Digital Commons Network^™

Optimizing And Scaling Up Tcfh–Nmi Pyrrole Acylation For Organic Syntheses, Grant H. Miller

Pomona Senior Theses

Traditional ketone synthesis often depends on toxic reagents and hazardous solvents, which limits its scalability and environmental compatibility. The TCFH–NMI method has shown strong potential for amide, ester, and thioester formation, but its use in ketone synthesis has only been recently described, and only on small scales. This thesis addresses that gap by optimizing a scalable synthesis of 2-(monomethyl succinyl)-3,5-dimethylpyrrole using monomethyl succinate and 2,4-dimethylpyrrole as model substrates. Key reaction parameters were systematically refined to improve yield, reproducibility, and sustainability. The final protocol avoids chromatography, operates at room temperature, and consistently delivers high yields. These features position it as a …

Huchum: The Legacy Of Fire Suppression, Indigenous Land Management, And Media Representation, Carolyn Coyne

Pomona Senior Theses

In my thesis, I examine how various forms of news media from the 1900s to present day in Ohlone territory have framed a particular hegemonic ideology around fire that matches early colonial journal entries – an ideology that is fueled by fear, sensationalism, and exclusion and directly commits violence against the Ohlone people. I investigate this time period because this is when modern news corporations, like The New York Times, rose into prominence. Specifically, I question how media representations of fire inform regulations over controlled burns; what are the similarities in discourse between media framing and policy? What tactics are …

Swimming In Sh*T: Quantifying Lagoon Flushing Impacts On Fecal Indicator Bacteria In Surf Zones Of Three Beaches On The East End Of Long Island, Ny, Brody C. Eggert

Pomona Senior Theses

This thesis investigates how lagoon flushing influences fecal indicator bacteria (FIB) concentrations—specifically enterococcus bacteria—in the surf zones of East Hampton and Southampton, New York. Focusing on the coastal lagoons of Georgica Pond, Sagg Pond, and Mecox Bay, the study analyzes how episodic inlet openings and environmental conditions affect enterococcus levels at adjacent recreational beaches. Using over 700 observations from the Surfrider Foundation’s Blue Water Task Force (BWTF) database, I construct a series of statistical models ranging from ordinary least squares to mixed effects frameworks; this thesis shows my process in developing this model. My analysis reveals that open inlets between …

Rwanda's Natural Remedies: A Fresh Look At The Fight Against Malaria, Leandre Nsabimana Ndisanze

Pomona Senior Theses

Malaria remains one of the most devastating parasitic diseases globally, disproportionately affecting sub-Saharan Africa, where Rwanda continues to face high transmission rates and rising resistance to conventional interventions. Despite decades of control efforts, the emergence of drug-resistant Plasmodium falciparum and insecticide-resistant Anopheles mosquitoes threatens to reverse recent gains. This research responds to the urgent need for sustainable and culturally relevant alternatives by exploring the therapeutic potential of Rwandan traditional medicinal plants. These indigenous remedies, long used by local healers, offer an underexplored reservoir of bioactive compounds that may provide the basis for novel antimalarial drugs.

The central hypothesis of this …

A Vascular Flora Of The Sacatar Trail Wilderness, Sierra Nevada, California, Kimberly Schaefer Pivetti

CGU Theses & Dissertations

The Sacatar Trail Wilderness in Inyo and Tulare counties, California, encompasses a bioregional transition zone in the southeastern Sierra Nevada. The ca. 233 km 2 (90 mi 2 ) study area, located 32 km (20 mi) northwest of the city of Ridgecrest, ranges from 930 to 2698 m (3051–8851 ft) in elevation. The highly diverse California Floristic Province, Great Basin, and Mojave Desert converge in the region including the Wilderness creating conditions to support a broad spectrum of vegetation assemblages. The Bureau of Land Management has prohibited vehicular activity in this area since its wilderness designation in 1994; consequently, recent …

Deepgridmclp: A Deep Reinforcement Learning Approach To Solve The Maximal Covering Location Problem With Facilities In Continuous Regions, Yang Zhong

