Digital Commons Network^™

Increased Backbone Rigidity Of Artificial Transcription Factors, Jasmine Glover, Emma Otey, Joanna K. Kwao, Nicholas Truex

Senior Theses

Programming DNA-binding proteins is an effective strategy for developing therapeutics that regulate gene expression. These proteins can directly bind to DNA to activate or repress transcription of specific genes. Zinc finger proteins are a class of DNA-binding proteins commonly found in eukaryotic organisms. Their DNA-binding function is derived from unique amino acid sequences within each domain that recognizes specific nucleotides, allowing each finger to selectively recognize three DNA base pairs. Adjoining of multiple domains in tandem allows recognition of a specific DNA sequence. Artificial transcription factors can be made of multiple zinc finger domains arranged in tandem and engineered to …

Studying Quantum Optics And Spdc With Single Photon Experiments, Chloe Pistelli

Physics Student Projects

Quantum optics is a specialized area of physics that focuses on using light sources, lenses, mirrors, beam splitters, photon detectors, and other optics equipment to demonstrate the wave-particle nature of light. We take advan tage of the spontaneous down-conversion of photons through a beta-barium borate (BBO) crystal, which splits one higher energy photon into two lower energy photons, conserving energy. We confirm the down conversion in our experiment by precisely aligning two detectors in each of the expected paths of the two down-converted photons and counting the number of coincidences detected, or number of times a photon was detected in …

Standing Firm On Sustainability, Helge Muenkel

Asian Management Insights

As priorities evolve, sustainability continues to shape key business decisions for organisations.

Competitive Reaction Pathways In The Fully Green Synthesis And Surface Modification Of Silver Nanowires Under L-Ascorbic Acid-Limited Conditions, Finley Neal

Honors Theses

Silver nanowires (AgNWs) are critical building blocks for transparent conductive films (TCFs) in flexible electronics, yet their commercial viability is hindered by environmentally hazardous, energy-intensive synthesis methods and limited intrinsic chemical stability. This study investigated a fully green, room-temperature (25℃) batch synthesis of pristine AgNWs using tannic acid as a biodegradable dual reducing and capping agent under strict kinetic pH control (pH 1.25). To enhance oxidative resistance, a subsequent surface modification protocol was evaluated to deposit a protective palladium (Pd) shell using L-ascorbic acid (LAA) as a secondary reducing agent. The pristine green synthesis yielded one-dimensional Ag nanostructures with a …

Algorithm Performance In The Search For Hamiltonian Cycles, Chance Davis

Honors Theses

The Hamiltonian cycle problem is ubiquitous in both computer science and graph theory: Given a connected graph, a solution would either confirm the existence of a cycle which visits each vertex only once or its nonexistence. The importance of this problem, as well as its difficulty, is described in the Clay Mathematics Institute’s Millenium Prize Problems and Karp’s 21 NP-complete problems. Despite its “hardness,” solutions to the Hamiltonian cycle problem are desired in logistics, electronic circuit design, and network routing, among other fields. In this work, we benchmark a promising exhaustive enumeration algorithm on various graphs, including ones derived from …

Ai-Assisted 3d Pre-Visualization: Streamlining Animatics For Filmmakers, Nishit Thapa

Honors Theses

Pre-visualization is a core part of film pre-production. Creators use it to test blocking, lighting, camera movement, and spatial relationships before committing to a shot. Despite this, three-dimensional pre-visualization remains out of reach for many entry-level filmmakers, as the software is expensive and takes substantial time to learn.

Recent AI developments have produced generative systems capable of creating highly re-alistic imagery and video from text prompts. These systems open new possibilities for visual sto-rytelling but are not built for the iterative, hands-on process that pre-visualization requires, where creators must adjust scene parameters, camera logic, and spatial configurations throughout.

