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Managing Multi-Drug Resistance: An Evolutionary Game Theory And Optimal Control Approach, Shukhrat Nasrulloev

Theses and Dissertations

Multi-drug resistance is an evolutionary process in which treatment eliminates sensitive cells, allowing resistant clones to dominate. This thesis investigates this process using a framework integrating population dynamics, evolutionary game theory, and optimal control theory. We develop a two-population logistic growth model describing competition between drug-sensitive and drug-resistant cells under treatment, construct dose-dependent payoff matrices and replicator dynamics to characterize evolutionary competition, and derive a critical drug level D_crit = (r_S - rR)/(dS - d_R) at which resistant cells gain a fitness advantage. An optimal control problem is formulated via Pontryagin's Maximum Principle to identify schedules …

Decomposing Shadow Prices Under Climate-Driven Growth Scenarios: Insights From An Elk Herd Case Study, Ranjit Bawa, Drew Bennett, Wai Yan Siu, Bailey Kirkland, David Finnoff, Jacob Hochard

ODU Articles

Natural capital accounting provides a framework for integrating ecological processes with economic valuation, but the mechanics of shadow price formation often remain opaque to resource managers and policymakers. Using the Clarks Fork elk herd in northwestern Wyoming as a case study, we decompose the shadow price of natural capital into its ecological, economic, and institutional components. Population dynamics are estimated using a linearized Ricker model and projected forward using a logistic projection, incorporating climate-driven reductions in intrinsic growth rates. These ecological scenarios are linked to a shadow pricing formulation that explicitly accounts for marginal benefits, harvest policy responses, discounting, and …

Chemical Load: An Unseen Herbicide Filter In Restored Prairies?, Rylie Franklin

Electronic Theses and Dissertations

Community Assembly Theory is a framework used to describe the process by which species from a regional species pool disperse and encounter various abiotic and biotic conditions that act as filters, limiting which species will populate a specific local community. Prairie restoration success can be improved by understanding abiotic and biotic filters. As agricultural practices have adopted integrated weed management plans, that include the use of both chemical and non-chemical techniques, another filter needs to be considered during restoration: the chemical load of soils, i.e., herbicide residue from recent on-site applications and herbicide drift from adjacent areas. To examine the …

Scope Of Microbial Transglutaminase For Site-Specific And Oriented Immobilization Of Native Antibodies From Various Host Species, Emily Beitello, Kwame Osei, Faith E. Breausche, Jon A. Friesen, Jeremy D. Driskell

Faculty Publications – Chemistry

Modification of antibodies to chemically couple labels or immobilization reagents is essential for developing biosensors. Typically, conjugation occurs through chemical methods that leverage reactive amines and thiols on native antibodies; however, this nonspecific approach can interfere with antibody function. Microbial transglutaminase (mTG) is an enzyme that has been used for site-specific conjugation of chemical modifiers to the F_c region of native antibodies, but thus far mTG-mediated conjugation has been limited to production of antibody-drug conjugates with human IgGs. Here, we assessed the scope and versatility of mTG to target IgGs, with the goal of site-specific conjugation to facilitate oriented …

Neighborhood Embeddings And Scalable Learning For Optimal Transport And Unbalanced Optimal Transport, Muhammad S. Rana

Mathematics Dissertations - Archive

Dimensionality reduction techniques are developed from the assumption that high-dimensional data often arises from low-dimensional structures embedded into the high-dimensional ambient space. Classical dimensionality reduction methods rely on the Euclidean distance, which may fail to capture the geometric structures of the datasets. This dissertation includes alternative metrics for dimensionality reduction techniques and challenges in applying these techniques.

