Biomedical Engineering and Bioengineering Commons^™

Advancing Novel Contrast Agents For Applications In Fluorescence-Guided Neurosurgery Using Fluorescence Cryotomography, Augustino Vittorio Scorzo

Dartmouth College Ph.D Dissertations

Fluorescence guided surgery (FGS) is an emerging surgical technique that aims to help surgeons identify tissue types to assist in surgical decision making - ideally providing “cut-by-color” guidance. A primary application for this approach is the identification of tumor tissue to achieve more accurate and complete tumor removal while simultaneously minimizing damage to surrounding normal tissue. The cornerstone of tumor visualization for FGS is the administration of fluorescent contrast agents, or in some cases metabolic precursors, designed to accumulate specifically in tumor tissue, and a wide range of agents that use different targeting mechanisms are currently under investigation. Although these …

Mechanistic Insights Into The Flash Effect: The Role Of Oxygen And Radiation Chemistry In Ultra-High Dose Rate Radiation Therapy, Jacob Pierce Sunnerberg

Dartmouth College Ph.D Dissertations

The development of new cancer therapies focuses on widening the therapeutic ratio between tumor control and normal tissue toxicity. Over the last decade, ultra-high dose rate (UHDR) radiation therapy, commonly known as FLASH radiotherapy (FLASH-RT), has shown promising potential to reduce normal tissue toxicity while maintaining tumor control. However, the underlying mechanisms of the FLASH effect remain poorly understood. This thesis explores the radiation-chemical basis of FLASH-RT, focusing on the role of oxygen and reactive oxygen species in modulating biological outcomes.

A comprehensive set of in vitro studies demonstrated that UHDR delivery significantly alters radiation chemistry compared to conventional dose …

Image-Based Models For Left Heart Flow Morphodynamics In Hypertrophic Obstructive Cardiomyopathy, Abdelrahman A. Sultan

Theses and Dissertations

Relieving flow obstruction in hypertrophic obstructive cardiomyopathy is highly effective in reducing symptoms and promoting left ventricular remodeling. However, existing characteristics in the disease, such as the systolic anterior motion of the mitral, mitral regurgitation, and papillary muscle motion, and their effect on ventricular flow and vortex formation, have not been thoroughly addressed. This study aims to develop image-based computational fluid dynamics models to evaluate flow morphodynamics in hypertrophic obstructive cardiomyopathy. A computational fluid dynamics model is constructed to investigate the interaction between inflow and outflow in hypertrophic obstructive cardiomyopathy, with a focus on how the motion of the left …

Advances In Bone And Orthopedics 2025 – 5th Edition, Jean-Philippe Berteau, Laurent Pujo-Menjouet, Hélène Follet, Aurélie Levillain

Publications and Research

This volume brings together selected works from the 2025 Bone and Orthopedics Interdisciplinary Symposium (BONITOS), underscoring our community’s ongoing commitment to advancing research in biomechanics, bone health, and orthopedic science. The symposium unites leading experts from around the world, fostering collaboration and the exchange of ideas across disciplines. Organized in partnership with the French-speaking Society of Biomechanics, the French National Institute of Health and Medical Research (INSERM), the University of Lyon, the College of Staten Island of the City University of New York (CUNY), and the American Association of Physical Therapists (APTA) – Brooklyn Staten Island Chapter, BONITOS 2025 represents …

Computational Fluid Dynamics And Fluid Structure Interaction Modeling In Healthy Vertebral Arteries: A Comparative Study, Bryce Clinkenbeard

Electronic Theses and Dissertations

Cerebral perfusion is critical for maintaining proper brain function, with each cerebrovascular artery playing an integral role in the overall cerebrovascular system. When these arteries become damaged or develop plaque, cardiovascular disease (CVDs) such as atherosclerosis can arise, leading to conditions like arterial stenosis. While CVDs are most prevalent in older individuals, they are also observed in young adults, particularly those engaged in high-endurance occupations such as military service. Diagnosis and prediction of CVDs often rely on imaging modalities supported by computational fluid dynamics (CFD) which account for low resolution in fluid flow. CFD models assume rigid arterial walls, which …

Tunable Methacrylated Decellularized Heart Matrix: A Versatile Scaffold For Cardiac Tissue Engineering, Valinteshley Pierre, Douglas H. Wu, Chao Liu, Elif Ertugral, Chandrasekhar R. Kothapalli, Samuel E. Senyo