CGU Theses & Dissertations

The Maximal Covering Location Problem (MCLP) is a classic Combinatorial Optimization Problem (COP) in spatial optimization and operations research, predominatnly used for strategic public facility placement. The model’s objective is to determine the optimal locations for a fixed number of facilities in order to serve the largest possible demands within a desired service distance. In its original form, the MCLP model is formulated with discrete facility candidate points. However, in many practical situations, the facilities can be positioned anywhere in a continuous region. For example, in environmental planning or wireless network design, the prospective facility placements may be established in …

Mathematical Modeling Of Cancer Tumor Evolution, Belgacem Al-Azem

CGU Theses & Dissertations

Several mathematical models of cancer tumor evolution are presented. The aim of this endeavor is to write a thesis that fosters numerical and analytical understanding of certain mathematical models in the area of oncology as well as to offer potential predictive tools of therapeutic and clinical applicability. In this work, we give a panoramic view of the cancer phenotype, for to understand cancer, we need to "see" its biophysics. Indeed, the discovery of oncogenes led to the thinking that cancer tumor is perhaps a genetic disease. But the role of angiogenesis and other microenvironment-related discoveries (such as the role of …

Optimization Of A Vertical-Axis Wind Turbine Airfoils Using Machine Learning, Numerical And Experimental Methodologies, Leovigildo Torres Angel

CGU Theses & Dissertations

This study aimed to enhance the aerodynamic performance of a Vertical-Axis Wind Turbine (VAWT) airfoil through a multidisciplinary approach that combines Machine Learning (ML), Computational Fluid Dynamics (CFD), and experimental validation. The focus was on enhancing the lift-to-drag coefficients ratio (퐶 푙 /퐶 퐷 ), particularly at higher Angles of Attack (AoA ≥ 20°), a critical operational regime for VAWTs. A baseline airfoil of 12-inch chord length and 10-inch wingspan was analyzed using ANSYS Fluent across a range of AoA (0°–90°) at a constant freestream velocity of 10 m/s (Re ≈ 2.0 × 10 5 ). This served as a …

Physics-Informed Deep Learning With Kalman Filter Mixture For Traffic State Prediction, Niharika Deshpande, Hyoshin (John) Park

Engineering Management & Systems Engineering Faculty Publications

Accurate traffic forecasting is crucial for understanding and managing congestion for efficient transportation planning. However, conventional approaches often neglect epistemic uncertainty, which arises from incomplete knowledge across different spatiotemporal scales. This study addresses this challenge by introducing a novel methodology to establish dynamic spatiotemporal correlations that captures the unobserved heterogeneity in travel time through distinct peaks in probability density functions, guided by physics-based principles. We propose an innovative approach to modifying both prediction and correction steps of the Kalman Filter (KF) algorithm by leveraging established spatiotemporal correlations. Central to our approach is the development of a novel deep learning model …

Predictive Maintenance In Naval Vessel Propulsion Systems For Enhanced Marine Operations Using A Bigmm-Hmm Framework With Divergence-Based Clustering, Farshid Javadnejad, Hyoshin John Park, Samuel Kovacic, Andres Sousa-Poza

Engineering Management & Systems Engineering Faculty Publications

This study introduces a BiGMM-HMM Integration Framework designed to improve predictive maintenance strategies for naval vessel propulsion systems, addressing the need for efficient and reliable operation in marine engineering applications. The framework effectively manages multimodal sensor data by leveraging a unique combination of Gaussian Mixture Models (GMMs) and Hidden Markov Models (HMMs) in a bidirectional architecture. It analyses the dynamic interactions between sensors and subsystems. Two preprocessing methods are evaluated: Method 1 focuses on subsystem interactions, employing divergence-based root cause analysis to identify key sensor variables by clustering of sensors and subsystems. In contrast, Method 2 processes the entire dataset …

Optimizing Port Logistics Through Generative Ai: Revolutionizing Efficiency And Resilience In The Maritime Industry, Minodora Badea, Olga Bucovetchi, Adrian V. Gheorghe, Gabriel Raicu

Engineering Management & Systems Engineering Faculty Publications

The maritime industry faces growing challenges in optimizing port logistics due to increasing trade volumes, environmental regulations, and supply chain disruptions. This comprehensive literature review examines the transformative role of artificial intelligence (AI), with particular focus on generative AI, in enhancing efficiency and resilience in port operations. Through systematic analysis of 23 peer-reviewed studies published between 2021-2025, this review synthesizes advancements in real-time data integration, machine learning, digital twins, IoT, and autonomous systems that collectively improve operational decision-making, risk management, and environmental sustainability. Key findings reveal that machine learning applications achieve 90% effectiveness ratings in operational optimization, while predictive analytics …

