Digital Commons Network^™

Robust Thermodynamic Analysis Of Flexible Protein-Ligand Binding Using Statistical Mechanics, Mitchell Dulaney

Create@State

Understanding how proteins bind small molecules is essential for accurate computational modeling of biological systems. However, calculating binding free energy (delta G), enthalpy (delta H), and entropy (delta S) becomes unreliable when proteins are flexible, and ligands are between multiple binding positions. This motion causes traditional computational methods to produce inconsistent thermodynamic values.

A computational workflow was implemented that included docking to predict likely binding positions, molecular dynamics simulations to sample how the protein and ligand move over time, and statistical mechanics analysis to calculate thermodynamic quantities. A new theoretical framework was developed and implemented in a custom program to …

Swosu Research And Scholarly Activity Fair 2026, Swosu Office Of Sponsored Programs

SWOSU Research and Scholarly Activity Fair Programs

On behalf of the University Research and Scholarly Activity Committee (URSAC) and the Office of Sponsored Programs (OSP) at Southwestern Oklahoma State University, we are pleased to welcome you to the Thirty-Fourth SWOSU Research and Scholarly Activity Fair.

Designing, Integrating, And Evaluating Blockchain Assignments In The Undergraduate Computer Science Program, Karol Lejmbach

Dissertations (1934 -)

Blockchains as a technology rely heavily on a wide range of computer science topics. These topics include: algorithms, data structures, network communication, cryptography and many more. These topics align nicely with topics often covered in undergraduate computer science course. Blockchain technology offers an interesting opportunity for computer science educa- tors. Blockchains rely heavily on a wide range of computer science topics. These topics include: cryptography, networking, data structures, and algorithms. Many of these top- ics are explored in undergraduate computer science programs either in core or elective classes. This offers an opportunity for teaching students about emerging technologies, such as …

The Impact Of State And Federal Policies On Academic Researchers: Findings From A National Survey, Dylan Ruediger, Chelsea Mccracken, Jonathan Barefield

Copyright, Fair Use, Scholarly Communication, etc.

Key findings

● State and federal policies targeting divisive concepts or DEI are shaping research agendas at scale and across disciplines. Twenty percent of all respondents, and 29 percent of researchers working in states with divisive concepts or similar laws, reported having avoided certain research topics because of state laws and policies.

● Eight percent of respondents representing a wide range of disciplines reported having had a federal grant cancelled in 2025.

● Eleven percent of respondents reported that federal and state policies restricting research activities are compelling them to seek employment out of state, to leave the academy, or …

Design And Application Of Collaborative Simulation System For Satellite Constellation Flight Missions, Dong Yan, Hanzhe Yang, Fangfang Jiang, Chengbao Liu, Peng Zhang

Journal of System Simulation

Abstract: To meet the requirements of the collaborative drill for the ground operation and control system of the satellite constellation, as well as the verification and evaluation of in-orbit complex missions, the design ideas and implementation methods of the collaborative simulation system for satellite constellation flight missions were proposed. By adopting the time correction mechanism of the time-scale distributor, the time synchronization problem among the simulation nodes and the operation and control simulation system was solved. By adopting the communication technology based on improved PDXP + UDP, the problem of cross-node data interface and inter-satellite communication simulation was resolved. A …

Fairhiveframes-1k: A Public Fair Dataset Of 1265 Annotated Hive Frame Images With Preliminary Yolov8 And Yolov11 Baselines, Vladimir Kulyukin, Reagan Hill, Aleksey Kulyukin

Computer Science Faculty and Staff Publications

In precision apiculture, the portable digital camera is a cost-effective sensor for capturing hive images or videos used to quantify different colony variables. Openly accessible, well-annotated, interoperable cell-level image datasets are still the exception rather than the norm. This shortage constitutes a major barrier to AI-driven approaches aimed at automating image-based comb analysis. In this article, we present FAIRHiveFrames-1K, a publicly available dataset of 1265 annotated hive frame images (1920 × 1080 PNG) designed to facilitate research in AI-intensive image-based comb analysis automation. The dataset, derived from a 2013–2022 U.S. Department of Agriculture–Agricultural Research Service multi-sensor research reservoir, includes 124,669 …