This thesis …

Synthesis Of Piperidine Heterocycles With Specific Functional Groups Via Sn2 Reactions, Teyanna Monroe

Honors Theses

Piperidine is a heavily utilized nitrogen containing heterocycle found in numerous pharmaceutical agents, solidifying its importance as a building block in drug development. The focus of this research is to investigate different mechanisms of action for adding and replacing various functional groups utilizing readily available lab materials. These findings would lead to determining the overall influence of substitution patterns and functional groups have on stereochemistry, reactivity, and overall conformation of the piperidine ring. The synthetic approach involves the formation of 3-bromo-5-methoxy-tosylpiperidine intermediate through acid promoted cyclization, followed by nucleophilic substitution reactions to introduce various functional groups. Reaction progress and product …

Rethinking News Classification Through A Multi-Dimensional Framework, Luana De Jesus Ferreira

Honors Theses

This thesis proposes a multi-dimensional framework for news classification that evaluates articles across three independent dimensions: headline accuracy, language neutrality, and content reliability. These dimensions produce both a continuous reliability score and a five-tier interpretive scale, while additionally classifying articles by genre and topic. To operationalize this framework, a structured annotation protocol was developed and applied to a dataset of 373 news articles drawn from 79 outlets spanning a wide range of contemporary media ecosystem. A binary Logistic Regression classifier trained on the ISOT Fake News Dataset was then evaluated against this dataset to examine how a model trained on …

Deep Learning-Based Automated Pneumonia Detection From Chest X-Rays: A Comparative Study Of Custom Cnn And Transfer Learning Architectures, Ahmed Sajim

Honors Theses

Pneumonia is a leading global cause of mortality, claiming approximately 2.5 million lives an-nually and placing exceptional diagnostic pressure on radiologists in resource-limited settings. Manual interpretation of chest X-ray (CXR) images is time-consuming, subject to inter-observer variability, and limited by radiologist availability. This thesis presents a systematic investiga-tion into deep learning-based automated pneumonia detection comparing five convolutional neural network (CNN) architectures: a custom-designed 2D CNN and four pretrained transfer learning models—ResNet, DenseNet, MobileNet, and VGG19.

A targeted data augmentation pipeline addresses the severe class imbalance in the Kag-gle Chest X-Ray Pneumonia dataset, expanding the Normal class from 1,583 to 9,495 …

Taphonomy And Fossil Record Of Eufistulana Mumia In The Owl Creek Formation Of The Mississippi Embayment, Riley Rilette

Honors Theses

This study examines the taphonomy and preservation of Eufistulana mumia, a boring bivalve, within the Owl Creek Formation of northeastern Mississippi. The formation was deposited in a shallow marine environment of Maastrichtian age within the Mississippi Embayment. A total of 66 specimens were collected from exposures within the formation and analyzed to evaluate morphometric variation and orientation patterns. Field measurements of trend and plunge of each specimen were recorded in situ using a geological compass, and specimens were later prepared and measured in the laboratory with digital calipers. Morphometric results show consistent tube morphology, with basal widths larger than distal …

Revisiting The Hydrostatic Assumption In The Marine Atmospheric Surface Layer, Karina Griffin

Honors Theses

The marine atmospheric surface layer (MASL), defined as the lowest ~100 m of the atmosphere overlying the ocean, is a complicated environment influenced by air-sea interactions and regional  weather patterns. In the absence of air motion, air pressure in the MASL decreases with altitude at  a constant rate due to the reduction in weight of the overlying air column. This relationship is  defined by a linear hydrostatic equation and is applied under the assumption that any dynamic  vertical pressure gradients will be small relative to the hydrostatic pressure gradient. The  hydrostatic assumption is commonly applied in the MASL despite the …

Radiation Protection Factor Research: The Keystone For Conventional-Nuclear Integration (Cni), Andrew W. Decker

Faculty Publications

This article briefly describes Defense Threat Reduction Agency (DTRA) vehicle Radiation Protection Factor (RPF) research and explains its critical role in enabling future Operations in a Nuclear Environment (ONE) and Conventional-Nuclear Integration (CNI) on behalf of the US Department of War (DoW).1 As such, the background and practical utility of RPF values is discussed, as well as the justification for renewed Army and DoW investment into RPF research to enhance Joint military planning, survivability, and lethality on tomorrow’s nuclear battlefields. Advances in DTRA RPF research directly strengthen US strategic and extended deterrence efforts and support all Agencies and Departments responsible …

Downstream Effects Of Post Aerobic Digestion And Divalent Cation Treatment: Dewaterability, Phosphorus Mitigation, And Process Odors, Maya Marisol Quijano Garcia