Multipliers On Weighted Sequence Spaces, Gilbert Acheampong, Raymond Cheng

Mathematics & Statistics Faculty Publications

The space ℓp,α of complex sequences a = (a0, a1,a2,...) for which

[[formula omitted]]

is studied. Each such sequence can be identified with the analytic function with power series

[[formula omitted]]

In this setting, the point evaluation and the difference quotient mappings are shown to be bounded; the cases are identified in which ℓp,α is boundedly contained in ℓr,β. Conditions on the parameters are derived for the analytic functions of ℓp,α to have radial limits almost everywhere on the boundary, and for ℓp,α to be an algebra. Smoothness properties of the boundary function are investigated. Basic properties of multipliers on …

Comprehensive Benchmarking Of Several Machine Learning And Bayesian Models For Early-Stage Diabetes Risk Prediction: A Large-Scale Comparative Study, Md. Iqbal Hossain, Najila Alam Porno

Mathematics & Statistics Faculty Publications

Diabetes remains a critical global health challenge, with early detection is crucial for effective management. This study presents a comprehensive benchmarking analysis of 14 diverse machine learning and Bayesian models for early-stage diabetes risk prediction using clinical data [2] from Sylhet, Bangladesh. This research evaluated traditional methods (Logistic Regression, Decision Trees), ensemble techniques (Random Forest, XGBoost, LightGBM), Bayesian approaches (BART, Bayesian Logistic Regression), and advanced neural architectures (Deep Belief Networks) using both 70-30 train-test splits and 10-fold cross-validation. The results demonstrate that ensemble methods consistently outperformed other approaches, with Random Forest(RF) achieving the highest cross-validated AUC (0.9951) and accuracy (0.9699). …

Suntan (And Other Solar Tigonometric Functions), John Adam

Mathematics & Statistics Faculty Publications

Question 1: If I₀ is the solar irradiance (power per unit area, W/m²) reaching my head, express the intensity on the side of my face (I_s) in terms of θ. Assume for now that the irradiance is independent of path length through the atmosphere and that my face is normal to the direction θ = 90°.

Using the 1962 U.S. Standard Atmosphere,² Hottel (1976)³ expressed the solar irradiance using the formula

I = I₀(a₀ + a₁e^{−k sec θ}), where A is the elevation in kilometers and

a₀ = 0.4237 − 0.00821(6 − A)²; a₁ = 0.5055 …

Golden Spirals Everywhere?, John Adam

Mathematics & Statistics Faculty Publications

The article explores different types of spirals, including Archimedean, hyperbolic, and logarithmic spirals, with a focus on the golden ratio and golden spirals. It discusses the misconception that golden rectangles and spirals can be found in various natural and man-made objects, emphasizing the importance of understanding the properties of logarithmic spirals. The text provides mathematical equations for logarithmic spirals and poses questions for readers to explore the concept further. The author, John Adam, invites readers to engage in Fermi Questions and submit ideas for consideration.

Model-Free Organization Of Patient Reported Outcomes Data: Geometrical Rep-Resentation Of The Modified Compartmen-Talization Method, Manasi Sheth, N. Rao Chaganty

Mathematics & Statistics Faculty Publications

There is a recent advancement in the field of mathematics and statistics to understand the geometry or connectedness of the data due to the massive amounts of data being generated. The data provided for analyses are usually very large and need to be organized and minimized in order to make it more useful and meaningful. In biostatistics or medical field, it is important for patients to have access to high-quality, safe and effective and/ or efficacious medical products. It is quite necessary to ascertain that the patients and their care-partners stay at the center of the regulatory decision-making process. In …

A Comparative Analysis Of Preprocessing Filters For Deep Learning-Based Equipment Power Efficiency Classification And Prediction Models, Sang-Ha Sung, Chang-Sung Seo, Michael Pokojovy, Sangjin Kim

