VictorJuiz/thesis huggingface dataset:
Multi-scale models of amphiphilic assemblies

Nature utilizes amphiphilic assemblies to compartmentalize different chemical environments, modulate interfacial properties and reaction rates, and create complex materials with mesoscopic order. Many models explain the phase behavior of amphiphiles, but our understanding of the non-equilibrium behaviors of amphiphilic assemblies is limited. There exists a vast and rich space of structural and functional variations unexplored by equilibrium methods and models. A recent set of amphiphilic self-assembly experiments have suggested that non-equilibrium pathways of amphiphilic assemblies are complex and poorly understood\cite{Griffith2014}. In the experiments, assembly of 2-oxooctanoic acid was photoinitiated and eventually yielded monodisperse aggregates of long-term stability. In this dissertation, I explore various states of amphiphilic assemblies and the non-equilibrium processes that interconnect these states in the context of the photoinitiated assembly model system. In Chapter 2, I used molecular dynamics simulations to study structural variations and mechanisms of formation of the early nuclei from aqueous solution. Importance sampling and classical nucleation theory were employed to estimate the rate of nucleation. I found that the kinetics of coaggregation, where a mixture of more than one amphiphilic species, could differ significantly from that of single-species aggregation. Specifically, the participation of a second species could open up new pathways of growth and introduce microscopic phase separation of the two species within the aggregates and as a result modulate the growth rates. In Chapter 3, I computed the solutions to master-equation chemical kinetic models of amphiphilic aggregation pathways. I found that a large critical nucleus size is an important factor that contributes to the production of a narrow aggregate size distribution, a highly desirable characteristic in the preparation of self-assembled nanoparticles. I incorporate the elementary steps of nucleation, growth, and a source of precursor molecules to observe the effects of competing elementary rates on the aggregate size distribution. In Chapter 4, I furthered the development of the charge-frustrated Ising model to represent amphiphilic species with non-zero spontaneous curvatures. I also built in the correct interfacial roughness by using two lattice spacings in the same lattice model.

Advisor: Geissler, Phillip
Smart and Robust Biomedical Interfaces

Wearable biosensing devices are becoming more and more ubiquitous, and new medical devices are being used to relieve previously untreatable diseases. Smart biomedical interfaces such as these depend on some form of device intelligence, enabling local processing of recorded biosignals to perform tasks such as hand gesture recognition or detection of neurological disease states. The devices and the algorithms they employ, however, must be robust to a variety of interferers and confounding factors that often prevent their practical use./nThis thesis descries methods to improve robustness in implantables and wearables through a variety of means, demonstrating them in two different applications. The first part presents the Wireless Artifact-free Neuromodulation Device, or WAND, which enables closed-loop neuromodulation by cancelling self-interference artifacts that normally prevent simultaneous neural recording and stimulation. The second part then describes the FlexEMG system for hand gesture recognition using electromyography, which employs a hyperdimensional computing algorithm capable of incrementally learning hand gestures in a variety of situational contexts such as changing limb positions. These systems have been deployed in realistic animal and human subject experiments that better approximate real-world use to demonstrate the hardware and algorithmic improvements towards robustness.

Advisor: Rabaey, Jan M
Muller, Rikky
Infrastructure Support for Datacenter Applications

Cloud computing enables operators to spin up resources on-demand, and orchestrators enables the automatic deployment of complex distributed applications. As deployment of applications in datacenter environments grows increasingly automated and accessible, the logical next step is to consider how the infrastructure can support the operator in critical configuration tasks./nIn this dissertation, we build and evaluate a number of infrastructure-based approaches that automate a few of these critical configuration tasks. First, we present AutoTune, an orchestrator-based tool that tunes an application's resource allocation in order to improve end-to-end performance and resource efficiency. Next, we describe Privoxy, a system which automatically checks that SQL queries issued by web applications are compliant with operator-defined privacy policies. Finally, we build a trace-driven packet simulator that evaluates how an architectural change to the datacenter networking fabric impacts the training time of convolutional neural networks for image recognition.

Advisor: Shenker, Scott J
Part I: Dearomative Synthetic Entry into the Altemicidin Alkaloids, Part II: Efforts Towards the Total Synthesis of Harringtonolide

Part I: Altemicidin and related Streptomyces-derived monoterpene alkaloids possess, highly-polar, dense azaindane cores as well as potent cytotoxic and tRNA synthetase inhibitory properties. The congested alpha-amino acid motif decorating their presumed ten-carbon iridoid-like core structure has proven both a synthetic challenge and biosynthetic mystery. This work relates the synthetic process which culminated in a distinct and concise synthesis of altemicidin from simple chemical feedstocks. Key chemical findings include the exploitation of dearomative pyridinium addition and dipolar cycloaddition sequence to stereospecifically install the quaternary amine moiety, and a chemoselective molybdenum-mediated double reduction to establish the fully functionalized azaindane nucleus with minimal redox manipulations.Part II: Synthetic efforts to the tropone-containing cephalotaxane natural product, harringtonolide, are disclosed. The synthetic approach involves construction of the 7-6-5-6 ring system through a Diels-Alder-Barbier coupling sequence followed by ring-closing metathesis. Subsequent advancement efforts via oxidation and stereocenter epimerization are reported.

