Digital Commons Network^™

Deep Learning Framework For Graph-Based Molecular Drug Discovery, Daniel Manu

Electrical and Computer Engineering ETDs

This dissertation proposes the GraphGANFed framework, which combines Graph Convolutional Networks (GCN), Generative Adversarial Networks (GAN), and Federated Learning (FL) to generate novel molecules while preserving data privacy. FL allows learning from distributed clients without sharing local datasets, GCN extracts molecular structural properties, and GAN generates new molecules retaining the learned properties. Extensive simulations on three benchmark datasets show GraphGANFed's effectiveness, producing molecules with high novelty (≈ 100) and diversity (> 0.9). Results indicate a trade-off among evaluation metrics, and the right dropout ratio avoids mode collapse. Additionally, Conditional GraphGANFed (cGraphGANFed) incorporates a critic network from Reinforcement Learning (RL) to …

Board 125: Work In Progress: Faculty Experiences And Learning Through Oral-Assessment Implementation In Engineering Courses, Minju Kim, Carolyn L. Sandoval, Josephine Relaford-Doyle, Torus Washington Ii, Saharnaz Baghdadchi, Nathan Delson, Marko Lubarda, Alex M. Phan, Curt Schurgers, Huihui Qi

Psychology Faculty Articles and Research

This WIP qualitative research paper explores faculty experiences with implementing oral exams in high-enrollment undergraduate engineering courses at a research university. With a primary goal to improve conceptual mastery, as well as a desire to ensure academic integrity in the sudden move to remote instruction at the height of the pandemic, a group of faculty in Mechanical and Aerospace Engineering and Electrical and Computer Engineering departments implemented oral assessments in their own engineering courses across several quarters. They formed a research group with educational developers in a teaching and learning center on campus, and investigated the impact of oral assessments …

Anonymized Identity Recognition And Classification Using Privacy Preserving Facial Encoding, Manas Sanjay Pakalapati

USF Tampa Graduate Theses and Dissertations

The need for sharing large-scale datasets to train deep neural network models, particularly in healthcare, raises significant data security and privacy concerns. To address these issues, methods such as data encryption or encoding are utilized. These techniques can encrypt the data and make it unreadable to humans, while still retaining its usefulness for training models.

In this study, we investigate various image encoding techniques designed to protect privacy by making images unrecognizable while still retaining their usefulness for model training. Our investigation utilized publicly available facial databases and focused on evaluating the trade-offs inherent in image encoding techniques, with a …

Cellular Energy Cycle Mediates An Advection-Like Forward Cell Flow To Support Collective Invasion, Jian Zhang, Jenna Mosier, Yusheng Wu, Logan Waddle, Paul V. Taufelele, Wenjun Wang, Heng Sun, Cynthia A. Reinhart-King

Biomedical Engineering Faculty Publications and Presentations

Collective cell migration is a model for nonequilibrium biological dynamics, which is important for morphogenesis, pattern formation, and cancer metastasis. The current understanding of cellular collective dynamics is based primarily on cells moving within a 2D epithelial monolayer. However, solid tumors often invade surrounding tissues in the form of a stream-like 3D structure, and how biophysical cues are integrated at the cellular level to give rise to this collective streaming remains unclear. Here, it is shown that cell cycle-mediated bioenergetics drive a forward advective flow of cells and energy to the front to support 3D collective invasion. The cell division …

Continuum Mechanics Modeling Of High Strain Rate Impact Of Thermoplastic Polymer Particles, Jeeva Muthulingam

Theses and Dissertations

The study of particle impact at high strain rates is crucial in fields ranging from materials science and engineering to space exploration and environmental science. In the particular case of cold spray, a particle undergoes intense plastic deformation upon impact, causing it to adhere to the target substrate. While metallic particles impacting on metallic substrates have been extensively studied, understanding the mechanical characteristics of polymeric particles on polymer and metal substrates requires further research. This study focuses on single particle impact modeling, analyzing impact parameters such as particle size, velocity, and angle of incidence using continuum mechanics finite element modeling …

Water Quality Impacts Of Recycling Nutrients Using Organic Fertilizers In Circular Agricultural Scenarios, W. Lisenbee, A. Saha, P. Mohammadpour, R. Cibin, Jason Philip Kaye, C. Grady, Indrajeet Chaubey

Biological and Agricultural Engineering Faculty Publications and Presentations

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OBJECTIVE

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Ocean Rain Detection And Wind Retrieval Through Deep Learning Architectures On Advanced Scatterometer Data, Matthew Yoshinori Otani Mckinney

