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Computational Approaches To Understanding The Proton-Coupled Electron Transfer Reactions In Ribonucleotide Reductase, Jiayun Zhong
Computational Approaches To Understanding The Proton-Coupled Electron Transfer Reactions In Ribonucleotide Reductase, Jiayun Zhong
Yale Graduate School of Arts and Sciences Dissertations
Proton-coupled electron transfer (PCET) is a fundamental chemical process where both an electron and a proton are transferred simultaneously or sequentially, playing a key role in various biological and chemical systems, including enzymatic reactions and energy conversion. This thesis investigates the PCET reactions in ribonucleotide reductase (RNR), a critical enzyme responsible for DNA synthesis and repair in all living organisms. While significant progress has been made in understanding RNR's PCET pathway, several gaps remain, particularly regarding the specific mechanisms and energetics of individual PCET steps, the role of conformational dynamics, and the influence of water molecules. Through quantum mechanical/molecular mechanical …
Resolving The Three-Dimensional Interactome Of Human Accelerated Regions During Human And Chimpanzee Neurodevelopment, Atreyo Pal
Yale Graduate School of Arts and Sciences Dissertations
Human Accelerated Regions (HARs) are regulatory elements highly conserved across species but exhibit a significant excess of human-specific sequence changes. They include transcriptional enhancers with human-specific activity and have been implicated in the evolution of the human brain. However, our understanding of how HARs contributed to uniquely human features of the brain is hindered by a lack of insight into the genes and pathways that HARs regulate. It is unclear whether HARs acted by altering the expression of gene targets conserved between HARs and their chimpanzee orthologs or by gaining new gene targets in human, a mechanism termed enhancer hijacking. …
Continization And Language Representation Of Chemical Information, Haote Li
Continization And Language Representation Of Chemical Information, Haote Li
Yale Graduate School of Arts and Sciences Dissertations
Throughout human history, our ancestors have continuously expanded the frontiers of their interests in nature. Chemistry is one of the essences of such explorations. Yet, despite countless discoveries and experiments, we are still on a journey to examine the possibilities within our finite time. With an ever-growing amount of information and open access to public resources, we are experiencing an inflection point. This moment redefines how efficiently we can solve problems, and the key lies in integrating increasing insights from the entire history of knowledge. Algorithms, in contrast to human efforts, are scalable with the amount of available hardware. In …
Essays On Demand-Driven Political Methodology, Amanda Weiss
Essays On Demand-Driven Political Methodology, Amanda Weiss
Yale Graduate School of Arts and Sciences Dissertations
This dissertation demonstrates a demand-driven approach to political methodology research. The demand-driven approach entails studying and addressing technical problems while remaining in dialogue with political science as actually practiced. This dissertation, in particular, focuses on conducting credible research in politics and policy amid problems related to causal inference, statistical power, and data limitations. Chapter 2, "How Much Should We Trust Modern Difference-in-Differences Estimates?," takes up the challenge of estimating policy effects in observational settings. In particular, this chapter asks how well a range of difference-in-differences (DID)-style methods work for the empirical settings and sample sizes commonly used in political science, …
Methodological Innovations In Causal Inference: Estimation, Testing, And Decision Making, Yitan Wang
Methodological Innovations In Causal Inference: Estimation, Testing, And Decision Making, Yitan Wang
Yale Graduate School of Arts and Sciences Dissertations
Causal inference has been an important topic across many fields, such as computer science, statistics, econometrics, epidemiology, psychometrics, and political science, for decades. In this dissertation, we present methodological innovations in causal inference for three problems: estimation, testing, and decision making. In the first chapter, we provide an overview of this dissertation and introduce potential outcomes framework and confounded contextual bandit. In the second chapter, we describe a new design-based framework for drawing causal inference in randomized experiments. Causal effects in the framework are defined as linear functionals evaluated at potential outcome functions. Knowledge and assumptions about the potential outcome …