Chemical & Biomedical Engineering Faculty Publications

Therapeutic tissue regeneration remains a significant unmet need in heart failure and cardiovascular disease treatment, which are among the leading causes of death globally. Decellularized heart matrix (DHM) offer promising advantages for tissue engineering, including low immunogenicity and seamless integration into biological processes, facilitating biocompatibility. However, DHM is challenged by weak mechanical properties that limit its utility to biomedical applications like tissue engineering. To address this limitation, we functionalized DHM with methacryloyl functional groups (DHMMA) that support UV-induced crosslinking to enhance mechanical properties. By modulating the degree of methacryloyl substitution, a broad range of stiffness was achieved while maintaining cell …

Highly Adaptable Dendrimer Gel Nanoparticles With Dual Targeting Of Upar And Ribonucleotide Reductase R2 For Better Retention And Improved Therapeutic Outcomes In Triple-Negative Breast Cancer, Hsin Yin Chuang, Da Huang, Lin Qi, Vidit Singh, Anna Chernatynskaya, Yue-Wern Huang, Hu Yang

Biological Sciences Faculty Research & Creative Works

Triple-negative breast cancer (TNBC) accounts for approximately 15% of breast cancers and lacks estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2), rendering it unresponsive to hormonal or anti-HER2 therapies. Due to its poor prognosis and limited treatment options, there is an urgent need for targeted therapies. In this study, we developed highly adaptable polyamidoamine (PAMAM) dendrimer-based gel nanoparticles with dual-targeting capabilities against urokinase-type plasminogen activator receptor (uPAR) and ribonucleotide reductase R2 (R2). These nanoparticles were designed to target both TNBC cells and cancer-associated stromal cells by leveraging uPA-uPAR interactions and delivering the antisense oligonucleotide …

Selective Anti-Tumor And Normal Tissue Sparing Effects Of Flash Radiotherapy In A Simple Algebraic Model Of Radiochemical Kinetics, Charles F. Babbs

Weldon School of Biomedical Engineering Faculty Working Papers

Background: This short paper presents the solution to an open problem in medical physics: how and when FLASH radiotherapy can have a selective anti-tumor effect. FLASH radiotherapy gives a single large dose of ionizing radiation to a cancer patient within a time span of a few milliseconds, unlike conventional radiotherapy which is divided into several dose fractions given weekly, each lasting about 10 minutes. In some animal models FLASH seems to improve tumor cell killing without damaging normal tissues. However, the mechanism of the selective anti-tumor effect remains elusive. Methods: To explore effects of tissue hypoxia in tumors, a model …

Microfluidic Intracranial Pressure Monitoring Sensor, Andrea Pader, Anthony Sukendro, Tripti Pandey

Bioengineering Senior Theses

This thesis presents the design of a novel microfluidic sensor for continuous monitoring of intracranial pressure (ICP), intended as a less invasive alternative to current monitoring techniques. The sensor targets patients with critical and chronic neurological conditions, aiming to provide real-time data on ICP fluctuations. The microfluidic intracranial pressure sensor is designed for implantation beneath the skull, on the dura mater, and integrates a PDMS-based microfluidic strain sensor with wireless data transmission. Initial testing focuses on optimizing sensor design and integration with a microcontroller. Preliminary benchtop testing demonstrates the sensor's capability to detect ICP with a minimum sensitivity of 5 …

Continuous Monitoring Of Dynamic Levels Of Sepsis-Associated Biomarkers In Blood For Early Diagnosis, Aidan Burke, Jake Chansky, Anders Kouhia, Brian Mostofi

Bioengineering Senior Theses

Sepsis is a general diagnosis related to a dysregulated immune response to a source of infection that, if left untreated, will most likely result in organ failure and eventual death. Sepsis affects 49 million people annually, and is responsible for 11 million annual deaths, according to Jarczak 1. A recent study has shown that over 80% of sepsis deaths may be preventable with earlier diagnosis and treatment, and that the risk of mortality increases by 8% for every hour that sepsis goes untreated 5. Thus, our team identified that the timeliness of sepsis diagnosis is a paramount healthcare need.