Theses and Dissertations

The Advanced Scatterometer (ASCAT) is a satellite-based remote sensing instrument designed for measuring wind speed and direction over the Earth's oceans. This thesis aims to expand and improve the capabilities of ASCAT by adding rain detection and advancing wind retrieval. Additionally, this expansion to ASCAT serves as evidence of Artificial Intelligence (AI) techniques learning both novel and traditional methods in remote sensing. I apply semantic segmentation to ASCAT measurements to detect rain over the oceans, enhancing capabilities to monitor global precipitation. I use two common neural network architectures and train them on measurements from the Tropical Rainfall Measuring Mission (TRMM) …

Hardware Acceleration Of Numerical Methods For Solving Ordinary Differential Equations, Soham Bhattacharya

Theses and Dissertations

Along with the advancement in technology, the role of hardware accelerators is increasing consistently, delivering advancements in scientific simulations and data analysis in scientific computing, signal processing tasks in communication systems, matrix operations, and neural network computations in artificial intelligence and machine learning models. On the other hand, several high-speed computer applications in this era of high-performance computing often depend on ordinary differential equations (ODEs); however, their nonlinear nature can present a challenge to obtaining analytic solutions. Consequently, numerical approaches prove effective in delivering only approximate solutions to these equations. This research discusses the implementation of a customized hardware accelerator …

Detection Of Wintertime Green Vegetated Cover Using Object-Based Classification With Open-Source Remote Sensing And Geospatial Technologies, Jae Sung Kim, Sara P. Syswerda, Sigrid D. P. Smith

Michigan Tech Publications

It is important to detect wintertime green vegetated cover (WGVC), since it includes cover crop information, which is one of the most important agricultural best management practices used today. Related to this, cover crop area, which is part of WGVC, has been estimated using survey methods traditionally, but remote sensing can be used as a more time- and cost-effective assessment. Previously developed pixel-based methods to assess cover crops using remote sensing can have a salt-and-pepper effect, which lowers classification accuracy. Therefore, object-based classification was applied to estimate the spatial distribution of WGVC across the entire state of Delaware. To reduce …

Design And Characterization Of 3d-Printed Hydrogel Lattices With Consistent Structural And Mechanical Anisotropy, Daniel Yoon

McKelvey School of Engineering Graduate Student Theses & Dissertations

This thesis explores the use of 3D printing to fabricate soft hydrogel lattice structures with consistent properties, including varying levels of mechanical anisotropy. Magnetic resonance elastography (MRE) is a non-invasive imaging tool to estimate and characterize the mechanical properties of tissue. MRE “phantoms” (physical surrogate models) have been used to assess how well MRE can measure and estimate mechanical properties. While gel phantoms generally simulate brain tissue, almost all have been isotropic. Prior studies have shown that white matter brain tissue is structurally and mechanically anisotropic. To validate anisotropic MRE, phantoms with controllable, reproducible anisotropic material properties are needed. This …

A Country-Level Primary-Final-Useful (Cl-Pfu) Energy And Exergy Database: Overview Of Its Construction And 1971–2020 World-Level Efficiency Results, Paul E. Brockway, Matthew Kuperus Heun, Zeke Marshall, Emmanuel Aramendia, Paul Steenwyk, Thomas Relph, Michelle Widjanarko, Jeonghoo (James) Kim, Anjana Sainju, Julian Irtube

University Faculty Publications and Creative Works

Societal exergy analysis examines the flows of energy and exergy through societies, from primary (e.g. oil) to final (e.g. gasoline) to useful (e.g. propulsion) energy stages. By extending the study of energy to the useful stage, new insights into the under-represented role of energy in economic growth have been made. However, currently (a) country coverage is patchy and incomplete, (b) available data are based on varying methods and assumptions including efficiencies based on economic rather than engineering data, and (c) datasets are constructed using piecemeal computational approaches. To address these gaps, we construct a country-level primary-final-useful (CL-PFU) energy and exergy …

Effect Of Oxidation Of Graphene On Agglomeration And The Mechanical Properties Of Thermosetting Resins, Matthew A. Reil

Electronic Theses and Dissertations

Thermosetting resins are used extensively worldwide in applications ranging from adhesives to structural components. However, these resins generally fail in a brittle fracture mode which is undesirable in most situations. Graphene (G) and its derivatives have been considered as additives to epoxy for material property enhancement and varied results have been reported in the literature. In this work, the effects of the oxidation of G to graphene oxide (GO) on polymer interactions and plate agglomeration were studied by classical molecular dynamics (MD). Results from those simulations concluded that agglomerates were likely present in all G-based nanocomposites. The effect of these …