The Digital Neuron: Neural Cellular Automata For Neural–Symbolic Translation, Nicole Assenza

SMU Data Science Review

A neural cellular automata (NCA) architecture, referred to as Pluto’s NCA, was developed to characterize bilateral communication and semantic reciprocity between symbolic representations and a spatially distributed update field. The architecture employs an encoder–automata–decoder pipeline that maps symbolic inputs into a multichannel state field and reconstructs them through agreement-driven attractor convergence within a stable semantic attractor landscape. System behavior was evaluated under controlled perturbations, including rhythmic desynchronization, graded ablations, correlated and independent noise, and percolation-based structural degradation. Quantities such as Agreement(t), internal coherence Aᵢ(t), the recovery time constant τ, and the critical percolation threshold pc were measured to assess stability, …

Phishing Restraint: University Simulated Phishing Campaigns, Alexander M. Abou Khir

Cybersecurity Undergraduate Research Showcase

Universities face heightened vulnerability to phishing attacks due to their open information-sharing culture and diverse user populations. This study examines how phishing exploits human factors within campus environments and evaluates three major training strategies: embedded phishing, microlearning, and role-based instruction to understand their individual and combined effectiveness. I explored studies that implement these strategies in pairs and use the strategies alone, identified trends in susceptibility reduction, behavioral reinforcement, and contextual relevance. I suggest that, while each method independently improves user awareness, multiple approaches offer stronger, more adaptable protection by addressing both psychological triggers and role-specific risks. The paper contributes a …

Draft Final Butte Priority Soils Operable Unit Unreclaimed Sites: Ur-03 Construction Completion Report, Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Tracing The Milky Way’S Evolution Through Its Star-Planet Systems, Rayna Rampalli

Dartmouth College Ph.D Dissertations

From individual planetary systems to the Milky Way's structure, stars are the linchpin connecting astrophysical scales. Through three complementary projects, my thesis leverages these connections and large stellar surveys to offer insight into the Galaxy's dynamical and chemical history and its role in shaping planet formation and evolution. (I) I developed Protify, an automated pipeline to measure stellar rotation periods in TESS light curves, enabling rotation-based ages for thousands of stars. Applying it to overdensities of stars in eccentric Galactic orbits, thought to be post-resonant signatures of spiral arm passages, revealed unexpectedly young rotators in dynamically old populations. Because such …

Bremsstrahlung Photons Emissions Measured At Different Rf Power In 28 Ghz Ecr Ion Source, Mwingereza John Kumwenda

Tanzania Journal of Engineering and Technology (TJET)

High-performance electron cyclotron resonance ion sources (ECRISs) generate large amounts of bremsstrahlung photons that affect the cryogenic systems due to the extra heat load that is produced. Thus, this study investigates the bremsstrahlung photons energy spectra at various RF powers, presenting some insight about the trends of the electron heating process inside the plasma. Bremsstrahlung photons from a 28 GHz ECRIS were measured at Busan center of Korean Basic Science Institute (KBSI). The gamma-ray detection system consists of three round-type NaI(Tl) scintillation detectors placed 620 mm radially from the beam axis at the extraction side of the ECRIS, and a …

Correcting Faraday Cup Measurements Using Rutherford Backscattering, Spencer Hughes, A. Bunnell, J. Kim

25th Annual A. Paul and Carol C. Schaap Celebration of Undergraduate Research and Creative Activity (2026)

Faraday cup is a conductive cup that measures the current of an incident beam of charged particles. Faraday cups are frequently used in particle accelerator-based studies where the beam intensity must be measured. A previous study determined the systematic error in Faraday cup measurements for a 3.4 MeV proton beam using Rutherford scattering at large angles. Our study builds upon this previous work to include six different beam energies ranging from 3.0 MeV to 0.6 MeV and two different incident masses (H and He). A silicon surface barrier detector measured the energy of back-scattered ions from a copper target. The …

