Physical Sciences and Mathematics Commons^™

3bb: Loss And Remembrance In The Anthropocene, Amanda J. Woolsey

Dissertations, Theses, and Capstone Projects

Undisputedly, we are living in a time of tremendous and unprecedented ecological loss. Various forms of life on earth are disappearing at a rate unheard of in human history, with a growing amount of evidence suggesting that we are in a period of mass biodiversity loss and extinction. This extinction event is marked by a series of environmental catastrophes that vary in acceleration, intensity, and impact, such as climate-change driven weather events wiping out an endemic island species, to habitat loss and fragmentation leading to the slow death of a once-common species. One such piece of supporting evidence is Rosenberg …

The Role Of Confined Hydration And Water Reorganization In Molecular Binding, Joe Z. Wu

Dissertations, Theses, and Capstone Projects

An important factor in guiding the development of drug discovery efforts is the comprehensive assessment of a ligand or drug’s ability to bind its receptor. The metric used to measure this interaction strength is by calculating the binding free energy (BFE). To achieve this accurately, we combine two concepts: (1) Grid Inhomogeneous Solvation Theory (GIST) returns the local water thermodynamic and structural contributions to free energy; and the (2) Alchemical Transfer Method (ATM) obtains the absolute (ABFE) and relative binding free energy (RBFE) estimates between ligand pairs. In this work, we employ Alchemical Water-Transfer to tether bridging water(s) during the …

Silver-Alloyed Cigs Thin-Film Solar Cells On Flexible Stainless-Steel Substrate, Zhi Huang

Dissertations, Theses, and Capstone Projects

Our dissertation demonstrates the optimization of ACIGS (Ag-Cu-In-Ga-Se) thin-film solar cells, achieving an efficiency of 20.4% through the combined effects of silver incorporation and alkali metal post-deposition treatment (PDT). The incorporation of 2.8% Ag into the CIGS lattice enhanced crystal quality, reduced disorder, and widened the bandgap by 0.103 eV, as evidenced by a significant reduction in Urbach energy. These improvements resulted in stronger light absorption, increased carrier generation, and enhanced photovoltaic parameters, including a short-circuit current density Jsc of 35.31 mA/cm², an open-circuit voltage Voc of 0.74 V, and a fill factor (FF) of 75.8%. PDT using rubidium fluoride …

Project Title: Maximizing The Volume Of A Cardboard Box To Save Trees– An Application Of Polynomial Functions To Address Global Issues [Mathematics], Lucie Mingla

Open Educational Resources

MAT 115 College Algebra & Trigonometry/Precalculus

Project Title: Maximizing the Volume of a Cardboard Box to Save Trees– An Application of Polynomial Functions to Address Global Issues

Reflective Narrative:

This project was inspired by my participation in the "Designing and Implementation of STEM Co-Curricular Activities" CTL seminar in Spring 2023. I am grateful to Drs. Bukurie Gjoci, Daniel Gertner, Ingrid Veras, and Midas Tsai, along with fellow participants, for their invaluable feedback that helped shape its development. The project was implemented in two College Algebra and Trigonometry courses. I participated in two seminars to further develop this project. The Community …

Chatgpt Didn’T Write This: Evaluating The Impact Of Llms With A Case Study In Grading Cuny Language Immersion Program Student Essays, Benjamin Inbar

Dissertations, Theses, and Capstone Projects

This study evaluates the capabilities and limitations of large language models (LLMs), specifically OpenAI’s ChatGPT-4o, in grading essays from students in the City University of New York’s Language Immersion Program. The program serves English language learners with diverse linguistic and demographic backgrounds, offering intensive language instruction to prepare students for academic success in college. Using a dataset of 30 pre- and post-program essays scored by program instructors and ChatGPT-4o under three paradigms, this research explores the alignment between human and AI-generated scores across five rubric-based competency areas. Findings reveal that ChatGPT-4o aligns moderately with human grading, with the strongest agreement …

Investigating Dna Damage Caused By Reactive Oxygen And Nitrogen Species Via Guided-Ion-Beam Scattering And Computational Techniques, Jonathan Benny

Dissertations, Theses, and Capstone Projects

Among DNA nucleobases, guanine (G) is the primary target for one-electron ionization and oxidation, generating G●+ through various processes, including photooxidation, electrocatalytic oxidation, DNA-binding transition metals, ionizing radiation, and photolysis. This is due to the low adiabatic ionization potential and oxidation potential of guanine. Electron holes from other nucleobases can move to guanine, proving that G●+ production traps oxidative DNA damage. G●+ formation can exacerbate DNA damages and cause secondary reactions from reactive oxygen species (ROS) and reactive nitrogen species (RNS) during pathological processes. The following three projects were conducted using a customized electrospray ionization (ESI) guided-ion-beam tandem mass spectrometer, …