Civil & Environmental Engineering Theses & Dissertations

This study evaluated post-aerobic digestion (PAD) with aeration, mixing, and divalent cation addition to improve phosphorus capture, dewaterability, and odor control in thermal hydrolysis process (THP)–treated anaerobic digestate at the Hampton Roads Sanitation District’s Atlantic Treatment Plant. A three-day PAD process was operated under constant air flow (5 LPM) and dissolved oxygen (DO)-setpoint (0.2 mg/L) aeration conditions with Ca(OH)₂ or Mg(OH)₂ dosing. Aeration and mixing alone increased polymer demand by 14–46 % relative to untreated influent, indicating enhanced extracellular polymeric substance release. Chemical conditioning partially mitigated this increase but did not restore polymer demand to baseline levels. Dewatered cake total …

Observations Of An Oscillatory Mechanochemical Reaction Between Tetrathiafulvalene And Chloranilic Acid, Alastair Deans

Physics Theses & Dissertations

Mechanochemistry is the study of chemical reactions driven by the input of mechanical en ergy in addition to thermal activation. Mechanochemical reactions from powders are carried out by manual grinding or milling using various types of ball mills, or in twin extruders. While mechanochemistry has great potential affording economically and environmentally advantageous “green” synthetic methods, a drawback is that its chemical mechanisms are not well understood. One example of such a reaction currently under study involves tetrathiafulvalene, an organic elec tron donor with two polymorphs (orange and brown), and chloranilic acid, an electron acceptor. Previous results show that neat grinding …

Dissecting The Etiology Of Alcohol Use Disorder By An Integrative Heritable Component Approach, Ivy Garrenton

Computer Science Theses & Dissertations

Alcohol Use Disorder (AUD) is a pervasive condition characterized by complex interplay among genetic, phenotypic, and environmental factors. Although previous studies have identi fied genetic loci associated with alcohol consumption, these efforts have not captured the genetic heterogeneity and gene-environment interactions underlying AUD pathogenesis. To address this critical gap, we developed a novel statistical methodology that integrates phenotypic, genotypic, and environmental data through an environmentally modified Genetic Relationship Matrix (GRM) to derive AUD-related traits with enhanced heritability.

This approach demonstrated superior performance in both simulated and real-world datasets. Traits derived using the environmentally modified GRM exhibited significantly higher estimated heritability …

Optimization Of Niobium Film For Particle Accelerators And Quantum Applications, Bektur Abdisatarov

Electrical & Computer Engineering Theses & Dissertations

Niobium (Nb) films play a central role in superconducting technologies used in particle accelerators and superconducting quantum circuits. Optimizing the physical properties of Nb films is therefore critical for improving both radiofrequency (RF) performance in superconducting radiofrequency (SRF) cavities and coherence in superconducting qubits. This thesis investigates the relationship between Nb film microstructure, impurity content, and electromagnetic response across these two application domains.

For particle accelerator applications, we studied Nb films deposited using high-power impulse magnetron sputtering (HiPIMS) with DC bias onto a 1.3 GHz elliptical SRF cavity. Nb film cavities exhibit a pronounced medium-field Q-slope, limiting their achievable accelerating …

Implementing A Clustering Framework On Distributional Bee Data, Roheel Nawaz

Research and Creativity Symposium

Understanding spatial patterns in biodiversity is important for identifying how ecological communities are structured across landscapes. Clustering methods provide a useful way to detect non-random species distributions and reveal potential environmental or geographic influences. In this study, we applied a clustering framework to a large long-term bee abundance dataset from the Mid-Atlantic United States to evaluate community structure across regions of Maryland, Delaware, and Washington, D.C.

The dataset included over 1,100 sites and more than 3,000 transects. Because sampling methods were not fully standardized, abundance data were converted to presence/absence and analyzed using the Jaccard index to measure site similarity. …

Traveling Waves In Reaction-Diffusion Equations With Delay In The Diffusion Term, William Barker, Van Minh Nguyen

Faculty Scholarship

We investigate the existence of traveling wave solutions for the reaction–diffusion equation ∂u(x,t)∂t=Δu(x,t−τ1)+f(u(x,t),u(x,t−τ2)), where τ1, τ2 > 0. This model is motivated by ecological applications in which migration rates incorporate historical effects and reproduction/death processes are subject to time delays at a given location. To address such systems under standard monotonicity assumptions, we extend the classical monotone iteration method. A key step involves a thorough investigation of the Green function associated with the functional equation x″(t)−ax′(t+r)−bx(t+r)=f(t), where a ≠ 0 and b > 0. Building on the resulting framework, we construct quasi-upper and lower solutions for the Belousov–Zhabotinski equations, thereby demonstrating the …

Quantifying Nutrient Fluxes Across The Sediment-Water Interface In The Lafayette River Estuary, Adriana E. Amrhein

