Biomedical Engineering and Bioengineering Commons^™

Integrating Neural Control And Finite Element Muscle Modeling: A Predictive Neuromusculoskeletal Framework For Investigating Neurodegenerative Disease, Colton Babcock

Boise State University Theses and Dissertations

Neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) disrupt the interplay between neural control and musculoskeletal function, leading to progressive motor decline and loss of force control and production. Traditional experimental and clinical approaches are limited in their ability to capture the multiscale, nonlinear mechanisms driving these impairments. This dissertation presents a novel predictive neuromusculoskeletal (NMS) modeling framework that integrates physiologically accurate motor neuron dynamics with three-dimensional finite element (FE) muscle models. Using subject-specific muscle geometry and fiber architecture of the tibialis anterior, the model simulates realistic force generation under both healthy and ALS-affected conditions. The neural component incorporates a …

Harnessing The Mechanical And Gelation Behavior Of Tyramine-Substituted Silk Fibroin Bioinks Through Integration Into A Modular And Low-Cost 3d Bioprinting Platform, Sourjjadeepta Biswas

Boise State University Theses and Dissertations

3D printing has become an indispensable tool in research labs across the globe. Yet, when it comes to bioprinting with custom or sensitive bioinks, accessible options remain limited. Commercial systems are often prohibitively expensive and restricted to proprietary materials, while DIY setups frequently lack the precision and compatibility needed for biologically relevant printing. Moreover, tunable bioinks that align with real-world biological constraints are still hard to come by. To address these gaps, we developed a modular, low-cost bioprinting platform tailored for tyramine-substituted silk fibroin (TA-SF) hydrogels-biocompatible materials known for their rapid gelation, tunable stiffness, and potential to support cell differentiation …

Harnessing Bioscaffold-Coupled Stimulation Through Electroactive Graphene Foam For Enhanced Cellular And Mechanical Responses: Applications In Cartilage Tissue Engineering, Mone't Sawyer

Boise State University Theses and Dissertations

Osteoarthritis is a leading cause of joint degeneration, with limited treatment options that fail to restore native cartilage. Tissue engineering offers a promising strategy by combining cells, scaffolds, and bioactive cues to regenerate functional tissue, though challenges remain in developing systems that integrate and precisely control these signals in three-dimensional environments. This work establishes a scaffold-coupled electrical stimulation (ES) platform using electroactive graphene foam (GF) to modulate cellular and mechanical responses relevant to cartilage tissue engineering. Custom stereolithography-printed bioreactors were developed to deliver low-voltage biphasic square waves (20–60 mVpp, 1 kHz) directly to GF scaffolds under submerged culture, maintaining waveform …

Stimulation And Recording Interfaces For Data Transmission To And From A Micro Neural Stimulation Device, Morgan Riley

Boise State University Theses and Dissertations

Advancements in neuromodulation for treating neurological disorders increasingly rely on selective peripheral nerve stimulation rather than whole-nerve activation. Traditional approaches engage all fascicles, causing off-target effects such as involuntary muscle contractions and pain. To address these challenges, this research proposes a minimally invasive microdevice that integrates wireless galvanic impulse communication with an epineural multi-contact nerve cuff. This design facilitates high-throughput, low-power stimulation, recording, and data transfer. Development efforts include optimizing neural stimulation protocols, validating deep tissue galvanic transmission, and fabricating a multi-channel nerve cuff for stable electrode–tissue interfacing. In parallel, custom depth-controlled intramuscular arrays enable high-density electromyography (EMG) recording during …

Optimal Control Of Human Exercise Using An Individualized Physiological Three-Tank Model And Dynamic Programming, Asal Lotfi

All Theses

This thesis develops a physiologically inspired three-tank model of human bioenergetics to describe and optimize fatigue and recovery during exercise. The aerobic, phosphagen, and glycogen systems are modeled as coupled reservoirs whose states constrain instantaneous power output. Building on this representation, dynamic programming is used to compute pacing strategies that respect physiological limits while maximizing task-specific goals such as peak power or total work over a fixed duration, enabling individualized, goal-driven exercise prescriptions. The three-tank dynamics are formulated in continuous time and then discretized under a zero-order-hold assumption for simulation and optimal control. Model parameters are linked to standard field …