Mathematics & Statistics Faculty Publications

The quality of input data is critical to the performance of time-series classification models, particularly in the domain for industrial sensor data where noise and anomalies are frequent. This study investigates how various filtering-based preprocessing techniques impact the accuracy and robustness of a Transformer model that predicts power efficiency states (Normal, Caution, Warning) from minute-level IIoT sensor data. We evaluated five techniques: a baseline, Simple Moving Average, Median filter, Hampel filter, and Kalman filter. For each technique, we conducted systematic experiments across time windows (360 and 720 min) that reflect real-world industrial inspection cycles, along with five prediction offsets (up …

A Decision-Space Model Explains Context-Specific Decision Making, Dirk W. Beck, Cory N. Heaton, Luis D. Davila, Lara I. Rakocevic, Sabrina M. Drammis, Danil Tyulmankov, Atanu Giri, Shreeya Umashankar Beck, Qingyang Zhang, Michael Pokojovy, Kenichiro Negishi, Alexis A. Salcido, Neftali F. Reyes, Andrea Y. Macias, Serina A. Batson, Paulina Vara, Raquel J. Ibáñez Alcalá, Safa B. Hossain, Graham L. Waller, Laura E. O'Dell, Travis M. Moschak, Ki A. Goosens, Alexander Friedman

Mathematics & Statistics Faculty Publications

Optimal decision-making requires consideration of internal and external contexts. Biased decision-making is a transdiagnostic symptom of neuropsychiatric disorders. We created a computational model demonstrating how the striosome compartment of the striatum constructs a context-dependent mathematical space for decision-making computations, and how the matrix compartment uses this space to define action value. The model explains multiple experimental results and unifies other theories like reward prediction error, roles of the direct versus indirect pathways, and roles of the striosome versus matrix, under one framework. We also found, through new analyses, that striosome and matrix neurons increase their synchrony during difficult tasks, caused …

A Bridge Too Low: Solutions For Fermi Questions, May 2025, John Adam

Mathematics & Statistics Faculty Publications

The article discusses a low bridge in Keswick, England, near the River Greta, with an arch shaped like a semiellipse. It presents Fermi questions related to the bridge's dimensions, such as the maximum distance a person of a certain height can walk under it without hitting their head. The solutions involve mathematical calculations and approximations, including the use of formulas provided by the Indian mathematician Srinivasa Ramanujan.

Impacts Of Tick Parasitism On The Rodent Gut Microbiome, Robert J. Brinkerhoff, Joshua Pandian, Meghan Leber, Isabella D. Hauser, Holly D. Gaff

Biological Sciences Faculty Publications

Host microbiota may impact disease vector behavior and pathogen transmission, but little is known about associations between ectoparasites and microbial communities in wildlife reservoir species. We used Illumina metagenomic sequencing to explore the impacts of tick parasitism on the rodent fecal microbiome in both a field and laboratory setting. We found that tick parasitism on wild hosts was associated with variation in the fecal microbiota of both the white-footed deermouse, Peromyscus leucopus, and the southern cotton rat, Sigmodon hispidus. In a lab experiment, we detected significant changes to the fecal microbiome after experimental exposure to immature ticks in …

Multi-Locas Gwas Mapping And Candidate Gene Analysis Of Anticancer Peptide Lunasin In Soybean (Glycine Max L. Merr), Rikki Locklear, Jennifer Kusumah, Layla Rashad, Felicia Lugaro, Sonia Viera, Nathan Kipyego, Faith Kipkosgei, Daisy Jerop, Shirley Jacquet, Mythy Addelmajid Kassem, Jiazheng Yuan, Elvira De Mejia, Rouf Mian

Biological Sciences Faculty Publications

Soybean (Glycine max) peptide lunasin exhibits significant cancer-preventive, antioxidant, and hypocholesterolemic effects. This study aimed to identify quantitative trait nucleotides (QTNs) associated with lunasin content and to annotate the candidate genes in the soybean genome. The mapping panel of 144 accessions was gathered from the USDA Soybean Germplasm Collection, encompassing diverse geographical origins and genetic backgrounds, and was genotyped using SoySNP50K iSelect Beadchips. The lunasin content in soybean seeds was measured using the enzyme-linked immunosorbent assay (ELISA) method, with lipid-adjusted soybean flour prepared from seeds obtained from the Germplasm Resource Information Network (GRIN) of USDA-ARS in 2003 and …