Eigenmode Decomposition Analysis Of Resistive Magnetic Reconnection, Isaac Q. Evans

25th Annual A. Paul and Carol C. Schaap Celebration of Undergraduate Research and Creative Activity (2026)

Recent work demonstrates that specific aspects of nonlinear magnetic reconnection in a collisionless regime are directly attributable to linearly damped eigenmodes. In this work, we apply similar eigenmode analysis tools to characterize nonlinear magnetic reconnection driven by resistivity. In contrast to the collisionless case which contains a single unstable/stable eigenmode pair, the resistive case contains an unstable eigenmode and a wide spectrum of stable modes. Calculating eigenmode amplitudes allows for a determination of the significance of each eigenmode in the nonlinearly-evolved resistive reconnection. Linearly stable modes are found to be important in determining properties of nonlinear systems. We discuss how …

A Computer Vision Approach To Analyzing Taxane Effects On Prostate Cancer Cells, Diana Elizabeth Dancea

Electronic Theses and Dissertations 2020 - Present

Actin is a family of proteins that help create the structure of the cytoskeleton, which gives shape to the cell. In many chemotherapy treatments, researchers target actin because it controls the cell division process. Therefore, if they are able to understand the actin fibers, that may help in formulating methods to stop or slow down cancer cells from reproducing. Another important protein is PAK6, which regulates actin. In our research, a collaborative effort with Prof. Michael Lu’s lab at Florida Atlantic University, we use machine learning techniques to analyze cells which had their PAK6 protein knocked out, and compare them …

Draft Final Butte Priority Soils Operable Unit Unreclaimed Sites: Ur-03 Construction Completion Report, Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Re: Comment Letter For The Silver Bow Creek/Butte Area Npl Site Butte Priority Soils Operable Unit, 60% Remedial Design Documents For The Blacktail Creek Area Groundwater Hydraulic Control System (Dated March 2, 2026), Emma Rott

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Loan Risk Classification Model, Giulio Palombo

Celebration of Research

I created a model that classifies the customers as good or bad for possible loaners. The model is XGBoost Classification model. I used as target variable the variable “default”. The target variable indicates whether the customer has previously defaulted on a loan or not. The dataset provides a representation of customer behavior and financial status. On top of that, the dataset contains detailed information about banking transactions.

Emergent Dynamics In Multiplex Social Networks: Agent-Based Modeling Of Information Diffusion For Misinformation Control, Harshvardhan Prabhakar Ghongade, Anjali Ashokrao Bhadre, Shivani Agarwal, Harjitkumar Uttamrao Pawar, Harshal Subhash Rane

Northeast Journal of Complex Systems (NEJCS)

Information misrepresentation is widespread in multi-layered social networks which provide multiple avenues to communicate information. As such, it presents significant opportunities for both information integrity and public discourse to be undermined by disinformation. This paper outlines a new agent-based model, developed to capture emergent dynamics of multi-layered social networks and to help identify technical means to mitigate information misrepresentation in complex systems. A key component of this research includes a novel Multi-Layer Information Diffusion Model (MLIDM), integrating both cross-layer communication among agents, as well as heterogeneous agent behaviors and adaptive intervention strategies. Our methods employ a three-stage process to model …

Asymptotic Sensitivity And Adjoint Methods For Equation Discovery With Open-Source Implementation, Nathan Schill

Theses and Dissertations

The "on-the-fly" (OTF) method is a gradient-based approach to equation discovery. It makes use of (potentially limited) observational data, a data assimilation technique such as continuous data assimilation (also called nudging), and an error metric. From these it computes an asymptotic approximation of a simulated system's error sensitivity with respect to unknown parameters and utilizes any gradient-based optimization algorithm to perform parameter updates. These parameter updates may be done online or offline, and the model may be of a precisely specified form or simply a library of possible terms with potentially nonlinear parameters. We have applied the adjoint method to …

