VictorJuiz/thesis huggingface dataset:
Projection inferences with clause-embedding predicates in RSA models

Projection inferences are inferences about speaker commitment to content embedded that project through an entailment-canceling operator. In this thesis, we investigate projection inferences in polar interrogatives with clause-embedding predicates (e.g., Does John know that Julian dances salsa?). Inferred speaker belief regarding whether Julian dances salsa is modulated by multiple factors, including the predicate used, interlocutors' prior beliefs about the content, and the content's at-issueness. In a behavioral study, we investigate the beliefs about contents embedded under the predicates “think” and “know” that listeners ascribe to the speaker and a potential attitude holder (John). We propose three different probabilistic models couched in the Rational Speech Act (RSA) framework, in an attempt to provide a unified computational account of projection inferences about content embedded under clause-embedding predicates. The empirical data are used to infer the parameters and evaluate the model predictions. The predictions of each model mirror some, but not all, of the qualitative empirical patterns. This is a step towards a systematic analysis of projection inferences using probabilistic pragmatic models.

Keywords: Projection inerences
Clause-embedding predicates
Experimental pragmatics
Probabilistic pragmatics
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Thesis
Advisor: Degen Judith
Promoting Equitable Pathways in Engineering and Career Technical Education

My dissertation addresses three studies which ask broadly: What are the predictive metrics of functioning AS-CTE pathways? Can students’ perceptions of these pathways be changed? Are these pathways equitable for female students? In my first study, I take a step toward better understanding the metrics that explain functioning AS-CTE pathways. Through ethnography, I observed that when social mobility was added as a metric of high-quality PBL with AS-CTE in a predictive framework of education success, attendance levels improved. In my second study, I investigated an opportunity gap (Ladson-Billings, 2013) contributing to students’ perceptions that AS-CTE does not lead to advanced STEM degrees. That perception forms a resistance to AS-CTE pathways, hindering efforts to include underrepresented demographics such as women. This study aims to explain to what degree the opportunity gap influences perceptions of obscure high-wage, high-skill careers by youth of an underrepresented demographic. In my final study, I investigated how AS-CTE pathways present barriers to inclusion through hegemonic masculinity (Connell & Messerschmidt, 2005). Building on the work of (Tarantino et al., 2016), this study employs a feminization of PBL mentor intervention to help break down the barriers of hegemonic masculinity in secondary STEM-CTE classrooms. Through ethnographic action research (Hartmann et al., 2009), I found evidence that the humanizing of our VDC-PBL intervention allowed for sites of resistance to gender norms. These studies make three important and timely contributions to the field of AS-CTE and engineering education more broadly. First, I uncover and remediate an ineffective metric of program efficacy, then reveal an opportunity gap which impacts marginalized youth more acutely, and finally I reveal a toxic masculinity within AS-CTE pathways which further impacts those with compounding marginalizations. While uncovering these trends, I offer recommendations to remediate these issues, while also highlighting what is working for these pathways.

Keywords: Engineering Education
Career Technical Education
Equity
STEM
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Thesis
Propagule size has context-dependent effects on colonization success in mixtures of gut microbial communities

Colonization plays an important role during assembly of the gut microbiome and influences microbiome composition throughout the life of the host, but determinants of colonization success are not yet fully understood. The size of introduced populations and frequency of their introduction can be important drivers of colonization success for introduced species. However, the effect of these factors, which are known together as “propagule pressure,” varies across environments and can be modulated by the strength of competition between introduced and resident species. In vitro microbial communities provide a tractable, high-throughput experimental system to interrogate the influence of propagule pressure on colonization. To quantify the importance of propagule size during colonization in gut microbial communities, we derived in vitro communities from human stool samples and systematically mixed eight pairs of communities at seven ratios ranging from 1:1000 to 1000:1. We compared our results to the predictions of a neutral model in which the relative abundance of each species remains proportional to its inoculation dose, a measure of propagule size. We observed that community co-cultures maintained similar levels of species diversity to the parent communities regardless of mixture ratio, suggesting that community diversity may be limited by resource competition even when many species are initially present. Likewise, community composition was generally maintained across mixture ratios, in contrast to neutral predictions. However, certain bacterial taxa showed varying levels of dose-dependence across mixtures, suggesting that the effect of propagule size depends on community composition and may be affected by the strength of competitive interactions in each mixture. Our results highlight the importance of both propagule pressure and competition in determining colonization success in gut microbial communities.

