VictorJuiz/thesis huggingface dataset:
Silicon carbide on insulator quantum photonics with color centers
Keywords: Electrical Engineering.

Color centers --- crystal defects that act as artificial atoms trapped in the solid state --- are contenders for realizing network-based quantum computation. An outstanding challenge has been the integration of color centers into scalable nanophotonic circuits, a prerequisite for efficient entanglement generation between the nodes of a quantum network. Silicon Carbide (SiC), a material traditionally used for abrasives, LEDs and transistors, has the potential to realize such circuits in a wafer-scale, CMOS-compatible platform. However, material fabrication challenges precluded the realization of high-quality SiC photonics. We overcome these limitations by developing new nanofabrication techniques and establish SiC as a high-performance classical photonics material. This development of classical photonic devices in SiC constitutes the first part of this dissertation. Then, we adapt the classical photonics techniques to fabricate devices that host coherent color centers, to demonstrate the basic building blocks of quantum networks based on color centers in SiC photonics. We isolate coherent single emitters in SiC photonic cavities, observe near-unity emitter-cavity cooperativity, and demonstrate superradiance of a pair of color centers in a single microresonator. Taken together, these results suggest that SiC is a candidate for closing the long-standing ''classical-quantum photonics gap'', characterized by a large disparity between the excellent performance of classical photonic devices and comparatively non-scalable and inefficient performance of the quantum-photonic counterparts. In the final part of the dissertation, we discuss electrical control of single color centers in SiC, a key element of the realization of homogeneous, scalable qubits compatible with large-scale, foundry-fabricated color-center quantum circuits
Simulating exoskeletons to assist walking : tools and applications
Keywords: Mechanical Engineering.

Wearable robotic exoskeletons provide a promising opportunity to improve human mobility. Recent advances in assistive technology have produced reductions in energy cost of walking, but exoskeleton design can often be a time-consuming and unintuitive process. Musculoskeletal simulation is a promising approach for speeding device design by revealing how exoskeleton assistance affects muscle behavior and alters walking motions. However, few studies have yet to effectively utilize simulations for device design, and simulation pipelines are often difficult to recreate and share. This dissertation work includes three projects aimed at developing better simulation tools and using them to design exoskeleton assistance. First, my labmate Chris Dembia and I created OpenSim Moco, a flexible software package that makes it easy to create simulations for biomechanics research using optimal control. Second, I used simulations to show that exoskeletons that assist multiple joints can effectively reduce the metabolic cost of walking using a simplified control strategy. Finally, I used simulations to reveal how exoskeleton torques affect the motion of the center of mass during walking. This work can be used by designers to make informed decisions when developing exoskeleton devices to reduce metabolic cost or improve walking stability. The simulations and software I created are freely available for other researchers to build upon and to accelerate future work
Single-Cell Profile of Human Corneolimbus Reveals Cellular Diversity and Novel Putative Stem Cell Markers
Keywords:  Department of Biology
Biology
Single Cell Sequencing
RNA Sequencing
Cornea
Limbus
Stem Cell
Transcriptomics
Ocular Surface
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Thesis

The cornea and limbus compose the regenerative portion human ocular surface, whose function is critical to maintain clear vision. We present one of the first transcriptomic profiles of the human corneolimbus using single-cell RNA-sequencing data. Our data shows significant cellular diversity, with multiple distinct cell clusters representing multiple cell types. Expression of established biomarkers for differentiation, including KRT12, were higher in central corneal cell types versus limbal epithelia, potentially representing more differentiated and senescent states. The limbal epithelial clusters expressed known progenitor biomarkers, such as KRT14, KRT15, and ITGB1, but also expressed newly identified cell growth, migration, differentiation, and proliferation pathways. We identified SLC6A6 and TMEM158 as novel markers for transit amplifying cells in maintaining the limbal stem cell niche. Furthermore, we identified C7, SELE, and TCIM as novel markers specific to limbal stem cells. For all tissues, we utilized CytoTRACE, a novel computational framework that predicts differentiation state from the number of expressed genes per cell, to identify, in an unbiased fashion, stages of progenitor cells. This transcriptomics resource provides the first functional human ocular surface single-cell profile, serving as a foundation for future stem-cell based vision loss therapies.
Snapshot hyperspectral polarization imaging
Keywords: Electrical Engineering.

