Other Biomedical Engineering and Bioengineering Commons^™

Plasma-Generated Ozone For Odor Removal, Jordan Marot

Seton Hall University Dissertations and Theses (ETDs)

Ozone (O₃) is gaining popularity for its use in industrial and environmental applications, including water treatment, air purification, disinfection, and odor remediation. As a powerful oxidizing agent, ozone is highly effective in destroying harmful bacteria and degrading hazardous gas pollutants such as hydrogen sulfide (H₂S). Dielectric barrier discharge (DBD) reactors are widely used for commercial ozone production under atmospheric-pressure conditions. However, ozone yield and selectivity are strongly influenced by operating parameters, particularly gas flow rate, which affects residence time, energy transfer, and competing byproduct chemistry.

This study explores the influence of the air flow rate on …

A Functional Ultrasound Imaging (Fusi) Pipeline For Investigating Brain-Wide Hemodynamics During Torpor-Like Hypothermia, Owen J. Culver

McKelvey School of Engineering Graduate Student Theses & Dissertations

Torpor is a regulated state of reduced metabolic demand that enables animals to conserve energy under unfavorable environmental conditions. The controlled induction of a similar state, termed synthetic torpor, has potential applications in ischemic protection, organ preservation, cancer treatment, radiation protection, and long-term spaceflight. Although neuronal populations within the preoptic hypothalamus have been shown to initiate hypothermic and hypometabolic states, the distributed cerebral hemodynamic dynamics accompanying their induction and maintenance remain poorly understood. In this thesis, we developed an accessible functional ultrasound imaging (fUSI) acquisition and analysis pipeline and applied it to investigate cerebral hemodynamics during chemogenetic activation of the …

Bowl-O-Matic, Nathan Lin, Luis Torres, Jill Worthington, Aiden Foote

Mechanical Engineering

Adaptive physical education presents the unique challenge of accommodating individuals with diverse physical and cognitive abilities. Instructors and program designers must often integrate specialized equipment, fixtures, or features to ensure activities remain safe, inclusive, and user-friendly. Beyond accessibility, adaptive physical education highlights the importance of empowerment— enabling every participant to experience personal growth, confidence, and connection through movement. Friday Club, a local San Luis Obispo program supported by Cal Poly’s Kinesiology Department, embodies these values by providing adaptive physical activities that promote health and well-being for individuals with varying abilities. One of the most popular and regularly held activities is …

Electrically Evoked Emg Decomposition Using The Perturbative Generalized Series Expansion, William R. Walker

Master's Theses

Electrically evoked electromyography records the muscle's response to nerve stimulation and has been used for clinical assessment of neuromuscular function, as well as treatments such as functional electrical stimulation or stroke rehabilitation. In every muscular contraction, an electrical signal is generated. These signals come from the summation of simultaneously recruited motor units, enabling decomposition techniques to reveal information about motor unit recruitment.  By improving the ability to decompose and analyze these signals, clinical treatments involving neuromuscular electrical stimulation can be optimized and better understood. Much of the research on EMG analysis focuses on voluntary EMG, leaving a gap in the …

Cardiac Twitch Force Measurement System, Tara Hoffman, Sebastian Carrascal Gómez, Julian Macdonald

Biomedical Engineering

The goal of this project is to develop a low-cost and accurate force measurement system and method of measurement to be used in the testing of grown cardiac tissue samples. The primary stakeholder in this project is Dr. Luke Perreault, a biomedical engineering professor at California Polytechnic State University San Luis Obispo who is studying grown cardiac tissue rings, and any of his student lab personnel. Other stakeholders include other researchers in the tissue engineering field who require a similar form of testing to the methods developed in this project.

This document will introduce the identified problem and background as …

Cathy’S Catcher, Marlee Scott, Regen Worsley, Alessandra Valenzano, Aviv Ben Zeev

Mechanical Engineering

Deep-sea fishing presents significant challenges for individuals with upper-limb differences, particularly when using prosthetic devices that are not designed for recreational fishing activities. This project developed a custom prosthetic fishing rod attachment for a user who had lost her forearm and desired a safe, comfortable, and independent method of fishing. Through interviews with the sponsor and an iterative design process, a lightweight aluminum attachment was created to interface directly with the user's existing prosthetic quick-connect system.