Keywords:  Department of Biology
Biology
Microbial ecology
Ecology
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Thesis
Advisor: Relman David
Long Sharon
Punish or Play it Down? China’s Reactions to Border Standoffs with India

Despite regular border standoffs between China and India since 2012, including one that resulted in deaths in 2020, little research has been done into the specifics of Beijing’s recent foreign policy strategy towards New Delhi. It is time to move beyond studying the border dispute as the dependent variable, and instead situate the border dispute within the broad China-India relationship by looking at standoffs as independent variables that impact China’s diplomatic and economic policies towards India. Using content analysis, I find that standoffs have a moderate negative association with the Chinese MFA’s diplomatic rhetoric, but that during a standoff Beijing continues to portray India in a generally positive light, and often ignores standoffs completely. Additionally, on average the value of China’s imports from India, either in the aggregate or for a few key products, does not dip during or in the immediate aftermath of a standoff, suggesting so far China has not responded to standoffs with economic punishment.

Keywords:  Stanford Global Studies
China
India
Foreign policy
Coercion
Content analysis
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Thesis
Advisor: Mastro Oriana
Quantifying and mitigating the contribution of model uncertainty to predictions of the terrestrial carbon cycle

The terrestrial biosphere is an integral component of the Earth system, serving as a buffer against the impacts of anthropogenic climate change and providing a wealth of ecosystem services to communities across the globe. However, its behavior and responses to environmental perturbations are challenging to model, mainly due to uncertainties involving model structure and parameterization. Despite a proliferation of targeted model development efforts, persistent disagreement between predictions from different state-of-the-art terrestrial biosphere models hinders the establishment and prioritization of robust management and restoration initiatives. In this dissertation, I develop methods for quantifying and mitigating the role of model uncertainty in predictions of the terrestrial carbon cycle. This was made possible via diverse, multi-scale Earth observations, which I integrate within a flexible ecosystem model--fusion framework. Together, this research provides new insight into the inter-relationship between structural and parametric uncertainties, and also highlights opportunities for using novel data to develop model parameterization strategies that yield realistic variability across the global land surface

Keywords: Sustainability.
Earth System Science.
Advisor: Konings Alexandra
Field Christopher B.
Jackson Rob
Michalak Anna M.
Quantifying Pacific Ocean nitrous oxide cycling using intramolecular isotope measurements and modeling

Nitrous oxide is one of the lesser-known greenhouse gases, yet its potential to warm the environment, on a per-molecule basis, is immense. Marine nitrous oxide production is concentrated in and around oxygen deficient zones, whose steep redox gradients allow for overlapping microbial processes that produce nitrous oxide. But the rates of these processes, and their relative importance in contributing to hotspots of nitrous oxide production, remain uncertain. This dissertation uses the intramolecular nitrogen isotopes (or isotopomers) of nitrous oxide to quantify its production in and around the eastern tropical North Pacific oxygen deficient zone. In Chapter 1, I find that high, near surface accumulations of nitrous oxide in this region are produced mainly by denitrification, with a smaller contribution from nitrification. In some core anoxic depths of the oxygen deficient zone, nitrous oxide cycling is not in steady state, while elsewhere, the isotopic content of nitrous oxide can be explained by denitrification with a positive site preference. In Chapter 2, I present a software package for isotopomer data processing and discuss the performance of this software. Ammonia-oxidizing archaea can produce nitrous oxide via a hybrid mechanism, so-called because it combines nitrogen derived from ammonium and nitrite to form nitrous oxide. In Chapter 3, I show that hybrid nitrous oxide production is inhibited by oxygen and reaches high yields at oxic-anoxic interfaces where ammonia oxidation is active. Integrating the information learned from these biogeochemical measurements, Chapter 4 presents a 1D advection-diffusion-reaction model constrained with nitrous oxide isotopomers to quantify nitrous oxide cycling in the eastern tropical North Pacific and test the sensitivity of that cycling to ocean deoxygenation and changes in organic matter export. Together, the results described in this dissertation show that nitrous oxide cycling in this region is a dynamic system that depends on low oxygen conditions and an organic matter source, conditions subject to change with ocean warming, deoxygenation, and increasing atmospheric N deposition. The constraints and parameters identified in this dissertation should provide a starting point for better implementations of nitrous oxide cycling in global biogeochemical models, making it possible to predict feedbacks between marine nitrous oxide cycling and climate change