Taming Biological Complexity Through The Use Of Symmetries, Luis A. Álvarez-García

Dissertations, Theses, and Capstone Projects

The study of biological systems is, inherently, the study of very complex systems. This is essentially due to the fact that they are made up of numerous, often very complicated, interactions between an extensive number of components. Often necessitating an abundance of quantitative parameters and details for a precise description. The human brain for ex- ample, consisting of ∼ 80 billion neurons with ∼ 800 to 100 trillion connections between them, each of them depending on a large set of parameters. Even simpler examples such as bacterial organisms, such as E. coli and B. subtilis, which we focus on …

Novel Alchemical Methodologies For Modeling Molecular Binding, Solmaz Azimi

Dissertations, Theses, and Capstone Projects

Molecular recognition is fundamental to all biological and biochemical processes. Understanding the interactions between molecules is the foundation for drug discovery and development, for understanding biological processes, and for the design of biosensors and nanomaterials. There is tremendous interest in the development of computer models to predict molecular association equilibria. In structure-based drug discovery enterprises, predicting the strength and selectivity of a small molecule to a biological target can advance target identification, aid ligand design, and accelerate high-throughput screening of drug compounds. This work focuses on free energy models, a class of computational methodologies grounded on the fundamental physical and …

Testing Toxicity: Two Approaches To Toxicity Detection, Nelson E. Jarrin

Dissertations, Theses, and Capstone Projects

The current online environment is increasingly being polluted by polarization, echo chambers, and a lack of constructive dialogue between individuals with differing viewpoints. Social media algorithms, while intended to personalize user experiences and marketing areas, have been heavily criticized for inadvertently amplifying extremist content and contributing to the spread of toxic commentary. The current state of the internet hinders productive conversations, fuels misinformation, entices disinformation and contributes to online and offline societal division. This is fueled by algorithms that can create echo chambers and by the anonymity given by online platforms. While tools like the Perspective API exist to identify …

Consequences Of Oxidative Dna Damage: Base-Pair Dissociation, Singlet Oxygenation And Dna-Protein Crosslinking, May Myat Moe

Dissertations, Theses, and Capstone Projects

8-Oxo-2′-deoxyguanosine (OG) is a common DNA lesion resulting from oxidatively generated damage and pairs with complementary cytidine (C) in Watson Crick base-pairing within duplex DNA. The WC-OG·C lesion, if not recognized or repaired, not only leads to G⋅C→T⋅A transversion mutations (through Hoogsteen (HG) base pairing of OG⋅A), but also renders the base pair being more vlunerable to ionizing radiation and singlet oxygen (1O2) damage. Leveraging on our previous accomplishments on the study of gas-phase reactions of 1O2 with 2′-deoxyguanosine radical cations, my research thesis expanded to the investigation of reaction dynamics of 9-methyl-8-oxoguanine (9MOG) radical cations. The experiments of following …

The Role Of Secondary And Tertiary Structure In The Cap-Independent Translation Of Fgf-9 And Hif-1-Alpha, Amanda Michelle Whittaker

Dissertations, Theses, and Capstone Projects

Under normoxic conditions, eukaryotes initiate translation of RNA through eIF4E recognition of the 5’ cap. However, under cellular stress, eukaryotic translation must be initiated through a 4E-independent, or “cap-independent” mechanism, involving eukaryotic initiation factor 4G (eIF4G) binding directly to the 5’ untranslated regions (5’ UTR) of the RNA. eIF4G binding then recruits the ribosome to the transcript. While this mechanism is useful for translation of apoptotic transcripts and transcripts involved in cell survival, cap-independent translation is also utilized by oncogenic RNA for tumorigenesis. Previous work by our lab and others has categorized this recruitment and initiation mechanism as either internal-ribosome-entry-site …

Studies On The Synthesis, Function, And Properties Of Troponoids, John-Charles A. Baucom

Dissertations, Theses, and Capstone Projects

Troponoids are a unique class of non-benzenoid aromatic compounds with a wide range of demonstrated applications in pharmaceuticals and molecular sensing. The cycloheptatrienone scaffold possesses a noteworthy degree of tunability as a function of ring oxygenation. This manuscript describes our efforts toward a better understanding of the physical consequences of the scaffold to better utilize the motif. Chapter the first discusses our efforts at elucidating the mechanism of troponoid inhibition of the Hepatitis B virus reverse transcriptase RNAse H enzymatic domain. Using homology modeling in conjunction with traditional in vitro assays we were able to establish the likely mechanism of …

Tracing The Sources Of Nitrogen In Submarine Groundwater Discharge And Primary Producers In The Great South Bay Estuary, Nia H. Rene