First, we investigate the Wasserstein distance based neighbor embeddings for dimensionality reduction methods and compare the classification and clustering performance with the classical Euclidean based methods. The Wasserstein distance models the data as probability distributions and compares two distributions applying optimal transport (OT) …

Exploratory Investigation Of Greenhouse Gas Emissions In A Natural And Restored Salt Marsh, Sophia Motta

Open Access Master's Theses

Coastal wetlands are typically considered greenhouse sinks, specifically playing an important role in the global carbon cycle (Chmura et al., 2003), but new studies have pointed to anthropogenic interference leading to the understanding that altered tidal salt marshes may also be producers of methane to the atmosphere, contributing to the greenhouse effect. Hydrologic alteration including due to sea level rise (SLR), peat subsidence, impounded water, and decreased accretion rate disruption can have negative effects on marsh biochemistry leading to potential changes in electron acceptor availability, redox gradient shifts, and microbial community structure within the environment. This research is intended to …

Exploring The Limitations Of Substrate Scope In Dimethylallyltryptophan Synthases, Evan T. Miller

Theses and Dissertations--Pharmacy

Natural products (NPs), are the largest source of bioactive compounds in Nature, and are essential to the treatment of human disease. Nearly 50% of drugs approved for use from 1981 to 2019 owe some aspect of their development to NPs, either in terms of their structure, pharmacophore, or mechanism of action. However, NPs are difficult to structurally optimize. Chemoenzymatic methods for NP derivatization have been increasingly seen as practical alternatives to traditional synthetic methods. Prenyltransferases (PTs) are involved in the primary and secondary metabolism of plants, bacteria, and fungi, and they are key enzymes in the biosynthesis of many clinically …

Using Camera-Based Unmarked Spatial Capture-Recapture Modeling To Estimate Reintroduced Elk (Cervus Canadensis) Population Parameters And Distribution In Southeastern Kentucky, Claire Marie Muia

Theses and Dissertations--Forestry and Natural Resources

Estimation of population parameters is important for wildlife management decisions. Elk reintroduced to southeastern Kentucky experienced early irruptive population growth and are currently monitored using a statewide harvest-based statistical population reconstruction model (SPR) across the Kentucky Elk Restoration Zone (KERZ). Because the SPR model is spatially coarse and difficult to scale to the smaller management units comprising the KERZ, we conducted a spatially explicit capture-recapture study using a clustered camera-trapping array deployed for 10 weeks from June–August 2024 to estimate elk population parameters within Management Unit 4. Due to a lack of resights of GPS-marked elk, population parameters were estimated …

Iere Annual Report 2026, Erin Largo-Wight, Heather Barnes Truelove, Kelly Rhoden, Jessica Barnes, Lauren Canady, Nicole Lowe, Ruby Cox, Sydney Barrett, Kathleen Hutton

Annual Reports

2026 Annual Report of the Institute for Environmental Research and Education

Impacts Of Management Practices And Soil Properties On Free-Living Nitrogen Fixation In Eastern South Dakota, Laura Galvan Nuevo

Electronic Theses and Dissertations

Free-living nitrogen (N) fixation (FLNF) may represent a sustainable pathway to supplement crop N demand in agroecosystems, yet edaphic and management factors regulating this process under field conditions remain poorly understood in the Northern Great Plains. Using 15N2 direct method to quantify potential FLNF (pFLNF) and baseline FLNF (bFLNF), this thesis investigates how crop rotations (2-, 3-, and 4-year systems), tillage management (conventional vs. no-till), cover cropping, and soil properties affect the potential of free-living diazotrophs to supply N via FLNF in a long-term no-till corn-based system in Southeastern South Dakota. A two-year field study evaluated pFLNF across four growing …

Linking Phytoplankton Physiology And Ecology To Global Biogeochemical Cycles: A Modeling Approach, Margaret Bernish

Open Access Dissertations

Phytoplankton, or microscopic primary producers, contribute to carbon export through the biological transformation of carbon dioxide into organic molecules. Phytoplankton are responsible for approximately half of global net primary production, while only contributing minimally to total photosynthetic biomass. Despite their important role in the global cycling of nutrients, phytoplankton physiology and ecology are often highly simplified in global biogeochemical models. This dissertation elucidates the role of phytoplankton physiology and ecology within biogeochemical cycles, allowing for better characterization of marine microbial distribution and better representation of nutrient cycling for interpretive and predictive models. The development of formulations that link physiological responses …