Keywords: Sustainability.
Earth System Science.
Advisor: Casciotti Karen Lynn
Arrigo Kevin R.
Dekas Anne
Francis Christopher
Quantitative analysis of observed filamentation structure in high energy electron beam-plasma interaction

Filamentation instability is a primary candidate mechanism that contributes to the dynamics of collisionless shock. It is of great significance to study the dynamics in the shock front, since the filaments are populated there. This mechanism is responsible for various cosmological physics phenomena and high-energy density physics, such as inertial confinement reactions, gamma burst. This report presents the first experimental evidence of filamentation structure formed by relativistic electron beam-plasma interactions. This study, conducted at the Omega laser facility at the University of Rochester, focuses on dynamics of a hot electron beam interacting with uniform, slowly expanding plasma electrons. Drawing from an extensive literature review on theoretical and simulation studies of Filamentation instability in relativistic high-energy physics, the observations and analysis from this experiment reveal a filamentation structure with a spatial scale range from 0.150 - 0.350 nm. Its linear stage persists for 50 ps, which serves as its temporal scale. Diagnostic methods, including the Electron-Positron-Proton spectrometer and proton radiography, have been employed. Further analysis for retrieving the magnetic field strengthen has been reported as of the order of O(0.8) T. This findings identify the regime where electron Filamentation instability is ongoing and provide valuable data for future exploration.

Keywords: Engineering.
Mechanical Engineering.
Advisor: Edwards Matthew R. (Matthew Reid)
The quantum anomalous Hall effect : uses in electrical metrology and understanding residual dissipation

When a company manufactures and sells a resistor, they typically aim to traceably link its resistance value to a quantum Hall (QH) effect measurement. When a thin semiconductor is cooled to a low enough temperature and exposed to a large enough magnetic field, it exhibits zero longitudinal resistance and quantized Hall (transverse) resistance. This quantized resistance is a topological phenomenon, insensitive to sample details, and since 1990 has been used to define the ohm. Magnetic topological insulators exhibit the same resistance properties, but at zero magnetic field — this is the quantum anomalous Hall (QAH) effect. QAH materials offer significant advantages as possible replacements for QH resistance standards. Eliminating the need for large magnetic fields not only allows simplifying measurement infrastructure, but also allows a quantum resistance standard to be directly integrated with a Josephson voltage standard to produce a quantum current standard. However, all measurements of the QAH effect to date have observed non-zero longitudinal resistance despite quantization of the Hall resistance to h/e^2 (where h is Planck's constant and e the electron charge) being confirmed to within one part per billion. This residual dissipation is strongly temperature-dependent, lowering the temperature at which the QAH effect is well-quantized and thus limiting industrial applications. This dissertation will focus on our efforts to understand and find metrological applications for the QAH state of the canonical magnetic topological insulator — Cr-doped (Bi,Sb)2Te3. The nature of non-equilibrium dissipationless current flow in this system will be explored by comparing the measured potential profile in a QAH Hall bar to numerical simulations of the Poisson equation. Separately, residual dissipation will be studied by decoupling edge and bulk contributions using an annular geometry known as the Corbino disk. We will also show that despite their limitations, these materials are already useful within the field of electrical metrology. We will discuss how metrological measurements of resistance are made and highlight the construction of a novel quantum current sensor based on a single-cryostat combination of a QAH resistor with a programmable Josephson voltage standard.

