Biological Engineering Commons^™

Design And Validation Of A Wearable Respiratory Protection System For Wildland Firefighters, Oliver Pilon

Master's Theses

Wildland and Wildland–Urban Interface firefighters are routinely exposed to hazardous smoke with fine particulate matter, carbon monoxide, volatile organic compounds, and other toxic combustion products. Existing protective gear has significant limitations and shortcomings for these conditions. Respirators with tight-fitting facepieces make it difficult to breathe and speak. On the other hand, self-contained breathing apparatuses are too heavy, have a limited duration of use, and do not work well with long wildland fire scenes, while smaller protective equipment like N-95’s and gaiters provide very little protection. These constraints contribute to low adoption rates and prolonged occupational exposure.

This thesis presents the …

Jaundease Phototherapy Vest Test Plan, Sujay Panthulu, Jasdev Banwait, Gwynn Moss, Solomon M. Fernandez

Biomedical Engineering

Neonatal hyperbilirubinemia is a common condition affecting more than 60% of newborns, caused by an excess buildup of bilirubin in the blood due to the liver’s limited ability to process it efficiently [1]. The standard treatment involves hospital-based phototherapy, where infants are placed in incubators under blue light to break down bilirubin in the skin. Although effective, this approach requires infants to remain under the lights for 12–18 hours per day, often with eye protection, and separated from their parents—disrupting early bonding and potentially contributing to toxic stress that can impact neurological and emotional development [2]. While at-home phototherapy solutions …

Raw Data Files Contributing To "Changes In Apoe And Timp-1 Expression Correlate With Outer Blood-Retinal Barrier Disruption In An In Vitro Model Of Retinal Aging", Elizabeth Vargis

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Age-related macular degeneration (AMD) is a leading cause of blindness worldwide. Unfortunately, the early stages of this disease are poorly understood, which has led to limited treatment options. Investigating normal changes in tissues eventually affected by AMD can further elucidate the mechanisms of disease progression and lead to novel therapeutic targets. The primary cell layer affected in AMD is the retinal pigment epithelium (RPE), which forms the outer blood-retinal barrier (oBRB). Beneath the RPE lies Bruch’s membrane, a proteinaceous layer that naturally thickens and stiffens with age. These changes to Bruch’s membrane are also implicated in RPE dysfunction and AMD …

Stentrx, Emma Barna, Minuthi Cooray, Bruce Newlands, Joseph A. Sabetta

Williams Honors College, Honors Research Projects

This project aims to develop a biodegradable, drug-eluting biliary stent for the treatment of biliary cancers. Current metal stents that restore bile flow bit are non-degradable, prone to migration, and unable to deliver drugs locally. The proposed stent will be biocompatible, biodegradable, and capable of controlled drug release to both maintain bile flow and treat tumors. The end goal is to produce a functional prototype that can be deployed via a minimally invasive catheter and maintain bile duct patency for at least three months. The project is expected to be involved in the NEOMED Bench-to-Bedside competition and provisionally patented.

Bioprinted Scaffolds For Investigating Fibroblast Alignment, Lillian Thro, Daeha Joung Ph.D.

Undergraduate Research Posters

Fibroblasts play a vital role in tissue repair, ECM remodeling, and maintaining structural integrity in human tissues. However, their behavior in engineered 3D microenvironments remains poorly understood. Traditional 2D cultures fail to capture the complex cell-cell and cell-matrix interactions that govern fibroblast alignment, migration, and proliferation in vivo. To address this gap, this project uses bioprinted scaffolds that mimic native ECM structures and provide a platform for studying fibroblast behavior in controlled microenvironments. The project focuses on varying scaffold channel properties—such as width, depth, and geometry—to investigate how physical cues influence fibroblast organization and collective migration. A biodegradable gelatin-based ECM …

The Role Of Laminin Isoforms In Glioblastoma Migration, Aseel Ahmed, Faezeh Ghobadi, Hanna Devillier, Qi Cai

Distinguished Undergraduate Researcher Program

Glioblastoma (GBM) remains the most prevalent and lethal invasive brain tumor, denoted by a median survival of 12-15 months despite standard procedures such as safe surgical resection, radiotherapy, and chemotherapy. This limited effectiveness largely arises from the infiltrative nature of GBM cells, which interact with the brain’s extracellular matrix (ECM) by migrating along blood vessels and axonal pathways. The ECM contains the interstitial matrix (IM) and the
basement membrane (BM) made up of proteins and glycans which interact with the malignant cells. While research has mainly been focused on understanding how GBM cells interact with IM components, our knowledge about …

The Healing Power Of Nanoparticles: Bioengineering Gelatin Films With Lignin-Graft-Plga Nanoparticles For Enhanced Tissue Repair, Marie Howe, Cristina Sabliov, Thanida Chuacharoen, Willyam Nikiema

