VictorJuiz/thesis huggingface dataset:
Semiconductor technology and circuit techniques for high-performance MHz-range power converters

Conventional power converters contain semiconductor devices switching in the tens to hundreds of kilohertz (kHz) range. Extending the switching frequency to the multi-MHz range brings opportunities to reduce the size and weight of power converters as the energy storage requirements decrease. Additionally, MHz-frequency power converters and amplifiers enable new applications such as plasma generators for semiconductor processing equipment, medical sanitation, and CO2 reforming. Despite these promises and opportunities, building efficient power converters at much higher frequencies still poses a significant challenge. In MHz-frequencies, wide bandgap (WBG) semiconductor devices, such as gallium nitride (GaN) and silicon carbide (SiC), have the potential to improve the performance of these systems as they have orders of magnitude lower specific on-resistance compared to silicon (Si) devices. One of the main issues is the soft-switching Coss losses in WBG devices, which have not been previously well-studied and modeled in the literature, and these losses significantly degrade the efficiency of power converters. We present the measurement results and techniques to characterize the Coss losses in wide bandgap devices, as well as discuss the physical root causes of these losses in SiC power devices. In addition to the Coss losses, effectively utilizing SiC MOSFETs poses a challenge, as designing fast transitioning and low loss gate drivers at MHz frequencies is difficult. As a solution, we develop resonant gate drivers that can drive SiC MOSFETs up to 30 MHz while conserving over five times as much gating power compared to available commercial counterparts. Lastly, we utilize these WBG devices in broadband power amplifier demonstrations suitable for radiofrequency (RF) plasma generation applications at 13.56 MHz. To achieve high performance across broadband, we employ various RF circuit techniques including reactance compensation, phase-switched impedance modulation, and power combining. As a result, these amplifiers showcase some of the highest efficiencies published in the literature, including over 90% across a 4 MHz bandwidth for a 300 W system and over 95% efficiency across 4 MHz for a 1 kW system

Keywords: Electrical Engineering.
Advisor: Rivas-Davila Juan
Perreault David J. 
Plummer James D.
Sensory-Friendly Design in the United States

In the United States, the accessibility of public space design is largely guided by the requirements of the Americans with Disabilities Act, passed in 1990. These criteria largely detail physical accessibility guidelines intended to ensure accessibility of public spaces by individuals with varying physical ability levels. While these requirements undoubtedly have a positive impact on the experiences of people with physical differences, current ADA standards provide little - though not zero - guidance on making spaces accessible for individuals with autism spectrum disorder or other neurological differences which increase sensitivity to sensory stimuli, despite this being a protected disability category as defined by the most recent Standards for Accessible Design published in 2010. As the number of children diagnosed with autism spectrum disorder in the United States increases each year, engineers and architects have the opportunity to further improve accessibility of public spaces to children and adults with autism by incorporating thoughtful sensory design strategies into public design schemes.
This thesis utilizes research on existing accessibility standards with an examination of the intention of public space design to include and exclude certain members of society from the public eye. In addition, this work draws upon the author’s personal experiences as a sibling of someone with autism, as well as supplementary interviews of experts with many hours of experience interacting with individuals with autism spectrum disorder in order to determine which design strategies might be most effective in ensuring sensory accessibility for individuals with sensitivities to sensory stimuli. These conclusions result in several recommendations for design requirements which may be added to existing accessibility design standards. These key recommendations for public spaces include the implementation of shading and thoughtful lighting strategy, the use of auditory barriers and noise-dampening surfaces, and increase of access to privacy within public spaces. When applied on a broad scale, public spaces may become generally more accessible to individuals of all sensory sensitivities and to the broader community as a whole.

Keywords: ADA Amendments Act of 2008 (United States)
Barrier-free design
Design
Autism
Sensory-friendly
Accessibility
Public spaces
Architecture
Americans with Disabilities Act of 1990 (United States)
Sensory stimulation
Sensory discrimination
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Thesis
¿Sequía o saqueo? Scarcity, Power, and Inequality in Chilean Water Markets

“No es sequía, es saqueo” (it’s not drought, it’s plunder) is a common phrase in activist circles to argue that it is not just drought that threatens Chile’s water resources, but rather a market-based model for water management that results in an extremely unequal distribution of water. This phrase exists in stark contrast to the worldwide acclaim Chile—the only country in the world with fully-privatised water rights—has received for its model’s potential to combat worsening water scarcity. Despite these opposing viewpoints and their implications for water markets as a drought-response mechanism in other parts of the world, empirical understanding of how scarcity and inequality impact Chile’s water markets remains limited, especially on a broader geographic and temporal scale. This study draws upon a dataset of nationwide water rights transactions, combining them with Standardised Precipitation Index data to identify water scarcity’s impact on market outcomes. I then employ Social Network Analysis methods to quantify market power and inequalities across time and space. I find that a small group of agents dominates the market through their involvement in the vast majority of transactions and volume transacted, their ownership of the lion’s share of water volume, and their strong tendency to trade with one another. Markets only respond to scarcity in the areas with the most unequal distribution of water volume, and scarcity decreases the tendency of highly-powerful agents to trade amongst themselves, suggesting that drought merely serves the interests of the powerful through predatory market behaviour.

