Digital Commons Network^™

Computational Modeling Of Poly-Peptide Chains, Nathan F. Surles, Kaitlin A. Edwards

ATU Scholars Symposium

Investigations of the structural properties of polypeptides are essential for understanding their conformational behavior, stability, and potential biological interactions. In this study, we employed computational techniques to determine the optimized structures of two model polypeptides: tri-glycine and di-tryptophan.

The Effects Of Climate Change On The Advancement Of West Nile Virus, Mackenzie R. Epperson

ATU Scholars Symposium

The West Nile virus (WNV) first emerged in the United States in the year 1999 within the state of New York and has become endemic throughout the country over time. This virus is contracted from an avian species acting as the reservoir host, by the vector species which are mosquitoes. From this point, the mosquitoes transmit the virus to humans and other mammals, which are the dead end hosts. The WNV often presents itself as flu-like symptoms, but in serious cases can cause severe arboviral neurological disease. Since this is an arbovirus, it is important to have the ability to …

Self-Supervised Learning And Its Applications In Medical Image Analysis, Siladittya Manna

Doctoral Theses

Self-supervised learning (SSL) enables learning robust representations from unlabeled data and it consists of two stages: pretext and downstream. The representations learnt in the pretext task are transferred to the downstream task. Self-supervised learning has appli- cations in various domains, such as computer vision tasks, natural language processing, speech and audio processing, etc. In transfer learning scenarios, due to differences in the data distribution of the source and the target data, the hierarchical co-adaptation of the representations is destroyed, and hence proper fine-tuning is required to achieve satisfactory performance. With self-supervised pre-training, it is possible to learn repre- sentations aligned …

From The Ground Up: Community-Based Participatory Research Reclaiming The Science Of Lead, Juan Manuel Rubio, Bavisha Kaylan, Anthony Diaz, Patricia Flores, Maya Cheav, David C. Bañuelas, Ashley Green, Annika Hjelmstad, Ariane Jong-Levinger, Tim Schütz, Maya Carrasquillo, Alana M. W. Lebron, Jun Wu

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

For decades, the dominant approach to lead poisoning has been to focus on homes affected by lead paint and to treat children who are already suffering from lead poisoning. This individualizing approach developed in the context of the defunding and deregulation of government agencies in the 1980s. In recent years, however, community–academic partnerships have reframed lead as an environmental issue produced by the development of the lead industry in the twentieth century and connected to overlapping histories of exploitation, discrimination, and inaction. These community-based projects have contributed to shifting research agendas (by emphasizing historical analysis and the study of the …

One Size Doesn’T Fit All: Towards Design And Evaluation Of Developmentally Appropriate Parental Control Tool, Prakriti Dumaru, Mahdi Nasrullah Al-Ameen

Computer Science Student Research

As children progress through developmental stages, they undergo substantial biological, cognitive, and social changes, creating unique needs for online safety across different age groups (e.g., young children, tweens, teens). The existing parental control tools fail to account for these differences, leaving a notable gap in the literature on parental mediation. To this end, we conducted 10 focus group sessions with a total of 20 parents to understand their preferences for age-appropriate design components that promote self-regulation and open communication, followed by an ideation workshop with four UX design experts to translate these preferences into customized features. We then evaluated these …

Synthesis Of Organosilicon Substituted Fₓpczn For The Preparation Of Silica-Based Photo-Catalysts, Reagan E. Daly

Seton Hall University Dissertations and Theses (ETDs)

This study began with the synthesis, purification, and catalytic application of hexadeca fluoro phthalocyanine zinc (F₁₆PcZn) derivatives functionalized with organosilane consuming thiol groups. The F₁₆PcZn was synthesized by reacting tetrafluorophthalonitrile (TFPN) with zinc acetate (Zn(OAc)₂) in 1-chloronaphthalene as a solvent, under a controlled heating process at 185°C for 90 minutes. The resulting blue solid was purified via vacuum filtration and recrystallization techniques to remove residual solvents and by-products, yielding pure F₁₆PcZn. The purity of the product was assessed through UV-Vis spectroscopy, MALDI analysis, and a molar extinction coefficient was determined.

