VictorJuiz/thesis huggingface dataset:
Removing black boxes in materials science : two-component droplet tilings and distributed manufacturing of fibrous media

The interaction of liquids with materials is fundamental to many areas of science, industry, and human health. The first half of this thesis explores how a specific type of liquid (specifically, Marangoni-contracted, two-component liquids) can be used to create a new class of deliberately designed lattice system at the macroscale. The second half builds an experimental context for distributed manufacturing of fibrous materials used in essential products such as face filtering respirators and menstrual pads. Advances in material fabrication have made it possible to produce materials with an increasing range of geometries, including those with no precedent in nature. However, the relationships between geometry and state or the dynamics governing transitions between states in condensed material systems are not well understood and remain difficult to observe. Here, we have developed a system that exploits the properties of two-component, marangoni-contracted droplets to rapidly explore the properties of systems with novel geometries. In particular, the ability to move in response to vapor gradients over long distances enables the observation of the dynamics of many body systems governed by a non-additive potential energy function subject to non-trivial geometric constraints. The resulting systems are highly frustrated and display relaxation dynamics over two-timescales, a characteristic feature of systems with long-ranged interactions. We show further that the system is amenable to control by a global gravitational field, enabling partial reduction in frustration through the implementation of hysteretic annealing. Finally, we show that specific geometric configuration can give rise to non-reciprocal interactions, a property common to many non-equilibrium systems but with few artificial realizations. The availability of many essential products are determined by access to engineered materials. While the production of many materials is highly efficient, this often comes at the cost of robustness, resiliency, and distribution. During the COVID-19 pandemic, production of raw material for personal protective equipment could not quickly respond to surge demand and left many in low and middle income countries without adequate resources. Here, we explored the potential for centrifugal melt spinning for the production of non-woven air filtration media. Meanwhile, access to another essential product, disposable menstrual pads, suffers from many of the same constraints. We develop a mild delignification chemistry for the small scale production of absorbent medium for use in disposable menstrual pads. We show that Agave sisalana, a drought tolerant succulent that can be grown on marginal land, can be treated under mild conditions to yield an absorbent material with an absorption and retention capacity meeting and exceeding performance of absorbents found in commercially available products.

Keywords: Engineering.
Materials Science and Engineering.
Advisor: Heilshorn Sarah
Prakash Manu
Appel Eric (Eric Andrew)
Resilience in the face of trauma : how sexual violence shapes economic well-being

Sexual violence can be physically, emotionally, relationally, and financially devastating, resulting in major disruption to survivors' everyday lives. However, about 70% of trauma survivors will be resilient—defined as maintaining a stable equilibrium in one's everyday life in the months and years following a traumatic event. Given that over half of women will experience sexual violence at some point in their lifetime, my dissertation asks: How are women doing well, despite the sexual trauma they face? I directly intervene in this debate by highlighting the roles that social support and social institutions play in facilitating and constraining survivors' resilience trajectories. I do this by examining the case of sexual violence and economic resilience. In the first paper of my dissertation, I provide a theoretical framework for explaining how economic resilience is empowered and constrained through an integration of micro-level, meso-level, and institutional-level social processes. This integration of a survivor's agency at the micro-level with the social structure in order to be resilient is a social process I term integrated resilience. The second dissertation paper zooms in on resilience in the context of educational persistence. Despite the high rates of sexual violence that school-aged women face, I explain how women are doing academically well through their strategic deployment of institutional support. The third dissertation paper traces how the workplace can be a site of both constraint and empowerment for survivors of sexual violence. In this paper, I show how these constraining and empowering experiences in the workplace shape survivors' future job search processes and occupational destinations. My body of work aims to show not only the harms done to women, but their strength and ingenuity in response to social constraint.

Keywords: Humanities and Sciences.
Sociology.
Advisor: Ridgeway Cecilia
Grusky David
Jackson Michelle
Jimenez Tomas
Resonances and symmetries in photonics

Resonances and symmetries are fundamental concepts in physics. This thesis presents my research on resonances and symmetries in photonics. The first part of this thesis investigates Fano resonances in nonlocal metasurfaces, including their basic principles and potential practical applications such as all-optical edge detection, free-space squeezing, and the generation of light bullets. The second part of this thesis focuses on the internal symmetries of linear photonic systems, particularly Lorentz reciprocity. I propose an extended Kirchhoff's law of thermal radiation applicable to all thermal emitters. I also investigate the impact of Lorentz reciprocity on reflection. I hope this thesis will contribute to a better understanding of resonances and symmetries in photonics and their practical applications