Comparative Assessment Of Lower Limb Neuromusculoskeletal Activation And Joint Kinematics In Normal And Impaired Gait, Jack Ryan Schule

Theses and Dissertations

This thesis evaluates whether accessible and affordable technologies can provide clinically significant, quantifiable gait analysis comparable to traditional marker-based motion capture systems. Modern high-end systems offer excellent accuracy but remain financially and logistically inaccessible to many clinicians and researchers. To address this gap, a framework was developed using markerless pose estimation using the model, MediaPipe, inertial measurement units (IMUs) processed through an Extended Kalman Filter (EKF), and surface electromyography (sEMG) to measure joint kinematics and neuromuscular activity during gait. An experiment was performed where data was collected from participants with both normal gait and pathologies including: Osgood–Schlatter disease, Plica Band …

Establishing Procedures For Primary Human Myoblast Cell Culture, Erica Duffy

Biomedical Engineering

Peripheral Artery Disease (PAD) affects an estimated 200 million people worldwide and is the leading cause of amputation in the United States. PAD is characterized by atherosclerotic narrowing of arteries, resulting in ischemia from reduced blood flow to distal tissues. Although surgical and percutaneous interventions can restore perfusion, fewer than 50% of patients experience sustained benefit, highlighting the need for alternative therapeutic strategies. One promising approach is promoting arteriogenesis, the growth and outward remodeling of pre-existing collateral vessels that improve blood flow around the occluded arteries. Arteriogenesis is regulated by regenerative, M2-polarized macrophages, making macrophage polarization a key therapeutic target. …

Reverse (Bio)Engineering: A Machine Learning Approach To Optimize Baseball Pitcher Health And Performance, Robert C. Moore

All Dissertations

Ball tracking systems are becoming ubiquitous in sport, creating an unprecedented opportunity for big data applications to optimize human health and performance. These applications are especially common in baseball, a sport known for analyzing ball flight data to quantify performance. Analysts routinely use ball flight data to identify the attributes of top performing pitchers, finding that the best pitchers throw with optimal combinations of release speed and spin to precise locations. However, for certain pitchers, the throwing motion required to produce optimal ball flight places exceedingly high biomechanical load on the elbow, and consequently injury rates continue to rise. This …

On The Scalability Of Anisotropic Mesh Adaptation On Distributed And Shared Memory Architectures For Numerical Approximations, Kevin Mark Garner Jr.

Computer Science Theses & Dissertations

Mesh generation is a critical component in numerical approximations of Partial Differential Equations (PDEs). One such example includes Computational Fluid Dynamics (CFD), as CFD simulations in turn are crucial for applications in many industries, such as personalized healthcare and the design of aerospace vehicles. Generating high quality meshes for large-scale CFD problems presents a significant bottleneck in the CFD workflow. This dissertation proposes “fast,” parallel 3D mesh generation methodologies that are designed to leverage the concurrency offered by emerging High-Performance Computing (HPC) architectures. First, a distributed memory method is presented that integrates a sequential state-of-the-art isotropic, advancing front local reconnection-based …

Diabetes-Induced Mitral Valve Degeneration: Tissue-Engineered Solutions And Antioxidant Therapy, Samantha Hahn

All Theses

Mitral valve (MV) fibrosis is a progressive pathological condition characterized by leaflet thickening and stiffening, ultimately compromising valve function. This process is accelerated in diabetes, where chronic hyperglycemia elevates reactive oxygen species (ROS) and alters the mechanics of the extracellular matrix (ECM), collectively promoting the activation of valvular interstitial cells (VICs). Under healthy conditions, VICs maintain a quiescent, fibroblast-like phenotype responsible for sustaining ECM homeostasis. However, pathological biochemical cues or mechanical stress drive VICs toward a myofibroblast phenotype. While this transformation is essential for short-term repair, its persistence contributes to maladaptive MV remodeling and fibrosis. Diabetic stressors may be mitigated …