Keywords: Humanities and Sciences.
Physics.
Advisor: Goldhaber-Gordon David
Feldman Ben
Kastner Marc
Quantum chemistry and quantum simulation at scale : leveraging modern computing paradigms and hardware

Quantum chemistry has strong connections to important technologies and applications like quantum computing, machine learning, chemical or materials design, and drug discovery. At the heart of these connections is an increase in high-performance computing (HPC) power, largely driven by accelerators like GPUs. Improving how quantum chemistry methods are formulated and implemented to use current and emerging computing power is therefore crucial. In this work, I focus on two directions: scaling quantum chemistry methods to distributed, GPU-accelerated hardware to enable studying large chemical systems, and using tensor network methods to simulate and study quantum circuits for quantum computing. The fast evaluation of electronic structure is essential for studying the dynamics of molecular systems, for reaction discovery, or for generating high quality training data for machine learning models. I develop a multi-node, multi-GPU implementation of the electron-repulsion integrals—the computational bottleneck in many electronic structure methods—using the task-based parallel programming language Regent. This allows performing a calculation that treats the entire green fluorescent protein (GFP) molecule (3000+ atoms) quantum mechanically with high parallel efficiency. I go on to parallelize across molecular systems by implementing a distributed client-server ab initio exciton model, and present results using this model to study the excited state dynamics of the LH2 light-harvesting protein complex. Quantum computers are a promising emerging technology, but while real quantum devices remain error-prone and composed of small numbers of qubits, classical simulations of quantum circuits are important for studying the behavior of quantum algorithms. Here I present work using a classical simulator built on tree tensor network methods to study quantum circuits. I discuss the benefits and relevance of approximate methods like tensor networks which represent a quantum state in a compressed form, and discuss insights on Shor's algorithm for integer factorization

Keywords: Humanities and Sciences.
Chemistry.
Advisor: Martinez Todd J. (Todd Joseph)
Aiken Alexander
Markland Thomas E.
Quantum control and characterization of phononic crystal cavities

The nonclassical behavior of mechanical objects is of both fundamental interest and potential technological utility. Mechanical resonators can be combined with superconducting microwave circuits to realize quantum technologies, acting as memories for computation and on-chip delay lines, with small footprints and large achievable coupling rates. The nonlinearity of the circuit enables quantum control of the mechanical mode, as well as nondemolition readout of the prepared mechanical states. This hybrid platform has seen great progress in recent years as both a flourishing technological avenue and as a platform to explore quantum behavior of mechanical motion. In this work, we describe a series of experiments which explore the versatile uses of a quantum acoustics platform built from piezoelectric nanomechanical resonators. First, we describe the design and experimental realization of a Purcell filter composed of lithium niobate Lamb-wave resonators. Next, we combine a superconducting transmon qubit with two phononic crystal resonators, also made of lithium niobate. We demonstrate full quantum control of the mechanical modes and perform quantum state tomography to extract the density matrices of the prepared states. In this effort, we also prepare and characterize a mechanical Bell-state between the two resonators, demonstrating a small-scale quantum acoustic processor. Last, using the same device, we use the qubit to perform phonon number-resolved detection of dissipation and dephasing of coherent states in the mechanical oscillator. We develop a model showing that the dissipation signatures are consistent with emission into a small ensemble of long-lived two-level system defects, thus elucidating the need for further refinement of fabrication techniques. Altogether, this dissertation represents an exploration of a wide range of different applications for a hybrid quantum acoustic platform

Keywords: Humanities and Sciences.
Applied Physics.
Advisor: Safavi-Naeini Amir H.
Hogan Jason
Schuster David (David Isaac)
Quantum controlled cold scattering between simple atoms and diatoms