Distinguished Undergraduate Researcher Program

Fish gelatin, a biocompatible material, can be methacrylated to enable its photo-crosslinking and formation of hydrogels for tissue-repair applications (1). This study investigated the incorporation of lignin-grafted PLGA nanoparticles (LNPs) into 3D-printed fGelMA hydrogels as controlled drug delivery systems. Lignin has UV absorbing properties, which could potentially interfere with photocrosslinking of fGelMA (2). These LNPs possess hydrophobic PLGA core and hydrophilic lignin forming the shell providing ample opportunities for delivery of drugs of different chemistries (3). Fluorescent LNPs (FLNPs) were engineered by covalently bonding a fluorophore to the shell prior to nanoparticle synthesis to allow for fluorophore tracking. The understanding …

Probing Proficiency-Related Neural Representations With Pca And Ica, Onila R. Narayana Mudalige Don

Graduate Student Theses, Dissertations, & Professional Papers

How proficiency-related information is represented in task fMRI depends not only on the data themselves, but on the representational lens used to summarize them. This thesis examines second-language (L2) proficiency as a problem of representational organization rather than as a simple classification exercise. Using task fMRI from adult language learners performing semantic animacy judgments in their native language (L1) and second language (L2), I derive shared low-dimensional network representations with principal component analysis (PCA) and independent component analysis (ICA), then evaluate those representations under matched leakage-controlled decoding pipelines.

Across analyses, the central comparison is between representational frameworks rather than between …

De Novo Protein Binding To Zinc Oxide Through Biomineralization Pathways, Jean-Mark A. Francis

Theses and Dissertations

De novo proteins are structurally distinct from proteins found in nature and thus capable of having their amino acid sequence modified to accomplish tasks such as increasing protein-nanoparticle binding without unfolding or decomposing. Zinc Oxide nanoparticles are functionally distinct from their bulk counterparts and are widely used as semiconductors in a variety of fields such as medicine and agriculture. With demand for these nanoparticles increasing, environmentally sustainable methods of Zinc Oxide nanoparticle synthesis are being investigated as an eco-friendly alternative to currently utilized but environmentally hazardous chemical and physical techniques. This research investigates the binding characteristics between Zinc Oxide nanoparticles …

Design And Validation Of A Novel Patterned Microfluidic Culture Platform For Hipsc-Cm Maturation, Anisia Gabriela Țiplea

Dartmouth College Master’s Theses

Adult cardiomyocytes (CMs) are among the most challenging cells to culture in vitro, given their poor adherence to plastic culture wells and poor maturation outside the native extracellular matrix (Narkar et al., 2022). Human induced pluripotent stem cell-derived CMs (hiPSC-CMs) offer a viable alternative to study heart development and disease progression. While not comparable to adult CMs in their maturity (Narkar et al., 2022), they mimic the clinical phenotypes of heart failure and are more feasible to culture. Nevertheless, hiPSC-CMs require specialized culture conditions that cannot be achieved with 2D static culturing, which fail to replicate native tissue environments (X. …

Biomechanical Advancements In Hydroxyapatite, Magnesium-Substituted Hydroxyapatite, And Strontium-Substituted Hydroxyapatite In Clinical And Non-Clinical Studies For Maxillofacial Bone Tissue Engineering: A Review, Elham Zafarrazzaghnia, Stuart Hampshire, Aran Rafferty, Dermot Brabazon, Eamonn Debarra, Maura Kelleher

Articles

Hydroxyapatite (HA) is a bioceramic known for its bioactivity and osteoconductivity, which should make it an ideal candidate for maxillofacial bone regeneration. However, its brittleness limits its suitability for load-bearing applications. Over recent decades, substantial efforts have focused on enhancing its performance, particularly through ionic substitution, including magnesium-substituted HA (Mg-HA) and strontium-substituted HA (Sr-HA). This review summarises the available information on the structural, physical and mechanical properties of facial bones (maxilla, mandible, zygoma and frontal bone). The crystal structure, physical, and mechanical properties and in-vitro biological responses of dense and porous HA, Mg-HA and Sr-HA ceramics are described, with particular …

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 …

Comprehensive Mechatronic Design Methodology For 6-Dof Stationary Lower Limb Rehabilitation Exoskeleton Robot With Safety-Integrated Control Architecture, Javlonbek Rakhmatillaev Mr., Nodirbek Kimsanboyev Mr., Umidjon Takabaev Mr., Zafar Juraev3 Dr.