Submesoscale Dynamics Of Phytoplankton And Carbon Export Revealed By High-Resolution Airborne And Satellite Remote Sensing Of Currents And Ocean Color, Sarah E. Lang

Open Access Dissertations

Satellites and airborne sensors reveal submesoscale (1 - 10 km) variability in ocean color in the form of filaments, eddies, and patches. The variability in ocean color is closely tied to the physical dynamics that restructure phytoplankton distributions and drive active biological responses like changes in primary productivity and community structure. As the base of the marine food web and a key component of the biological carbon pump, phytoplankton are crucial to the overall health of marine ecosystems and to the ocean's role in climate. This dissertation focuses on the use of airborne and satellite remote sensing to study the …

Dcmm-Transformer: Degree-Corrected Mixed-Membership Attention For Medical Imaging, Huimin Cheng, Xiaowei Yu, Shushan Wu, Luyang Fang, Chao Cao, Jing Zhang, Tianming Liu, Dajiang Zhu, Wenxuan Zhong, Ping Ma

Computer Science Faculty Research & Creative Works

Medical images exhibit latent anatomical groupings, such as organs, tissues, and pathological regions, that standard Vision Transformers (ViTs) fail to exploit. While recent work like SBM-Transformer attempts to incorporate such structures through stochastic binary masking, they suffer from non-differentiability, training instability, and the inability to model complex community structure. We present DCMM-Transformer, a novel ViT architecture for medical image analysis that incorporates a Degree-Corrected Mixed-Membership (DCMM) model as an additive bias in self-attention. Unlike prior approaches that rely on multiplicative masking and binary sampling, our method introduces community structure and degree heterogeneity in a fully differentiable and interpretable manner. Comprehensive …

Adversarial Robustness In Biomedical Time-Series Models, Rohan Tiwari

Bioengineering Theses

This study investigates adversarial vulnerabilities in deep learning models for biomedical time-series classification across two clinically important modalities: electrocardiography (ECG) and electroencephalography (EEG). Using the MIT-BIH Arrhythmia and CHB-MIT seizure datasets, I evaluate time-domain attacks (FGSM, PGD), Fourier-domain constrained attacks, and learned spectral perturbations designed to reveal modality-specific sensitivity patterns. Across both tasks, a consistent trend emerges low-frequency components (0–5 Hz) constitute a dominant axis of adversarial vulnerability, with perturbations in this range producing the steepest degradation in classification performance. In ECG models, protecting the physiologically relevant QRS band (5–20 Hz) significantly improves robustness, whereas EEG models remain highly sensitive …

Drivers Of Phytoplankton Bloom Interannual Variability In The Amundsen And Pine Island Polynyas, Guillaume Liniger, Delphine Lannuzel, Sébastien Moreau, Michael S. Dinniman, Peter G. Stutton

CCPO Publications

The Amundsen Sea Embayment (ASE) experiences both the highest ice shelf melt rates and the highest biological productivity in West Antarctica. Using 19 years of satellite data and modelling output, we investigate the long-term influence of environmental factors on the phytoplankton bloom in the Amundsen Sea (ASP) and Pine Island (PIP) polynyas. We test the prevailing hypothesis that changes in ice shelf melt rate could drive interannual variability in the polynyas' surface chlorophyll-a (chl a) and Net Primary Productivity (NPP). We find that the interannual variability and long-term change in glacial meltwater may play an important role in …

Ecological Feedbacks In The Earth System, Eugene J. Murphy, Jessica J. Williams, Isla H. Myers-Smith, Vivienne P. Groner, David M. P. Jacoby, Lester Kwiatkowski, Jess Melbourne-Thomas, Emma Ransome, Cristina Banks-Leite, Laurent Bopp, Marion Gehlen, Eileen E. Hofmann, Babette Hoogakker, Nadine M. Johnston, Yadvinder Malhi, Emma L. Cavan