Wavelength and polarization are fundamental properties of light that are widely used in astronomy, biology, geology, metrology, and other scientific applications. Standard color cameras are insufficient for wavelength and polarization measurements; specialized hardware is required. Existing solutions operate by scanning over a scene or changing filters for wavelength and polarization -- a slow, time-consuming process. We present a system that can acquire an image and its spectrum and polarization at every pixel with a single image exposure. This snapshot hyperspectral polarization camera has an image resolution of 40 x 30 pixels, samples wavelengths from 400 -- 700 nm in increments of 15 nm, detects both linearly- and circularly-polarized light, and costs less than $1000. I also present a Mueller spectropolarimeter, a tool capable of a complete polarization and wavelength analysis of a 100 mm semiconductor wafer. The compact size, low cost, and minimal data post-processing required of the system makes it suitable for high-speed scientific measurement and remote sensing
SNEAD: Solving Nash Equilibria with Adversarial Deviation
Keywords: Algorithms
Game theory
Adversarial
Optimization
Numerical analysis
Convex functions
Nash Equilibrium
Nash Equilibria
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Thesis

We present SNEAD, an extension of an algorithmic framework by McKelvey (1998) under which one can reduce the problem of finding Nash equilibria in finite games to a tractable unified optimization problem. Specifically, we adapt the method to tractably optimize continuous-strategy games and improve asymptotic running time over finite-strategy games. We further prove that convergence of our algorithm to zero loss guarantees a Nash equilibrium in quasiconcave games. Experimentally, our algorithm achieves state of the art performance on a variety of games, even in the face of high-dimensional, complex payoff functions. Finally, we provide supplementary theoretical frameworks which further adapt SNEAD to locate symmetric equilibria or subgame-perfect equilibria with novel algorithmic efficiency.
SOBREVIVIENDO DETRÁS DEL SUEÑO AMERICANO: LATINO IMMIGRANTS IN THE COVID-19 CRISIS
Keywords: COVID-19 (Disease)
Health disparities
Latino Immigrants
Latinos
Immigrant communities
Latinx Communities
COVID-19 (Disease) > Economic aspects
COVID-19 (Disease) > Prevention > Social aspects
Transnational networks
Undocumented Latinos
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Thesis

Over the past two years it has been evident that Latino immigrants in the U.S. have been notably impacted as a result of the health and economic crises resulting from the COVID-19 global pandemic. Since the start of the pandemic, it has been reported that higher rates of Latino immigrants have had trouble affording basic needs and paying bills as well as maintaining regular work hours and jobs. Further, this group has experienced higher rates of infection, COVID-19 exposure, and hazardous work environments in essential industries. This has been the case while many Latino immigrants, especially those without U.S. citizenship, lack membership to health insurance. Through a close look at in-depth interviews of Latino immigrants conducted after the start of the pandemic, this paper adds perspective to these pandemic-related developments. This report (a) captures ways in which networks that transcend borders have provided a sense of community and support but also created anxiety in the lives of Latino immigrants over the past two years, and (b) brings to light how the pandemic has exacerbated and exposed health and economic social inequities for certain Latino immigrant communities.
The social choreography of rape : race, gender, sexuality, and sexual violence in queer performance
Keywords: Theater and Performance Studies.

This project is a queer of color critique of Emma Sulkowicz's durational performance art piece Mattress Performance (Carry That Weight) (2014-2015), Hannah Gadsby's standup show Nanette (2018), Wanda Sykes' comedy special Sick and Tired (2006), Lucía Puenzo's film XXY (2007), and Lisset Barcellos' motion picture Both (2005). Via these examples of queer performance and cinema, I argue that rape is a socially choregraphed phenomenon. The social choreography of rape speaks to the role that rape (as an act and an idea) plays in the ways that people are socialized to move (including both bodily movements and movement in and through the world). The concept of rape, particularly myths about rape, compels people to "contort and comport their bodies" (62), in Imani Kai Johnson's words, to produce and uphold a particular social order, an order structured by white cishetero patriarchy. These socialized movements are evident in and reinforced by day-to-day experiences as well as the aesthetic movements and social dynamics within artistic performance. Reference: Johnson, Imani Kai. "Battling in the Bronx: Social Choreography and Outlaw Culture Among Early Hip-Hop Streetdancers in New York City." Dance Research Journal, vol. 50, no. 2, 2018, p. 62-75
Social Determinants of Perception: Investigating the Role of Key Sociodemographic Variables in Self-Perceived Vaping Risk
Keywords: Risk perception
Electronic cigarettes
Vaping
Nicotine
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Thesis

E-cigarette use has increased dramatically in the United States over the past decade. Risk perceptions play a strong role in the likelihood of undertaking risky behaviors, including use of e-cigarettes. However, there is a dearth of understanding regarding the various factors associated with risk perceptions of nicotine e-cigarettes. In particular, despite some demographic differences in e-cigarette use, we know little about how e-cigarette-related perceived risks vary by demographic variables. The aim of this study was to identify differences in perceived risk of nicotine e-cigarettes among different sociodemographic groups. An online Qualtrics survey of individuals (N = 6,131) in the United States between the ages of 13-40 was conducted to examine patterns and predictors of e-cigarette use. Surveys queried participants on both sociodemographic variables such as race/ethnicity, gender, LGBTQIA+ status, and financial comfort; vape ever/never-usage; and perceived risk of various nicotine devices. Findings showed that perceived risks of e-cigarette use was lower among current e-cigarette users (defined as any e-cigarette use in the past 30 days), Black and Latino groups, those aged 21-24, and non-binary individuals. The findings of this study suggest that greater focus should be placed on addressing certain sociodemographic groups’ risk perceptions towards e-cigarette devices as these groups may be the most vulnerable to future use. There is a need for more research on why these groups experience a lower perceived risk and the degree to which these pressures may manifest in other risky behaviors.
The social, technical, and musical construction of deafness in Japan
Keywords: East Asian Languages and Cultures.