Sonic Booms From Rockets: Measurements And Modeling, Mark Charles Anderson

Theses and Dissertations

Rocket sonic booms are produced when launch vehicles or boosters travel faster than the local speed of sound in the atmosphere, generating systems of conical shock waves. The purpose of this dissertation is to perform high-fidelity measurements of rocket sonic booms and to explain the physics behind the unique phenomena observed. After a thorough literature review on sonic booms produced during spaceflight operations, Part I of this dissertation deals with measurement and analysis challenges. One challenge is reducing contaminating noise effects on sonic boom perception metrics, addressed using a low-pass filtering method tied to the noise floor. A second challenge …

Real And Perceived Barriers To Effective Use Of Cataract Surgical Supplies, Caitlin Davie, Lindsay K. Cloud, Scott Burris, Shaina Shiwdin, Brooke Sherry, Christina R. Prescott, Joel Schuman, David Palmer, David Chang, Daniel Parra, Cordelia Kwon, Margaret A. Tharp, Cassandra L. Thiel

Wills Eye Hospital Papers

INTRODUCTION: Cataract surgery, among the most common procedures worldwide, significantly contributes to climate change through both solid waste and air pollution, highlighting the urgent need for targeted interventions. Implementation faces hurdles including legal constraints and concerns about infection risks and malpractice.

METHODS: This article examines federal and state regulatory structures around two key waste reduction strategies: reduction of multidose medications and distribution of partly-used operating room medication to patients post-surgery.

RESULTS: We find little-to-no legitimate regulatory barriers to either waste reduction practice. Dispensing and redistributing partly-used medication has been codified in law in some states. Evidence-based reports indicate minimal risks …

Image Processing Technique To Find The Burden Rock Velocity And Its Interdependency On Bench Blasting Parameters – A Case Study, Channabassamma N, Akhil Avchar, Sahas V Swamy, Vedala Rama Sastry, Hemant Agrawale

Journal of Sustainable Mining

In any rock engineering or excavation project, optimizing blast design is essential for controlling post-blast phenomena such as flyrock, burden throw, and burden rock velocity (BRV). This study investigates the dynamic response of BRV in bench blasting operations by employing a high-speed camera and ProAnalyst software to quantify rock displacement. The relationships between BRV and key blast parameters, number of holes (NH), explosive charge per hole (EPH), total explosive charge (TEC), stiffness ratio (K), and stemming ratio (STR), were analyzed to identify linear or non-linear trends. Non-linear trends, …

Accelerated Coupled Mode Model For Fiber Laser Amplifiers As An Averaged Dynamical System, Rebecca Bryant, Jacob Grosek, Jay Gopalakrishnan

Mathematics and Statistics Faculty Publications and Presentations

We apply a known theorem for simplifying dynamical systems with bounded error to a specific optical fiber waveguide problem, thereby supplementing the physical intuition and heuristics used in the optics community with proper mathematical justification. Using techniques from the averaging theory of dynamical systems, a reliable accelerated model based on the coupled mode theory (CMT) approach for a common fiber laser amplifier application is derived. Computational testing reveals that this accelerated model achieves a ∼4000x increase in computational speed compared to the CMT model while preserving high accuracy in key figures of merit such as output power and amplification efficiency. …

Evaluating Sand Characteristics And Their Influence On Sea Turtle Nest Incubation Conditions, Thomas Naylor

Honors Theses

The embryonic development of sea turtles is strongly influenced by the environmental factors experienced during incubation within the nest. These environmental factors can influence hatchling sex ratios, body condition, and their success emerging from nests. Adult female sea turtles lay nests across a range of sites throughout the nesting season, resulting in each nest encountering unique abiotic conditions. This study aims to identify how variation in sand characteristics, such as grain size proportions, permeability, and color, influences nest temperature and subsequent hatchling outcomes of Loggerhead Sea Turtles (Caretta caretta) and Green Sea Turtles (Chelonia mydas) from …

Dimensionless Ratios And Processes Controlling Volumetric Bioretention Performance, Andrew Charles Hiestand

Master's Theses (2009 -)