New Statistical Methods For Mediation Analysis With Independent And Correlated Data, Chao Cheng
New Statistical Methods For Mediation Analysis With Independent And Correlated Data, Chao Cheng
Yale Graduate School of Arts and Sciences Dissertations
Causal mediation analysis is a popular statistical tool for evaluating the extent to which an observed exposure-outcome relationship is mediated by an intermediate variable, also referred to as the mediator. Through mediation analysis, the total effect (TE) from the exposure on the outcome can be decomposed into a natural indirect effect (NIE) through the mediator and a natural direct effect (NDE) whose impact is due solely to the exposure and possibly other mediators. Causal mediation analysis has been applied in a variety of empirical research fields, including but not limited to epidemiology, implementation science, economics, and psychology. In implementation science, …
From Em To Depth Estimators: An Overparametrization View, Jiyi Liu
From Em To Depth Estimators: An Overparametrization View, Jiyi Liu
Yale Graduate School of Arts and Sciences Dissertations
This paper introduces the heated idea of overparametrization in the field of neural nets training into the statistical scenario, establishes the theoretical properties of the overparameterized Expectation-Maximization (EM) algorithm and its connections to deep learning and robust statistics. We establish a global convergence result for overparameterized EM in Gaussian mixture models (GMMs), demonstrating that overparameterization reshapes the optimization landscape and facilitates convergence. Inspired by its success in deep learning, we show that overparameterized EM mitigates initialization sensitivity while maintaining statistical consistency. Beyond EM, we introduce the Penalized Tangent Depth (PTD) estimator, a novel framework linking GAN training and depth-based robust …
Real-Time Synthesis And Characterization In Quantum Materials: Insights From Superconducting Nickelate Research, Wenzheng Wei
Real-Time Synthesis And Characterization In Quantum Materials: Insights From Superconducting Nickelate Research, Wenzheng Wei
Yale Graduate School of Arts and Sciences Dissertations
This dissertation reports on developments in quantum materials synthesis and characterization, with an emphasis on the study of superconducting nickelates through molecular beam epitaxy (MBE) and real-time synchrotron hard X-ray data analysis. The work elaborates on the developments in MBE synthesis, real-time characterization, and strategic materials design, and leads to the discovery of a nickelate superconductor. High resolution X-ray diffraction measurements were taken at the Advanced Photon Source, Argonne National Laboratory.The dissertation reports on the development of real-time analysis frameworks for both synthesis and characterization. This includes dynamic MBE source flux calibration techniques using RHEED and the shutter-control method, as …
Hardware Accelerators For Post-Quantum Cryptography - A Comprehensive Study Of Pqc Hardware Accelerators Belonging To Different Families., Sanjay Deshpande
Hardware Accelerators For Post-Quantum Cryptography - A Comprehensive Study Of Pqc Hardware Accelerators Belonging To Different Families., Sanjay Deshpande
Yale Graduate School of Arts and Sciences Dissertations
The rapid advancement in the field of quantum computing promises groundbreaking developments across various fields. While quantum computing possesses unparalleled capabilities in solving complex mathematical problems, it also undermines the very foundation of our current pre-quantum classical cryptographic systems. The quantum algorithm known as Shor's algorithm has the potential to efficiently break widely used public-key encryption algorithms such as Rivest-Shamir-Adleman (RSA) and Elliptic Curve Cryptography (ECC), rendering sensitive information vulnerable to compromise. Examples of such sensitive information include, but are not limited to, biometric data and encryption keys. Consequently, there is an imminent need to migrate to quantum-safe alternatives to …
Capital Market Effects Of Fake Social Media Accounts, Brett Campbell
Capital Market Effects Of Fake Social Media Accounts, Brett Campbell
Yale Graduate School of Arts and Sciences Dissertations
Fake social media accounts, or bots, are often used to spread or amplify content on social media platforms. I examine the effect of this artificial amplification on capital markets. I obtain a large dataset of posts from the social media platform Twitter (now X) and use several methods to identify accounts that are likely bots. The descriptive analysis suggests bot accounts produce about a third of all tweets mentioning company tickers. Bot tweets are associated with higher market activity, particularly among retail traders. Bot tweets are generally not associated with return reversals, but those with stock price-related content are. Bot …