Aging-Related Changes In The Mechanical Properties Of Single Cells, Amarnath Singam, Chandrabali Bhattacharya, Seungman Park

Mechanical Engineering Faculty Research

Mechanical properties, along with biochemical and molecular properties, play crucial roles in governing cellular function and homeostasis. Cellular mechanics are influenced by various factors, including physiological and pathological states, making them potential biomarkers for diseases and aging. While several methods such as AFM, particle-tracking microrheology, optical tweezers/stretching, magnetic tweezers/twisting cytometry, microfluidics, and micropipette aspiration have been widely utilized to measure the mechanical properties of single cells, our understanding of how aging affects these properties remains limited. To fill this knowledge gap, we provide a brief overview of the commonly used methods to measure single-cell mechanical properties. We then delve into …

Shape Memory Alloy Capsule Micropump For Drug Delivery Applications, Youssef Mohamed Kotb

Theses and Dissertations

Implantable drug delivery devices have many benefits over traditional drug administration techniques and have attracted a lot of attention in recent years. By delivering the medication directly to the tissue, they enable the use of larger localized concentrations, enhancing the efficacy of the treatment. Passive-release drug delivery systems, one of the various ways to provide medication, are great inventions. However, they cannot dispense the medication on demand since they are nonprogrammable. Therefore, active actuators are more advantageous in delivery applications. Smart material actuators, however, have greatly increased in popularity for manufacturing wearable and implantable micropumps due to their high energy …

Statistical Modeling Of Knee Morphology And Material Properties Considering Diverse Populations, Gabrielle Jeannine Kindy

Electronic Theses and Dissertations

Total Knee Arthroplasty (TKA) is a widely performed surgical procedure aimed at alleviating pain and restoring function in patients with severe knee osteoarthritis. Despite its general success, disparities in postoperative outcomes have been observed across different racial and ethnic groups, with minority populations often experiencing less favorable results. One potential avenue for improving the generalizability of orthopaedic implants is using Statistical Shape and Intensity Models (SSIMs), which can be used to incorporate patient variability directly into the orthopaedic medical device development workflow through population-based finite element analysis.

This work aimed to construct an SSIM from a diverse subject set, incorporating …

Differentiating Dynamic System Outcomes In Cam Photosynthesis Through Sonification, Duncan Turley

Civil and Environmental Engineering Undergraduate Honors Theses

Sonification is a powerful tool that is harnessed by modern engineers to represent information through audio, and is beginning to be used to interpret more complex data sets. Sonification can be used to facilitate the listeners' ability to grasp microscopic or complex changes in the state of a system. This study uses the assigning of sound patterns to model outputs that indicate chaotic or non-chaotic systems in Crassulacean acid metabolism photosynthesis. Using sound allows the interpretation of chaotic data without the more time intensive processes typically used, such as of Fast Fourier Transformations. Based on past research, it is known …

Optimization Using Central Composite Design For Continuous Absorption Of Co2 Gas With Green Sodium Silicate In A Packed Bed Column, Dalia A. Ali Eng, Mohamed Essam Ibrahim Eng.

Chemical Engineering

If absolutely nothing is taken to reduce carbon dioxide (CO2) emissions, atmospheric concentrations of carbon dioxide will rise to 550 parts per million by 2050, which will have disastrous effects on the world's climate and food production. An apparatus has been designed and setup to convert CO2 into a useful and vital product which was silica. The effect of different experimental factors on the compositions by weight percent of SiO2 and Na2CO3 were studied including the CO2 gas flow rate (1.037, 1.648 and 2.26 L/min), initial concentration of sodium silicate (Na2SiO3) solution (5, 7.5 and 10 %wt) and the packing …

Sensitization Of Europium Oxide Nanoparticles Enhances Signal-To- Noise Over Autofluorescence With Time-Gated Luminescence Detection, Hunter Miller, Jessica Q. Wallace, Hui Li, Xing-Zhong Li, Ana De Bettencourt-Dias, Forrest Kievit

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Clinical translation of nanoparticle-based therapeutics has been limited, and a lack of preclinical delivery characterization is partly to blame, limiting our understanding of the mechanisms of failure. The improvement of the preclinical delivery assessment requires nanoparticles with higher detectability. This work focused on the exploration of several aromatic carboxylic ligands (terephthalic acid, quinaldic acid, and kynurenic acid) for the sensitization of europium oxide nanoparticles with a long emission lifetime to overcome cellular autofluorescence, a key confounder of detection in luminescence-based bioimaging. A facile one-pot synthesis and ligand exchange process generated and sensitized ultrasmall Eu₂O₃ cores. As reflected …