The design process included concept generation, CAD modeling, rapid prototyping with 3D-printed models, manufacturing, and user-centered refinement. The final design consists of a welded …

Cloud-Deployed Rna-Seq Analytics For Identifying Imaging And Therapeutic Targets In Chemotherapy-Induced Toxicities, Zhimu Wang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Chemotherapy has significantly improved cancer survival rates; however, many anticancer agents induce severe acute and chronic side effects that substantially reduce patient quality of life and limit therapeutic efficacy. Despite their clinical importance, the molecular mechanisms underlying chemotherapy-induced toxicities across different organs remain incompletely understood, in part due to the lack of integrated, scalable, and accessible analytical platforms capable of synthesizing large transcriptomic datasets across tissues and experimental models.

This thesis describes the development of a cloud-deployed RNA-seq analytics platform designed to identify candidate imaging biomarkers and therapeutic targets associated with chemotherapy induced toxicities. The platform integrates large-scale transcriptomic datasets …

An Experimental Study Of The Morphology Of Dna-Carbon Nanotube Hybrid Structures In Direct Dna Sequencing, Avery P. Davis

Biomedical Engineering Undergraduate Honors Theses

Hybrid structures formed between single-stranded DNA (ssDNA) and single-walled carbon nanotubes (SWCNT) have emerged as promising components in future direct DNA sequencing technologies due to their unique morphological and electronic properties. The nanoscale configuration of these hybrids, including the DNA wrapping angle, pitch, and contour behavior, directly influences their potential for stable electronic readout. This thesis presents an experimental study of DNA-SWCNT hybrid morphology using a fixed, reproducible wrapping protocol designed to minimize environmental variability and isolate the influence of DNA nucleotide sequence on hybrid structure. As described in prior work, this protocol produces well-dispersed hybrids suitable for high-resolution imaging. …

Fluorescence-Based Quantification Of Hepatic Ldl Uptake And Donor Hepatocyte Engraftment Using Atto 700–Labeled Ldl, Victor Agustin Cortes Flores

All Theses

Familial hypercholesterolemia (FH) is an inherited disorder characterized by elevated low-density lipoprotein cholesterol (LDL-C) that increases the risk of premature atherosclerotic cardiovascular disease. In severe FH, including low-density lipoprotein receptor (LDLR), hepatic LDL clearance is profoundly impaired and many lipid lowering treatment strategies have limited effectiveness. Current advances in ex vivo CRISPR–Cas9 hepatocyte gene editing in vivo and ex vivo approaches for treatment of FH are under development.

However, a central barrier to translation is the ability to quantitatively measure the percentage of healthy gen edited hepatocytes in the liver while simultaneously assessing functional hepatic LDL handling. This thesis establishes …

Methods For Radiation-Sparing Navigation In Endovascular And Spine Surgery, William Ross Warner

Dartmouth College Ph.D Dissertations

Modern surgical navigation systems improve procedural accuracy, limit complications, and can reduce reliance on intraoperative ionizing radiation, yet their adoption remains uneven across surgical domains. Informed by clinical immersion, this thesis identifies and addresses two unmet needs revealed through contrasting image-guidance practices in endovascular and spine surgery, where existing guidance techniques are costly, intermittent, or fundamentally limited. Specifically, these needs include (1) the absence of radiation-sparing navigation techniques for endovascular procedures, which rely heavily on 2D x-ray angiography, and (2) the need for dynamic registration methods in open spine surgery, where navigation accuracy can degrade after initial registration and intraoperative …

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 …

The Development And Implementation Of A Computational Framework To Simulate Patellofemoral Joint Mechanics, Mahmood Rashedi

Master’s Theses

Anterior knee pain affects approximately 25% of adults and is associated with altered joint mechanics. Patellofemoral joint (PFJ) models vary widely in complexity, with no established gold standard. Musculoskeletal models efficiently estimate joint loading but do not capture tissue-level mechanics, whereas finite element (FE) models provide tissue-level predictions at greater computational cost. This thesis developed a workflow to evaluate relationships between musculoskeletal model-predicted PFJ loads and FE-predicted cartilage mechanics, examined the impact of altered quadriceps activation, and introduced improved computational models.