Mitral Annular Calcification In Diabetes: Valvular Interstitial Cells, Antioxidant Therapy, And Tissue Engineering Approaches, Raleigh J. Keenan

All Theses

Mitral annular calcification (MAC) is a chronic, progressive, and degenerative condition that impairs mitral valve function and increases the risk of cardiovascular disease. The mitral annulus is a saddle-shaped, fibrous structure that is primarily composed of collagen and elastin. The annulus also contains interspersed lipids that are involved in cellular metabolism, as well as inflammatory and osteogenic signaling. These lipids increase the annulus’ susceptibility to calcification, under conditions that increase mechanical stress (hypertension) and promote atherosclerosis (diabetes mellitus). These conditions intensify calcification by promoting the activation of valvular interstitial cells (VICs), increasing fibrosis, and inducing osteogenic differentiation. Although it is …

Developing A Metabolic Engineering Chassis From A Metabolically Versatile Organism, Rhodopseudomonas Palustris Cga009, Mark William Kathol

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Metabolic engineering has made it possible to develop biological processes that were once considered economically unfeasible or uncompetitive. This field has enabled both a robust niche market, whereby products, such as pharmaceutical substances like monoclonal antibodies, are produced exclusively through biological means, as well as an emerging commodity production market. Nonetheless, significant challenges remain in harnessing the unique metabolic capabilities of genetically non-tractable organisms. This dissertation focuses on Rhodopseudomonas palustris CGA009 as a potential chassis for metabolic engineering. To address the issue of genetic intractability, a synthetic biology toolkit was developed to facilitate the expression of heterologous proteins in R …

Strategic Enhancement Of Biofuel Production Using Bacillus Subtilis As A Model Organism: A Dual Approach Of Gene Essentiality Mapping And Optimization, Angela A. Zebede

Electronic Theses and Dissertations

With rising global demand for renewable energy, enhancing microbial platforms for biofuel production is vital. This study engineered Bacillus subtilis to improve resilience to solvent stress by targeting membrane lipid biosynthesis pathways essential for integrity. Growth curve analysis (OD₆₀₀) showed that phosphatidylserine (PS) and phosphatidylethanolamine (PE) knockout strains grew significantly slower than wild type (168), indicating the importance of these lipids under stress. Laurdan fluorescence spectroscopy was used to assess membrane properties. Generalized polarization (GP) analysis revealed a concentration-dependent reduction in membrane order upon 1%–2% 1-butanol exposure. GP values declined progressively from control to 2% treatment, reflecting increased membrane fluidity …

Extending Touch: Investigating Sensorimotor Integration, Cognitive Workload, And Presence With Neuro-Haptic Feedback In Virtual Reality, Aliyah Khadijah Shell

Graduate Theses and Dissertations

Sensory feedback from the hand is fundamental for the coordination of fine motor skills and overall sensorimotor function. Impaired somatosensation during task execution has been associated with the development of inaccurate motor plans, which can hinder motor learning. Virtual Reality (VR) has emerged as a promising tool for motor rehabilitation; however, most VR-based interventions overlook the critical role of tactile feedback in motor control. The absence of touch feedback, which is integral to conventional rehabilitation and training, may limit the full therapeutic potential of VR. Integrating functionally relevant neurostimulation based haptic feedback (neuro-haptic feedback) into VR-based interventions may enhance functional …

Evaluating Toggle-Out Testing For Pedicle Screw Failure Prediction, Rebecca Elayne Shelby

Master of Engineering Theses

Pedicle screw loosening is a common failure mode in spinal instrumentation, particularly in osteoporotic bone, where cancellous strength averages 0.944 MPa compared to 1.5-7.8 MPa in healthy bone. This study evaluated toggle-out testing for predicting pedicle screw failure and examined how material strength affects failure behavior. Polyurethane blocks underwent progressive cyclic loading from 100 N to 400 N in 100 N increments, with displacement recorded throughout. A 200 N load reflects forces typically carried by a screw during walking in an osteoporotic patient, placing the test range within expected clinical loading. Displacement behavior and stiffness decay were quantified using a …