Keywords: Water justice
Drought
Chile
Water markets
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Thesis
Advisor: Naylor Roz
Serial X-ray crystallography : pushing the boundaries of structure and dynamics

Over its long history, macromolecular X-ray crystallography has proven to be the most popular method for structural biology. Recent advent of serial X-ray crystallography at X-ray free-electron laser facilities and synchrotrons have revolutionized the field allowing scientists to study proteins that were previously inaccessible. Radiation damage-free structures from microcrystals at room temperature are routinely studied these days. The next frontier of serial X-ray crystallography will be in studying the function of the proteins by reconstructing a detailed movie of the protein in motion. Conformational variations/changes of proteins are studied using diffuse scattering and pump-probe type of experiments. My research is focused on developing advanced data analysis methods in the field of macromolecular X-ray crystallography to extract more information from massive datasets and push the boundaries of the status quo. Here is a summary of projects I would like to highlight. The first project advances the analysis of pump-probe and mixing-jet experiments by applying machine learning to correct for uncertainty/inaccuracy of measured pumping or mixing times in serial femtosecond X-ray crystallography (SFX) experiments. In pump-probe or mixing-jet experiments, we either excite the crystals using an optical light or mix the crystals with a catalyst to trigger motion, followed by an X-ray probe after a certain delay. Although these methods have been broadly used to study protein dynamics, few people have considered the effects of jitter in these inaccurate timestamps, which can be critical in the study of ultrafast protein dynamics. In our work, we have applied the diffusion map method to embed high-dimensional diffraction images into low-dimensional latent space to correct for the time jitter. The second project is a reproducibility study of diffuse scattering in crystalline isocyanide hydratase in three forms, its wild type and two mutants. Different from ultrabright Bragg peaks that arise from the coherent diffraction of periodic crystal lattices, diffuse scattering is much weaker and is induced by imperfections inside the crystal lattice, such as protein motion and/or other forms of disorders. I have developed advanced methods to extract much weaker diffuse scattering signals from diffraction images, and then studied possible protein motions that cause these diffuse signals, by comparing liquid-like motions model to the experimental data. This work demonstrates a potential utility for selecting a preferred atomic displacement parameter model from diffuse scattering data

Keywords: Applied Physics.
Advisor: Dunne Anthony Michael
Reis David A.
Hedman B. (Britt)
Si vis pacem, para bellum : essays on military preparations and deterrence

This dissertation focuses on how military preparations made 'in peace' shape the dynamics of deterrence and the ability to prevent a crisis from occurring. Resolve has received most of the attention in past studies of deterrence, yet military capability and how it is developed has major implications for deterrence as well as peacetime force posture and security assistance through military alliances. I assemble empirical evidence and provide formal theoretical logic that highlight the role of military preparations in deterrence. In doing so, this dissertation contributes to an area of deterrence studies that has been understudied by past scholars and is of immediate relevence to policy-makers confronting problems of interstate tensions and conflict

Keywords: Political Science.
Advisor: Schultz Kenneth A.
Fearon James D.
Sagan Scott Douglas
Sidestepping hardness in statistical problems

Recent increases of the availability of data have led to more demand for solving large-scale, computationally intensive statistical problems. Unfortunately, many such problems are provably hard and can require excessive amounts of data or computational resources. I will start out by showing an example hardness result and the implications the result has for practitioners. Keeping that in mind, we will discuss several approaches to sidestepping such hardness results. We will examine applications to the robotics problem of navigation among obstacles with estimated shape and location, the nonparametric statistics problem of log-concave density estimation and synthetically enlarging datasets

Advisor: Reingold Omer
Valiant Gregory
Tan Li-Yang
Silicon carbide on insulator quantum photonics with color centers

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

Keywords: Electrical Engineering.
Advisor: Vuckovic Jelena
Safavi-Naeini Amir H.
Solgaard Olav
Simulating exoskeletons to assist walking : tools and applications

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

Keywords: Mechanical Engineering.
Advisor: Delp Scott
Collins Steve (Steven Hartley)
Liu Cheng-Yun Karen
Simulations of flexural-gravity wave response of Antarctic ice shelves to tsunami and ocean wave impacts

