VictorJuiz/thesis huggingface dataset:
Control and tomography of phonons in cavity optomechanical nanostructures
Keywords: Applied Physics.

Phonons are the quanta of mechanical motion. One possible toolbox for manipulating phonons is provided by the field of cavity-optomechanics, in which light and motion interact via radiation pressure. Of particular importance to applications are cavity-optomechanical nanostructures, whose properties are entirely engineered and which can be integrated on the surface of a chip. In such platforms, new possibilities for the control of phonons emerge. Two key questions arise in these systems where phonons carry information: How can we control the propagation of phonons, and how can we use light to prepare and verify quantum states of mechanical systems? In this thesis, I present three main results using cavity optomechanical nanostructures. First, I will show that phonons confined to a resonator can be made to deterministically couple to an external channel. We propose, and demonstrate via cryogenic measurements, that a particularly simple symmetry-breaking perturbation in nanopatterned silicon allows for the efficient transduction of localized phonons into de-localized phonons. Second, we design and experimentally demonstrate a single-mode phononic wire. Our design incorporates a patterned silicon film with a complete two-dimensional acoustic bandgap. We show through optical measurements that only a single propagating mode is supported for GHz frequency phonons within the bandgap. Low-loss propagation over millimeter length scales is observed. In addition, methods to generate optically induced non-linearities for phonons are discussed. Finally, I describe recent results from our experiment combining photon counting and continuous measurement of mechanical position to perform quantum state tomography. By heralding our measurement on the detection of a single inelastically scattered photon, a single phonon is added to a nanomechanical oscillator. Despite the large thermal occupancy of the oscillator at room temperature, the addition, or subtraction, of a single phonon produces a distinctly non-Gaussian state of motion. The results open up new possibilities for preparing and verifying macroscopic quantum mechanical states using light
Controlling color and photoisomerization pathways in photoactive proteins : the role of the protein environment
Keywords: Chemistry.

Proteins are a remarkable class of macromolecules. With a limited number of building blocks, amino acids, they adopt an incredible diversity of three dimensional structures, each with unique functions that are essential to virtually all cellular processes. In many cases, specific small molecules (i.e., ligands, cofactors, substrates, solvent) bound within the three dimensional protein structure are required to help perform that protein's function. The environment created by the protein around the small molecule imparts unique functionality not attainable for the free small molecule alone. For example, fluorescent proteins contain a covalently attached small molecule chromophore that absorbs and emits photons at particular wavelengths. When free in solution, the chromophore is essentially nonfluorescent, but within the protein environment, the chromophore's photon emission efficiency dramatically improves. It is easy to recognize and demonstrate the exquisite control that a protein has over the reactivity of its bound ligands, cofactors, and substrates. However, we do not understand how the protein environment controls function, specifically what factors at the molecular level are important in creating this immense functional diversity. In some cases, crystal structures provide obvious atomic interactions that prove to be essential, such as a particular hydrogen bond or electrostatic attraction. Yet, designing proteins with desired functions is still quite difficult, if not unattainable in many cases, even with current state-of-the-art computational and experimental methods. In my work as a graduate student, I focused on identifying the underlying factors that link a protein's function to its structure and on how to manipulate those factors in a rational way to efficiently achieve a desired function. Using green fluorescent protein (GFP) and its many relatives and derivatives, I have applied various biophysical, spectroscopic, structural, and protein engineering techniques to address this issue, with projects that focus on gaining mechanistic insights into relevant light-induced processes, creating quantitative and predictive models to relate structure and energetics to protein function, and using this deeper understanding to engineer new and improved photoactive protein variants. Together, these projects tell a cohesive story about the functional role of the protein environment on bound molecules and my efforts to elucidate design principles for the engineering of new and improved proteins
Convergence concepts : he political construction of stability, legitimacy, and authority
Keywords: Political Science.

This dissertation defines a broad class of normative political concept - the 'convergence concept' - named to highlight the distinctive mode by which these concepts are evaluated: the evaluation of convergence concepts at the collective scale of the polity derives from the consolidation and convergence of individual citizens' normative judgements. Thus, convergence concepts reflect citizens' own conceptual definitions and assessments, as well as the processes of both private and discursive reasoning which guide these judgements. These concepts are of central concern in the study of political coordination and cooperation (as well as crisis and conflict), since citizens' judgements and behaviors can either establish and reinforce, or undermine and erode, shared structures of governance and coercive political authority. This project investigates three such concepts: stability, legitimacy, and authority. It offers a normative framework for conceptualizing these concepts, and presents an empirical approach by which to investigate political processes of discursive conceptual reasoning
Conversion and braiding rules of band-structure nodes
Keywords: Physics.