Use Of Nanoparticle Additives To Achieve Desirable Properties In Fluorine-Free Firefighting Foams, Annelise Kathleen Curtin

USF Tampa Graduate Theses and Dissertations

Class B Firefighting foams play a crucial role in protecting equipment and people fromliquid fuel fires but concerns regarding the impacts of per- and poly-fluoroalkyl substances (PFAS) have resulted in bans on the use of aqueous film forming foam (AFFF). Fluorine-free replacements are yet to achieve the same level of performance. Nanoparticles including silica and clay have been used to improve foam stability, especially in environments where hydrocarbon fuels are present. These materials have also been used in solid composites to improve fire resistance. The stability of aqueous foams containing silica and Laponite RD nanoparticles along with surfactants of different …

Chemical Herding As A Multiplicative Factor For Top-Down Manipulation Of Colloids, Mark N. Mcdonald, Douglas R. Tree, Cameron K. Peterson

Faculty Publications

Colloidal particles can create reconfigurable nanomaterials, with applications such as color-changing, self-repairing, and self-regulating materials and reconfigurable drug delivery systems. However, top-down methods for manipulating colloids are limited in the scale they can control. We consider here a new method for using chemical reactions to multiply the effects of existing top-down colloidal manipulation methods to arrange large numbers of colloids with single-particle precision, which we refer to as chemical herding. Using simulation-based methods, we show that if a set of chemically active colloids (herders) can be steered using external forces (i.e., electrophoretic, dielectrophoretic, magnetic, or optical forces), then a larger …

Emergent Magnetism And Hyperthermia In Phase- And Size-Tunable Iron Oxide Nanostructures, K Mudiyanselage Tharindu Supun Bandara Attanayake

USF Tampa Graduate Theses and Dissertations

Iron oxide nanoparticles (IONPs) hold immense potential across diverse fields, from spintronics, magnetic hyperthermia to drug delivery, biodetection, and magnetic resonance imaging. Unlocking these applications hinges on our ability to tailor the magnetic properties of IONPs, and this dissertation presents novel and powerful approaches for enhancing magnetic and hyperthermic responses of multiphase iron oxide nanostructures. This is achieved by manipulating their phase volume fraction, size, and shape with a focus on the magnetic tunability of nanostructures via strategic control over structural and environmental parameters. The aforementioned has been achieved by the following three key approaches: (i) phase-tunability of iron oxide …

An Efficient Method For Recognition Of Human-In-Motion Action Based On Foot-Lift Features, Khin Cho Tuna, Hla Myo Tunb

ASEAN Journal on Science and Technology for Development

In the age of Industry 4.0, recognition of human moving actions becomes an essential element in smart surveillance systems at public places. The requirement of a large number of frames, view dependency and the requirement of big database are still challenging issues for human action recognition in real-time applications. This study proposes an efficient method for basic moving actions, “Walking” and “Running”, based on foot-lift features aiming at the recognition of ongoing moving action by reducing the number of frames required. The plane of moving path and foot-lift are estimated during the action by means of BLOB analysis. The performance …

Transforming Orthopedic Surgery: Autonomous Image-Guided Techniques For Femur Fracture Robotic Surgery, Marzieh Sadat Saeedi-Hosseiny

Theses and Dissertations

Long-bone fractures, particularly femur fractures, are prevalent and necessitate surgical intervention due to traumatic forces. Manual reduction procedures pose challenges, including excessive traction forces and reliance on limited X-ray imaging, resulting in malalignment-related complications and repeated surgeries. Current methods for femur fracture reduction are prone to inaccuracies, prolonged surgical times, and postoperative complications. This research introduces image-guided methods to automate a surgical robotic system, Robossis, to enhance femur alignment accuracy, reduce procedure times, and improve patient outcomes. To address these challenges, a marker-based approach utilizing a few X-ray images is developed to detect the spatial relative position of the femur …

Design And Fabrication Of Passive Microfluidic Devices For Enhancing Membrane-Based Biosensors, Tanner N. Wells