Advisor: Maimone, Thomas J.
Empire of Luck: Trust and Suspicion in Early China

This dissertation proposes a new framework for examining the problem of “trust” (xin) in China’s early empires, from the third century BCE to the third century CE. Much of the current scholarship on trust in early China focuses either on trust as one of the virtues or the problem of personal trust as an organizing principle of imperial institutions. My dissertation brings the ethical and the institutional discussions together. I show that the ethical problem of trust is much more complex than its meaning as a virtue and the institutional problem of trust goes beyond problems of personal trust and favoritism. The dissertation proposes two paradigms to understand debates about trust in early China: (1) the paradigm of the invisible seer; and (2) the paradigm of the visibly blind. In the first paradigm, rulers, courtiers, and thinkers argue that reliable, trustworthy institutions come about by positing the possibility of a view from nowhere, inhabited by the ruler, that surveils and measures all. In that position one is invisible, but nevertheless sees everything. In the second paradigm, it is incumbent upon the ruler or gentleman to be exposed and visible. He assumes that other people are looking at him as a guide for action, so he tries to make himself appear more legible and reliable. At the same time, he works to be blind to the faults and possible deceptions of others. He is visible to all, yet blind to others. These two paradigms concern the distribution of visibility in imperial life. The dissertation further argues that regardless of paradigm, “trust” was set against “luck” and “favor” (xing). Reliable institutions required the elimination of luck. Through an examination of debates about social status and social hierarchy, on the one hand, and amnesty and law, on the other, I show how this struggle against luck—the empire over luck—marked out the limits of both of the paradigms of trust examined in the dissertation.

Advisor: Nylan, Michael
Black Girl Lit: The Coming of (R)age Performances in Contemporary U.S. Black Girlhood Narratives, 1989-2019

Amid the popularity of representations of Black girls in U.S. media over the past thirty years, my dissertation charts how literature, film, television, and social media has helped shape our cultural understanding of what it means to be young, Black, and female in the U.S. I argue that the Black girl attitude is a misunderstood trope. It is not a singular attitude. Rather, the Black-girl attitude is a sequence of gestures and choreographic acts used to survive a moment. Combining extensive research from African American literary studies, Black girlhood studies, and performance and media studies, my dissertation assembles compelling cultural artifacts that call attention to the increasing love for and theft of youthful Black femininity in American culture between 1989 and 2019. My critical framework plays on the term “literature,” truncating it to “lit,” a word that refers not only to the past participle of “light” but also colloquially connotes the brilliance and outstanding nature of the Black girls on which I focus. I argue that to be lit is to be young, Black, and female experiencing the light and shadows that results from life’s euphoria and its withdrawals. I define “lit” as: 1) the liminal space between Black girlhood and Black womanhood 2) the affective spectrum between Black girl joy and Black girl rage. As a result of these “lit” experiences, I assert that Black girls do not come of age, but rather, they “come of (r)age.”/nI delineate four valuable articulations of rage as the foundation for why coming of (r)age is the paradigm shift desperately needed in apprehending how Black girls experience their maturation processes. These articulations include: 1) to become raged upon, 2) to rage against, 3) to become all the rage, and 4) to become enraged. This framework troubles existing notions about the maturation processes of Black girls by highlighting rage as an integral part of their survival as they transition into Black women. In doing so, coming of (r)age provides scholars with the necessary framework for dismantling mediated representations of the “Black-girl attitude” and the “angry-Black woman” tropes. By pivoting away from these antiquated stereotypes to coming of (r)age, we now have new language and groundbreaking knowledge to dismantle the images that pin Black girls as culturally deviant. Through coming of (r)age, mediated representations of Black girls can now be seen as not only culturally relevant, but also culturally vital.