Topological semimetals are characterized by topologically protected band-structure nodes. One prominent example is the Weyl semimetal, characterized by Weyl points carrying topological Chern numbers. In this dissertation, we explore the topology of band-structure nodes with three ingredients: crystal symmetry, non-Hermiticity and periodic driving. First, we show that point group symmetry facilitates a new type of topological invariant from relative homotopy theory, which determines the rules for converting generic band nodes to nodes at high-symmetry momenta (and vice versa) as we tune the lattice Hamiltonian. Secondly, we show that exceptional lines in non-Hermitian bands act as Alice strings. This is manifested by the reversal of the topological charge of a node, if it is braided around an exceptional line. Finally, we discuss the Nielsen-Ninomiya no-go theorem in Floquet bands and the possibility of simulating chiral Weyl particles in the adiabatic limit
Convex projective geometrically finite structures
Keywords: Mathematics.

In this thesis, we explore two phenomena involving geometrically finite hyperbolic manifolds, and extend them to convex projective geometry. The first phenomenon involves the limit set of a Zariski dense geometrically finite structure. Greenberg studied limit sets of geometrically finite hyperbolic manifolds in order to understand their commensurators, and Mj extended his result to symmetric spaces. We extend this line of results to convex projective geometry, where our motivation is to understand when two geometrically finite structures define similar limit sets. We show that, when the limit of a Zariski dense geometrically finite structure is not the entire boundary at infinity, it determines the structure up to a finite index. The second phenomenon involves the characterization of geometrically finite structures. We introduce the notion of generalized geometrically finite structures, following the works of Danciger-Guéritaud-Kassel on convex cocompactness and Ballas-Cooper-Leitner on generalized cusps. We show an equivalence between a geometric and a dynamical description of such structures, similar to Bowditch's work on geometrically finite hyperbolic manifolds
Cortical Development in a Human 3D Cellular Model of 22q11.2 Deletion Syndrome
Keywords:  Department of Psychiatry and Behavioral Sciences
22q11.2 Deletion Syndrome
human cortical spheroids
single-cell RNA-sequencing
Thesis

22q11.2 deletion syndrome (22q11DS) is a multi–system disorder characterized most frequently by a 3 Mb hemizygous deletion on chromosome 22. This disorder is the most common chromosomal microdeletion in humans and leads to significantly increased rates of neuropsychiatric disorders. Defects in corticogenesis are hypothesized to play a role in pathogenesis and have been investigated through MRI studies, postmortem studies, and mouse models, but have not been studied in human cells. Here, we investigated corticogenesis in 22q11DS using human cortical spheroids (hCS) differentiated from human induced pluripotent stems cells derived from 22q11DS and control subjects. We found that hCS differentiation showed no major differences in morphology and size between 22q11DS and control subjects. Transcriptional profiling of hCS using single–cell RNA–sequencing revealed similar cell composition and highly correlated gene expression. We found that genes within the 22q11.2 deletion exhibited, on average, a 50% reduction in 22q11DS patient derived hCS, including DGCR8, a miRNA processor. Differentially expressed genes, including 9 from the 22q11.2 locus, were enriched for transcriptional regulation, specifically of mRNA and RNA metabolic and catabolic pathways in gene ontology analysis. These findings indicate that early cortical differentiation may not be a significant contributor to developmental defects in 22q11DS, which makes hCS a reliable cellular model to study this disorder. Furthermore, we show that gene expression within the 22q11.2 locus, including DGCR8, is significantly downregulated and may play a role in dysregulating transcription in 22q11DS patient derived hCS.
Cortical neural population dynamics for flexible motor control and motor learning
Keywords: Biology.