Separating The Control Of Moving And Holding In Human Post-Stroke Arm Paresis, Alkis M. Hadjiosif, Kahori Kita, Scott T. Albert, Robert A. Scheidt, Reza Shadmehr, John W. Krakauer

Biomedical Engineering Faculty Research and Publications

Moving and holding-still (holding) have been posited to be separately controlled. The paretic arm after stroke exhibits different abnormalities during rest vs. movement, providing an opportunity to ask whether control of these behaviors is independently affected in stroke. We quantified resting postural abnormalities in human stroke patients by measuring their biases in force production as they held their hand still in various locations in a planar workspace and then assessed whether these resting force biases influenced reaching in the same workspace. Patients displayed marked resting force biases at each location, even when the arm was supported. However, these …

Effective Transfer Of Tumor Annotations From Hematoxylin And Eosin To Fluorescence Images Of Breast And Lung Tissues, Tianling Niu, Emi Ampo, Julie M. Jorns, Mollie Patton, Tongtong Lu, Dong Hye Ye, Tina Yen, Bing Yu

Biomedical Engineering Faculty Research and Publications

Significance: Accurate transfer of annotations from histological images to fluorescence images is essential in developing deep learning (DL)-based optical imaging systems for intraoperative assessment of tumor margins. Manual annotation is time-consuming, prone to interobserver variability, and impractical for large-scale datasets.

Aim: We present a semi-automated method that can effectively transfer tumor annotations from pathologist-annotated hematoxylin and eosin (H&E) images to fluorescence images captured using microscopy with ultraviolet surface excitation (MUSE). This method is not intended for intraoperative use but rather to facilitate the creation of annotated datasets for DL model development.

Approach: Our semi-automated method consists of nonrigid image registration, …

Flash Effect Is Diminished By Daily Fractionation Of Electron Rt In Mouse Skin, Aleksandra Ilina, William S. Thomas, Xu Cao, Matthew S. Reed, Kendall Jarvis, Albert Van Der Kogel, Nathaniel Van Asselt, Wesley S. Culberson, Brian W. Pogue

Dartmouth Scholarship

Objective. While FLASH radiotherapy is known to reduce skin damage in vivo from ultra-high dose rate (UHDR) irradiation relative to conventional dose rates (CDR), it is not clear whether this sparing is preserved when delivered as fractionated. This study was designed to directly assess whether three daily fractions would maintain the sparing effects in murine leg models and preserve the murine skin sparing with single fraction treatments. Approach. C57Bl/6j female mice were irradiated with 9 MeV UHDR and CDR beams from a FLASH-capable Mobetron system, in a dose escalation study with doses ranging from single dose 22–30 Gy in a …

Mechanisms Of Correlated Neuronal Activity In The Globus Pallidus, Hamza Albawaliz

Electronic Theses and Dissertations

This thesis investigates the mechanisms of correlated neuronal activity in the globus pallidus externus (GPe), a key structure in the basal ganglia. Neuronal activity in the GPe is reportedly decorrelated in healthy subjects but can become highly correlated in Parkinson’s disease. However, high-density neuronal recordings in the GPe of healthy rats reveal a surprising degree of correlated activity. This raises the question of whether intrinsic properties or network connectivity alone can account for such patterns. To explore this, a computational model was developed in which GPe neurons are represented as coupled phase oscillators influenced by experimentally derived phase-response curves and …

Development Of A Non-Faradaic Impedimetric Biosensor Based On Reduced Graphene Oxide For The Detection Of Brain-Derived Neurotrophic Factor (Bdnf), Mariana N. Martins

Electronic Theses and Dissertations

Neurological disorders affect millions of people worldwide. In the case of Alzheimer’s disease (AD), the rising number of cases significantly increases global healthcare costs. Therefore, early detection of biomarkers at the onset of the disease is essential for early diagnosis. This study presents an electrochemical biosensor designed for the detection of Brain-Derived Neurotrophic Factor (BDNF) in human plasma, incorporating reduced graphene oxide (rGO) to enhance signal sensitivity. Dielectrophoresis (DEP) was employed to deposit rGO flakes on the electrode surface, improving conductivity and sensor performance. Electrochemical impedance spectroscopy (EIS) was used to monitor changes in impedance associated with BDNF binding events, …