Chemical Technology, Control and Management

This paper presents the mechatronic design of a proposed six-degree-of-freedom (6-DOF) stationary lower limb rehabilitation exoskeleton (SLLRE) robot, developed through a comprehensive mechatronic design methodology that includes mechanical design, actuator and sensor selection, and the development of a control structure based on a safety-oriented control approach. The proposed 6-DOF SLLRE mechanical design introduces a comprehensive mechanical structure comprising bilateral hip, knee, and ankle joints, degrees of freedom, joint ranges of motion, human parameters for rehabilitation training, as well as the frames and structural elements of the proposed system. Furthermore, the selection of appropriate sensors, actuators, and control architecture for the …

Optimization Of Research Pipeline To Characterize The Effects Of Atp-Sensitive Potassium Channels Mutations On Native Skeletal Muscle Fibers And Evaluate Potential Drug Therapy, Yuezhou Chen

McKelvey School of Engineering Graduate Student Theses & Dissertations

The ATP-sensitive potassium (KATP) channel is a critical metabolic sensor in skeletal muscle, yet its definitive molecular composition and functional roles remain contested. In this study, I conclusively demonstrate that the Kir6.2/SUR2 complex forms sarcolemmal KATP channel in mouse fast-twitch muscle. Genetic knock-out (KO) of Kir6.2 (Kcnj11−/−) or SUR2 (Abcc9−/−) resulted in a similar phenotype with increased fatigue resistance and a pathological rise in unstimulated resting tension at high-frequency stimulation. In contrast, SUR1 (Abcc8−/−) KO was ineffective. Furthermore, a CRISPR/Cas9 knock-in mouse model of a human SUR2A truncation variant (KCGV/KCGV) recapitulated the abnormal force accumulation, demonstrating that even loss-of-function of …

2d-Nanosilicate Carriers For Sustained Delivery Of Vaccine Components, Chih Yun Liu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Laponite® 2D Nanosilicates (NS) are disc-shaped platelets (~30 nm diameter, ~1 nm thick) with positively charged edges and negatively charged faces, capable of loading proteins, drugs, and nucleic acids via electrostatic interactions to form a house-of-cards gel that sequesters cargo. Here, we evaluated NS for sustained delivery of antigens and Toll-like receptor (TLR) agonists to extend germinal center duration and enhance antibody quality. The model antigen ovalbumin (OVA) was adsorbed onto NS at acidic pH in a ~1:1 ratio, with partial unfolding that remained stable at physiological pH. NS-OVA complexes were efficiently internalized by dendritic cells, with uptake driven primarily …

Space Agriculture: A Comprehensive Systems-Level Review Of Challenges And Opportunities, Hassan Fazayeli, Aaron Lee M. Daigh, Cassandra Palmer, Santosh Pitla, David Jones, Yufeng Ge

Biological Engineering Faculty Publications

As humanity prepares for prolonged space missions and future extraterrestrial settlements, developing reliable and resilient food-production systems is becoming a critical priority. Space agriculture, the cultivation of plants beyond Earth (particularly on the Moon and Mars), faces a constellation of interdependent environmental, biological, and engineering challenges. These include limited solar radiation, elevated ionizing radiation, large thermal variability, non-Earth atmospheric pressures, reduced gravity, regolith substrates with low nutrient-holding capacity, high-CO₂/low-O₂ atmospheres, pervasive dust, constrained water and nutrient availability, altered plant physiology, and the overarching need for closed-loop, resource-efficient systems. These stressors create an exceptionally challenging environment for plant …

Unsaturated Fatty Acid Oil-Based Microdroplets: A Promising Novel Class Of Microdroplets, Ramiz S. Alejilat

Seton Hall University Dissertations and Theses (ETDs)

Droplet-based microfluidics has rapidly advanced numerous fields, including chemistry, biology, materials science, medicine, food science, and cosmetics. In these systems, fluorocarbon oil combined with fluorinated surfactants is the preferred medium for fluid encapsulation, offering exceptional stability and biocompatibility essential for sensitive biological and chemical processes. However, growing concerns about the environmental and biological risks associated with fluorinated chemicals have prompted a search for alternatives.

This study is the first to explore the use of unsaturated fatty acids derived from emu oil for microdroplet formation. We characterized droplet formation based on flow rates and the presence non-fluorinated surfactant at a certain …

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 …

Analysis On Modifications To An Outdoor Field-Scale Rotating Algal Biofilm Reactor With A Focus On Biomass Productivity And Power Usage, Davis R. Haag

All Graduate Theses and Dissertations, Fall 2023 to Present

A rotating algal biofilm reactor (RABR) was operated outdoors for one calendar year to see how the microalgae grown were affected. The algae are grown in wastewater that contains nitrogen and phosphorous, which are elements found in fertilizer. The design used was modified from a previous design, and this project tested the modifications to see if they improved how much microalgae were grown. In February 2025, the objectives of the field study were updated to focus on growing as much microalgae as possible instead of removing as much nitrogen and phosphorous as possible. This updated design increased the fluid flow …

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 …