Advisor: Catanese, Brandi
Electronic Structure Modelling of Catalysis and Complex Systems: Theory, Analysis and Application

This thesis contributes to three areas of electronic structure theory: First, chapters 2 to 5 cover the development of energy decomposition schemes based on absolutely localized orbitals (ALMO-EDA). In chapter 2, the second-order Møller-Plesset perturbation theory (MP2) based version of this decomposition scheme is generalized to restricted and unrestricted open-shell. This new method allows to decompose the interaction energy of radical species at the MP2 level. Furthermore in chapter 3, a variational forward-backward (VFB) approach is presented to decompose the overall charge transfer (CT) stabilization energy into contributions from forward and backward donation for the density functional theory (DFT) based ALMO-EDA scheme. The two “one-way” CT states are variationally relaxed such that the associated nuclear forces can be readily obtained. In chapter 4, the DFT based ALMO-EDA scheme is extended to intermolecular interactions in the solution phase by the development of ALMO-EDA(solv); a scheme that allows the application of continuum solvent models within the framework of energy decomposition analysis./nSecond, the performance of second- and third-order Møller-Plesset perturbation (MP3) theory wavefunction methods is probed for non-covalent interactions in chapter 5. The κ- regularization improves the energetics in almost all data sets for both MP2 and OOMP2. Scaled MP3 using κ-OOMP2 reference orbitals provides the most accurate results among all tested methods for non-covalent interactions across all data sets.Third in chapters 6–8, a robust computational model is presented to study mechanisms of molecular catalysts for the CO2 reduction reaction (CO2RR) to CO using DFT calculations. This model is applied and refined by the mechanistic studies of four pyridine based catalysts. In chapter 5, the bipyridine based [Fe(bpyNHEtPY2(H2O)2]2+ system is studied. In chapter 7, the mechanisms of [CoII(qpy)(H2O) ]2+ and [FeII(qpy(H2O)]2+ (with qpy = quaterpyridine) are investigated using DFT calculations to shed light on the contrasting catalytic pathways. In chapter 8, a terpyridine(tpy)-based iron polypyridine complex, [Fe(tpyPY2Me)]2+, is investigated in a combined experimental and computational approach to elucidate the different mechanisms at low and high overpotentials.

Advisor: Head-Gordon, Martin
The Race to Exclude: Residential Growth Controls, Rising House Prices, and Racial Inequality

Housing costs have grown substantially for United States households over the last several decades, and research has identified low rates of housing production as a major cause of this increase. In this dissertation, I first examine the role that race has played in the passage of residential land use regulations designed to curb residential growth, and in the effects of these regulations on housing production. I find that cities that were Whiter than their surrounding metropolitan area were significantly more likely to pass residential growth restrictions, consistent with theories that residential growth restrictions spread in the United States in the post-Civil Rights era as a way for residents of predominantly White cities to enforce racial residential segregation. However, I find no evidence that residential land use regulations have a stronger effect on housing supply. Finally, I demonstrate that rising house prices widen White-Black wealth gaps, due to White-Black gaps in both homeownership and house values. This dissertation contributes to a growing literature in the social sciences that identifies how housing policy in the United States has perpetuated various forms of racial inequality.

Advisor: Fligstein, Neil
Classical and Quantum Aspects of Black Holes and Spacetime

Understanding the microscopic structure of black holes and, more generally, of arbitrary spacetime regions, is one of the fundamental problems of quantum gravity. The holographic principle suggests that the information content of a spacetime region is encoded in degrees of freedom on the boundary of that region. To this aim, progress in AdS/CFT suggests that the emergence of spacetime from boundary degrees of freedom entails a deep connection between gravity and entanglement. In this thesis, we attempt to gain insight into this problem by following two different approaches. A particularly important step towards understanding the emergence of spacetime is explaining the origin of black hole entropy. Given that black holes are subregions of spacetime, a ``bottom-up'' approach to black hole entropy would first require understanding the gravitational degrees of freedom on the boundaries of subregions, at both the classical and quantum levels. A particularly powerful way to shed light on these degrees of freedom is by characterizing the symmetries and charges of gravitational theories with internal boundaries. In the first part of this thesis, we primarily focus on this question at the classical level. We start by considering subregions behind causal horizons, which we treat as null boundaries of the spacetime. We then extend the analysis to causal diamonds. We apply this formalism to event horizons, using the algebra of charges to derive the entropy of a black hole. Lastly, we study the measurability of gravitational charges at asymptotic boundaries when quantum corrections are included. While the first part of this thesis focuses on the purely gravitational aspects of black holes and spacetime, the second part aims to uncover the profound relationship between these concepts and quantum field theory (QFT). The classic example of this is the quantum null energy condition (QNEC), a novel inequality in quantum field theory relating energy and entanglement which was discovered through the classical focusing theorem in general relativity. We first study the relationship between the QNEC and quantum focusing using AdS/CFT. We then study the QNEC purely using QFT, and show that it is always saturated, which displays a deep connection between energy and entanglement. We also use black hole entropy to derive energy-minimizing states in QFT which are naturally understood in terms of modular flow. Finally, we derive the holographic dual of this modular flow.