Keywords: Humanities and Sciences.
Applied Physics.
Advisor: Fan Shanhui
Brongersma Mark L.
Fisher Ian R. (Ian Randal)
Responsibility and cooperation

This work begins with methodological issues upstream of traditional questions about moral responsibility, starting with just what the problem of responsibility is and why it matters. Articulating and motivating my interest in the problem shapes and constrains other methodological choices, such as how to delimit the subject matter and how to inquire into it. The approach I develop is functionalist: if we want to understand the nature and value (or lack thereof) of holding one another responsible, we should think about holding one another responsible does -- what needs or interests (if any) it serves; what functions it has in our lives. The answer, I suggest, is that our practices of holding one another responsible function to sustain and promote cooperation: the different ways in which we hold one another responsible function as solutions to different kinds of distinctively interpersonal obstacles that living and working together often face

Keywords: Humanities and Sciences.
Philosophy.
Advisor: Bratman Michael
Briggs R. A.
Dannenberg Jorah
Hussain Nadeem J. Z.
Maguire Barry
Rethinking power dynamics in software tools for artists

Computation has become an essential tool for art and design. Yet many creative software tools limit users to preset options and filters, which may be restrictive for professional artists who have unique goals and workflows. While artists can learn to code to circumvent this preset functionality, the structured and abstract nature of programming is in tension with the exploratory and concrete nature of visual art making. From Photoshop to Processing, tools give artists the power to create, but the designers of such tools also exert power over artists by dictating what is available to them. This dissertation offers three contributions towards understanding, enabling, and questioning power relationships in software tools for visual art. First, through a thematic analysis of interviews with over a dozen professional artists, I show that pre-existing software tools are most powerful when they enable fine grain aesthetic control and adaptable to artists' idiosyncratic workflows, and that artists learn to program their own tools to gain various forms of power. Second, to support visual artists in programming, I present the Demystified Dynamic Brushes (DDB) system. DDB is a creative coding environment that visualizes program information on the ongoing artwork and grounds debugging interactions with stylus inputs, giving artists the power to understand their programs in a way aligned with their existing expertise. Finally, I argue that the traditional way software tools empower their users---through defining abstractions and representations that align with user needs---also disempower them by exerting a ``normative ground'' that structures and limits how users can and should act, think, and express themselves. Backed by interviews with creative practitioners and tool designers, I build a preliminary theory of how power relationships manifest in creativity support tools, and what tool designers can do, both technically and methodologically, to mitigate imbalances in power relationships. Taken together, it is my goal to show that supporting creative practices beyond accomplishing tasks with more efficiency or lower mental load----supporting wonderful creative practices that are unpredictable, emergent, and messy---means taking power relationships---and creative practitioners themselves---more seriously in software design.

Keywords: Engineering.
Advisor: Agrawala Maneesh
Follmer Sean
Landay James
Retinal ganglion cell responses to extracellular stimulation for high-fidelity vision restoration

Future high-fidelity, large-scale electrical brain-machine interfaces will have the ability to restore population-level neural function to treat debilitating sensorimotor conditions. Achieving this will require fine, simultaneous, targeted closed-loop extracellular control of many individual neurons, carefully taking into account their natural physiological properties. Reconstitution of naturalistic neuronal activity in vivo necessitates advances in the engineering of bio-interfacing electrodes, understanding of population-level functional physiology, and mapping of biophysical responses to artificial external current. However, until recently, the electrophysiological exploration of neuronal responses to pulses of extracellular electrical current has been limited to either mostly non-primate cells, aggregated signals from hundreds or thousands of neurons, or peripheral nerve-fiber bundles. Additionally, most detailed explorations of single neuron biophysics have been conducted on cultured neurons with unnatural morphologies and extracellular environments. Using intact pieces of excised retinal tissue as a model system for ease of access, correlatability to therapeutic interventions for patients, and similarity to the cortex, our lab has previously independently characterized the recording and extracellular stimulus response properties of four macaque retinal ganglion cell (RGC) types: ON and OFF parasol and midget cells at a large scale using a densely spaced 512-electrode MEA. My graduate work builds on these initial studies by 1) systematically relating the recorded features of spontaneous activity of four RGC types at different eccentricities to their electrical response properties across dozens of different retinal preparations and thousands of individual cells, exploring the mechanism of this relationship using simulated neural models, and investigating the practical utility of such a characterization for future retinal implant engineering, and 2) generalizing the insights derived from the extracellular probing of macaque RGCs to human RGCs, which demonstrate very similar recording and electrical response properties. This work reveals that RGCs across different macaque and human eyes have near a uniform relationship between activity recording and electrical response properties that depend on broad cellular characteristics such as membrane morphology and ion channel density. It also demonstrates that these properties can be leveraged to aid in retinal implant design--specifically calibration of electrical stimuli--for use in treating acquired blindness. Finally, it implies that similar analyses are possible in various CNS circuits, making high-resolution artificial electrode access to these systems possible