CCPO Publications

Ecological feedbacks are fundamental features of the Earth system, affecting physical processes and chemical cycles. Our understanding of the interactions underlying these feedbacks at different spatial and temporal scales and the extent to which feedbacks affect Earth system functioning remains limited. Climate change and other anthropogenic pressures are already negatively affecting ecological processes in marine, freshwater, and terrestrial ecosystems. These will most likely be amplified in the coming decades under our current warming and socioeconomic pathways. The knock-on impacts on ecological feedbacks have the potential to cause rapid perturbations to the Earth system, and may significantly impact the structure and …

Investigations Toward A Unified Reaction Pathway Of Thermal And Tbsotf-Mediated Oxidopyrylium-Alkene (5 + 2) Cycloadditions, Adam J. Youman, Samantha N. Rokey, Wentao Guo, Jacob P. Grabowski, Susanna N. Angles, Jacob J. Bulandr, Qing Sun, John R. Goodell, Dean J. Tantillo, T. Andrew Mitchell

Faculty Publications – Chemistry

Oxidopyrylium-based (5 + 2) cycloadditions are crucial reactions to construct seven-membered carbocycles containing an ether bridge (i.e. oxabicyclo[3.2.1]octanes). Intramolecular silyloxypyrone-based (5 + 2) cycloadditions were investigated and revealed several features: (1) the TBDPS thermal process proceeds via a zwitterionic oxidopyrylium intermediate similar to previously reported TBS variants; (2) the TBSOTf-mediated reaction proceeds through a cationic oxidopyrylium intermediate; (3) quantum chemical calculations predict a stepwise process for an electron-rich dipolarophile for each set of conditions. The thermal silyloxypyrone-based (5 + 2) cycloadditions were extremely dependent on the nature of the dipolarophile and the silyl transfer group. The TBDPS enhances the …

Assessing The Diversity And Composition Of Crayfish Assemblages In The Ogeechee River Basin, Reginald Turner

College of Graduate Studies: Theses & Dissertations

Crayfish assemblage composition in the southeastern United States is understudied relative to other aquatic taxa, such as aquatic insects and fishes, and the Coastal Plain watersheds of that region are particularly underrepresented in the contemporary literature on this topic. For example, although 38% of the crayfish species in Georgia are considered “species of greatest conservation need,” most of the distributional data used to make these designations are outdated, with some dating back over 50 years. This thesis sought to update our understanding of the contemporary distributions of crayfish species within the Ogeechee River Basin (ORB), a watershed in southeastern Georgia …

Training Set Augmentation And Biology-Aware Harmonization Improve Radiomic Models For Lung Cancer Prediction In Indeterminate Nodules, Claire Huchthausen, Menglin Shi, Gabriel De Sousa, James Larner, Einsley Janowski, Jonathan Colen, Krishni Wijesooriya

Data Science Faculty Publications

CT radiomics-based machine learning has potential to predict lung cancer in pulmonary nodules (PNs) earlier than standard-of-care methods. Low malignancy rates in early-development PNs and variable image acquisition hinder development of radiomic models for diagnosing these PNs. To address these challenges, we augmented training using later-development PNs and harmonized for acquisition effects. We examine early-development benign and malignant PNs (n = 106) below the sensitivity of standard-of-care diagnosis. Classifiers predicting malignancy performed near chance when trained on ComBat-harmonized radiomic features from only early-development PNs. We then augmented training with later-development benign and malignant PNs (n = 225). We evaluated whether …

Laser Beam Shaping Using A Neural Network, Azeem A. Hakim

Honors Undergraduate Theses

Multiphoton lithography (MPL) is a method of laser-based 3D-printing for fabricating micron-scale structures point-by-point in a photopolymerizable medium. MPL’s high-resolution capabilities have made it a powerful method for the fabrication of many devices, such as microelectromechanical systems (MEMS) and tissue scaffolds.  The throughput of MPL processes can be increased by using spatially shaped laser beams that expose large areas or volumes simultaneously. A laser beam can be reshaped by passing it through a spatial light modulator (SLM) displaying a pre-designed phase mask. One type of laser beam profile used for this purpose is the Bessel beam, a type of structured …

