem, and build a forecasting toolkit to identify and anticipate students' career trajectories. Using transcript data capturing the academic careers of 26,892 undergraduates enrolled at a private university between 2000 and 2020, I describe enrollment histories using natural-language methods and vector embeddings to forecast terminal major on the basis of students' sequences of enrolled courses early in their college careers. I find (I) a student's very first enrolled course predicts major thirty times better than random guessing and more than a third better than majority-class voting; (II) modeling strategies substantially influence forecasting accuracy; and (III) that course portfolios vary substantially within majors, raising novel questions what majors mean or signify in relation to undergraduate course histories. In the third paper I deal with the issues of course shopping and course staffing as an optimal stocking problem. I describe the phenomenon of course shopping at scale at a large private research university. At this case institution shopping has increased over the past ten years. There also is substantial variation in shopping behavior by gender and academic tenure. Aided by the natural language methods developed in describing academic course histories, I predict which students will retain their enrollment decisions. I find that machine learning algorithms are both fairer and more efficient in this instance than more traditional rationing mechanisms that are used at many institutions

Keywords: Education.
Advisor: Domingue Ben
Bettinger Eric
Haber Nick
Stevens Mitchell L.
The poetics of organic damage : discursive and aesthetic functions of monstrosity and monstrous bodies in early Soviet 'mad science' literature

This dissertation examines the use of a particular type of imagery as a literary device and discursive metaphor in a series of literary works about the scientific transformation of the body from the Soviet 1920s and 1930s. The imagery in question, what I call broadly the imagery of monstrous or altered bodies, includes human bodies warped or transformed by disassembly, reassembly, atrophy, augmentation, and/or amputation. I argue that such imagery serves as a potent metaphor to writers in this time not only because of certain historical conditions, but also because of early Soviet transformation discourse and the role that the body and the biological sciences played in it. These writers, I argue, use the mechanisms of scientific transformation both as discursive markers to interrogate the Soviet transformation project and as metaphorical inspiration for their own literary practice. This dissertation seeks to articulate and elaborate a series of linguistic and aesthetic strategies that allow writers to investigate the aesthetic and ethical potentials of transformation in early Soviet rhetoric and constitute what I call a poetics of organic damage

Keywords: Slavic Languages and Literatures.
Advisor: Greenleaf Monika
Ilchuk Yuliya
Safran Gabriella
Politics aside : North Africans, Europeans, and the fight to transform postwar Algeria, 1945-1975

This dissertation tells the story of cross-cultural development initiatives and various local and international organizations during a particularly tumultuous moment in the history of France and Algeria: The Algerian War of Independence (1954-1962). This violent war of decolonization pitted anti-colonial Algerian nationalists against French paratroopers sent to defend one of France's oldest overseas territories. In this tense and divisive context, organizations, including the Association of Algerian Youth for Social Action, the Service Civil International, the Service des Centres Sociaux, the French government's High Committee for Youth, and Young Algerian Volunteer Workers, opted to put politics aside and claimed to be politically neutral or to operate outside of politics. During the war and its aftermath, these organizations and their members faced two challenges: first, how to best navigate highly polarized political contexts, and second, how to get Europeans and Algerians to work together to improve Algerian living conditions. These organizations' different approaches to both of these imperatives reveal how actors on the ground interpreted the political and social stakes of development, decolonization, and cross-cultural cooperation at the twilight of the French Empire in Africa

Keywords: History.
Advisor: Daughton J. P. (James Patrick)
Davis Muriam Haleh
Roberts Richard L.
Polymer-based vaccine delivery for enhancing immunity

Vaccines remain one of the most effective medical treatments to prevent infectious diseases. In modern vaccine design, the co-delivery of a subunit vaccine's antigen and adjuvant is essential for inducing an optimal immune response and the subsequent adaptive immunity that is acquired. Small-molecule Toll-like receptor agonists (TLRa) have been increasingly recognized as promising adjuvants due to their targeted pathways, allowing for specific immune signatures and response. However, the pharmacokinetics/pharmacodynamics (PK/PD) profiles of small adjuvants are often mismatched from large protein antigens due to vast differences in molecular weight. Polymeric-based delivery platforms offer a highly tunable approach for antigen/ adjuvant co-delivery. By conjugating adjuvants to a polymeric nanoparticle, PK/PD can be favorably altered to improve retention and trafficking into lymphoid tissues, while also reducing systemic toxicity. Simultaneous release of vaccine components prolongs the cytokine response profile for higher antibody titers and isotype switching. Further, augmenting the co-delivery platform for sustained release elicits a more robust humoral immunity and improved antibody longevity and breadth. Sustained release, as compared to a traditional bolus delivery, more closely mimics a natural pathogen infection, and as a result of the extended antigen presentation and germinal center lifetime, enables an increased quality and magnitude of antibody response. In this work, we mixed biopolymers with nanoparticles to create dynamically cross-linked polymer nanoparticle (PNP) hydrogels. These PNP hydrogels are supramoleculary crosslinked networks that transiently form and break, simultaneously releasing protein antigens and small-molecule adjuvants in a slow-release manner. Although vaccines are commonly thought of as prophylactic in nature, they can also be utilized in a therapeutic setting. Cancer immunotherapy with vaccines is a promising strategy to overcome the immunosuppressive tumor microenviroment to stage a potent anti-tumor response. Potentiating the immune response with PNP hydrogel delivery increases the short-lived effector T cell populations compared to a bolus-delivered vaccine. Additionally, supplementing the vaccine with a novel immune checkpoint blockade therapy further enhances the increased T cell populations for a robust immune response. In this dissertation, I will discuss polymeric strategies for spatiotemporal control in vaccine design, enabling improved co-delivery of antigen and adjuvant. Extending the co-delivery into sustained delivery further improves humoral immunity for disease protection and cellular immunity for anti-cancer response

Keywords: Bioengineering.
Advisor: Appel Eric (Eric Andrew)
DeSimone Joseph M.
Heilshorn Sarah
Polymer-nanoparticle hydrogels : from fundamentals to biomedical applications

Physically crosslinked hydrogels are an appealing class of materials for biomedical applications including drug delivery, 3D bioprinting, and cell therapies due to their unique mechanical properties, such as injectability. This thesis examines Polymer-Nanoparticle (PNP) hydrogels as one class of these materials that have been found to be effective in biomedical studies requiring minimally invasive injections. We elucidate criteria for the formation of robust PNP hydrogels and highlight key mechanical properties needed for applications. We demonstrate that chemical modifications of the outer corona of the nanoparticles lead to great changes in mechanical properties including extreme extensibility. Using this understanding of hydrogel mechanical properties, we also optimize these materials for the delivery of therapeutic cells for regenerative medicine and immunotherapy applications. We demonstrate the advantages of using PNP hydrogels over liquid saline injections, such as minimizing cell membrane damage during injection and increasing cell retention at the injection site. Leveraging these capabilities, finally we describe the development of PNP hydrogels for the treatment of solid tumors in in vivo cancer models through the improved co-delivery of CAR-T cells and stimulatory cytokines. Overall, this thesis demonstrates that carefully designed dynamic biomaterials enable unique opportunities in biomedicine.

Keywords: Chemical Engineering.
Advisor: Appel Eric (Eric Andrew)
Fuller Gerald G.
Heilshorn Sarah