Engineering 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 …

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 …

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 …

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 …

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 …

Patient-Informed Fluid-Structure Interaction Simulations Of Bicuspid Aortic Valve In Young Adults Reveal Regionalized Differences In Mechanical Stress, Hail B. Kazik, Harkamaljot S. Kandail, Joy Lincoln, John F. Ladisa

Biomedical Engineering Faculty Research and Publications

Bicuspid aortic valve (BAV) is a common congenital cardiovascular defect characterized by two, rather than three, cusps. Many BAV patients prematurely develop calcification and aortic stenosis by age 35, which is more severe with fusion of the right and noncoronary (RC/NC) cusps. The mechanisms underlying calcification observed within the coaptation, attachment, and fusion regions of BAV patients are unknown. While abnormal mechanical stimuli induced by the bicuspid anatomy likely plays a role, little is known about regionalized mechanical stimuli in these susceptible cusp regions of young patients prior to calcification. Strongly coupled fluid-structure interaction simulations were conducted using physiologic boundary …

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. …

Strategies For Increasing Methane Removal In Methanotroph Stirred-Tank Reactors For The Production Of Ectoine, Jaden Storrer, Tansley M. Mazurkiewicz, Bodee Hancock, Ronald C. Sims

Biological Engineering Student Research

Methane is a potent greenhouse gas that requires its emissions to be mitigated. A significant source for methane emissions is in the form of the biogas that is produced from anaerobic digestion in wastewater reclamation and landfill facilities. Biogas has a high valorization potential in the form of its bioconversion into ectoines, an active ingredient in skin care products, by halotolerant alkaliphilic methanotrophs. Cultures of Methylotuvimicrobium alcaliphilum 20Z were grown in bench scale stirred-tank reactors to determine factors to improve methane uptake and removal. Tangential flow filtration was also implemented for a bio-milking method to recover ectoine from culture media. …

Harvesting Aav By Tangential Flow Filtration Using Reverse Asymmetric Membranes, Xiaolei Hao, Ronny Horax, Xianghong Qian, April Wheeler, Hironobu Shirataki, Sumith Ranil Wickramasinghe

Chemical Engineering Faculty Publications and Presentations

Efficient bioreactor clarification for harvesting virus particles is often challenging. Tangential flow filtration is attractive as it can be easily adapted for batch and perfusion operations. Here the feasibility of using reverse asymmetric hollow fiber membranes, where the more open support structure faces the feed stream, has been investigated for harvesting adeno associated virus serotype 2. The open support structure of these membranes stabilizes a secondary membrane consisting of rejected particulate matter. It is essential that the stabilized secondary membrane remains highly permeable. Flux stepping experiments were conducted in total recycle mode in order to determine the critical flux. The …

Different Brain Network Connectomic Relationships Subserve Hand Dexterity During Task Versus Resting States In People With Brain Tumors, Timothy F. Boerger, Leon Taquet, Kaitlin Goetschel, Sarah Young, Jennifer Connelly, Jeffrey R. Binder, Brian Schmit, Max O. Krucoff

Biomedical Engineering Faculty Research and Publications

Purpose

The purpose of this study was to explore different brain network connectomic relationships subserving hand dexterity in patients with contrast-enhancing brain tumors during task and resting states.

Method

We measured hand dexterity, resting state functional connectivity, and task-based functional connectivity in 21 participants with newly diagnosed brain tumors. Hand dexterity was measured using the 9-hole peg test (9HPT), and patient-reported outcomes were assessed with the Duroz Hand Index (DHI).

Findings

We discovered the following: (1) The inability to complete dexterous tasks is most associated with low somatomotor-basal ganglia network connectivity during rest but high somatomotor-basal ganglia network connectivity during …

Characterizing Piezoelectric-Blended Polydimethylsiloxane For Use As A Mechanoelectrical Responsive Cell Culture Substrate, Alexis P. Applequist, Lance D. Cordes, Lais A. Ferreira, Kartik Balachandran

Biomedical Engineering Faculty Publications and Presentations

In this study, we developed a piezoelectric-polydimethylsiloxane (pz-PDMS) composite by blending poly(vinylidene fluoride-co-trifluoroethylene) (P(VDF-TrFE)) with PDMS to create a biocompatible, mechanoelectrical responsive material. The pz-PDMS was synthesized with varying piezoelectric concentrations (0%, 1%, 3%, and 5%) and characterized for visual properties, mechanical properties, mechanoelectrical sensitivity, and biocompatibility. Compression testing showed no significant change in mechanical strength with the addition of piezoelectric particles, while mechanolectrical sensitivity testing revealed a non-linear increase in voltage response, with 5% pz-PDMS producing the highest sensitivity. Fatigue testing demonstrated no change in sensitivity after 7 days of cyclic displacement. Additionally, microcantilever experiments demonstrated the high fidelity …

Fabrication Of Multimodal Anion Exchange Membrane For Chromatographic Purification Of Full Adeno-Associated Viral Capsids, Xiaolei Hao, Sumith Ranil Wickramasinghe, Xianghong Qian

Biomedical Engineering Faculty Publications and Presentations

A multi-modal anion exchange ligand 2-methyl-phenylimidazole has been successfully functionalized on highly porous electrospun regenerated cellulose membrane substrate for the separation of full and empty adeno-associated viral (AAV) capsids. The functionalized membrane has an average pore size of 0.5 mu m and exhibits both charge and hydrophobic functionality. The ligand is able to distinguish the subtle physio-chemical differences between the full and empty viral capsids. The multi-modal anion exchange membrane is able to separate the full capsids from affinity-captured mammalian AAV2 using both gradient and two-step elution methods with superior performance. A full capsid recovery of 72.9% at 85.3% purity …