OES Theses and Dissertations

The Lafayette River, a shallow, eutrophic tributary of the Chesapeake Bay, experiences seasonal harmful algal blooms (HABs). While management efforts focus on reducing external nutrient inputs, internal loading from benthic sediments remains poorly constrained. This study quantifies spatial and seasonal variability in nutrient and radium isotope fluxes across the sediment–water interface at three sites where HABs are known to initiate and represent contrasting sediment textures and hydrodynamic conditions. Sediment cores and porewater samples were collected in summer 2023 and winter 2024 to measure grain size, porosity, dissolved nutrients (NH₄⁺, NOₓ⁻, PO₄³⁻), and radionuclide activities (²²⁴Ra and ²²⁸Th). Radium isotope disequilibrium …

Pushing High-Performance Private Inference Towards Resource-Constrained Edge Clients, Xiangrui Xu

Computer Science Theses & Dissertations

The widespread adoption of Machine Learning as a Service (MLaaS) has enabled resource constrained edge clients, such as mobile and IoT devices, to leverage powerful deep learning mod els hosted on the cloud. However, this paradigm introduces critical privacy challenges regarding the client’s sensitive input data and the server’s proprietary model parameters. While cryptographic techniques like Homomorphic Encryption (HE) and Multi-Party Computation (MPC) enable Private Inference (PI), existing frameworks impose prohibitive computational and communication overheads that render them impractical for edge deployment. This dissertation introduces three novel frameworks—SPOT, LUTless, and PrivShap—to systematically address the efficiency bottlenecks of PI in edge …

Learning Techniques In Prediction Of Functional Epigenomic Events, Mohammad Shiri

Computer Science Theses & Dissertations

Accurately predicting functional epigenomic events from DNA sequences is critical to understanding gene regulation and the functional impact of non-coding variants. Despite considerable progress, critical challenges hamper the effectiveness and efficiency of existing deep learning approaches. These challenges include negative transfer in multi-task learning (MTL), suboptimal network architectures, and pervasive label noise, particularly the positive-unlabeled problem arising from data sparsity in single-cell assays. This dissertation presents a cohesive framework of novel learning techniques to effectively address these challenges. First, a highly scalable task grouping framework is presented to mitigate negative transfer in deep MTL. This method clusters tasks based on …

Radicals Transforming Organic Matter: Implications For Non-Pyrogenic Black Carbon And Nitrogen Formation, Molecular Dynamics In Tropical Soils, And Lignin Valorization, João Vitor Dos Santos

Chemistry & Biochemistry Theses & Dissertations

Radicals drive the transformation of organic matter in natural and engineered systems, altering its structure, reactivity, and stability. Condensed aromatic carbon (ConAC) and condensed aromatic nitrogen (ConAN) are among the most persistent forms of organic matter in soils and are traditionally interpreted as products of biomass burning. This dissertation challenges the long-standing assumption that these materials are exclusively pyrogenic, showing that iron-mediated radical chemistry can generate condensed aromatic structures under ambient conditions.

Chapters II and III show that Fenton-like radical oxidation of lignin-rich biomass produces condensed aromatic structures compositionally similar to pyrogenic black carbon and black nitrogen when assessed with …

Behavioral, System, And Informational Cyberattacks: A Human-In-The-Loop Driving Simulator Experiment, Samuel Petkac

Psychology Theses & Dissertations

Advanced technologies such as sensors and AI/ML algorithms have enabled increasing levels of automated driving system that detects, responds, and even predicts changes in a driving environment supported by wireless connectivity to nearby vehicles and infrastructure. Such connected and automated vehicles (CAVs) can be particularly vulnerable to cyberattacks targeting not only infotainment systems but also firmware and other applications, critically compromising driver safety. As we anticipate a “mixed” traffic where vehicles with various levels of automated technologies share the road for the foreseeable future, it is urgent to systematically examine types of possible cyberattacks and control human behaviors in such …

Personality Predictors Of Cybersecurity Vulnerability: Insights From Self-Reports And Stimulated Threat Scenarios, Saroja Roy Grandhi

Psychology Theses & Dissertations

In this cyber dependent and enabled era, understanding the role of human factors in digital security is essential. This study investigates the relationship between Big-Five personality traits and cybersecurity behaviors by examining both self-reported and stimulated behaviors in security threat scenarios. Participants completed validated questionnaires to report their personality traits, cybersecurity practices and engage in task-based stimulations to capture behaviors such as phishing detection, password creation, and response to security alerts. The study tested whether higher conscientiousness, openness, and agreeableness would be associated with stronger cybersecurity practices and smaller discrepancies between self-reported and observed behaviors. And, whether greater extraversion and …