We …

A Hybrid Ai-Based Framework For Real-Time Epileptic Seizure Detection In Intracranial Eeg Signals Using Brain-Computer Interfaces, Ahmed, M. Salaheldin Dr., Manal Abdel Wahed Prof., Neven Saleh

Future Engineering Journal

Epilepsy is a serious neurological disorder that can significantly impact an individual's quality of life. This study proposes a novel method for the detection and mitigation of epileptic seizures through the integration of artificial intelligence (AI) and a brain-computer interface (BCI) system. Statistical features were extracted from intracranial electroencephalography (IEEG) signals using a multi-resolution decomposition technique and used to train five classification algorithms: support vector machines (SVM), k-nearest neighbors (KNN), Naïve Bayes (NB), artificial neural networks (ANN), and long short-term memory (LSTM). The model demonstrated strong performance, achieving classification accuracies of 98.28% (SVM), 93.88% (KNN), 95.73% (NB), 95.73% (ANN), and …

Novel Electrospinning Techniques For Fabricating Scaffolds To Model Intracranial Atherosclerotic Disease In Tissue Engineered Blood Vessel Mimics, Isaac "Squeaky" Buentipo

Master's Theses

Novel Electrospinning Techniques for Fabricating Scaffolds to Model Intracranial

Atherosclerotic Disease in Tissue Engineered Blood Vessel Mimics

Isaac “Squeaky” Buentipo

Dr. Kristen Cardinal’s Tissue Engineering Lab at California Polytechnic State University specializes in fabricating customized vascular models, known as Blood Vessel Mimics (BVMs), for medical device testing. BVMs are simplified in vitro vascular models designed to bridge the gap between bench testing and in vivo evaluation of intravascular medical devices. BVMs are produced by combining a polymer scaffold with human vascular cells. Through novel scaffold fabrication techniques, such as silicone injection molding, silicone dip casting and electrospinning, the capabilities of …

Evaluation Of Antibiotic Testing Protocols For Biofilm-Forming Escherichia Coli In A Microfluidic Platform, Caleb R. Telander

Master's Theses

Catheter-associated urinary tract infections remain an ongoing clinical problem due to biofilm persistence and antibiotic resistance. Standard antibiotic susceptibility testing cannot accurately reproduce flow conditions and the spatial complexity of the in vivoenvironment and is thus questionable in relevance to device-related infections. This study examines a microfluidic device designed to simulate physiologically relevant wall shear stress and antibiotic gradients in Escherichia coli biofilms. The polydimethylsiloxane-based system integrates a 16-well culture chamber with a gradient generator. Biofilm growth was observed using fluorescence microscopy of green fluorescent protein-labeled bacteria. Simulations performed using COMSOL Multiphysics software estimated the appropriate range of wall …

Microplastic Eaters, Alanna Boze

Bioengineering Senior Theses

This thesis evaluated Alcanivorax Borkumensis’ (A. Borkumensis) ability to degrade polystyrene in a pyruvate-rich environment to determine if the bacteria could degrade the microplastic when grown in pyruvate. The thesis explored the metabolic behavior of A. Borkumensis when pyruvate is used to start the gluconeogenesis pathway, which is the start of the metabolic pathway when degradation occurs. The bacterium was grown in ONR7a medium, that was adjusted to a pH of 8.1, and 1% pyruvate; then it was processed by centrifugation and washing before experimentation began. Trials were conducted to iteratively refine the process and verify trial results. Bacterial growth …

Efficacy Of Monophasic And Biphasic Pulsed Field Ablation Waveforms: A Model Study, Natalia Dekock

Master's Theses

Cardiac arrhythmias are conditions where the heart’s normal sinus rhythm is interrupted by accelerated or premature rhythms. The most prevalent of these rhythms is atrial fibrillation (AF), where disorganized impulses cause the atria to quiver and pump blood inefficiently. As of 2025, AF affects over 10 million people. Aside from invasive surgical treatments, antiarrhythmic drugs, or one time cardioversions, atrial fibrillation is treated with catheter ablation. The longstanding ablation solutions for AF have been the cryoballoon or radiofrequency catheter ablation. However, limitations for these two ablation modalities are due to the nature of cell destruction; both thermal methods pose a …

Effect Of Foot Strike Pattern On Joint Kinetics On A Downhill Slope, Evan Manley

Master's Theses

With recent increases in participation in outdoor running events, there is a need for research in downhill gait biomechanics. One change that could impact joint loading is foot strike pattern. Foot strike patterns have been categorized into rearfoot-strike (RFS), midfoot-strike (MFS), and forefoot-strike (FFS) [1]. While 75-99% of distance runners naturally RFS on level surfaces, they tend to move towards FFS when it is necessary to reduce vertical loading conditions at the knee [1]. The purpose of this study was to examine differences in peak vertical knee and ankle forces, knee moment, and ankle power, as well as cumulative force …