Reproducibility In Modeling Of Knee Joint Mechanics, Maryam Nazem

Electronic Theses and Dissertations

Computational modeling of knee joint biomechanics can provide valuable insights into joint function, injury mechanisms, and patient outcomes, and can support surgical planning and informed clinical decision-making. However, achieving consistent and repeatable results, or reproducibility, is a significant challenge that affects the credibility of these models. This thesis addresses reproducibility through two studies related to the KneeHub Project, which is a multi-institutional collaboration designed to investigate reproducibility in finite-element modeling of the knee.

The first study involved model benchmarking, where predicted results of the calibrated models were compared with the experimental data to evaluate model reproducibility. While all models replicated …

Bending Energy Schemes For Discrete-Spring-Network Structural Modelling Of Red Blood Cells, Osayomwanbor Ehi-Egharevba, Mingzhu Chen, Fergal Boyle

Articles

Red blood cells (RBCs) undergo large structural deformation, including bending, when passing through capillaries. They also exhibit a range of complex shapes such as stomatocytes, discocytes and echinocytes that form due to altered blood pH and salt levels, ingested drugs and adenosine triphosphate depletion. Discrete-spring-network structural models of RBCs employ different numerical treatments of the continuum bending energy. This affects bending accuracy and the prediction of accurate RBC shapes. This research compares three representations called bending energy scheme (BES) A, B and C to evaluate their accuracy in shape predictions. BES A, seen throughout the literature, is based on the …

Advanced Plant Growth Using Halloysite Nanotubes (Hnts) And Waste Extraction For Medical Applications, Zeinab Jabbari Velisdeh

Doctoral Dissertations

This dissertation presents an integrated research framework that bridges nanotechnology, green chemistry, and sustainable agriculture, aiming to address two critical global challenges: enhancing plant growth under resource-limited conditions and valorizing agricultural waste for bioactive compound extraction. The study is divided into three major projects that together highlight the innovative application of magnesium oxide-coated halloysite nanotubes (MgO-HNTs) and the development of environmentally conscious extraction methods for high-value phytochemicals. The first component of this work investigates the design, fabrication, and functional evaluation of MgO-HNTs as advanced nanocarriers for promoting seed germination and early root development in tomato plants. MgO-HNTs were synthesized via …

Exploring The Effectiveness Of Virtual Reality Learning Through Use Of Visual Eye-Tracking Analytics (Veta) And Biological Measurements, Mckinley Anne Sherman

Master's Theses

Virtual Reality (VR) offers an immersive and interactive platform for experiential learning. The purpose of this thesis was to evaluate the relationship between physiological responses and cognitive workload within a VR learning environment and to explore VR as an effective instructional tool. This research compared participant engagement, stress, and learning performance within a 6th-grade science module developed in VR by incorporating biometric data collected via Polar H10 heart rate monitor and Varjo Areo VR headset eye-tracking. Thirty-three participants completed a pre-lesson demographic survey, post-lesson survey, VR sickness questionnaire, and the NASA Task Load Index (NASA-TLX). While completing the lesson, the …

Modeling Synaptic Dysfunction As Neural Contagion: A Graph-Based Sedr Framework For Simulating Signal Spread, Michelle Marfo, Dr. Padmanabhan Seshaiyer, Alonso Ogueda-Oliva

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Scientific Characterization Of Historic Mortars Dating From The 15th-Century Of A Historical Building In Algeria: A Case Study, M. E. Belgacem, N. Rabahi-Touloum, R. Neves, Y. Ouldkhaoua

Journal of Sustainable Construction Materials and Technologies

This research investigates the historic mortars (Aggregate/Binder (A/B) ratio) of a historical patrimony building, dating from the 15th century, in Algeria, for restoration purposes. It is well known that thorough characterization is essential for successful restoration. To this end, several techniques, including Scanning Electron Microscopy (SEM), X-ray Diffraction (XRD), and X-ray Fluorescence (XRF), optical microscope were used to characterize the historic mortars. A mechanical test was used to characterize the compressive strength of a historic mortar. For a comprehensive characterization, A/B ratios were estimated using both Digital Image Analyses (DIA) and chemical analyses. The results obtained provided clear information on …