Animals have a remarkable capacity to learn new motor skills while maintaining existing ones. Motor learning encompasses a wide range of phenomena, from relatively low-level mechanisms for calibrating movement parameters, to making high-level cognitive decisions about how to act in a novel environment. Yet the neural mechanisms of these behavioral phenomena, in particular their underlying neural population dynamics, remain largely unknown. Precise motor control and flexible motor learning involve distributed brain regions, among which motor cortex is a key brain hub involved in the control of skilled movements. The neurophysiological studies (Chapters 2 and 3) and the tool-development project (Chapter 4) presented in this dissertation aim to address the roles of neural population activity in motor cortex underlying different behavioral phenomena during movement control and motor learning. In the neurophysiological studies, we recorded hundreds of neurons simultaneously with high-density electrodes while monkeys were learning one or multiple motor skills. To investigate the neural population data, we used techniques based on the dynamical systems theories and applied different dimensionality reduction methods. In the tool-development project, we demonstrate a new imaging platform in behaving monkeys that was able to monitor the same neural population across weeks and could provide us a potential avenue for studying long-term motor learning. In Chapter 2, I first address the question of how neural population activity in rhesus macaque motor cortex changes when learning new arm movement from dynamic force perturbations. Chapter 3 reports the neural population activity patterns during interference and learning of multiple different skills. Chapter 4 demonstrates the development of chronic in vivo two-photon calcium imaging for rhesus macaques generating arm movements and the implementation of an optical brain-computer interface (oBCI), as well as the capability to combine functional and structural imaging of the motor cortical neural population
Counterexamples in digital system verification, channel coding, and electro-neural interface design
Keywords: Electrical Engineering.

This thesis contains chapters on several different topics. Chapter 2 explores hardware Trojan detection, by considering attacks that can be implemented when fabrication of the integrated circuits (ICs) is not trusted. Many other works focus on Trojan detection during IC testing or pre-silicon verification, but these cannot detect all attacks. We present a system architecture using randomized error-detection codes, which can detect any hardware Trojan on any digital IC, in real-time, during both testing and system operation in the field. It cannot produce false positives. In addition, it prevents a large variety of reverse-engineering attacks during chip design and fabrication. Chapter 3 explores channel coding a bit further. While channel capacity captures fundamental limits on communication under a transmit energy constraint, it fails to account for processing energy. Using VLSI complexity models from computer science, we analyze total power for regular-LDPC codes and iterative message-passing decoders. This specific code family is selected for analysis, based on its use in many real (wired and wireless) communication standards. We establish many counterexample scenarios, where it is actually more energy-efficient to use uncoded transmission than coding. Some post-layout circuit simulations of decoders help corroborate the theoretical results, at short communication distances on the order of 1m. Chapter 4 presents a proof-of-concept design of an invasive, electro-neural interface for neural recording and information telemetry in some sensory applications. The communication distance required is on the order of 1cm. Yet, even though the power constraints are solely transmit power constraints (unlike the counterexample scenarios of Chapter 3), it is not currently feasible to use capacity-approaching codes due to thermal and area constraints associated with implantation of the sensors in-body. We design a wireless, distributed, modular, and miniaturized opto-electronic system, that easily meets thermal and ocular safety limits. Chapter 5 provides conclusions for each chapter, future work, and a discussion of some follow-up works in the recent literature
Coupling single cell RNA sequencing with crispr perturbation and using single cell RNA sequencing to profile musculoskeletal injuries and disease
Keywords: Stem Cell Biology and Regenerative Medicine.

Single cell RNA sequencing (scRNAseq) has changed the way we understand cellular heterogeneity and overall tissue behavior. Using scRNAseq, we addressed three questions here, one technical, two biological. For the first question, we wanted to assess if Clustered regularly interspaced short palindromic repeats (CRISPR) perturbation information can be coupled with transcriptomic information in the drop-seq setting through direct capture of the small guide RNA (sgRNA). While capturing sgRNAs on drop-seq beads was achieved, we found that our downstream signal was scrambled. The first biological question we addressed was looking at an Hsl knockout mouse with faster fracture repair. Initial experiments suggested osteoimmunological causes behind the faster repair. Using scRNAseq, we found that pre-osteoclasts were the most perturbed cell type suggesting they may play a role in the improved fracture repair. Furthermore, pre-osteoclasts were some of the few cells in our dataset that expressed Pparg for which Hsl makes ligands. The second biological question we addressed was looking at tendon progenitor cells (TPCs) derived from either tendinopathic or normal patellar tendon. In our mechanical stress experimental system we found substantial differences between normal and tendinopathy TPCs. This dissertation illustrates the potential of scRNAseq applications to address a number of important biological questions while still have room to be further expanded
Cracks in the Sanctuary Walls: The Effects of Local Immigration Enforcement on Trust in the Police
Keywords:  Fisher Family Honors Program in Democracy
Political Science
Center for Democracy Development and the Rule of Law
immigration
Secure Communities
police
Thesis