This dissertation explores the historical intersection of D/deafness, music, and technological and media spectacle in 20th century and contemporary Japan. Each chapter in this dissertation is focused on a different case study in which different actors attempted to delineate specific expectations of D/deafness, often through holding public musical events. Chapter 1 covers hearing aid manufacturers and public music performances after 1945. Chapter 2 explores non-commercial assistive technologies and public events held by deaf school teachers and cyberneticists in the 1950s and 60s. Chapter 3 traces the development of sign language musical performance from the 1960s to the 2000s. Finally, Chapter 4 follows the rise and fall of Samuragōchi Mamoru from the 1990s to the 2010s, who built a successful public persona as a "miracle" deaf composer of symphonies. In each case, I ask: whose interests are represented in these musical events? What kinds of technologies and forms of media are being mobilized, and to what purpose? What can they tell us about sociopolitical struggles to define Deafness? Ultimately, I argue that examining these technological, cultural, and musical events enhances our understanding of similar technological and cultural initiatives in contemporary Japan and across the globe. These events draw upon and inform academic and popular conceptions of what music and technology can bring to the Deaf body: bringing spoken language and personal fulfillment by prioritizing hearing-centered ideas of what music means and consists of. These mostly hearing stakeholders, however, have not acted unilaterally. Deaf community members have responded to these developments with musical movements of their own, deploying Japanese Sign Language (JSL) in service of Deaf-centered logics of musicality. These different stakeholders continue to exert influence over overlapping and competing domains in Japanese technological development, politics, and popular culture within a post-2020 Olympics landscape
Solid-state structure formation and functional properties of semiconducting polymers and composites for TFTs
Keywords: Chemical Engineering.

Polymer semiconductors (PSCs) have experienced great innovation alongside the development of soft and wearable electronics on account of their mechanical ductility, synthetic versatility, and ease of processing from solution. The design of flexible integrated circuits based on PSCs relies on an understanding of PSC solid-state structure formation during deposition from solution. Although many useful frameworks have been developed to describe the behavior of well-studied commodity plastics (e.g. polyethylene, polystyrene), the extension of these descriptions to PSCs, typically comprised of uniquely rigid conjugated backbones and flexible alkyl sidechains, remains a persistent challenge. This dissertation describes the use of complementary characterization techniques to develop a more descriptive picture of solid-state structure formation in single-component and composite solution-deposited thin films of recently reported high-performance PSCs. Specifically, grazing incidence x-ray diffraction, UV-visible absorption spectroscopy, atomic force microscopy, rheology, and x-ray photoelectron spectroscopy measurements are combined. Insights into solid-state structure formation are correlated to functional properties. We investigate (1) the impact of thin-film morphology on thin-film mechanics during tensile deformation and (2) the impact of single-component and composite morphologies on the device performances of strained and unstrained thin-film transistors, which are the basic units of integrated circuits
Some applications of graph limits in probability and statistics
Keywords: Statistics.

In this dissertation, we discuss three different applications of graph limits in probability and statistics. The first part involves the study of atypical structures in canonical random graph models as an application of nonlinear large deviations. Next, we discuss how graph limit theory can be used to address matrix completion problems, where one has to recover a large matrix with lots of missing entries. The last part studies minimax thresholds of signal detection problems under dependence, in particular in the context of Ising models
Some numerical considerations for prediction of laminar-turbulent transition in boundary layers
Keywords: Mechanical Engineering.