Resonant Body Communication For Neurodivergent Contexts: A Multimodal, Temporally Elastic Blueprint For Inclusive Biometric Systems, Piper Hutson, James Hutson

Faculty Scholarship

Prevailing emotion-sensing systems privilege a facial-and-gaze paradigm that encodes neurotypical tempo, channel priority, and expression classes, thereby mischaracterizing or erasing neurodivergent communication. This article advances a design-oriented framework for biometric sensing that centers resonant body communication: temporally extended, multimodal, and environmentally situated patterns of posture, gesture, rhythm, and interoception that carry affective meaning. Through an integrative methodology that synthesizes cognitive neuroscience, embodied arts practices, and human–computer interaction, the study formalizes a theoretical model with four pillars: temporal elasticity, multimodal sensory hierarchies, resonant gestures and rhythmic entrainment, and environmental attunement. Building on this model, the article specifies technical requirements for next-generation …

A Convolutional Neural Network Approach To Breast Cancer Tumor Boundary Detection, James Leah Matlosz

Master's Theses

Breast cancer is the second most common form of cancer and often goes undetected in its initial stages due to its subtle symptoms. As the tumors grow, they become more difficult to surgically remove with clean borders. To minimize the chance of recurrence, a 2D convolutional neural network is developed in this work for delineating tumor boundaries. Specifically, the U-shaped network model is trained, validated, and tested with longitudinal MRI scans of patients diagnosed with breast cancer and undergoing neoadjuvant therapy. For training, image masks were generated as ground truths using signal enhancement ratio segmentation, thresholding, and contour detection. The …

Stress-Relaxation And Failure Properties Of Spinal Ligaments In Pigs With And Without Scoliosis-Like Deformity, Christian D'Andrea, Mattan Orbach, Dogerno Norceide, Madeline Boyes, Axel Moore, Jacob Jordan, Thomas Schaer, Anita Singh, Patrick Cahill, Edward Vresilovic, Brian Snyder, Sriram Balasubramanian

Student Papers, Posters & Projects

This study addresses the need for accurate tissue material properties in computational models of the spine. Fundamental to functional spinal unit (FSU) biomechanics are the stress-relaxation and failure properties of the interspinous and intertransverse ligaments (ISL and ITL, respectively). These were measured and compared in normative and scoliotic spines using a Yorkshire pig model. Skeletally immature female pig spines were posterolaterally tethered to induce scoliosis. 23 ISLs and 17 ITLs excised from normative and scoliotic spine segments underwent stress-relaxation and failure tests. Group comparisons tested the effects of scoliosis (magnitude, convexity versus concavity), spinal level (thoracic, lumbar), and pig age. …

Multiscale 3d Whole Joint Cellular And Molecular Mapping Reveals Disease-Specific Neurovascular Plasticity Underlying The Structure-Pain Relationship, Peng Chen, Jiaxin Chai, Abirami Soundararajan, R. Glenn Hepfer, Benjamin Kheyfets, Jiaxin Hu, Ishraq Alshanqiti, Swarnalakshmi Raman, Ikue Tosa, Jun Tae Huh, Matthew Yee, Brooke J. Damon, Shangping Wang, Yu Shin Kim, Man-Kyo Chung, Mildred C. Embree, Janice S. Lee, Tong Ye, Hai Yao

Publications

Understanding musculoskeletal joints from a 3D multiscale perspective, from molecular to anatomical levels, is essential for resolving the confounding relationships between structure and pain, elucidating mechanisms regulating joint health and diseases, and developing new treatment strategies. Here, a musculoskeletal joint immunostaining and clearing (MUSIC) method specifically developed to overcome key challenges of immunostaining and optical clearing of intact joints are introduced. Coupled with large-field light sheet microscopy, this approach achieves 3D high-resolution, microscale neurovascular mapping within the context of whole-joint anatomy without the need for image coregistration across various joints, including temporomandibular joints, knees, and spines, and multiple species, including …