Subsequent nucleophilic substitution of the fluorine atoms on F₁₆PcZn with …

The Attitudes And Perspectives Of Laboratory Professionals On The Use Of Machine Learning Combined With Maldi For Viral Identification: A Qualitative Study, Grace Johnson

Honors Projects

The use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with machine learning (ML) has been proposed by numerous studies as a novel approach for viral identification. However, the development and implementation of this instrumentation is still in its early stages, and laboratory professionals' perspectives on its feasibility, accuracy, implementation, and effect on current laboratory operating procedures remain underexplored.

This study aimed to investigate laboratory professionals’ attitudes and opinions regarding the use of MALDI-TOF-MS coupled with machine learning for viral identification, focusing on perceived benefits, barriers, and factors that would affect participants’ opinions on implementation.

A qualitative descriptive research …

From Clusters To Frameworks: Synthesis, Engineering, And Application Of Sub-2-Nanometer Nanoclusters And Microporous Covalent Organic Frameworks, Melika E Kenari

Chemistry Theses and Dissertations

In this dissertation, we have investigated the complex interplay of atomic composition, structural modifications in covalent organic frameworks (COFs), and atomic-level designs in bimetallic chiral nanoclusters (NCs). By synthesizing COFs and bimetallic NCs, we elucidated how these elements govern their exceptional catalytic, optical, and electronic properties. Our work demonstrates that precise atomic adjustments, tailored pore engineering in COFs, and the strategic use of chiral ligands in NCs enable fine-tuned reactivity and stability. These advancements were applied to enhance photocatalytic performance, optimize iodine adsorption, and facilitate asymmetric A3 coupling reactions, laying a robust foundation for practical applications and future innovations in …

Quantifying And Characterizing Microplastics In The Greater Philadelphia Region, Emily Lybashev

Biology Honors Papers

Plastic is one of the world's most useful and versatile materials, so it is no wonder that 400 million tons are produced yearly. When exposed to weathering, heat, water, and organisms, plastic degrades and produces microplastics. These microplastics have managed to leach into our oceans, local waterways, bodies, and even our atmosphere. The negative implications of microplastic contamination in our environment are slowly being uncovered with concerns of toxin buildup. Additionally, the amount of microplastics we are exposed to through local waterways is rarely quantified. Though microplastic research is picking up pace, the Schuylkill River which spans the Greater Philadelphia …

Quantifying The Rates Of Coastal Change Along Smith Island, Maryland, Sarah Lacy, Ravi Sankar

Longwood Senior Thesis Proposal

As increased climate variability continues to alter the environment, coastal landscapes are becoming increasingly vulnerable to geomorphic change. Coastal erosion, driven by rising sea levels, land subsidence, more intense storm events and human-induced activities poses a serious threat to the sustainability and resilience of island environments like Smith Island, a small marsh island located in the Chesapeake Bay. This study investigates the impacts of recent shoreline change along selected alongshore segments of the island’s coast. Using a combination of aerial imagery, field surveying techniques, and novel geospatial analyses, the project aims to identify areas at highest risk of erosion and …

The Chemistry Of Decomposition: The Mechanisms To Decay The Human Body, Lydia J. Buxa

Senior Honors Theses

Taphonomic analysis separates decomposition into four major stages: fresh, early decomposition, advanced decomposition, and skeletonization. It is easy to demarcate the observable changes to the body, but it is far more difficult to know what underlying biochemical processes are occurring. Fresh decomposition begins with algor mortis, livor mortis, and rigor mortis, which sets the stage for the major workforces of decomposition: autolysis and putrefaction. The external signs of decomposition appear in early decomposition, which can be attributed to the breakdown of proteins, lipids, carbohydrates, and nucleic acids. This also leads to major changes in the moisture levels during advanced decomposition, …

Mine Closure Planning Must Face The Challenge Of Delivering Nature Positive Outcomes, Luis E. Sanchez, Angus Morrison-Saunders

Research outputs 2022 to 2026

The need to address and reverse global biodiversity decline is imperative across all of society including the practices of mine closure planning. Nature Positive is the latest global biodiversity-focused initiative which calls for at least 30% of biodiversity to be enhanced through effective restoration relative to the 2020 baseline. This paper conceptualizes and explains what is necessary in mine closure planning and implementation to meaningfully contribute to this and other nature-positive goals, with some illustrative examples. Issues considered include application of the mitigation hierarchy, rehabilitation in mining and the time lag challenge for restoring biodiversity, biodiversity offsetting, conserving nature while …

Electrocatalytic Nitric Oxide Reduction To Yield Ammonia Over Fe3C Nanocrystals, Sen Lin, Lang Zhang, Tong Hou, Jun-Yang Ding, Zi-Mo Peng, Yi-Fan Liu, Xi-Jun Liu