Moderate Heating Renders 7.8-Million-Year-Old Sedimentary Organic Matter Bioavailable, Shuchai Gan, Verena B. Heuer, Frauke Schmidt, Lars Wormer, Faming Wang, Rishi R. Adhikari, Patrick Hatcher, Ann Pearson, Kai-Uwe Hinrichs

Chemistry & Biochemistry Faculty Publications

Marine sediments are a large reservoir of recalcitrant organic matter and host microbes at subsurface depths exceeding 2.4 kilometers and temperatures up to 120°C, yet the mechanisms supplying bioavailable substrates remain unclear. Here, we investigated 7.8-million-year-old sediment from IODP Site C0012 off the Nankai Trough, Japan, through incubations at 20°, 35°, 55°, and 85°C to simulate burial temperatures. Using 3D fluorescence spectroscopy and ultrahigh-resolution mass spectrometry, we tracked changes in dissolved organic matter (DOM). At 35°C, humic-like DOM was released alongside metal ions, exhibiting low bioavailability. At 55°C, abiotic decomposition of humic compounds generated smaller, more bioavailable DOM, promoting fermentation. …

Amorphous Quininium Aspirinate From Neat Mechanochemistry: Diffracting Nanocrystalline Domains And Quick Recrystallization Upon Exposure To Solvent Vapours, Silvina Pagola, James Howard, Johannes Merkelbach, Danny Stam

Chemistry & Biochemistry Faculty Publications

Quininium aspirinate is mechanochemically prepared as a crystalline solid by liquid-assisted grinding, or as an amorphous phase (as determined by X-ray powder diffraction), by neat grinding or neat ball milling. Our previous work demonstrated using FT-IR spectroscopy that a mechanochemical reaction had occurred in the mechanically treated neat mixtures. Herein is reported that microcrystal electron diffraction (microED) afforded the discovery of two diffracting micron-size particles in the amorphous powder synthesized by manual grinding, among a majority of non-diffracting particles. Remarkably, microED data of one of them led to the known lattice parameters of quininium aspirinate. Furthermore, this so-called 'X-ray amorphous' …

Calculation Of Proton Transmembrane-Electrostatic Interaction Force And Elucidation Of The Water Droplet Experiment With A Transient Protonic Front, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

The “transmembrane-electrostatically localized proton(s)/cation(s) charge(s) (TELC(s), also known as TELP(s)) model” may serve as a theoretical framework to explain protonic cell energetics including both delocalized and localized protonic couplings. TELCs are held by their corresponding transmembrane-electrostatically localized hydroxides anions (TELAs) across the membrane through mutual transmembrane-electrostatic attractive force, which is now calculated to be in the range from 1.96 × 10⁻¹¹ to 2.28 × 10⁻¹¹ newtons (N) across a 2.5 nm thick membrane in a range of transmembrane potential from 10 to 200 mV. At a moderate transmembrane potential (100 mV), the protonic transmembrane attractive force is now calculated to …

A Comparison Of Microcrystal Electron Diffraction And X-Ray Powder Diffraction For The Structural Analysis Of Metal-Organic Frameworks, Erik Biehler, Silvana Pagola, Daniel Stam, Johannes Merkelbach, Christian Jandl, Tarek M. Abdel-Fattah

Chemistry & Biochemistry Faculty Publications

This study successfully implemented microcrystal electron diffraction (microED) and X-ray powder diffraction (XRPD) for the crystal structure determination of a new phase, TAF-CNU-1, Ni(C₈H₄O₄)·3H₂O, solved by microED from single microcrystals in the powder and refined at the kinematic and dynamic electron diffraction theory levels. This nickel metal–organic framework (MOF), together with its cobalt and manganese analogues with formula M (C₈H₄O₄)·2H₂O with M = Mn ^II or Co^II, were synthesized in aqueous media as one-pot preparations from the corresponding hydrated metal chlorides and sodium terephthalate, as a promising `green' synthetic route to moisture-stable MOFs. The crystal structures of the …