Urbanization of previously natural land cover has spurred the innovation and implementation of green stormwater infrastructure (GSI) to combat increased surface runoff due to impermeable areas and a changing climate. Bioretention has been a popular choice in design due to its small footprint and proven effectiveness in retaining stormwater runoff and limiting discharges to receiving surface waters. However, their event-to-event performance variability is difficult to explain due to a number of confounding and interacting influences that distort cross-site analyses including inter-event drying and antecedent soil moisture conditions, geometric size and media properties, and event magnitude. This study applies and evaluates …

Cybersecurity Integration In Research Stage Connected Devices Within Healthcare Environments, Klemens Koszarek

Master's Theses (2009 -)

The rapid growth of connected devices in healthcare environments has significantly expanded the cybersecurity threat landscape, extending the potential risks beyond traditional hospital networks. Regulatory guidance from the FDA and risk management frameworks such as the NIST Cybersecurity Framework (NIST CSF) provide an approach for managing cybersecurity risk in connected systems. However, these principles are not always applied during early stages of device development. As a result, security consideration may be deferred until later stages of development, allowing for vulnerabilities to persist in systems as they move toward clinical or commercial deployment. This study presents a structured method for integrating …

Exploring The Synthesis, Characterization, And Aggregation Properties Of Perylene Diimide Derivatives, Erica Salinas

Honors Theses

Once widely used for its vivid presence in an array of industrial dyes, perylene-3, 4, 9, 10-tetracarboxylic dianhydride (PTCDA) is a known precursor for perylene diimides (PDIs). These compounds are an alternative for sustainable energy within organic solar cells (OSCs) and for improving organic light emitting diodes (OLEDs). PDIs are a great candidate for organic semiconductor applications because of their overall flexibility and low manufacturing cost as an organic photovoltaic. Its extended π-conjugation results in a planar structure promoting strong π- π intermolecular stacking, giving aggregated PDIs high electron mobility, allowing a flow of electrons to move through these stacked …

Brown Pelican (Pelecanus Occidentalis) Groundings On A Four-Lane Divided Highway In South Texas: A Comparative Study Using Citizen Science, Bradley Evan Beer, Kevin W. Ryer, Md. Saydur Rahman, John H. Young Jr., Richard J. Kline

School of Integrative Biological & Chemical Sciences Faculty Publications

The population of the once-endangered brown pelican (Pelecanus occidentalis) has increased over the past several decades and is now considered fully recovered. However, in south Texas, the combined effects of weather patterns, transportation infrastructure, and brown pelican biology have led to road mortalities on State Highway 48 (SH 48) at the Carl “Joe” Gayman Bridge. To mitigate these mortalities, the Texas Department of Transportation modified traffic barriers on SH 48. We aimed to examine the effect of the barrier change and determine which weather variables influence brown pelican groundings on SH 48. Citizen scientists monitored sections of SH …

The Impact Of An Interactive Open Education Textbook For An Undergraduate Introductory Chemistry Course For Nonmajors, Erin Avram

Chemistry Faculty Publications

Reading informational text is a critical skill across most professions. Unfortunately, students are less likely to purchase the required course materials now compared to 2010. A free, interactive text was developed for an introductory chemistry course for non-STEM majors. This involved remixing existing texts and incorporating interactive activities to engage students during the learning process and provide opportunities for them to gauge their learning. Based on the results of a student survey, 82% of students reported that it was very important to them that the text was free and 80% of students who responded reported that they used the eText …

Modeling Bitcoin Dynamics Using Differential Equations, Boone M. Fleenor

Departmental Honors & Graduate Capstone Projects

In this thesis, we develop and analyze two nonlinear systems of ordinary differential equations to model Bitcoin price dynamics. Analytical techniques are used to obtain exact or approximate solutions where possible. Then, numerical simulations using a fourth-order Runge–Kutta method are employed to explore system behavior beyond analytically tractable regimes. Finally, model outputs are compared to historical Bitcoin price data using normalized and resampled time series. These results suggest that deterministic models can provide meaningful insight into the structural behavior of Bitcoin markets, while highlighting the need for stochastic or time-dependent extensions for more realistic modeling.