Metabolic Insights Into Cyst Fluid Composition And The Role Of Taurine In Polycystic Kidney Disease, Vineetha Garimella

USF Tampa Graduate Theses and Dissertations

Polycystic kidney disease (PKD) is the most common genetic disorder affecting kidneys and the fourth leading cause of kidney failure. It occurs in two major forms, autosomal dominant PKD (ADPKD), and autosomal recessive PKD (ARPKD). ADPKD is typically adult-onset and caused by mutations in the PKD1 and PKD2 genes, and ARPKD generally manifests in utero and is caused by mutations in the PKHD1 gene. Despite the severity of the disease, only one FDA-approved drug, tolvaptan, is currently available for ADPKD and remains under clinical investigation for ARPKD. However, its use is limited by adverse side effects including polyuria, polydipsia, and …

Capacity Of Microbial Strains And Communities To Degrade Sewerage Fats, Oils, And Grease Clog Deposits, Allondra M. Woods, Catherine J. Pettinger, Catherine Harris, Tanya Soule, Garth Farley, Erica L.-W. Majumder

Biological Engineering Student Research

Fats, oils, and grease (FOG) deposits are hardened, sticky, insoluble solids that accumulate in sewage systems globally. These deposits contribute to pipe blockages and sanitary sewer overflows, releasing pathogens and pollutants into the environment, posing significant environmental and public health risks. Current removal methods are labor-intensive and costly, emphasizing the need for alternatives. While biological strategies offer a viable alternative, the microbial breakdown of FOG is poorly understood. In this study, we evaluated the potential of individual microbial strains and synthetic microbial communities to biodegrade wastewater-derived FOG deposit samples. These biological agents were applied to a range of FOG samples, …

Exploring The World Of Medical Exoskeleton Robots: A Classification Guide, Javlonbek Rakhmatillaev, Vytautas Bučinskas

Technical science and innovation

This article describes the classification of exoskeletons. This classification is based on the use of exoskeletons in the medical field, shape, power source, generation, parts related to the human body, structural material, and control forms based on sensor and actuator devices. In addition, examples of each category are given. The main goal is to comprehensively evaluate medical exoskeletons, pay special attention to their functions and goals, conduct scientific research, and further develop these devices. As a result, a completely new type of classification of medical exoskeletons was developed. The developed new type of classification serves as an important guide in …

Insights From A Simple Mathematical Model Of Autism Spectrum Disorders, Charles F. Babbs

Weldon School of Biomedical Engineering Faculty Working Papers

This preliminary report explores insights about mechanisms of autism spectrum disorders (ASDs) gained from a mathematical model of interconnected clusters of excitatory neurons. This local, integrate-and-fire, spiking neural network is subjected to random noise from other populations of excitatory and inhibitory neurons outside the network. Its emergent behavior in response to different ratios of inhibitory to excitatory noise mimics several aspects of ASDs. The spiking neural network functions according to rules of classical neurophysiology, involving resting membrane potential, threshold potential, excitatory or inhibitory post-synaptic potentials, action potential, and refractory period. Key parameters include the incremental change in membrane potential, p …

Evaluation Of An In Situ Forming Composite Hydrogel Based On Gelatin–Sodium Alginate– Polyethylene Oxide For Biomedical Applications: Effect Of Incorporated Sophora Japonica On Hydrogel Performance, Samar A. Salim

Nanotechnology Research Centre

Hydrogels are ideal candidates for biomedical applications such as wound healing, tissue engineering, and bone regeneration due to their porosity and similarity to the extracellular matrix of humans. A gelatin/ sodium alginate (SA) hydrogel with the inclusion of polyethylene oxide (PEO) was utilized to achieve enhanced mechanical strength. Hydrogels were prepared at different ratios of polymer solutions to select the hydrogel that exhibited an optimal gelation time. Sophora japonica, a plant leaf extract (SJLE) rich in flavonoids and isoflavonoids, was added to the hydrogel to enhance tissue repair. The developed hydrogels were extensively characterized for their morphology, porosity, and swelling …

Enhancing 6g Network Security With Quantum Key Distribution: A Comprehensive Review, Bassma M. Kamil

Al-Esraa University College Journal for Engineering Sciences

With the considerable progress of sixth-generation (6G) networks further on the horizon, security has attracted much attention in the face of increasingly sophisticated threats, especially from quantum computing. Classical cryptographic schemes based on computational hardness are becoming more and more brittle, as they can easily be attacked with a quantum computer. Quantum Key Distribution (QKD) arises as a promising tool for information-theoretic security through quantum mechanics to obtain an unbreakable key by exchanging unknown bit sequences. In this paper, we provide an extensive survey on the integration of QKD both in the envisioned 6G architecture, including current implementations, technical feasibility, …

Protection The Nfv Net-Work Using The Random Forest Classification, Mustafa H. Taha, Ibtesam Jomaa Hawi, Wafaa Waheeb Abdullah Ali

Al-Esraa University College Journal for Engineering Sciences

A misuse attack is the most common and dangerous type of attack that could target NFV (Network Function Virtualization). In a misuse attack, the attacker attempts to consume the NVF environment’s resources by sending a large amount of traffic. To protect the NFV environment, an early and accurate misuse attack detection system has been proposed based on NFV and Random Forest Classifier. The proposed model starts with importing the dataset and analyzing it then pre-processing and feature selection using a PSO (particle swarm optimization) Test algorithm, classification is based on the most common and efficient machine learning technique, which is …