The Shoreline Protection Potential Of Oyster Reefs: A Systematic Review And Meta-Analysis, Jessica R. Fergel, Robert E. Isdell, Gabriella Dipetto, Karinna Nunnez, Sean T. Gregory, Evan Hill, Donna Marie Bilkovic

Biological Sciences Faculty Publications

Nature-based solutions for erosion control that incorporate oyster reefs, alone or in combination with other habitats, are an increasingly popular approach due to their potential to protect shorelines and enhance oyster production. However, the extent to which natural or constructed oyster reefs provide shoreline protection remains unclear. We conducted a global systematic literature review and meta-analysis to summarize and evaluate the potential of oyster reefs in attenuating waves, promoting sediment accretion, and/or reducing shoreline erosion. Factors extracted from studies included shoreline protective measures examined, oyster reef structure type, and oyster reef tidal location. The results of the meta-analysis showed generally …

Differences In Biologic Clinical Trials For Chronic Rhinosinusitis With Nasal Polyps—Are We Comparing Apples With Oranges?, Marjolein Cornet, Peter W. Hellings, Martin Desrosiers, Martin Wagenmann, Richard Follows, Laura Walrave, Luz Adriana Jimenez, Lee Tombs, Dawn Edwards, Peter Howarth, Joseph K. Han

Department of Otolaryngology (ENT) Faculty Publications

In recent years, several biologics targeting Type 2 inflammation have been developed for treating chronic rhinosinusitis with nasal polyps (CRSwNP). These have been studied in registrational randomized controlled trials (RCTs), which vary in their patient populations, trial design, endpoints, geography, timing, or data-handling processes. While (in)direct treatment comparisons and meta-analyses have been carried out to compare efficacy results from RCTs, often these fail to properly account for these between-study differences. Here, we summarize the key between-study differences that can influence trial outcomes and highlight the resulting challenges faced when comparing outcomes from different Phase III RCTs of biologics in CRSwNP.

A Bioinspired Approach For Adaptive Solid-Solid Phase Change Material Coatings With Optimized Surface Features For Passive Thermal Regulation, Rajae Bousselham, Zhiying Xiao, Mingjiang Tao, Sergio Granados-Focil, Adriana Hera, Steven Van Dessel

Chemistry

The necessity to reduce global energy consumption calls for innovative strategies in building thermal management. Passive thermal regulation, particularly through bio-inspired designs, offers a promising avenue by mimicking nature's efficient control of optical properties. This research introduces a novel, climate-responsive coating that integrates optimized bio-inspired surface features with a solid-solid phase change material (SS-PCM) to dynamically manage solar absorptivity without adding additional thickness, enabling both heating and cooling as needed. Drawing on the photonic architectures of the Saharan silver ant and Morpho Didius butterfly, we employed a modeling and multi-objective optimization framework to tailor these surface features. Simulations reveal that …

Celebrating Faculty Scholarship 2026, Smith College Libraries

Celebrating Faculty Scholarship: Bibliographies

Bibliography of selected scholarly and creative work produced by Smith College faculty and submitted by faculty for the 2026 celebration in the Neilson Library Skyline Reading Room, Smith College on September 14, 2026.

Theoretical Study Of Long-Range Molecular Interactions, Adrian Luis Batista-Planas

Doctoral Dissertations

Describing intermolecular forces is fundamental to modeling and predicting the behavior of molecular systems. In particular, long-range molecular interactions—with electrostatic, induction, and dispersion as main components—play a critical role, especially for low-temperature and low-density regimes. Long-range interactions are often described through perturbation theory, representing the electronic charge distribution via multipolar series of the moments and polarizability tensors corresponding to each molecule. However, while the theory is well-established, obtaining the resulting analytical expressions (and their practical implementation) constitutes a highly complex and system-dependent task. To address this challenge, we developed Long-Range-Fit (LRF), an interactive and user-friendly software package designed to automate …