Digital Identity Infrastructure, Jonathan Evan Hochman
Digital Identity Infrastructure, Jonathan Evan Hochman
Yale Graduate School of Arts and Sciences Dissertations
This dissertation proposes a uniform infrastructure for identifying users and data on the Internet. It identifies the questions we need to ask, provides terminology to think and speak about digital identity, introduces new cryptographic primitives to support digital identity services, and finally presents a sequence of applications that could be built upon the foundation of a shared digital identity infrastructure. These solution sketches are not meant as final specifications. They are examples to demonstrate how digital identity infrastructure could make it easier for digital platforms to deploy new services, improve privacy, reduce user frustration, and support the rule of law …
Mechanics And Energetics Of Cytoskeletal Assembly, Gao Sun
Mechanics And Energetics Of Cytoskeletal Assembly, Gao Sun
Yale Graduate School of Arts and Sciences Dissertations
Active matter is a subfield of soft condensed matter physics that focuses on the emergence ofcollective phenomena, as components of the system consume energy, driving them out of thermodynamic equilibrium. Living matter, a specific subfield of active matter, lies between physics and biology. In this case, the components are biomolecules, whose interactions are not only constrained by the laws of physics but may exhibit purpose and intentionality. Biophysicists, who study living matter use reductionist approaches and focus on how different components of the system can collectively give rise to novel biological phenomena through continuous consumption of energy. An example of …
Mechanisms Of Heart And Major Vessel Development: Nup107 And Cacna1g As Novel Regulators, Valentyna Kostiuk
Mechanisms Of Heart And Major Vessel Development: Nup107 And Cacna1g As Novel Regulators, Valentyna Kostiuk
Yale Graduate School of Arts and Sciences Dissertations
Congenital Heart Disease (CHD) is the most common congenital malformation and a leading cause of infant mortality. While advances in genomic sequencing technology have enabled a fast and inexpensive candidate gene identification, the molecular mechanisms of CHD remain mostly unknown. Both nup107 and cacna1g are novel CHD genes identified in CHD patients with no plausible mechanisms explaining their roles in cardiac development. Here, we show that nup107 plays a key role in early embryonic patterning and subsequent organ development. The loss of Nup107 has a direct impact on germ layer specification, Left-Right patterning and downstream cardiac looping. Specifically, Nup107 depletion …
Visual Circuits For Distance Estimation In Walking Drosophila, Joseph Shomar
Visual Circuits For Distance Estimation In Walking Drosophila, Joseph Shomar
Yale Graduate School of Arts and Sciences Dissertations
Animals must infer the three-dimensional structure of their environment from twodimensional retinal images. They use visual cues like motion parallax and binocular disparity to judge distances to objects, and studies across several animal models have foundand characterized neural signals that correlate with visual distance. However, the causal role of these neurons in distance estimation and the range of their possible neural properties remain poorly understood. Here we show that both directional and non-directional feature-selective neurons in the Drosophila visual system are involved in distance estimation during free locomotion. We used a high-throughput behavioral assay to perform a targeted silencing screen …
Bioinformatic, Genetic, And Biochemical Investigations Of The Bacterial Ole Ribonucleoprotein Complex, Chrishan Malinda Fernando
Bioinformatic, Genetic, And Biochemical Investigations Of The Bacterial Ole Ribonucleoprotein Complex, Chrishan Malinda Fernando
Yale Graduate School of Arts and Sciences Dissertations
Bacteria are under significant evolutionary pressures to maintain compact genomes.Therefore, they typically have high coding density compared to eukaryotes. As a result, large and highly structured noncoding RNAs (ncRNAs) are extremely rare in bacteria. However, the few classes of known large ncRNAs have unique and fundamental biological roles and are often catalytic. Furthermore, these ncRNAs reveal what may have been possible under a hypothetical ancient RNA world in which all major biological functions in existing organisms were performed by RNA, rather than DNA and protein. Further study of large ncRNAs is likely to reveal new insights into RNA catalysis and …