Dissertations, Theses, and Capstone Projects

The primary aim of this research was to elucidate the impact of submarine groundwater discharge (SGD) and septic effluent on coastal primary producers in the Great South Bay (GSB). The study focused on three main objectives: assessing the impact of precipitation patterns on SGD, tracing nitrogen sources into the GSB, and determining the impact of these nitrogen sources on coastal primary producers. The research revealed that current precipitation patterns significantly influence SGD across different seasons, highlighting the seasonal variability in groundwater discharge and its implications for nutrient loading in coastal waters. A suite of tracers was employed to identify and …

Geospatial Machine Learning Approaches For Studying Urbanization Impact, Surface Reflectance Patterns, And Groundwater Health Risks, Bibhash Nath

Theses and Dissertations

Geospatial machine learning techniques have been used to study: the impact of urbanization on land use and land cover change, surface reflectance patterns in boreal regions, and groundwater health risks from arsenic in India. These studies combined spatial data, remote sensing, and predictive models to gain valuable insights for sustainable living and protecting human health.

Lowering The Barrier For Reading Primary Literature In Stem, Sebastian G. Alvarado, Maral Tajerian

Open Educational Resources

Building Bridges of Knowledge (BBK) is a cross‑CUNY initiative that integrates artificial intelligence (AI) and open educational resources to lower the barrier to primary literature and enhance research‑focused pedagogy. Recognizing that scientific papers are often dense and inaccessible to newcomers, we developed a suite of AI‑assisted instructional materials and activities to help students interpret complex data and methodology. A central component is the use of large language models (LLMs) and tools such as Scite.ai to provide citation‑context analytics and personalized research support. These tools allow students to filter literature by supportive, neutral, or contrasting citation statements and to troubleshoot laboratory …

Estimating The Amount Of Carbon Dioxide Gas Removed From The Atmosphere By The Bryant Park Tree Population, Edimarlyn Gonzalez

Open Educational Resources

No abstract provided.

Investigating The Impact Of Pfas Contamination On Mental Health, Jihyun Kim

Open Educational Resources

To explore the intersection of environmental injustice, racial disparities, and public health through an examination of PFAS contamination in drinking water and its impact on communities of color. This study will address environmental, social, and health implications of PFAS exposure, with a specific emphasis on promoting equity and advocating for policy changes to rectify systemic inequalities.

Identifying Intangible And Biocultural Heritage Elements Toward Environmental Understanding: Engaging Stakeholders Through Art, Martha B. Lerski

Publications and Research

Grounded in a case study in Barbuda in the Caribbean, this research examines sustainability from the perspective of what arts and heritage can contribute to community engagement and local and broader understandings about the environment. This article documents a growing body of literature recognizing the role of arts and culture, including local knowledge and traditional ecological knowledge (TEK), in climate change endeavors. Art and TEK present expansive world views. Contextual information situates research done on the island of Barbuda pre- and post-Hurricane Irma. Visual arts workshops engaged community members in mixed methods research. Results documented cultural elements, particularly intangible and …

Experiment 1--Density, Measurement And Significant Figures, Kevin Mark, Phil Mercier

Open Educational Resources

Lab objectives:

• To identify an unknown metal by measuring and calculating its density
• To determine the density of an unknown liquid by graphing mass and volume data
• To compare the accuracy and precision of water mass using measurements from a beaker and burette

Csc36000 - Modern Distributed Computing Assignment 2, Saptarashmi Bandyopadhyay

Open Educational Resources

This assignment is designed to help the student identify and mitigate common errors in Distributed Computing such as race conditions and reaching consensus, as well as reflecting on how Distributed Computing concepts apply to their class project.

Analyzing Acid Rain And Industrial Activity, Jooyoung Jeon

Open Educational Resources

This assignment by Jooyoung Jeon asks students to explore the relationship between acid rain occurrences and industrial activity by analyzing open datasets. It was created as part of a workshop on OER-based Active Learning at John Jay College in 2025.

Scp 231 Dictionary + Example Problems [General Physics 1], Daniel Capic

Open Educational Resources

Student-written definitions of key physics concepts that appear in SCP 231. There are also student-written word problems with links to instructor-created video solutions.

Developing Mathematical Maturity By Solving A Given Quadratic Equation, Armando A. Amador, Nieves Angulo, Juan B. Lacay

Publications and Research

This article explores the instructional challenges faced by mathematics educators when addressing students’ limited background knowledge and underdeveloped mathematical maturity, two critical barriers to success in college-level algebra. Using the quadratic equation 2x2+x−3=0, which is reducible over the field of rational numbers ℚ ⊂ ℝ, we analyze how diverse solution methods—factoring, completing the square, and the quadratic formula—can support learning. An additional strategy, “Slide and Divide,” was introduced to promote procedural fluency and conceptual flexibility. To gain insight into students’ evolving mathematical maturity, an online survey was conducted to students at various levels of mathematics. The survey captured their perspectives …

Dual View Of The Z2-Gauged Xy Model In 3d, Piers Coleman, Anatoly Kuklov, Alexei Tsvelik