Advisor: Bousso, Raphael
Oakland is a Vibe: Blackness, Cultural Framings and Emancipations of The Town

In this dissertation, I examine the ways that developers and Black community organizers in Oakland, California, utilize a situated concept of Black culture to produce value in the city. This value is constituted by a politics of Blackness rooted both in racial capitalism, shifting structures of community care, and their affective articulations. The affective qualities of Black Oakland – which includes a sense of relationality, creativity, and resistance – are understood colloquially as “vibe.” While representations of vibe are mobilized by both developers and community organizations to respectively advance and resist gentrification, I argue that the vibe of the city is constituted by a Black sense of place that cannot be reproduced through capitalist representations of cultural value alone. This study of vibe presents an opportunity to take seriously the invitation of Black geographic scholarship to work at the intersection of poetics and historical materialism by exploring relationality as a site that coproduces racialized space and experience. Where developers leverage notions of vibe to generate value through private investment, Black organizers utilize such representations in order to reclaim the physical space necessary to the very production of vibe. The latter strategy is, I suggest, an enactment of what I call “emancipatory framing,” in which hegemonic framing is mobilized in order to create alternative spaces for liberatory praxes. This dissertation explores vibe and emancipatory framing at three different scales: the Black body, the independent business, and the grassroots collective. I conclude that vibe as a material and metaphorical asset of Blackness, is at the root of contestations over place, and sometimes contradictory imaginaries of freedom.

Advisor: Scott Lewis, Jovan
Control of High-Dimensional Systems with Applications in Transportation

Important control applications in the fields of robotics and transportation frequently involve high-dimensional systems; for example, robots with many degrees of freedom, or groups of connected automated vehicles (CAVs). In safety-critical applications, the system of interest must also meet a complex set of requirements formalized in a control specification. Formal methods for control synthesis are useful in such applications since they partially automate the controller design process, while also providing guarantees that the control specification will be satisfied. However, when the system dimension becomes too large, such techniques cannot be directly applied due to their computational complexity./nThis dissertation focuses on addressing this challenge using hierarchical and distributed control techniques, with an emphasis on applications in transportation. To enable control synthesis for high-dimensional systems, in Chapter 2 we propose techniques for constructing approximate abstractions of a class of interconnected control systems, to be used in a hierarchical control framework. On the application side, in Chapters 3 and 4 we explore the potential for CAVs to improve the efficiency and safety of traffic flows at intersections. For improving efficiency, we discuss how traffic throughput at intersections can be increased by forming vehicle platoons. In particular, this is accomplished using a distributed model-predictive control approach, which is enabled by vehicle-to-vehicle (V2V) and vehicle-to-infrastructure (V2I) communication. For improving safety, we show how safe behaviors can be accurately characterized for certain challenging driving maneuvers, such as unprotected left turns.

Advisor: Arcak, Murat
Laboratories of Power: Federalism and Reform in the American Political Economy

This dissertation studies how the institution of federalism structures policy reform in the American political economy. It amends and expands the classic logic of states as “laboratories of democracy,” which suggests that successful state policy experiments diffuse across the federal system due primarily to mechanisms of learning and healthy competition. I argue that this perspective misses a crucial element of what state policy reforms do—which is to shape the political power of coalitions of organized interests active in the broader federal system./nIn three policy areas, I demonstrate how policy feedbacks on interest group politics operating across the federal system have structured policy reform pathways. First, in the case of rooftop solar policy, I show how solar power installers built their industry by first locating in states with favorable policy terrain, and then leveraged resources they accumulated to influence policy in other states, allowing them to expand into new markets. Turning to marijuana policy, the marijuana industry initially followed a similar pattern, but because of the context of a federal prohibition, industry political efforts soon focused much more heavily on influencing national policy than on spreading legalization state-by-state. I leverage exogenous variation in likelihood of legalization from ballot initiative rules to show that state legalization had a causal effect on support for marijuana policy reforms in Congress. Finally, in the case of charter school policy, I argue that as state-level experiments drove charter growth, charter advocates were able to recruit certain foundations, which saw charter schools as a vehicle for achieving their own education policy goals, as allies. Crucially, foundations used their extensive resources to promote pro-charter policies more broadly than charter school networks and other advocates would have been able to on their own./nBy highlighting the national-level political implications of state-level policy decisions, the dissertation supports the notion that state politics and policy is more consequential than traditional perspectives on federalism suggest, and in doing so, helps to explain why national groups have made such massive investments in state politics in recent years. Indeed, findings suggest that state policy reforms can be a crucial ingredient in building coalitions for (geographically) broader policy change.

Advisor: Pierson, Paul
Schickler, Eric