Analysis Of The Papillomavirus L2 Capsid Protein Structure And Protrusion, Patrick Michael Buckley
Analysis Of The Papillomavirus L2 Capsid Protein Structure And Protrusion, Patrick Michael Buckley
Yale Graduate School of Arts and Sciences Dissertations
Approximately 5% of human cancer worldwide is caused by Human Papillomavirus (HPV). Although there are highly effective prophylactic vaccines, HPV remains a serious public health challenge due to low vaccine uptake and the inability of the vaccine to treat anyone already infected. Understanding how HPV enters and infects cells is important, as this work may lead to the development of new antivirals or therapeutics and may also reveal new aspects of cell and protein biology. HPVs are non-enveloped viruses, containing an ~8000 base pair double-stranded DNA genome encapsidated by 360 copies of L1 major capsid protein and up to 72 …
Quantum Error Detection And Correction Of Bosonic Codes In A Superconducting Cavity, Akshay Koottandavida
Quantum Error Detection And Correction Of Bosonic Codes In A Superconducting Cavity, Akshay Koottandavida
Yale Graduate School of Arts and Sciences Dissertations
Detecting and correcting decoherence errors is essential for the preser- vation of encoded information in quantum systems. Quantum error correction (QEC) based on bosonic codes where the information is stored in the multiple levels of harmonic oscillators has shown much promise recently. Bosonic codes, specifically those implemented in superconducting cavities, suffer from microwave photon losses which lead to increase in entropy of the system. How can we reduce this entropy, or in other words, can we detect and/or correct the errors associated with microwave photon loss of the cavity? This thesis work proposes and implements novel codes to address these …
Cosine-100 And Anais-112: Two Experiments, One Search For The Annual Modulation Of Dark Matter, Sophia J. Hollick
Cosine-100 And Anais-112: Two Experiments, One Search For The Annual Modulation Of Dark Matter, Sophia J. Hollick
Yale Graduate School of Arts and Sciences Dissertations
Overwhelming evidence has been observed for the existence of dark matter; however, it has yet to be directly detected. Since 1997, the DAMA/LIBRA experiment has claimed to detect a dark matter signal, taking the form of an annual modulation consistent for over 20 yearly cycles. Though DAMA/LIBRA reports a 13.7 sigma significance, experiments utilizing different detector technologies have excluded their result by several orders of magnitude. To definitively test the validity of the claim, COSINE-100 and ANAIS-112 have mounted experiments with the same detector medium, NaI(Tl). Both experiments have reported results consistent with no modulation and are on the cusp …
Essays In Development Economics, Timothy Hersey
Essays In Development Economics, Timothy Hersey
Yale Graduate School of Arts and Sciences Dissertations
Over the last half century, global religious affiliation to new Pentecostal denominations has grown rapidly, with this growth concentrated in low income countries. This thesis investigates one economic factor influencing this growth - rural-urban migration. Religious institutions attract members by serving as hosts for economic and social networks, a service which interacts strongly with the migration process. I present new evidence from Ghana to test the link between migration and religious affiliation, using data from the ISSER Northwestern-Yale Panel Survey (GSPS) and a survey of Pentecostal churches in Accra.In the first chapter, I consider the effect of migration on the …
Asymmetric Synthesis Of Bioactive Scaffolds Via Organocatalysis, Melody Guo
Asymmetric Synthesis Of Bioactive Scaffolds Via Organocatalysis, Melody Guo
Yale Graduate School of Arts and Sciences Dissertations
Chiral catalysts allow chemists to access enantioenriched materials without the use of proportionate amounts of chiral reagents, while lowering the energy barrier of the original reaction. One way to form bioactive, heteroatom-containing scaffolds asymmetrically is through the use of chiral organocatalysts. This dissertation covers the development of stereoselective reaction methodology to access bioactive scaffolds and mechanistic investigations into intriguing features therein. Chapter 1 describes the development of the asymmetric synthesis of axially chiral quinazolinones. In this project, complementary applications for two different scaffold classes of chiral phosphoric acid (CPA) catalysts are found. We observe that while a C2-symmetric CPA catalyst …
The Role Of Local Factors In Shaping Microbial Communities And Biogeochemical Functions Across Scales, Alexander Polussa
The Role Of Local Factors In Shaping Microbial Communities And Biogeochemical Functions Across Scales, Alexander Polussa