Opensim Analysis Of The Aymara Indigenous People Performing Ancestral Tasks: Exploring Trends Of Muscle Activity With Tiwanaku Skeletal Indicators, Noah M. Taylor

Master's Theses

The Tiwanaku civilization (AD 500-1100) of the Andean highlands exhibited occupational specialization in communities, with archeological evidence suggesting the existence of labor- and residential-communities, or “taskscapes”, based on an individual’s livelihood. Prior bioarcheological studies have examined Tiwanaku skeletal remains for musculoskeletal stress markers, osteoarthritis, and cross-sectional geometry to infer activity patterns. Their descendants, the Aymara Indigenous people, currently live in the same highlands and until recently lived a lifestyle like their ancestors. Over the past 20 years, the global quinoa demand has risen, thrusting the Aymara into globalization and moving them away from the traditional tasks previously performed. This study …

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 …

A Manufacturing Process For Interdigitated Microelectrodes On Glass Wafers, Wyatt W. Warfield

Master's Theses

This study presents work done to optimize the process parameters to produce interdigitated electrodes on a borosilicate wafer. Using designed experiments and statistical analysis, the error in pattern transfer was minimized using for key process steps including exposure time, develop time and post exposure bake duration. Similarly, statistical analysis was used with profilometry data to fine tune the develop times. Qualitative analysis was used to assess thin film deposition. The resulting process produced wafers with improved pattern transfer and adequate film adhesion

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 …

Ambulatory Monitoring Of Biomarkers For Enhanced Recovery, Guneet Grewal, Grace Kurilo, Maggie Nostrand, Vismaya Panicker

Bioengineering Senior Theses

The objective of our project is to create, design and test a fully functional continuously monitoring hydrogen peroxide sensor. This sensor aims to identify early detection of diseases associated with oxidative stress which can include certain types of cancer, neurodivergent diseases and cardiovascular diseases. Early detection of hydrogen peroxide levels can provide patients with early treatment and can help reduce disease progression. Overall, the biosensor prioritizes early detection of ROS levels allowing various consumers such as healthcare sectors, patients, and research institutions to benefit from continuous monitoring for health management and disease prevention.

Emergency Bleeding Education Fixture, Nate Colley, Kennedy K. Austin

Biomedical Engineering: Graduate Reports and Projects

Despite the deadly nature and widespread occurrence of emergency bleeding events, there are currently no training devices or demonstrations which educate users on the urgency of these events and potential methods to address them. Additionally, current models often fail to replicate physiological conditions correctly. A fixture was created to demonstrate the urgency of hemorrhaging events and educate users on potential methods for treating hemorrhaging, namely tourniquets and pressure wraps. This fixture utilized gravity to replicate systolic blood pressure, a silicone model to replicate various adult leg sizes and correct tissue properties, and a tubing system with varying compliance to replicate …

Ray Collection: Forging A New Fashion Genre, Olivia R. Cooper

Graphic Communication

This senior project addresses a gap in the fashion industry by creating a new genre through a unique collection and comprehensive branding. The "RAY" collection draws inspiration from the designer's artistic roots and is a deeply personal homage to influential female artists like Frida Kahlo, Louise Bourgeois, and Leonora Carrington, whose works have inspired the designer's creative journey. Each piece in the collection draws direct inspiration from these artists, reflecting the creator's vision and self-expression, a key element of the streetwear genre incorporated into the designs.

The project also heavily emphasizes fashion branding, encompassing a logo, brand identity, social and …

Quantifying Harmful Trunk Postures: Inertial Sensor Analysis Of Trunk Angle To Support Low Back Pain Prevention, Elsa E. Bates

Master's Theses

Low back pain is a highly prevalent condition worldwide, impacting up to 80% of individuals at least once in their lifetime. A critical gap in current prevention strategies is the lack of tools to accurately measure trunk posture and movement in real-world environments. Accurate identification of biomechanical risk requires information about movement intensity, duration, and frequency, yet traditional assessment methods rely on self-reporting or visual observation, which are time-consuming and prone to error. To address this gap, a wearable monitoring method, consisting of two Inertial Measurement Units, was designed to quantify risk exposure to the spine by measuring angular position …