Marker trajectories and ground reaction forces were collected from four adults (2 male, 2 female) during walking and squatting. …

Computational Methods For Identification Of Molecular Signatures, Weijun Yi

Graduate Theses, Dissertations, and Problem Reports (ETD)

This work develops computational methods for identifying molecular signatures from high-throughput genomic data and for modeling long non-coding RNA (lncRNA) sub-cellular localization. The response of multiple myeloma to CB-6644, a selective RUVBL1/2 complex inhibitor with potential anti-tumor activity, is analyzed to identify drug-responsive pathways and molecular signatures. Conventional gene set enrichment analysis (GSEA) often excludes low-expression genes. Here, phenotype comparison is reformulated as a supervised machine learning problem: genes most informative for discrimination are first selected using a machine learning approach, and GSEA is then applied to these machine-learning derived gene sets. This framework improves detection of CB-6644-associated pathways. For …

Volumetric Fluorescence Microscopy For High-Throughput And High-Sensitivity Imaging: From Single Molecules To Tissues, Le-Mei Wang

Graduate Studies Theses and Dissertations 2026

Fluorescence microscopy is an indispensable tool in the biological sciences, enabling researchers to investigate intricate subcellular structures, particularly for volumetric studies. However, conventional optical microscopy for volumetric imaging remains fundamentally constrained by imaging speed and throughput. To bypass traditional serial z-scanning, we introduce an axially scan-free method using a phase layer cake to modulate the system's point spread function. This approach projects volumetric information onto a 2D plane in a single shot, offering high flexibility in tuning axial depth alongside simultaneous multicolor imaging with high spatial resolution and sensitivity. This dissertation divides these technical advancements into cellular and tissue imaging …

Towards Computational Methods In Medical Data Analysis: From Speech And Text To Imaging, Kristin Qi

Graduate Doctoral Dissertations

Early detection of cognitive decline and efficient medical image analysis remain critical challenges in healthcare. Traditional clinical assessments are infrequent and resource-intensive, while everyday speech data and unlabeled medical images remain largely unexploited. This dissertation develops computational methods integrating machine learning and artificial intelligence across speech, text, and imaging modalities to address challenges in medical data processing. For cognitive monitoring, this work first introduces methods using voice assistant systems to collect longitudinal speech data in home environments, demonstrating that incorporating historical session patterns significantly enhances detection of mild cognitive impairment. Building on this foundation, a framework combining large language model-driven …

Recreating Fiber Recruitment With Fiber Recruitment Using Additive Manufacturing, Natalia D. Mciver

Biomedical Engineering ETDs

Injured ligaments are often repaired with tendon grafts which may over or under constrain the joint; there is a need for an artificial graft option with the mechanical properties of a native ligament. Crimped fibers within ligaments allow for recruitment which means the viscoelastic properties of stress relaxation and creep are not inversely related. A feasibility study using ACLs and large-scale crimp models to study viscoelasticity, led to an in-depth analysis of the scapholunate interosseous ligament. Using the Modified Kelvin spring-dashpot model, for describing viscoelasticity with a variable stiffness property (time dependent fiber recruitment), we defined the relationship between creep …

Developing Deep Learning Methods For Cognitive Impairment Detection Based On Non-Invasive Data, Muath Alsuhaibani

Electronic Theses and Dissertations

Cognitive impairment detection is on the rise to help reduce the burden of healthcare costs on institutions and individuals. Mild Cognitive Impairment (MCI) is an early stage of cognitive decline progressing to Alzheimer’s disease (AD) or AD-related Dementia (ADRD). Detecting the early stages of AD/ADRD is crucial for early interventions among older adults to mitigate cognitive decline over time. However, the current diagnostic methods are often costly and/or invasive, such as MRI and PET scans. Thus, the search for non-invasive and cost-effective screening tools for the early detection of cognitive impairment using speech, language, visual, and motor data is growing. …

Advancing Single-Molecule Nanopore Sensing: From Protein Conformation And Metal Binding To Dna Transport Via Hybrid Nanostructures, Matthew J. Odonohue

Multidisciplinary Studies Theses and Dissertations

This dissertation presents the development and application of solid-state and hybrid nanopore platforms for single-molecule analysis of biomolecular interactions. First, a silicon nitride nanopore was employed to characterize the conformational states of the transferrin receptor (TfR), enabling discrimination between its monomeric and dimeric forms, as well as from its ligand, human serum transferrin (hSTf), despite their similar molecular weights. In a separate study, the same nanopore configuration was used to track the real-time binding of titanium ions to transferrin, demonstrating single-molecule sensitivity to metal-induced conformational changes. A hybrid microtubule–solid-state nanopore (MT–SSN) was then engineered, repurposing microtubules as electrostatically anchored conduits …