Secure Communities is a national immigration enforcement program that allows U.S.
Immigration and Customs Enforcement (ICE) to gain access to the fingerprints of all suspects booked at local jails. Upon receiving the fingerprints, ICE can request that the jail hold a suspect until they can be transferred into ICE’s custody. From 2009 to the present day, Secure Communities has led to the deportation of hundreds of thousands of immigrants and has garnered criticism for threatening to compromise the relationship between local law enforcement and the communities they serve. This thesis provides one of the first empirical examinations of the effects of the program on individuals’ trust in local law enforcement. I use millions of calls for service before and after the implementation of Secure Communities in Seattle, Washington as a proxy for residents’ trust in local law enforcement. Using this call for service data, I employ a difference-indifferences design to estimate the causal relationship between the implementation of the program and trust in local law enforcement. In particular, I examine whether we observe a decrease in calls for service in higher-density Hispanic areas compared to lower-density Hispanic areas postimplementation. Contrary to expectations, I find no significant effect of the programs’ implementation on rates of calls for service, in general, or on domestic violence calls, in particular. In light of these findings, I remark on the possibility that Seattle’s sanctuary policies may have provided a buffer against the potential negative consequences of Secure Community’s implementation on Hispanic residents’ trust in local law enforcement.
Crafting cosmologies : buddhist cartography and the spatial imagination in Medieval China
Keywords: Moerman, D. Max (David Max) degree committee member.
Religious Studies.

This dissertation traces written and visual discourses mapping the Buddhist cosmos in medieval China. This study is grounded in sixth- to eleventh-century Chinese manuscripts and murals preserved at the Mogao Grottoes, a bustling Buddhist cave complex in the Dunhuang region. I expand this localized focus with analysis of texts, images, and maps whose productions range from the Six Dynasties (220--589) to the Song Dynasty (960--1279), from sand-swept caves of Dunhuang to elite temples of central China, and from the hands of anonymous local scribes to imperially sponsored scholar-monks. Each chapter examines a unique method of crafting cosmologies in medieval China. These methods are demonstrated inductively, grounded in three distinct bodies of materials, each evincing a particular pursuit in the production. Chapter One highlights the method of crafting cosmologies through visual transformation, examining wall murals at Mogao that engage in the artistic pursuit of turning a Mainstream text into a collection of graphic narrative maps of two distinct universes and one micro-cosmos. Chapter Two uncovers the creative method of textual appropriation, examining two new texts added to the Lotus Sūtra which I identify as having been made from at least one pre-existing cosmology. Chapter Three explores an element of material culture, examining one cohesive manuscript in order to illuminate possible practical pursuits involved in the creation of a meta-cosmology through the practice of textual compilation. Throughout, this study strives to demonstrate the foundational role cosmology played in medieval Chinese Buddhist ontology and soteriology
Creating the Kibbutz Family in the 1920s: Between Revolution and Tradition
Keywords:  Department of History
anat peled
kibbutz
labor zionism
kibbutz family
socialism
a.d. gordon
moshav
shtetl
jewish family
jewish families
kadish luz
the family question
degania
dgania
zionism
nahalal
second aliya
Thesis

Labor Zionist kibbutzniks faced a dilemma in the 1920s with the birth of their first children in Palestine. As Socialists, they saw the bourgeois Jewish family as an outdated way to control women and property. In fact, according to Socialist critique by Engels and Bebel, the bourgeois family was destined to disappear with the abolishment of capitalism. But as Jews and Zionists, they understood that the family was important for preserving tradition and building the Jewish nation. This thesis aims to shed light on the tension between Zionism and Socialism through an analysis of the family question on the early kibbutz.
Critiquing counter-terror : the impact of security policy on American, British, and French publics post 9/11
Keywords: Theater and Performance Studies.

In this thesis, "Countering Counter-Terror: The Impact of Security Policy on American, British and French Publics Post 9/11", I reframe counter-terrorism law as performance; I argue it is a scenario or blue-print for military and civilian interactions in the public sphere. As evidence of how counter-terrorism is a form of performance, I explore the intersections between security policy in the United States of America, the United Kingdom, and the fifth French Republic and immigration practices, indeterminate detention, torture, and mass surveillance. More specifically, I demonstrate how the U.S. Patriot Act (2001), UK CONTEST (2007 -- 2019), and France's SILT law (2017) have significantly reduced peoples' privacy, impacted peoples' right to freedom of movement and of speech, and escalated racial, class, religious and ethnic divides. Though particular emphasis is placed on the violence perpetrated against disenfranchised Muslim and/or Arab communities, this dissertation argues that national security discourses are broadly betraying the democratic values and institutions they purport to protect