Floating ice shelves off the coast of Antarctica play an important role in buttressing the outflow of grounded ice. These ice shelves are subject to the continuous impact of ocean waves and tides which can induce their flexure, create bending stresses, and possibly facilitate rifting and calving. Ice shelves have complex geometries and spatially variable ice thickness and water depth. These features that are challenging or impossible to capture with the commonly used semi-analytical methods that have been used to study wave reflection, transmission, and propagation. In this thesis, we will address this challenge, firstly, by introducing a provably stable, higher-order-accurate finite difference method to solve the 2D (map view) problem of an incompressible ocean partially covered with an elastic plate. The method is based on the summation-by-parts--simultaneous approximation terms (SBP-SAT) framework, and uses curvilinear multiblock grids to handle complex geometries. The model solves the Euler-Bernoulli plate equation, with spatially variable properties, coupled with the 2D variable depth shallow water equations. We demonstrate the stability and accuracy of the numerical model using the method of manufactured solutions. Next, we apply the new method to study ocean wave forcing of the Thwaites Glacier Ice Tongue, Eastern Ice Shelf and Pine Island Ice Shelf, with ice thickness and water depth from BedMachine2. We also apply our model to Ross Ice Shelf, where seismic data exists for validation. We reproduce observed attenuation of waves in the infragravity band (IG, 0.003-0.03 Hz) and the absence of attenuation in the very long period band (VLP, less than 0.003 Hz). This attenuation is attributed to scattering losses that are captured by our model. Finally, we model the response of these ice shelves to tsunamis from the 2015 Mw 8.3 Illapel, Chile, earthquake and to a hypothetical Mw 8.6 earthquake in the Central American subduction zone. We calculate maximum wave amplitudes and bending stresses, in particular identifying regions that experience large bending stresses from wave focusing and amplification. One such region is on the upstream side of the pinning point of the Thwaites Eastern Ice shelf, a location of critical importance for the stability of the West Antarctic Ice Sheet

Advisor: Dunham Eric
Iaccarino Gianluca
Schroeder Dustin
Single-cell characterization of human immune cell histone modification profiles using machine learning

Histone post-translational modifications (HPTMs) regulate gene expression through coordinated interactions known as histone crosstalk. Variations in HPTM abundances or histone crosstalk are associated with cancer, infectious diseases, autoimmune disorders and mental illness. EpiTOF, a high-dimensional mass cytometry-based platform, measures abundances of HPTMs and histone variants across multiple immune cell sub-types at a single-cell resolution. However, the direct study of histone crosstalk in vivo in higher eukaryotes is very difficult due to experimental limitations in inhibiting or knocking-out HPTMs. In this thesis, we develop computational methods to infer directed associations between HPTMs from their abundances measured using EpiTOF. Leveraging the large number of immune cells from healthy human subjects profiled using EpiTOF, we first develop a neural network-based subject-specific method and train models to accurately predict HPTM abundances. We then infer directed associations between HPTMs from these models using a novel, perturbation-based interpretation algorithm. Lastly, we apply our trained models and interpretation algorithm and identify changes in HPTM associations due to the influenza vaccine and the cluster of cells that drive these changes. Our results provide insights into the histone crosstalk landscape in immune cells from human beings. The trained models and the interpretation framework can be applied to identify changes in the HPTM and histone crosstalk landscape due to a disease or external stimuli like vaccination. Our methods can also be applied to proteomic or transcriptomic datasets to infer directed interactions between proteins or gene expression respectively

Advisor: Khatri Purvesh
Hastie Trevor
Utz Paul
Single-Cell Profile of Human Corneolimbus Reveals Cellular Diversity and Novel Putative Stem Cell Markers

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.

Keywords:  Department of Biology
Biology
Single Cell Sequencing
RNA Sequencing
Cornea
Limbus
Stem Cell
Transcriptomics
Ocular Surface
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Thesis
Advisor: Wu Albert Y.
Morrison Ashby
Single-molecule and computational studies of DNA torsional dynamics : from fundamental biophysics to anticancer therapeutics

The torsional mechanics of DNA have been exploited by evolution to achieve exceedingly sophisticated levels of biological control. Yet, how these mechanics dictate genetic function remains underexplored, limiting both our understanding of basic biological phenomena and our ability to fine-tune synthetic systems for biotechnological applications. In this dissertation, I present a series of biophysical studies based on molecular modeling and single-molecule measurements, each providing mechanistic insight into genetic phenomena through consideration of DNA topology and supercoiling

Advisor: Bryant Zev David
Greenleaf William James
Spakowitz Andrew James
Snapshot hyperspectral polarization imaging

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

Keywords: Electrical Engineering.
Advisor: Fan Jonathan Albert
Rivas-Davila Juan
Solgaard Olav
SNEAD: Solving Nash Equilibria with Adversarial Deviation

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.

Keywords: Algorithms
Game theory
Adversarial
Optimization
Numerical analysis
Convex functions
Nash Equilibrium
Nash Equilibria
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Thesis
Advisor: Judd Kenneth
Clerici-Arias Marcelo