Journal of Electrochemistry

Nitric oxide (NO), which generally originates from vehicle exhaust and industrial flue gases, is one of the most serious air pollutants. In this case, the electrochemical NO reduction reaction (NORR) not only removes the atmospheric pollutant NO but also produces valuable NH₃. Hence, through the synthesis and modification of Fe₃C nanocrystal catalysts, the as-obtained optimal sample of Fe₃C/C-900 was adopted as NORR catalyst at ambient conditions. As a result, the Fe₃C/C-900 catalyst showed an NH₃ Faraday efficiency of 76.5% and an NH₃ yield rate of 177.5 μmol·h^–1·cm^{–2 …}

Autoradai: A Versatile Artificial Intelligence Framework Validated For Detecting Extracapsular Extension In Prostate Cancer, Pegah Khosravi, Shady Saikali, Abolfazl Alipour, Saber Mohammadi, Maxwell Boger, Dalanda M. Diallo, Christopher J. Smith, Marcio C. Moschovas, Iman Hajirasouliha, Andrew J. Hung, Srirama S. Venkataraman, Vipul Patel

Publications and Research

Preoperative identification of extracapsular extension (ECE) in prostate cancer (PCa) is crucial for effective treatment planning, as ECE presence significantly increases the risk of positive surgical margins and early biochemical recurrence following radical prostatectomy. AutoRadAI, an innovative artificial intelligence (AI) framework, was developed to address this clinical challenge while demonstrating broader potential for diverse medical imaging applications. The framework integrates T2-weighted MRI data with histopathology annotations, leveraging a dual convolutional neural network (multi-CNN) architecture. AutoRadAI comprises two key components: ProSliceFinder, which isolates prostate-relevant MRI slices, and ExCapNet, which evaluates ECE likelihood at the patient level. The system was trained and …

Prime Theta-Curves From Torus Knots, Sam Nieman, Jack Calcut

Research Symposium

Classical knot theory is the placement problem for a circle in Euclidean 3-space or in the 3-sphere. That problem has been generalized in numerous ways. Knotted graph theory replaces the circle with a graph. Knotting of certain graphs has been well-studied. That includes the theta-graph consisting of two vertices connected by three edges---a copy of the letter theta. A theta-curve is an embedding of the theta-graph in 3-space or in the 3-sphere. Connected sum of knots yields the notion of a prime knot. Similarly, one may sum two theta-curves at a vertex and one may sum a theta-curve and a …

Study Habits And Review Sessions, Lillian Gottstine

Fisher Showcase 2025

Seeing the outcomes of using and teaching different studying habits in a review session to see the effects on student preparedness for unit exams.

Identification Of Areas Of Weakness In Forensic Footwear Research, Kathryn Roy

Honors Projects

Forensic footwear examinations have been carried out for almost a century, but the foundational validity of identifying a questioned impression to a particular shoe has been questioned by the National Research Council and the President’s Council of Advisors on Science and Technology. The focus of this paper was to identify the current weaknesses present in forensic footwear impression research. Additionally, a future experiment was proposed to address these concerns and improve the foundational validity of footwear impression comparisons. A total of 15 footwear research studies varying in methodology and content were analyzed and contrasted. From this, a lack of studies …

The Analysis Of Reference Standard Storage Failures Through The Use Of Ibuprofen, Hope Vonder Brink

Honors Projects

Reference standards are commonly used in drug chemistry. They are used to calibrate the instruments and serve as a known point of reference for analysts’ ability to compare unknowns. Drugs can degrade over time or through environmental factors, causing contaminants to be present. In the event of environmental degradation while in storage, such as the exposure to high heat, it would be beneficial to have a database of known breakdown products in common drug reference standards for analysts’ reference. Using ibuprofen as an exemplar drug, this study attempted to identify the thermal breakdown products of ibuprofen and introduce the proposed …

Modeling Cis/Trans Preferences Of Sn("Acac")2cl2 Complexes, Luke L. Rising, Hanna Sunsdahl, Matthew Burrows, Juan Carlos Feregrino Ponce

Research & Creative Achievement Day

Tin(IV) complexes bearing two chloride ligands and two symmetric β-diketonate ligands exhibit octahedral geometries. As such, they can theoretically present in two geometric isomer forms, cis and trans. Modeling of isomeric forms of these Sn(IV) complexes with five different β-diketonate ligands has been conducted to identify overall preference as well as to attempt to ascertain any influence the ligand's own electronic properties has on exhibited isomeric preference. Additionally, modeled IR spectra of cis and trans forms were compared to determine the utility of that characterization method in distinguishing these isomers.

