Digital Commons Network^™

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 …

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

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

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

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

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

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 …

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

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

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

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

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

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

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 …

Spatial Control Of Nonlinear Interactions In Multimode Fibers, Kabish Wisal

Yale Graduate School of Arts and Sciences Dissertations

In recent years, there has been significant advancement in controlling optical scattering by structuring the wavefront of the incident light, or `wavefront shaping'. Most applications of wavefront shaping have focused on linear scattering, but there is a growing interest in tailoring nonlinear scattering. In this thesis, we explore a new approach based on wavefront shaping for suppressing certain instabilities induced by nonlinear scattering in passive and active multimode fibers (MMFs). Specifically, we focus on suppressing stimulated Brillouin scattering (SBS) and transverse mode instability (TMI). A key motivation for our work is power scaling in high power fiber lasers and amplifiers, …

Deep Learning For Large-Scale Harmonic Analysis: A Corpus Study Of Western Harmony From 1700-1900, Malcolm Sailor

Yale Graduate School of Arts and Sciences Dissertations

This dissertation trains deep learning models for the Roman numeral analysis and applies these to the analysis of a corpus of over 12,000 movements of Classical music composed between 1700 and 1900. The Roman numeral analysis models obtain performance that is, as of this writing, state of the art. At the same time, this is the first work of scholarship to employ such models at scale for a music-theoretic corpus study. Consistent with music-historical expectations, this corpus study shows that, along many dimensions, such as the distribution of keys employed or the proportion of chromatic scale degrees, harmonic complexity rose …

Graduate Bulletin 2025-2026, Cuny John Jay College

College Bulletins

Covers academic years 2025-2026

Undergraduate Bulletin 2025-2026, Cuny John Jay College

College Bulletins

Covers academic year 2025-2026

Jack Raverty Honors Portfolio, Jack Raverty

Honors Capstone Portfolios

Jack Raverty's honors portfolio captured in May 2025.

Oltjona Muca Honors Portfolio, Oltjona Muca

Honors Capstone Portfolios

Oltjona Muca's honors portfolio captured in May 2025.

Anne-Lyse Nono Honors Portfolio, Anne-Lyse Nono

Honors Capstone Portfolios

Anne-Lyse Nono's honors capstone portfolio captured in May 2025.

Design And Implementation Of A Low-Cost Raspberry Pi And Ai-Based Intrusion Detection System For Surveillance, Metrine Nyaboke Osiemo

All Graduate Theses, Dissertations, and Other Capstone Projects

As security concerns continue to rise, there is a growing demand for affordable and intelligent surveillance solutions to ensure safety in homes, businesses, and other environments. Many individuals are embracing AI-driven technologies such as Closed-Circuit Television (CCTV), smart doorbells, and automated security systems to protect their properties. This project presents a design and implementation of a cost-effective AI-powered intrusion detection system utilizing Raspberry Pi 5 for home surveillance, with adaptability for broader applications. The system integrates a camera module and an LCD screen running on a Linux-based platform, with Python, and OpenCV as key software components. It employs dlib’s deep …

Exploring Physiotherapist’S Ability To Identify Cauda Equina Syndrome Early, Khalid F. Althobaiti, Joshua R. Zadro, Fahad A. Alzhrani, Hosam A. Alzahrani

Neurosciences

ABSTRACT Objectives: To explore the ability of physiotherapists in Saudi Arabia to identify cauda equina syndrome (CES) in a timely manner, and to identify the methods used by physiotherapists to manage patients with suspected CES. Methods: This study utilized a cross-sectional research design and was conducted in the period May-October 2023. It included licensed physiotherapists working in Saudi Arabia. The data was collected using a survey that aimed to assess physiotherapists’ ability to identify CES early, using 12 statements. Based on the participants response to these statements, all responders were categorized into the following groups based on their ability to …

Impact Of Digital Courseware Use On Online Student Sense Of Belonging And Potential For Building An Online Community Of Inquiry, Kat Klement

All Graduate Theses, Dissertations, and Other Capstone Projects

Though interest in online education is rising, online programs have a lower retention rate than do in-person programs and a correspondingly higher dropout rate. One factor that drives online student retention is the degree to which students feel a sense of belonging in their online courses. As more interest in online education leads to larger course sizes and more online sections, instructors may turn to digital courseware offered by publishing companies to increase student engagement and provide formative assessment. Yet research shows little consistency in the impact of digital courseware use on course grades. The studies in this thesis explored …