Electroporation Protocol Development For Cal Poly Cell Therapy Laboratory Courses, Gabrielle Melamed

Biomedical Engineering

Cancer is a heterogeneous disease caused by unchecked cell proliferation. The disease contributed to 9.7 million deaths worldwide in 2022, with hematological malignancies (leukemias, lymphomas, and myelomas) accounting for over 1.4 million deaths in the United States from 1999 to 2020. This thesis focuses on the treatment of these cancers, with an emphasis on non-Hodgkin lymphomas (NHLs). R-CHOP (Rituximab-Cyclophosphamide, Doxorubicin hydrochloride, Oncovin/Vincristine, and Prednisone) is the standard of care first-line treatment for diffuse large B-cell lymphoma (DLBCL), the most common subtype of NHL, and encompasses a mixture of chemotherapy, immunotherapy, and corticosteroids. The R-CHOP regimen cures 50% to 70% patients, …

Biofeedback For Upper Limb Bionics, Arissa Anaya, Adam Moger, Connor Bly, Theodore R. Hughes

Biomedical Engineering

The purpose of this document was to present a senior design project from Cal Poly sponsored by Matt Robinson at the Hanger Clinic in San Luis Obispo to provide biofeedback for users of upper limb protheses. This project focuses on individuals with trans-radial upper limb amputations, including patients with congenital limb deficiencies who use trans-radial prosthesis, who receive very little or no sensory feedback from their prosthetic device. This sensory feedback device was intended to be used as a training tool with a myo-electric hand-like upper limb prosthesis in a clinical setting. This document provides an overview of the different …

Hands-Free Balance Protocol And Development Of An Iphone App For Self-Assessment, Jacob Matties

Master's Theses

For many clinical populations, the measurement of balance is a critical task. Previous studies have agreed that smartphone IMUs provide a valid measure of balance that can be significantly correlated with force plate measurements and is sensitive enough to distinguish between various balance poses, but many balance assessment protocols require uncommon equipment or the use of hands during assessment. These limit accessibility of balance assessment. To eliminate the need for hands or any additional equipment, this study assessed the use of a smartphone recording the root mean square of 3D acceleration magnitude. The goal of the study was to determine …

Biostride - Prosthetic Charging Stand, Abigael Howard, Brett Matich, Allie Mcauliffe, Liam Harwood

Biomedical Engineering

This Final Report outlines the development of a lower limb prosthetic docking and charging station to address a critical need for individuals with unilateral transfemoral amputations who use microprocessor-controlled prosthetics. This project is focused on designing and producing a secure, accessible, and aesthetically pleasing stand to store and charge prosthetic limbs overnight, targeting the lack of commercially available, functional prosthetic storage. The absence of a functional storage solution points to a failure in meaningfully addressing the human needs of prosthetics users, exacerbating user frustration through the perpetuation of issues including prosthetics falling over into inaccessible positions, and tripping hazards due …

Force Mapping Wand For Individuals With Upper-Limb Amputations, Max Bosse, Cole Capitani, Eddie Grassini

Biomedical Engineering

Technology relating to upper-limb amputations has seen many advances in recent years, especially in terms of function and aesthetic appeal. Although these improvements exist, comfort is often a primary concern among prosthetic users and can lead to prosthetic abandonment [1]. Without a standardized method of measuring force concentrations in patients, high rates of discomfort and potential tissue damage remain. The goal of this project is to create a force mapping system for upper-limb amputees to help minimize discomfort in socket fit during the fitting process using real-time data and software to view force concentrations. To accomplish this goal, background research …

Intraoperative Dynamic Contrast-Enhanced Fluorescence Imaging For Navigating Open Orthopedic Surgeries, Yue Tang

Dartmouth College Ph.D Dissertations

Infection following trauma is one of the most prevalent and challenging complications faced by orthopedic surgeons. Inadequate tissue perfusion plays a critical role in this complication, as poorly perfused bone can be a nidus for bacterial biofilm formation and promote resistance to antibiotic treatments. Consequently, the management of open fractures and fracture-related infections relies on aggressive and thorough debridement to remove all poorly perfused bone. This thesis focuses on developing an indocyanine green (ICG)-based dynamic contrast-enhanced fluorescence imaging (DCE-FI) to objectively measure bone perfusion during open orthopedic surgeries and guide surgical debridement of devitalized bone.

Novel methodologies were developed to …