Theses and Dissertations

Microfluidic devices and systems have demonstrated wide applicability in sample processing and analysis. The ability to integrate sample processing and analysis into a single platform is a key benefit of microfluidic technologies. This dissertation describes the design and fabrication two types of microfluidic devices developed to enhance membrane-based biosensors. First is a device for collecting particles into a highly confined region, locally enhancing their concentration. Second is a device for size-based particle separation capable of separating differently sized particles into separate streams. Both types of devices are fabricated with a thin top layer, providing a platform for synthetic membrane-based technologies. …

The Design, Prototyping, And Validation Of A New Wearable Sensor System For Monitoring Lumbar Spinal Motion In Daily Activities, Brianna Bischoff

Theses and Dissertations

Lower back pain is a widespread problem affecting millions worldwide, because understanding its development and effective treatment remains challenging. Current treatment success is often evaluated using patient-reported outcomes, which tend to be qualitative and subjective in nature, making objective success measurement difficult. Wearable sensors can provide quantitative measurements, thereby helping physicians improve care for countless individuals around the world. These sensors also have the potential to provide longitudinal data on daily motion patterns, aiding in monitoring the progress of treatment plans for lower back pain. In this work it was hypothesized that a new wearable sensor garment that makes use …

Manipulating Colloidal Particles Using Chemical Gradients And Top-Down Control, Mark Nichols Mcdonald

Theses and Dissertations

Colloidal particles provide the ideal building blocks for the next generation of microdevices, such as advanced sensors and precision drug delivery systems. However, many such applications require the use of top-down (i.e. humanly controllable) forces to manipulate colloidal particles with single-particle precision, and current methods can only achieve such precision for small numbers of particles at a time. To address this challenge, we propose using chemical forces in combination with existing top-down techniques to enable the control of larger numbers of particles simultaneously. Controlling colloids using chemical reactions is a novel technique not typically utilized. Due to its distinct difference …

Preclinical Examination Of A Nerve Specific Fluorophore Using Ex Vivo Human Tissues, Logan Michael Bateman

Dartmouth College Master’s Theses

Fluorescence-guided surgery (FGS) is a nascent field which seeks to improve patient safety and surgical outcomes using fluorescent agents known as fluorophores. Fluorophores are molecules which upon excitation with a specific wavelength of light emit a photon of a specific wavelength which can be detected using a modified camera system. Creation and translation of a fluorophore for clinical use is a costly, laborious, and time intensive process. Only a handful of fluorophores have received FDA approval and they required multiple years of tightly regulated clinical trials. Prior to these first-in-human studies these agents are subject to a litany of preclinical …

Quantifying Variation Across 16s Rrna Gene Sequencing Runs In Human Microbiome Studies, Andrew J. Hoisington, Christopher E. Stamper, Joseph C. Ellis, Christopher A. Lowry, Lisa A. Brenner

Faculty Publications

Recent microbiome research has incorporated a higher number of samples through more participants in a study, longitudinal studies, and metanalysis between studies. Physical limitations in a sequencing machine can result in samples spread across sequencing runs. Here we present the results of sequencing nearly 1000 16S rRNA gene sequences in fecal (stabilized and swab) and oral (swab) samples from multiple human microbiome studies and positive controls that were conducted with identical standard operating procedures. Sequencing was performed in the same center across 18 different runs. The simplified mock community showed limitations in accuracy, while precision (e.g., technical variation) was robust …

Performance Evaluation Of A Novel Dual-Bed Gasification Reactor For The Production Of Green Energy, Ogooluwa Philip Ojo

Theses and Dissertations

The need to maximize current energy sources and create new ones has increased due to the world's growing energy demand and the depletion of major energy sources. Biomass and solid waste, such as wood, sawdust, plant wastes, paper, cardboard, and plastics, present promising carbon-neutral alternatives, collectively accounting for over 10% of global energy generation. The concept of integrating fixed and fluidized bed reactors in industrial applications needs additional research to ascertain the optimal configuration and interplay between these reactor types. Hence this research focuses on the utilization of a unique hybrid modular gasification system that combines fixed and fluidized bed …

Mathematical Modeling And Understanding The Physiological Mechanisms Of Vibration On Wound Healing And Scar Remodeling, Devin Rion Needs

Theses and Dissertations

Chronic wounds and pathological scars reduce the quality of life for millions of people worldwide. Through mathematical modeling and clinical testing, understanding of how these conditions occur continues to increase. These tools have also been employed to investigate the efficacy of treatments that could impact wound healing and scar remodeling. The purpose of this work is to investigate the physiological effects of vibration treatment on wound healing, blood flow, and scar remodeling through mathematical modeling and experimental testing. This work presents and validates a mathematical murine model for whole body vibration enhanced wound healing (VEWH). This VEWH model builds on …