Extended Inter-Laboratory Characterization Of The New Coastal Seawater Dissolved Organic Matter Reference Material Trm-0522, Alexander J. Craig, Lydia Babcock-Adams, Maxime C. Bridoux, Charlotte Brun, Juliana D'Andrilli, Aleksandar I. Goranov, Patrick G. Hatcher, Oliver Lechtenfeld, Hang Li, Rebecca Matos, Garrett Mckay, Amy M. Mckenna, Madelyn Miller, Sasha Wagner, Margot E. White, Alexander Zherebker, Jeffrey A. Hawkes

Chemistry & Biochemistry Faculty Publications

Dissolved organic matter (DOM) reference materials are critical to ensuring reliable comparability of measurements across experiments and between labs. TRM-0522, isolated in 2022 from 45 m deep seawater off of Sweden’s west coast, fills the niche of a previously unavailable coastal marine DOM reference material. After its isolation, we detailed a limited number of metrics for TRM-0522, initially disclosing Orbitrap high-resolution mass spectrometry, nuclear magnetic resonance, carbon proportion, absorbance, and fluorescence data. With TRM-0522 becoming more widely used, a variety of labs have generated different metrics that help to characterize and define the chemical properties of this coastal reference material. …

Co₂ Isotopologues From The Ace Satellite, D. English, P. Bernath, C. Boone

Chemistry & Biochemistry Faculty Publications

Carbon dioxide isotopologues have been studied thoroughly in the troposphere. In the stratosphere, the minor oxygen CO₂ isotopologues have anomalous abundances due to their exchange reactions with isotopically fractionated ozone, differentiating them from tropospheric CO₂. Previously a model predicted that this anomalous isotopic abundance continues into the mesosphere but lacked verification from experimental observations. Here we use the Atmospheric Chemistry Experiment Fourier Transform Spectrometer which records infrared transmittance spectra of the Earth's limb from low Earth orbit using solar occultation. These infrared spectra provide measurements of global CO₂ isotopologue volume mixing ratios (VMRs) from the upper troposphere to the lower …

Analysis Of Aerosols In The Asian Monsoon Anticyclone As Observed By The Atmospheric Chemistry Experiment, M. Lecours, R. Dodangodage, C. D. Boone, P. F. Bernath

Chemistry & Biochemistry Faculty Publications

During the Asian summer monsoon season, pollutants from the lower troposphere are transported through deep convection to the upper troposphere and lower stratosphere. Surface pollutants such as CO are transported upward and trapped in the anticyclone during this unique atmospheric phenomenon. Associated with the anticyclone is a layer of enhanced aerosols located near the tropopause often referred to as the Asian tropopause aerosol layer (ATAL). The chemical and physical properties of aerosols in the ATAL are not yet fully understood as direct observations of the aerosols are limited. The Atmospheric Chemistry Experiment (ACE) is a satellite mission that provides high-resolution …

From Biophysics To Cellular Function: Neural Telcs-Membrane-Anions Capacitor Transmembrane Potential, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

Based on the transmembrane-electrostatically localized protons/cations charges (TELCs) theory, neural transmembrane potential including both resting and action potential is now well elucidated as the voltage contributed by the TELCs-membrane-anions capacitor biophysics in a neuron. Accordingly, neural transmembrane potential has an inverse relationship with TELCs surface density, which may represent a substantial progress in bettering the fundamental understanding of neuroscience. In this article, I will present a review on the latest development of the TELCs neural transmembrane potential theory and address Silverstein’s interesting arguments regarding the TELCs model that may constitute a complementary development to both the Hodgkin-Huxley classic cable theory …

Metathesis Or Isomerization: Counteranion Directed Reactivity Of Grubbs I, Paul D. Miller, Joe B. Calkins, Craig A. Bayse, Trandon A. Bender

Chemistry & Biochemistry Faculty Publications

Catalytic isomerization of alkenes has garnered interest for many years, but there are remaining challenges when it comes to thermodynamic selectivity and uncontrolled isomerization. Nonbiased substrates, be it sterically or thermodynamically, remain challenging for many catalysts, with a few examples available in the more modern literature. Herein, we present the controlled isomerization of linear alkenes with a cocatalytic mixture of commercially available catalyst and reagents: Grubbs I, tris(pentafluorophenyl)borane, and triethylsilane. DFT calculations indicate that an observed alkylidyne hydride intermediate is in rapid equilibrium with an alkylidene that binds the alkene substrate. This combination results in a pi-acidic metal and a …