Hydrogeochemical And Redox Controls On Nitrate And Arsenic Co-Occurrence In The Western Kansas High Plains Aquifer (Usa): A Composite Health Risk Assessment And The Case For Risk-Informed Private Well Governance, Jonathan Kuffour Owusu

Master's Theses or Doctor of Nursing Practice

Fifty-one private domestic wells across western Kansas were sampled to quantify nitrate and arsenic occurrence, identify geochemical controls, and evaluate carcinogenic and non-carcinogenic health risks for adult and child receptors in a region where groundwater serves as the primary drinking water source with no routine regulatory oversight. Samples were analyzed for major ions, nutrients, and trace elements by ICP-MS, ion chromatography, and UV-Vis spectrophotometry. Shapiro-Wilk testing confirmed non-normal distributions for both contaminants; inter-county comparisons were therefore conducted using Kruskal-Wallis tests with Dunn's post-hoc correction. Health risk was quantified via chronic daily intake (CDI), hazard quotient (HQ), HQ-based Water Quality Index …

An Introduction To Field Excursions For The 2026 Geological Society Of America Cordilleran Section Meeting In Loreto, Baja California Sur, México, Scott E.K. Bennett, Michael H. Darin, Genaro Martínez Gutiérrez

Geology Faculty Publications and Presentations

The 122nd annual meeting of the Geological Society of America (GSA) Cordilleran Section will be held in Loreto, Baja California Sur, México, an idyllic and historic Sonoran Desert city nestled on the eastern shore of the Baja California peninsula. The 2026 Loreto meeting marks a milestone for GSA as it is the first time in the Section’s century-plus history that the meeting has been held on the Baja California peninsula and only the third time that the meeting has been held in México. Thus, the 2026 Loreto meeting and related field trips represent a meaningful expansion of the Section’s engagement …

Electronic Bills Of Lading And Blockchain Technology: A Regulatory Perspective, Hsin-Hua Tsai

Journal of Marine Science and Technology–Taiwan

Information and communications technology (ICT) systems are increasingly relevant to the maritime sector. Regarding the revolution of the bill of lading, many shipping lines and other technology startups have been looking into developing viable electronic transport documents that have the same functions as paper bills of lading to reduce supply chain risks. The limitations of the paper-based process have become increasingly visible in the COVID-19 crisis. The main purpose of the article is to analyze the application of blockchain bills of lading, which utilizes computational logic to create the digital ledger, and users can set up algorithms and rules to …

Intelligent Formation Control Using Orfbls And Adaptive Backstepping Sliding-Mode Control To Address Uncertain Tilting In Multi-Quadrotors During Wind Gusts, Ching-Chih Tsai, Chun-Fu Mao, Kumail Hussain

Journal of Marine Science and Technology–Taiwan

In terms of aerial robotics, stable and precise formation control is a significant challenge for tilting multi-quadrotors during disturbances. This paper proposes a fixed-time formation control strategy for tilting multi-quadrotors to address the effect of external wind gusts. The observer accurately predicts environmental disturbances and an adaptive backstepping sliding-mode control (ABSMC) method with an output recurrent fuzzy broad learning system (ORFBLS) addresses these disturbances within a finite time. ORFBLS dynamically adjusts its structure through a growing ORFBLS structure to allow nodes to be added as needed. The method's stability is validated using Lyapunov stability theory and ensures the convergence of …

Visually Guided Landing System On Ship Deck For Multicopter, Dong-Lin Li, Shih-Kai Lee, Tzu-Hsiang Chou

Journal of Marine Science and Technology–Taiwan

Traditionally, high-value fish have been located at sea using helicopters. However, with advancements in technology, maritime drones have become increasingly important in recent years. Compared to traditional helicopter-based methods, drones offer significantly lower operational costs, making them cost-effective. However, the challenging sea conditions, including strong winds and the swaying motion of vessels, pose significant challenges for drone landings.

This paper proposes a stable approach for multicopter landing on ships at sea, incorporating improved marker detection, enhanced wind resistance control, and more accurate deck motion prediction. In the marker detection phase, we introduce a method to improve the accuracy of ArUco …