Yale Graduate School of Arts and Sciences Dissertations
Microorganisms play a vital role in carbon cycling, driving the decomposition and transformation of organic matter (OM) in soils. This dissertation examines how both broad climatic and local factors shape microbial communities and influence organic matter decomposition. Through a combination of microcosm and field experiments, I demonstrate that local conditions like soil moisture, depth and plant identity impact microbial function, although these effects can be masked by broader climatic influences. I also investigate how the ericoid shrub, Kalmia latifolia, differentially affects fungal communities under arbuscular and ectomycorrhizal trees. Finally, integrating results from multiple forest sites in the eastern US, I …
Machine Learning In Finance: Applications To Understanding Investor Behavior And Asset Prices, Kangying Zhou
Machine Learning In Finance: Applications To Understanding Investor Behavior And Asset Prices, Kangying Zhou
Yale Graduate School of Arts and Sciences Dissertations
This dissertation consists of three essays on machine learning in finance, focusing on its applications to understanding investor behavior and asset prices. The first essay is titled "Professional Investors and Media Narratives." I investigate the impact of media narratives on the portfolio strategies of active equity mutual funds. Using 1.5 million Wall Street Journal articles from 1984 to 2023, I use ChatGPT to distill media narratives into 59 distinct topics, and quantify each topic's time-varying share of news attention and sentiment. I then define a fund as having exposure to a topic if it overweights stocks expected to perform well …
Understanding The Mechanisms Regulating Neuronal Metabolic States In Vivo, Milind Singh
Understanding The Mechanisms Regulating Neuronal Metabolic States In Vivo, Milind Singh
Yale Graduate School of Arts and Sciences Dissertations
Glycolysis, a glucose-consuming pathway required for cellular energy production, iswell conserved across species and has been extensively characterized biochemically. Less is understood regarding how it is subcellularly organized, or coordinated across tissues in vivo. Previous work from our lab found that during transient hypoxia or neuronal stimulation, the rate-limiting glycolytic enzyme phosphofructokinase-1 (PFK-1.1) dynamically re-localizes from the cytoplasm to condensates near synapses in C. elegans neurons. My research examined mechanisms by which PFK-1.1 localization is regulated in neurons, and resulted in two main findings: 1) PFK-1.1 condensate formation in neurons is regulated by a non-cell-autonomous signal derived from hypodermal (epidermal) …
Quantum Control Of An Oscillator With A Kerr-Cat Qubit, Andy Zhenghao Ding
Quantum Control Of An Oscillator With A Kerr-Cat Qubit, Andy Zhenghao Ding
Yale Graduate School of Arts and Sciences Dissertations
Noise presents a major obstacle to scaling up quantum computers, causing logical errors and preventing the reliable execution of quantum algorithms. Quantum error correction provides a path toward fault-tolerance, but this typically comes at the cost of significant resource overhead. Bosonic codes offer a hardware-efficient strategy for quantum error correction by redundantly encoding quantum information in the large Hilbert space of a harmonic oscillator. These codes have been employed to achieve landmark experimental demonstrations. However, these demonstrations are limited by transmon ancilla errors propagating to the encoded logical qubit during syndrome measurements. The Kerr-cat qubit has been proposed as a …
Characterizing And Improving The Readout Of Superconducting Qubits, Wei Dai
Characterizing And Improving The Readout Of Superconducting Qubits, Wei Dai
Yale Graduate School of Arts and Sciences Dissertations
The development of fault-tolerant quantum computers relies critically on fast and accurate readout of qubit states. In state-of-the-art superconducting quantum processors, the readout operations exhibit higher error rates and longer execution times compared to single- and two-qubit gates, bottlenecking their performance. How can we realize faster readout with lower error rates in superconducting circuits? In this dissertation, we answer this question through addressing two pressing limitations in the dispersive readout scheme: readout-induced state transitions and Purcell decay of the qubit. We introduce the "readout channel benchmarking" technique for the faithful benchmarking of readout performance accounting for the readout-induced state transitions. …
The Linc Complex Component Kms1 And Cenp-B Protein Cbp1 Cooperate To Enforce Faithful Homology-Directed Dna Repair At The Nuclear Periphery, Alyssa Laffitte