Keywords: Medicine.
Advisor: Chichilnisky E. J.
Baccus Stephen A.
Huguenard John
Mitra Subhasish
Palanker Daniel
Rewiring oncogenic signaling to therapeutic viral activation for treatment of metastatic cancer

Despite recent advances in cancer treatments, improvements to long-term survival in metastatic solid tumors, such as pancreatic or ovarian cancer, remain limited. Current medical therapies suppress growth-promoting biochemical signals or activate immune responses to tumor-associated antigens (TAAs). However, these approaches are limited by toxicity to normal cells that utilize the same signaling pathways or express the same antigens. Previously we developed a method for Rewiring Aberrant Signaling to Effector Release (RASER) to selectively redirect hyperactive ErbB signaling, found in many solid tumors but not normal tissues, to programmable responses. Here in my thesis, I report the engineering of viral vectors that express and are regulated by RASER, resulting in the selective ablation of cancer cells exhibiting hyperactive ErbB signaling. In mice, RASER-restricted vesicular stomatitis virus (VSV) exhibited 10000-fold less toxicity per dose than parental VSV, and 10-fold less than the attenuated VSV-∆M51 variant. RASER-restricted VSV conferred a larger survival benefit in non-immune mouse models of peritoneally disseminated ErbB-hyperactive pancreatic and ovarian cancers. Thus, RASER-restricted viral activation may represent a new approach for treating ErbB-hyperactive metastatic cancers that is independent of adaptive immunity. I also successfully extended the RASER concept to additional signals caused by oncogene mutations including hyperactive c-Met and KRAS and successfully developed Ad and VSV controlled by c-Met and KRAS RASER. With its generalizability and application in vivo, RASER controlled viruses will thus build a completely new type of cancer therapy, in which synthetic proteins are engineered to specifically identify and destroy cancer cells.

Keywords: Engineering.
Bioengineering.
Advisor: Lin Michael Z.
Qi Lei (Professor of Bioengineering)
Wang Bo (Researcher in bioengineering)
Ring-opening metathesis polymerization of 2,3-dihydrofuran

Plastics are critical to every modern industry, but the chemical stability of common polymers causes them persist for decades. As a result, plastics are accumulating in the environment at an alarming rate. To address the growing plastic pollution crisis, new end-of-life strategies must be developed. One important approach is the development of new polymers that can be broken down on demand. These degradable polymers may be converted back into monomers or into building blocks for second-generation materials. This thesis introduces the surprising ring-opening metathesis polymerization (ROMP) of 2,3-dihydrofuran (DHF), a commercial cyclic enol ether. Enol ethers have historically been used as quenching agents in ROMP, reacting rapidly with Grubbs catalysts to form thermodynamically stable electron-rich Fischer carbenes. However, these Fischer carbenes remain competent metathesis catalysts. Using Grubbs catalysts, DHF can be both homopolymerized and copolymerized with common norbornene ROMP monomers. Furthermore, rapid acid-catalyzed hydrolysis enables degradation of enol ether-containing materials. Chapter 1 introduces the challenge of polymer recycling for both thermoplastics and thermosets. Special attention is paid to modern approaches and recently commercialized recycling technologies. The foundation for the discovery of DHF ROMP is also described. Chapter 2 summarizes the synthesis of degradable and depolymerizable polyDHF. Chapter 3 explores copolymerization of DHF with common norbornene monomers. Finally, Chapter 4 describes the use of DHF in ROMP of dicyclopentadiene. In addition to enabling hydrolysis of polydicyclopentadiene thermosets, the unique reactivity of Ru Fischer carbenes suppresses crosslinking in these materials