Ultra-High Vacuum Outgassing Characterization Of Thermally Processed Low-Carbon Steel For Advanced Particle Accelerator And Gravitational Wave Detector Applications, Aiman H. Al-Allaq

Mechanical & Aerospace Engineering Theses & Dissertations

This dissertation investigated AISI 1020 low-carbon steel as an alternative vacuum chamber material to conventional stainless steel for ultra-high vacuum (UHV) and extreme-high vacuum (XHV) applications. After a 400 °C/48 h bake, AISI 1020 tube chambers achieved a hydrogen outgassing rate of 2.4 × 10⁻¹⁶ Torr·L·s⁻¹·cm⁻², approximately 2,300 times lower than the prebaked 316L stainless-steel comparator, among the lowest hydrogen outgassing rates ever reported for an uncoated metallic vacuum chamber. Bare and magnetite-coated AISI 1020 chambers were then compared using throughput and rate-of-rise methods. The magnetite coating yielded 5× lower water outgassing at room temperature, but this advantage disappeared after …

Do Purpleair Monitors Democratize Data For The Environment?, Christopher Rick, Kyla Lorden

Student Publications

PurpleAir monitors may serve a vital role in marginalized or under-monitored communities nationwide. These low-cost monitors—roughly $300—give communities the ability to monitor their air quality at local geographies in ways that are infeasible for expensive, regulatory-grade air monitors. They also have the potential to aid community advocacy efforts around environmental and transportation policy by giving community members literal ownership over the monitoring, including precise locations, and philosophical ownership over the advocacy efforts. To determine the potential democratization of air quality data by PurpleAir monitors in socially disadvantaged communities, we analyze the sociodemographic characteristics of neighborhoods with PurpleAir monitors. We find …

The Importance Of Body Size And Spatial Scale In Modeling Winter Bird Distributions, Carissa M. Mobley

Student Publications

Birds’ annual cycles include biologically linked breeding and non-breeding seasons, yet most research and bird atlases focus exclusively on the breeding season. There have been very few winter bird atlas projects in North America, and none have been published for the northeastern United States. Short daylight hours and harsh weather limit winter survey coverage, making species distribution models (SDMs) essential for addressing spatial gaps.

I evaluated the optimal spatial scale for SDMs across bird species differing in body size and tested whether optimal scale varies with body mass. Using 16,967 eBird checklists collected during the first winter survey period (December …

Fallen Light (Video Game), Joshua Do

Presentations - 2026

Problem:

•People misunderstand Lucifer’s deception

•(shown through Temptation of Jesus in Matthew 4) •Lack of engaging ways to teach theological concepts   •Background: Lucifer corrupts not through force, but subtle self-elevation and doubt   Motivation:   •Just initially wanted to make a game of how sin entered the world for fun   •Just thought it was a cool idea in general.

Solution:

•Dialogue-driven narrative game   •6+ story chapters   •10+ regions   •Focused on spiritual conflict, deception, and discernment   •Uses event-based progression   •Presents Lucifer through subtle manipulation, by being a false light by choosing self-pleasure over what is right.

Fisheasy, Jake Rankin

Presentations - 2026

Problem: 
Inexperienced and experienced anglers lack necessary tools to begin fishing

Motivation:
Fishing is a fun hobby everyone should be able to enjoy – the lack of resources makes that difficult

Solution:
An application that integrates learning tutorials with helpful practices tools for both novice and experienced anglers

Automation Of Discovery And Classification Of Compact X-Ray Binaries In Globular Clusters, Justin Brooks

Theses and Dissertations from DePaul University

The discovery and classification of Compact X-ray Binaries (CXRBs) within globular clusters improves our understanding of stellar encounters, the evolution of globular clusters, accretion physics, and the high-energy physics of the compact objects involved in these systems. For this reason, scientists compare X-ray observations from the Chandra X-ray Observa?tory with visible and UV observations from the Hubble Space Telescope to find objects of unusual colors and magnitudes which might be CXRBs. However, this process is time-consuming and requires significant amounts of data and expertise to achieve reliable classifications. This paper de?scribes this process, as well as a proposed automated process …