Teaching Object-Oriented Design Through Interactive Uml: A Dual-Approach Framework For Code-Based Generation And Direct Diagram Manipulation, Moses Kayuni

Masters Theses & Specialist Projects

This thesis introduces an interactive educational framework for teaching object-oriented design through UML class diagrams. The framework implements a dual-approach methodology: code-based generation, where students write Java code that automatically transforms into UML diagrams, and direct diagram manipulation, where students build diagrams by interacting with highlighted terms in problem descriptions. This approach addresses common challenges in teaching UML, including cognitive load difficulties, visualization problems, and the disconnect between code implementation and visual design. Built on the Mermaid diagramming framework, the system features a React frontend for diagram creation and manipulation, and a Flask backend that handles some code parsing and …

Makers Of Identity: Those That Hold It, Or Those That Create It?, Valentina K. Quintero

SPARK Symposium Presentations

Throughout the semester, the topic of AI potentially achieving personhood has been a deeply debated topic. Issues rise and fall depending on perspective, and there are still too many unknowns to be completely certain that AI has either managed to become a person or has not. One of the key details of personhood is the modern understanding of the word identity. This paper will go into the origins of the word and how it may have changed, and how it is important in regards to AI and its potential. Wittgenstein’s language games, personal opinion, and cultural influences will be explored …

The Economic And Environmental Impact Of Shinkansen And High-Speed Rail Infrastructure: A Comparative Analysis Of Economic Growth And Carbon Emissions Reduction, Dillan R. Victory

SPARK Symposium Presentations

The development of Japan's high-speed rail system, the Shinkansen, has played a pivotal role in the country's post-war economic resurgence. Introduced in 1964 with the Tokaidō Shinkansen, this transformative infrastructure investment significantly reduced travel times, bolstered economic activity around station hubs, and facilitated regional development by enabling urban decentralization. This paper explores the long-term economic benefits of high-speed rail, including its impact on land value, business expansion, and carbon emissions. The case study of the Linear Chuo Shinkansen, Japan's latest maglev project, underscores both the economic promise and the political resistance to expansion, particularly in regions such as Shizuoka.

Using …

Beyond The Editorial Analogy: First Amendment Protections For Platform Content Moderation After Moddy V. Netchoice, Alan Rozenshtein, Kyle T. Langvardt

Articles

This Article examines the Supreme Court’s 2024 decision in Moody v. NetChoice and its implications for social media platform regulation. In Moody, which addressed state laws requiring platforms to host certain content, the Court issued a complex set of opinions that left the scope of platforms’ First Amendment rights uncertain. On the procedural question of how such laws may be challenged, the Court provided a clear holding: it rejected facial challenges to broad content-moderation laws, instead requiring case-by-case analysis of how specific regulations affect different platform features—a shift that undermines the tech industry’s longstanding litigation strategy. But on the …

Women And Corporate Governance: Time Horizons And Stakeholder Analysis, June R. Carbone

Articles

This Article will build on my earlier work with Naomi Cahn and Nancy Levit to use the fate of women in individual companies to shine new light on the temporal orientations underlying corporate and labor and employment law and provide a basis for a new foundation for a combined approach. This Article will first explain why the shift to shareholder primacy, and the accompanying emphasis on short-term results tied to high stakes bonus pay, disproportionately short-changes female employees, whether in management or in line positions. The Article will maintain that it is not the shift to shareholder primacy in isolation, …

Abuse Of Power In The Workplace: The New Gender Discrimination Claims, June R. Carbone, Nancy Levit, Naomi Cahn

Articles

This article draws on our book, Fair Shake: Women and the Fight to Build a Just Economy, to show how the fight for gender equality has changed. Antidiscrimination laws took hold during an era of relative economic equality; the fight for gender equality was a fight to gain access to the rights of white men. Today’s economy creates much greater inequality and reserves the greatest rewards for a much smaller group, again predominately white and male, who can defy the rules and get away with it. In such contexts, anti-discrimination law premised on a fight for equality can provide only …