Publications and Research

The Z₂ gauged XY model is of long-standing interest both in the context of nematic order, and the study of fractionalization and superconductivity. This paper presents heuristic arguments that no deconfinement of the XY field occurs in this model and presents results of a large-scale Monte Carlo simulations on a cubic lattice which are consistent with this conclusion. The correlation radius determining the confinement is found to be growing rapidly as a function of the parameters in the phase featuring the nematic order. Thus, mesoscopic properties of the system can mimic deconfinement with high accuracy in some part of …

Quantum-Mechanical Definition Of The Classical Scalar Potential In Schrödinger-Pauli And Schrödinger Theory, Viraht Sahni

Publications and Research

According to the Bohr correspondence principle, the external temporal scalar potential in the classical equation of motion is replicated in quantum theory as a multiplicative operator. An equivalent quantum-mechanical definition of the scalar potential in Schrödinger-Pauli/Schrödinger theory is provided. The potential is a known universal functional of the wave function. At each instant of time, it is the work done in a conservative “classical” field representative of internal properties of the system: Pauli and Coulomb correlations, kinetic effects, the density, the Lorentz force, an internal magnetic component, and the current density response. The Hamiltonians are thus rewritten in a …

Explorations Of Dna-Single-Walled Carbon Nanotube Interactions To Develop Multiplexed Molecularly Specific Biosensors For Inflammation, Amelia K. Ryan

Dissertations and Theses

Inflammatory cytokines such as interleukin-6 (IL-6) and interleukin-12 (IL-12) are central regulators of immune signaling and key biomarkers of disease, yet existing assays for their detection remain slow, invasive, and lack multiplexing ability. This dissertation advances the development of single-walled carbon nanotube (SWCNT) optical nanosensors capable of real-time, multiplexed, and molecularly specific cytokine detection through innovative use of single-stranded DNA (ssDNA) interfaces.

First, an IL-6-specific DNA aptamer was employed as both a dispersing agent and recognition probe for SWCNT fluorescence sensing. Sequence modifications, including anchor domains, truncations, and thermally induced refolding, were systematically tested to optimize sensitivity and selectivity. The …

Development Of An Quadcopter Unmanned Aerial Vehicle For Atmospheric Remote Sensing, Omar J. Addasi

Dissertations and Theses

This paper explores the development of a quadcopter unmanned aerial vehicle (UAV, a.k.a. drone) for atmospheric remote sensing of temperature, pressure, humidity, and PM2.5 particulate matter quantities. A 3-D printed drone body is designed and flight tuning is performed. An optimal length for an upward extending mast for the drone body is determined. Low cost, lightweight sensors are compared against higher precision sensors in both static and dynamic conditions. In addition, an initial investigation into the design of a pressure sensor based anemometer is performed.

Classification Of Variable Stars Using Convolutional Neural Network, Abhina Premachandran Bindu

Dissertations and Theses

This research focuses on developing Convolutional Neural Networks (CNNs), for the process of classifying and identifying variable stars through the analysis of unprocessed light curves from Transiting Exoplanet Survey Satellite (TESS). As astronomical data is becoming increasingly complex, and as advanced missions deploy sophisticated instruments for data collection, both the quality and quantity of the data are improving at a rapid pace. This has created an urgent need to automate the analysis process using efficient and effective methods, such as those based on machine learning. While previous research has explored machine learning approaches, there has been limited focus on implementing …

Metasurfaces And Their Applications In Photonic Devices, Shuwei Guo

Dissertations and Theses

Metasurfaces are flat artificial optical elements composed of dielectric and/or metallic nanostructures. They can manipulate light in unprecedented ways by altering amplitude, phase, and polarization at subwavelength scales. The ability of these two-dimensional elements to perform multiple optical functions within compact optical systems—while offering high functionality, small form factors, and easy integration into optoelectronic devices—has sparked significant interest across various fields and industries. These applications span imaging, sensing, nonlinear and quantum optics, optical computing, automotive technology, augmented and virtual reality, and more.

In this dissertation, we explore and design new multifunctional metasurfaces with a focus on manipulating spectral responses. First, …

Using Deep Neural Nets In Writer Identification & Analysis, Aditya Majithia

Dissertations and Theses

This thesis focuses on developing automated deep learning methods for writer identification and writer attribute prediction from handwriting. It introduces two novel architectures: Convolutional Transformer Encoder (CTE) and Convolutional Swin Encoder (CSE). CTE is designed for determining authorship from handwritten text, be it modern or historical handwriting. CTE tracks subtle features and cues from handwriting strokes to distinguish authorship. It is the first of its kind capable to operate on historical handwritten fragments, setting it apart from existing methods that rely on entire document pages. CSE is designed to determine multiple attributes of an author such as authorship, gender, age …