Disturbances in an incompressible laminar boundary layer can grow over time and lead to the transition to turbulence. This laminar to turbulent process can be computationally expensive for modern CFD solvers and has led to the emergence of streamwise marching techniques that accurately compute the disturbance growth in the laminar and transition regions at a fraction of the cost. The common streamwise marching techniques in slowly evolving shear flows, however, retain some undesirable limitations motivating the development of a novel marching algorithm presented here and known as the Spatial Perturbation Equations (SPE). The SPE couples the marching of boundary layer equations along with the perturbation equations. This coupling results in an accurate capturing of the mean flow distortion for high-amplitude disturbances; which existing methods have under-predicted. The SPE is also able to capture the growth of linear, multi-modal, and nonlinear growth of time-periodic disturbances once the projection operator is introduced to stabilize the marching procedure. The SPE is able to accurately capture the linear evolution of a Tollmien-Schlichting (TS) wave and the multi-modal transient growth for time-periodic disturbances. Nonlinear interaction is also observed for high-magnitude TS waves. For compressible flow, the laminar to turbulent process also has a major impact on many engineering quantities of interest such as surface heating in hypersonic atmospheric flight. In high-speed atmospheric flight, the so called Mack's second mode disturbances are observed as a common route of transition. Capturing the evolution and growth of the mode can be difficult when numerical dissipation from shock capturing techniques are introduced. Linear stability theory (LST) and streamwise marching techniques are used to estimate the growth of the second mode and compare the growth as predicted from direct numerical simulations. However, the choice of inflow conditions and shock-capturing techniques can have a major influence on the predicted growth. The effect of numerical dissipation is examined and explained for various shock-capturing methods and inflow conditions
Some probabilistic aspects of Yang-Mills
Keywords: Statistics.

This thesis develops some of the mathematical aspects of Yang-Mills theories, primarily in the setting of probability theory. First, we analyze finite gauge group lattice gauge theories at weak coupling, and in this setting compute expectations of Wilson loop observables as well as show exponential decay of correlations for local observables. Then, we shift to working directly in the continuum and analyze the Yang-Mills heat flow with random distributional initial data. Finally, we construct a state space which should support the 3D Yang-Mills measure - for some progress towards this end, we then use the previous results on the Yang-Mills heat flow to make some partial progress towards constructing the 3D Yang-Mills measure as a probability measure on our state space
Some problems in quantitative genetics and modifier theory
Keywords: Biology.

The dissertation includes two parts and is divided into five chapters. The first part (chapters 1-3) involves rigorous analyses of some important quantitative genetic problems with related methodologies. The problems we study can be roughly divided into three categories: genetic nurturing analysis (chapter 1), heritability analysis (chapter 1-3) and the apportionment of human diversity (chapter 3). The methodological tools we use for genetic nurturing analysis and heritability analysis are mainly from traditional population genetics, gene-culture coevolution theory, and modern causal analysis, which is introduced in detail in chapter 1. Chapter 2 gives a more detailed review of the historical background of the issue of heritability and connects that with the latest researches. Chapter 3 forms a systematic review of Lewontin's lifetime contribution in human genetics and addresses some of the related disputes and misunderstandings. The second part (chapters 4-5) deals with some problems in modifier theory, with a focus on the Reduction Principle (chapter 4) and the mode of transmission (chapter 5). Chapter 4 extends the traditional modifier theory and studies whether the Reduction Principle still holds in a more general context, i.e. the null modifier case, where the leading eigenvalue of the dynamical system is 1, or when there can be a stable cycle . Chapter 5 models different structural assumptions about preferential oblique transmission and traces the corresponding evolutionary dynamics
Sophisticated mammalian cell engineering with CRISPR/Cas12a
Keywords: Bioengineering.

The application of CRISPR/Cas systems for programmable DNA manipulation has revolutionized the field of genome engineering. In addition to their use for cutting DNA, nuclease-dead versions of Cas proteins fused to different effectors are a powerful tool for cell engineering and synthetic biology. In this thesis, I will discuss two projects from my Ph.D., both demonstrating how Cas12a can be used for constructing next-generation genetic circuits in human cells. For my first project I developed a split Cas12a protein, which spontaneously re-assembles into a functional gene-activating effector when all components are present. Therapeutic cell engineering, in which cells are programmed to sense and respond to complex disease states, requires integration of information about the cellular environment and execution of a functional response only in response to the specified combination of inputs. By linking the expression of individual components of the split Cas12a system to different input signals, it forms the functional core of multi-input, multi-output logic circuits in mammalian cells. The system is highly programmable and can generate expandable AND gates, as well as incorporate NOT logic by using anti-CRISPR proteins as an OFF switch. For my second project I established a platform for parallel signal recording using a hyper-efficient Cas12a base editor. Biological signal recording enables the study of molecular inputs experienced throughout cellular history, by encoding a transient signal as a permanent, targeted DNA mutation that can be read out at a later time by sequencing. However, current methods are often limited in their ability to scale up beyond a single biologically relevant signal in mammalian contexts. This novel implementation of Cas12a for signal recording provides a powerful platform for scalable recording, demonstrated by the recording of up to four signals in parallel in human cells. This method is plug-and-play with diverse inputs in different cell types, including tumor antigen recording in CAR-T cells. It can also be easily extended for more sophisticated applications, such as time-delimited recording and dual recorder-effector cells. Overall, these two projects demonstrate the utility of Cas-based effectors in complex genetic circuits, for both understand-ing fundamental biological processes as well as constructing smarter cellular therapeutics