Modeling Sod1 Enzyme Mutations: Biochemistry Ii Lab Class Project, Jenna Bolduan, Elle K. Haumont

Research & Creative Achievement Day

Superoxide Dismutase 1 (SOD1) is an enzyme that catalyzes the detoxification of reactive oxygen species that cause damage to the body. Mutations of this protein can cause diseases, such as Amyotrophic Lateral Sclerosis (ALS). The structures of the SOD1 wild type and two of its deleterious mutations (A4V and L126*) were digitally modeled using the AI program AlphaFold3. Although a literature structure exists for A4V, no experimental structure data has been collected for L126*. The wild type and A4V structures were virtually identical, whereas the wild type and L126* structures had quite different features, with the mutant being smaller and …

A Comparison Of The Bacterial Communities Of The Yamuna River (India) And Mississippi River (Usa), Jacob Gareis, Osvaldo Martinez, Silas Bergen

Research & Creative Achievement Day

This study compared the bacteria in the Yamuna River in India and the Mississippi River in the USA. Water samples were taken from 11 sites (2 in the Mississippi River and 9 in the Yamuna River). The bacteria were identified using 16S rRNA gene sequencing. Some phyla such as Proteobacteria and Bacteroidetes were seen in abundance regardless of country. However, principal-component analysis showed three distinct groupings: Mississippi/Ganga/Tons and other Yamuna River locations (7 sites), Yamuna River at Delhi (2 sites), Yamuna River below Glacier (2 sites) Additionally, the Yamuna River below Glacier had the highest bacterial diversity, with a Shannon …

Plasma Profiling Reveals Proteins Specific To Primary Disease Origin Of Retroperitoneal Fibrosis, Thomas J. Pelowitz, Benjamin Hurr, Matthew Koster, Jaeyun Sung

Research & Creative Achievement Day

Retroperitoneal fibrosis (RPF) is a rare inflammatory disease characterized by the formation of scar-like tissue in the retroperitoneum, which can lead to life-threatening obstructive nephropathy. RPF is typically a secondary disease, arising from various underlying conditions. Currently, no objective and highly accurate diagnostic methods exist. Identifying blood protein biomarkers specific to RPF could facilitate the development of objective minimally invasive diagnostic tests.

In this study, blood plasma samples were collected from 45 participants spanning 5 different primary causes of RPF, including idiopathic cases where no underlying condition was identified. Six participants without significant diseases at the time of sample collection …

An Exploration Of Simple Methods For The Purification And Separation Of Natural Curcuminoids, Eion S. Hinkle

Research & Creative Achievement Day

The separation of curcumin from other naturally occurring curcuminoids, such as demethoxycurcumin and bisdemethoxycurcumin, presents significant challenges due to their similar chemical structures. Conventional methods like column chromatography are energetically and environmentally costly, requiring large amounts of solvents and extended processing times. Alternatively, preparatory scale high-performance liquid chromatography (HPLC) offers high precision but necessitates expensive equipment, making it less accessible for routine laboratory use. This research explores simpler and more sustainable approaches to purify curcumin, aiming to reduce both the environmental impact and the financial burden associated with traditional separation techniques.

The Conditioning Of Reservoir Computing And Ng-Rc For Forecasting And The Effects Of Temporal Overparameterization, Daniel Jensen

Theses and Dissertations

Reservoir computing and "Next-generation reservoir computing" built on nonlinear vector autoregression are algorithms for predicting time series given past observations. Both algorithms have been successful in predicting some chaotic dynamical systems, but this success is not theoretically well understood. This paper considers the conditioning of both algorithms and the nature of the solutions found. With either algorithm, the least squares problem which is solved to give parameters as a function of the time series data is ill-conditioned, leading to parameter non-identifiability. Both algorithms fall into the class of "sloppy models." Standard practice to regularize either algorithm includes a bias towards …

2025 Acssc Program, Acssc Planning Committee

Annual Celebration for Student Scholarship and Creativity

No abstract provided.