Polyphenols For The Mitigation Of Vascular Calcification; In Vitro And In Vivo Studies, Abdullah Altuhami

All Theses

Globally, cardiovascular diseases, in most cases associated with calcification, are the main cause of death. However, currently, the only effective cure is to undergo surgery to augment or receive a healthy donor heart, which could be very difficult due to the long waiting list and the associated risks. The possibility of body rejection of the foreign organs is attributed to immunoreaction or the risk of infection, since the donor must be on immunosuppressant drugs that lower the body's immunity and facilitate the body's acceptance of the new organ as one of its own. Taking that into consideration, using tissue-engineered vascular …

Crevice Corrosion Mechanisms Of Cocrmo Alloys In Orthopedic Implants: Retrieval Analysis, Nano-Tribocorrosion And Cellular Responses, Hwaran Lee

All Dissertations

Mechanically assisted corrosion and non-mechanically (chemically) driven corrosion in modular junctions of orthopedic implants using cobalt-chromium-molybdenum (CoCrMo) alloys remain clinical concerns and may contribute to implant failure. The underlying corrosion mechanisms are not yet fully understood, leaving a critical research gap. We hypothesized that corrosion in modular junctions may be driven by aggressive local environments, including fretting, metal ion release (cobalt ion, Co²⁺), low pH and reactive oxygen species (ROS). This dissertation aims to (1) analyze corrosion modes and potential causes in modular junctions; (2) identify chemically driven corrosion modes on CoCrMo alloys using simulated inflammatory modular taper …

Mathematical Modeling Of Effects Of Tumor Location On Lung Function., Lamargaret Temukisa Johnson

Master of Engineering Theses

Lung cancer has the highest rates of incidence and mortality of all cancers. Most lung cancer tumors are Non-Small Cell Lung Cancer (NSCLC). NSCLC patients with lesions in the upper lobes are found to have better prognosis compared to those with lesions in the middle and lower lobes. Previous studies have suggested various causes for this discrepancy at both the organ-scale and tissue-scale. To model NSCLC growth in different locations within the lung, an organ scale lung model and tissue scale tumor model were coupled through the tissue pressure, and oxygen and carbon dioxide partial pressures. The coupling was used …

Impact Of Cysteine And Tyrosine Dipeptides On Cho Cell Performance In A Perfusion Mimic, Corrin L. Pruitt

All Theses

Perfusion cell cultures typically achieve higher cell densities and generate higher volumetric productivities than fed-batch cultures due to continuous nutrient supply and spent media removal. Despite these advantages, perfusion cell cultures remain underutilized for licensed product manufacturing, primarily due to the lack of small-scale perfusion models for high-throughput process development and the complexities involved in media formulation capable of supporting high cell densities during long-term continuous operation. To avoid nutrient limitation at high cell densities, current perfusion processes rely on using higher perfusion rates, which results in significant media wastage and downstream product dilution. Therefore, there has been an effort …

A Deep Learning Approach For Semantic Segmentation And Its Application On Ctc., Samir Farag Harb

Electronic Theses and Dissertations

This dissertation explores the modeling and analysis of medical images, focusing on the intricate task of colon segmentation and subsequent 3D reconstruction, which are critical steps in Computed Tomography Colonography (CTC) systems. The primary objective of this research is to develop precise segmentation approaches to enhance the accuracy of colon identification and reconstruction from abdominal CT scans. Three distinct segmentation approaches are proposed and evaluated: a Markov Random Field (MRF)-based approach, a convolutional neural network (CNN)-based deep learning (DL) approach, and a sequential episodic training with dual contrastive learning Approach (G-SET-DCL) that has a flavor of few-shot learning (FSL). To …

Synthesis And Characterization Of Magnetic Nanoparticles To Study Effective Magnetic Anisotropy For Biomedical And Catalytic Applications, Alexander Malaj

All Dissertations

This dissertation focuses on understanding how to tune the magnetic properties of nanoparticles through controlling the effective magnetic anisotropy (Keff), which is a key variable in determining a nanoparticle’s Néel relaxation time, which will dictate its magnetic behavior in various applications. In this work, magnetocrystalline anisotropy is tuned by synthesizing tri-metallic substituted ferrite (Fe3-x-yMnxCoyO4) nanoparticles with specific metallic compositions that were informed by computer simulations using density functional theory (DFT) to target magnetocrystalline anisotropy values. A drip synthesis was used to control the size and composition of the tri-metallic ferrites, which were revealed to be monodisperse and compositionally mixed by …