Keywords: Humanities and Sciences.
Chemistry.
Advisor: Xia Yan
Moore Jeffrey
Waymouth Robert M.
RNA structures in non-coding RNA : from the SARS-CoV-2 genome to S. cerevisiae introns

Structured RNAs play critical roles across the domains of life, whether facilitating viral packaging and replication or regulating complex eukaryotic RNA processing pathways like pre-mRNA splicing. Understanding RNA in the context of its folding can give us a better picture for the mechanism and regulation of these processes, and moreover, this understanding could inform attempts to intervene in these pathways. In the first section of this dissertation, I will discuss the capabilities of computational RNA structure prediction and RNA structure determination. I will highlight our efforts towards evaluating de novo computational prediction methods for RNA tertiary structures, along with our work on building RNA structures in cryo-EM density maps for large RNA or RNA-protein complexes. Then I will focus on our application of de novo RNA structure modeling in making predictions for secondary and tertiary structures in the SARS-CoV-2 RNA genome, providing candidate target regions for diagnostics and anti-viral therapeutic development. In the second section of the dissertation, I will focus on our characterization of the RNA structure landscape in S. cerevisiae pre-mRNA through biochemical experiments and computational prediction. We identify intron secondary structures through transcriptome-wide dimethyl sulfate (DMS) probing experiments, enriching for low-abundance pre-mRNA through splicing inhibition. These data reveal structures bridging splice sites present across yeast introns, along with previously uncharacterized long stems that distinguish pre-mRNA from spliced mRNA. With high-throughput structure-function experiments, we measure the effects of modulating a set of candidate intron structures, finding that some structured elements can increase spliced mRNA levels despite being distal from canonical splice sites, while other structures can increase intron retention. To more deeply interrogate these functional intron structures, we explore the potential protein-binding partners and tertiary structure for a candidate functional structured domain. Our transcriptome-wide inference of intron RNA structures suggests new ideas and model systems for understanding how pre-mRNA folding promotes splicing efficiency and regulation of gene expression. This approach provides a blueprint for computational, structural, and functional experiments that can help dissect the role that RNA structure plays in various biological processes

Keywords: Humanities and Sciences.
Advisor: Das Rhiju
Ares Manuel
Puglisi Joseph D.
Robotic mobility using extendable booms : design, control, and experimentation

Space exploration drives us to push the boundaries of engineering, especially in the fields of robotics and autonomous systems. Innovations such as satellite communication, GPS technology, and advancements in materials science, originally developed for space missions, have significantly enhanced everyday life on Earth. As we aim to tackle increasingly ambitious space missions -- from the Lunar Gateway to Martian colonization to asteroid mining -- the mobility and manipulation requirements of our robotic platforms exceeds current capabilities. Many of these missions involve environments characterized by adverse gravity conditions and sparse footholds that impede traditional means of locomotion. The solution offered by this thesis, ReachBot, provides unique access to previously inaccessible terrain, broadening our capability to make new scientific discoveries and expanding humanity's reach into space. ReachBot realizes mobility in challenging terrain by combining the portability and maneuverability of small mobile robots with the long reach and high force capability of large robots. It does this by merging two technologies with little previous overlap: mobile manipulation robots and lightweight extendable booms. This thesis begins with a discussion of ReachBot's design, optimized via a trade study method to tailor an extendable-boom architecture to mission-specific parameters and objectives. We demonstrate this method by applying it to a Martian lava tube mission, resulting in a final configuration of booms, joints, and sensors that will provide a continuing example throughout the thesis. Subsequent chapters develop models to describe ReachBot's kinematics and dynamics, including a contact model that addresses uncertainties inherent to grasping in rocky terrain. We then incorporate these models into a robust motion planning algorithm to move ReachBot through its environment while maintaining grasp contact. In particular, we leverage optimal control techniques to generate trajectories that maximize the probability of successful execution. Finally, we validate ReachBot's system capabilities, in addition to our modeling and simulation approaches, with a series of hardware experiments ranging from low-fidelity prototypes using tape measures as deployable booms to a mission-realistic field test in the Mojave Desert. Collectively, this thesis lays the foundation for extensive future work on robotic systems using extendable booms; in particular, the tools used for design, modeling, and control will enable the development of extendable-boom robots built to explore complex adverse gravity environments previously inaccessible to robotic or human exploration.

Keywords: Engineering.
Aeronautics and Astronautics.
Advisor: Pavone Marco
Bohg Jeannette
Cutkosky Mark R.