The Significance Of Symmetry: Exploring T-Numbers And Their Role In Virus Survival And Behavior, Jenna Franco, Taylor Ligozio

Mathematics & Computer Science Student Scholarship

Jenna Franco ’25, Biology major

Taylor Ligozio ’25, Biology major

Faculty mentor: Dr. Su Jeong Kang, Mathematics and Computer Science

We studied the symmetry of different structures in common viruses and their T-numbers. We related these T-numbers with characteristics of the virus. Next we researched how the T-number of each virus was optimal for its survival and reproduction in its environment. We can use this information to infer or predict the behavior of viruses in the future based on their T-numbers.

Exploring The Role Of Azoreductase Enzymes In Drug Metabolism: Implications For Personalized Medicine, Najoude Claude, Robert Ghergurovich

Chemistry & Biochemistry Student Scholarship

Najoude Claude ’26, Biology major

Robert Ghergurovich ’26, Biochemistry major

Faculty mentor: Dr. Tyler Stack, Chemistry and Biochemistry

The gut microbiome hosts trillions of microorganisms that metabolize xenobiotics such as drugs and food dyes. Individual differences lead to variable drug metabolism. We studied two azoreductases: E. coli’s P41407 and Alistipes sp. CHKCL003’s A0A143XFE8. Enzyme P41407 acted on methyl red and ethyl red, while A0A143XFE8 acted on these and also on phenol blue, HMND, and sunset yellow. We propose these enzymes function as quinone reductases, requiring a quinone-like intermediate. Three synthesized compounds confirmed similar kinetics. In conclusion, these insights significantly advance …

Discovery, Purification And Annotation Of Four Novel Mycobacteriophages In New England, Mason Krawczynski

Chemistry & Biochemistry Student Scholarship

Mason Krawczynski ’26, Biology and Psychology major

Faculty mentor: Dr. Kathleen Cornely, Chemistry and Biochemistry

Mycobacteriophages are viruses that infect bacteria of the Mycobacterium genus. Several thousand mycobacteriophages have been discovered, isolated, and characterized to advance the current understanding of their genomic diversity. The mycobacterium phage selection proves valuable, as they have a broad host range and potential for therapeutic application to treat pathogenic and antibiotic-resistant mycobacteria, such as Mycobacterium tuberculosis, the causative agent of tuberculosis infection. Kraw was isolated from a soil sample collected in Oaks Bluff, Massachusetts, on the island of Martha’s Vineyard in July 2023. FairyPath, Calvinny, …

Tools For Harnessing Atropisomerism In 1-Aryl-Β-Carbolines, Cristina Díaz, Malaquias Loiza, Josef Crenshaw, Brian Ladino, Elizabeth Perda, Alma Martinez, Joseph Mazzucca, John Stathoulopoulos

Chemistry & Biochemistry Student Scholarship

Cristina Díaz ’25, Chemistry major

Malaquias Loiza ’26, Biochemistry major

Josef Crenshaw ’28, Biochemistry major

Brian Ladino ’28, Biochemistry major

Elizabeth Perda ’26, Biochemistry major

Alma Martinez ’26, Biochemistry major

Joseph Mazzucca ’25, Biochemistry major

John Stathoulopoulos ’26, Chemistry major

Faculty mentor: Dr. Seann Mulcahy, Chemistry and Biochemistry

Axially chiral molecules with high barriers to rotation are becoming increasingly more prominent in drug discovery, chemical biology, and materials science. We have shown that 1-aryl-β-carbolines exhibit high configurationally stability, with barriers to rotation greater than 30 kcal/mol and have recently disclosed an asymmetric synthesis of these molecules. In this presentation, we …

Discovery, Purification And Annotation Of A Novel Mycobacteriophage Discovered On The Providence College Campus, Jenna Greene

Chemistry & Biochemistry Student Scholarship

Jenna Greene ’26, Biochemistry major

Faculty mentor: Dr. Kathleen Cornely, Chemistry and Biochemistry

Bacteriophages—viruses that infect bacteria—offer a promising alternative to antibiotics in the face of rising antibiotic resistance. In this project, I isolated a novel phage from a soil sample collected in front of Raymond Dining Hall at Providence College. Using Mycobacterium smegmatis as the host, the sample underwent multiple rounds of purification until a single phage, named GMonster (a nod to my family nickname, “Greene Monster”), was isolated. GMonster was submitted to the PhagesDB database and confirmed through sequencing to belong to the A1 cluster—the first of its …