Acoustic And Hemodynamic Analysis Of Phantoms: Roughness And Flow Dynamics, Ethan Erik Olof Sundberg

Master's Theses

The purpose of this study was to determine whether different vascular phantoms, with and without a surrogate arm, could serve as effective analogs to the human brachial artery for assessing endothelial dysfunction, an early indicator of cardiovascular disease, particularly atherosclerosis. Atherosclerosis is characterized by plaque buildup and endothelial damage, which precede more severe clinical events and are often detectable through changes in vascular function. A 40” water tower was used to simulate diastolic pressure, enabling water flow through each phantom. Strain gauge pressure transducers were placed at both ends of the phantoms to measure pressure drop, while a microphone captured …

Optimizing Microfluidic Murine Fibroblast And Human Epidermal Keratinocyte Cell Culture In 70Μm Microwells, Christian Navarro

Master's Theses

Cell culture is an essential technique utilized in biotechnology and medicine to remove systemic influences to study cellular behavior and morphological development of individual cell lines. However, conventional cell culture is two-dimensional and static meaning it can’t easily mimic in vivo conditions such as multicellular cell to cell interactions, fluid perfusion, or 3D structures which might alter cellular behavior and morphology. Microfluidic cell culture allows for the incorporation of in vivo conditions such as perfusion and chemical gradients allowing for more physiologically accurate models. The goal of this study is to develop a protocol for testing a microfluidic chip designed …

Insert Creation To Mimic Blood Vessels In Gel Phantoms, Courtney Bloom

Biomedical Engineering Undergraduate Honors Theses

Gel phantoms are commonly used in research settings due to their ability to mimic soft tissue. Creating these phantoms usually involves 3D printing an insert, embedding it in gel, and then washing the insert out. Polyvinyl alcohol (PVA) is typically used as the insert material, but it often swells and deforms the gel during the washout process. Aquapour, a water-soluble material, was investigated as a potential replacement for PVA. Unlike PVA, Aquapour comes in a powdered form that can be mixed with water to create a castable slurry. To create molds to cast Aquapour, SolidWorks was used to design two …

Design And Evaluation Of Antibody-Conjugated Microneedle Patch For Early Mrsa Biomarker Detection, Kylee Marie Pop, Alexis Richie, Nicholas Jenkins, Andrew Holmes

Honors Theses

Post-operative orthopedic surgical site infections (SSIs), specifically those caused by methicillin resistant Staphylococcus aureus (MRSA), present a significant clinical challenge due to delayed detection, increased morbidity, and current rising healthcare costs. Early detection of infection remains limited due to the current methods of diagnosis, which consist of observation of the surgical site and laboratory infrastructure for conformation of infection. To combat these issues, my team and I have designed and evaluated a minimally invasive microneedle diagnostic patch that continuously monitors for the presence of MRSA-associated biomarker PBP2a in interstitial fluids around surgical site incisions. Upon antigen detection, a colorimetric response …

Toward The Application Of Natural Language Processing In Electronic Health Record Analysis For Taxonomy Development, Latoya Mcdonald

All Dissertations

Electronic health records (EHRs) are pivotal resources for nurse practice because they increase the timeliness and reliability of patient information at the point of care and support access by multiple healthcare providers and the individual patients themselves. However, it is widely recognized that data extraction from EHRs is challenging due to the variability in the language used in clinical care notes and the lack of standardized terminology across healthcare systems. The broad objective of this dissertation is to develop taxonomy-based classification models for nursing care by applying feature engineering approaches to EHRs that include nursing care of ostomy patients following …

Investigating The Effects Of Hepatocyte Growth Factor On Primary Myoblast Proliferation, Grace Heller

Biomedical Engineering

Peripheral artery occlusive disease (PAOD) is a progressive vascular condition that affects over 200 million people worldwide and approximately 8 million in the United States. It is characterized by atherosclerotic narrowing of peripheral arteries, leading to reduced blood flow, ischemia, and, in severe cases, tissue loss and limb amputation. Although surgical revascularization is the gold standard, many patients—particularly those with comorbidities like diabetes— continue to experience poor outcomes, emphasizing the need for alternative therapies. One promising strategy is to enhance collateral arteriogenesis, the remodeling and enlargement of collateral arterioles that naturally bypass occluded vessels. Satellite cells (SCs), which give rise …