The Linc Complex Component Kms1 And Cenp-B Protein Cbp1 Cooperate To Enforce Faithful Homology-Directed Dna Repair At The Nuclear Periphery, Alyssa Laffitte
Yale Graduate School of Arts and Sciences Dissertations
DNA double-stranded breaks (DSBs) represent a danger to genome stability. Cells repair DSBs mainly through one of two pathways: canonical non-homologous end-joining (cNHEJ), which requires the direct ligation of the two DSB ends, or homologous recombination (HR), which involves the use of a homologous template to create a faithful repair product. While HR is often considered to be an error-free mechanism, the ultimate fidelity of this pathway depends on the ability of the cell to identify and engage with the correct homologous template. This is particularly challenging during repair of repetitive regions of the genome for which non-allelic sequences can …
Resource Efficiency At The Network Edge And Deep Learning Methods, Akrit Mudvari
Resource Efficiency At The Network Edge And Deep Learning Methods, Akrit Mudvari
Yale Graduate School of Arts and Sciences Dissertations
Next-generation networks, especially wireless and cellular networks, will feature massive IoT and embedded device deployments alongside various novel services, most of which may be constrained by energy and computational capabilities. As a result, these networks must address challenges such as device limitations, scalability, resource management, and energy efficiency for both computation and communication. The rise of deep learning has unlocked significant potential for various new AI-driven applications, meaning next-generation communication networks could benefit tremendously from these approaches, particularly for efficient resource allocation. Simultaneously, the growing prevalence of AI-driven applications on intelligent devices at the network edge implies that numerous applications, …
Computational Study Of Redox-Active Protein Residues And Biological Proton-Coupled Electron Transfer, Qiwen Zhu
Computational Study Of Redox-Active Protein Residues And Biological Proton-Coupled Electron Transfer, Qiwen Zhu
Yale Graduate School of Arts and Sciences Dissertations
Proton-coupled electron transfer (PCET) reactions are essential processes in biological systems, fundamental to various enzymatic functions and redox biology. Key to these reactions are redox-active residues, such as tyrosine and tryptophan, which enhance the efficiency and specificity of electron transfer events. This thesis investigates the thermodynamics, kinetics, and conformational influences of PCET in proteins involving these residues through three projects, each offering significant insights into the mechanisms and broader implications for biological function. The studies have focused on two protein systems: a simple de novo protein system, α3X, and ribonucleotide reductase, an enzyme critical to DNA synthesis. Combining a wide …
Creating Socially Competent Mobile Robots: Rethinking How To Measure Success, Nathan Tsoi
Creating Socially Competent Mobile Robots: Rethinking How To Measure Success, Nathan Tsoi
Yale Graduate School of Arts and Sciences Dissertations
Motivated by the value alignment problem, which is concerned with ensuring that an autonomous system's behavior matches user values, this dissertation proposes that creating socially competent mobile robots requires rethinking how success is measured in order to align evaluation metrics with human values and to this end, proposes the use of context-aware simulation systems and subjective human feedback. Social robot navigation is concerned with an agent that must traverse the navigable space in an environment that is shared with people. Conducting such motion in dynamic and densely populated environments demands that a robot understands how humans perceive its behavior and …
A Bioluminescent Approach To Coxiella Burnetii Pathogenesis: Development And Utilization Of An In Vivo Imaging Model, Jenna Myr Andrews
A Bioluminescent Approach To Coxiella Burnetii Pathogenesis: Development And Utilization Of An In Vivo Imaging Model, Jenna Myr Andrews
Yale Graduate School of Arts and Sciences Dissertations
Coxiella burnetii is a Gram-negative, obligate intracellular bacterium that infects livestock and causes Q fever in humans, which can range from acute flu-like symptoms to severe, persistent infections. C. burnetii relies on a Dot/Icm type IVB secretion system to translocate effector proteins, manipulating host cell processes to support intracellular replication. While axenic media have facilitated in vitro pathogenesis research, in vivo studies remain limited due to the classification of the virulent Nine Mile phase I strain as a category B select agent. Although the avirulent phase II strain RSA493 is exempt from this classification, it is rapidly cleared in immunocompetent …