This thesis presents the experimental studies of quantum-controlled cold scattering of H2 isotopologues (HD, D2) with simple rare gas atoms (He, Ne) and diatom molecules D2. In these experiments, we prepare HD and D2 molecules in specific rovibrational levels (v = 2, 4, j = 2, 4) with defined alignments, and study their rotational inelastic scatterings of the state-prepared molecules at low collision temperatures. From a time-of-flight apparatus, we extract information about the angular distributions of the scattered products, therefore providing insights into the dynamics of the collision processes. By combining quantum-state control and low-energy scattering, we are able to interrogate the fundamental interactions between such simple atoms and diatoms at an unprecedented level of detail. The thesis is structured as follows. Chapter 1 serves as an introductory point of the subject. A brief overview of the development and progress of cold scattering is given, and various techniques to achieve cold relative temperatures as well as quantum state control are discussed. The purpose is mainly to situate our experimental techniques in the broad field, and to demonstrate the similarities and difficulties we face. Chapter 2 presents the theoretical treatment of the scattering problem. They serve as the necessary background for analyzing the data in later discussions, and sometimes provide direct comparisons. Chapter 3 focuses on the experimental setup we use to achieve quantum-controlled cold scattering. Many details are elucidated at length. In the next two chapters (Chapter 4, 5), various experimental results of rovibrationally excited HD/D2 with other scattering partners are presented and discussed. Chapter 4 describes the Δj = 2 inelastic scattering results of D2 (v = 2, 4, j = 2, 4) with rare gas atoms He and Ne, as well as the Δj = 1, 2 relaxations of HD (v = 4, j = 2). Chapter 5 includes the scattering results between a pair of state-prepared diatoms D2 (v = 2, j = 2). In these two chapters, theoretical comparisons are provided alongside the data where available. In the last chapter (Chapter 6), we conclude the thesis with more thoughts on the summary and outlook of the project. Although complete satisfactory agreements between theory and experiments have not been necessarily achieved for all of the studies we present, we hope such discussions would inspire more future works of this kind

Keywords: Chemistry.
Advisor: Zare Richard N.
Dai Hongjie
Fayer Michael D.
Quantum dynamics of broadband nonlinear photonics : from phenomenology to function

In this thesis, we address the question of what new physics is expected to emerge as optical nonlinearity continues to increase towards the single-photon-level nonlinearity and how we can utilize the dynamics of photons in such a regime. In particular, we put special emphasis on broadband nonlinear photonics, where ultrashort pulses in nonlinear waveguides can provide significant enhancement of nonlinear coupling via tight three-dimensional field confinement. As such strong nonlinearity naturally leads to quantum features in broadband optical fields, the main aim of this thesis can be more precisely summarized as understanding the phenomenology of multimode nonlinear quantum dynamics of photons and engineering novel functions by leveraging the phenomenology

Keywords: Humanities and Sciences.
Applied Physics.
Advisor: Mabuchi Hideo
Hayden Patrick (Patrick M.)
Safavi-Naeini Amir H.
Quantum parametric oscillators coupled in time and frequency domains

This dissertation collects a sequence of case studies on the physics of coupled networks of quantum parametric oscillators. In the first part, we review the relevant formalism used to describe quantum parametric oscillators and quantum networks. In the second part, we examine a family of architectures based on time-multiplexed parametric oscillators, more widely known as coherent Ising machines for solving hard optimization problems. In the third part, we consider two case studies in frequency-multiplexed networks: a microwave architecture in which couplings can be arbitrarily synthesized, and an optical system in which the collective excitation of many frequency modes come together to form an ultrashort pulse. In the last part, we explore the quantum dynamics of ultrashort pulses of light undergoing traveling-wave parametric interactions

Keywords: Humanities and Sciences.
Applied Physics.
Advisor: Mabuchi Hideo
Fejer Martin M. (Martin Michael)
Safavi-Naeini Amir H.