Biomedical Engineering and Bioengineering Commons^™

Molecular Devolution For Gene Editing: Reverse Directed Evolution Of Cre Recombinase, Giovanna Esposito, Simran Sood, Katie Liu

Bioengineering Senior Theses

The principal objective of this paper is to provide a proof-of-concept of a novel protein engineering method called Molecular Devolution (MD). MD is an evolutionary protein engineering method that reduces the size of enzymes while retaining its functional properties. This paper outlines an MD protocol for Cre Recombinase. Cre Recombinase is an enzyme that is part of the Cre LoxP DNA Recombination System, which is a leading gene editing system widely used in genetic research. This paper outlines a MD approach that was used to miniaturize Cre Recombinase and remove unnecessary complexities, allowing for simpler and more e!cient use in …

A Point-Of-Care Hormone Monitoring Platform For Postpartum Health Assessment, Ava Mcdonald, Avary Torres, Frances Warneke

Bioengineering Senior Theses

Our point-of-care hormone monitoring device for postpartum health assessment uses paper-based microfluidics to provide an accessible and affordable hormone monitoring tool, tracking biomarkers correlated with postpartum depression (PPD). The device features a 3D-printed spring-box housing and platform containing chromatography paper testing sheets that are lined with polydimethulsiloxane (PDMS) and wax paper, embedded with specific reagents that generate colorimetric hormone readouts from saliva samples. This device was motivated by the need to address critical shortcomings in PPD care, where societal stigma surrounding mental health and reliance on self-reporting diagnostic methods prevent mothers from truthfully reporting symptoms and receiving timely support and …

Ai In Precision Medicine: Redefining Blindness Treatment Via Retinal Stem Cell Differentiation, Calissa Leong, Tiffany Nguyen

Interdisciplinary Design Senior Theses

Age Macular Degeneration (AMD) is currently the leading cause of blindness, driven by the degradation of Retinal Pigment Epithelial (RPE) cells. Stem-cell based therapies, particularly those involving induced pluripotent stem cells (iPSCs), typically consists of differentiating stem cells into RPE cells in vitro and transplanting them into the subretinal space. Our goal is to improve the accuracy of differentiation into RPE cells to better promote retinal regeneration. Traditional methods to alleviate symptoms of AMD is through therapeutic medications to slow disease progression, though stem cell therapy has emerged as a promising alternative. However, despite its potential, stem cell therapy presents …

Peridevice: A Packed Bed Reactor For Integrated Peritoneal Dialysis, Jake Wood, Gurtej Singh, Orion Cook, James Bell

Bioengineering Senior Theses

Chronic kidney disease affects approximately 800 million people worldwide, with more than 800,000 Americans living with end-stage kidney disease. Peritoneal dialysis provides patients with greater :flexibility and independence than traditional hemodialysis, but it is limited by the buildup of urea in the dialysate, which requires frequent fluid exchanges. Developing a system that continuously regenerates dialysate could help improve the efficacy of this treatment.

In this study, we developed the PeriDevice, a compact packed-bed reactor designed to remove urea from dialysate through enzymatic degradation. The 3D-printed device, using stereo lithography, filled with alginate microcapsules ( d = 1.5 mm) containing urease. …

Automated Optimization Of Membrane Bioreactor Performance Using Machine Learning, Janessa Cayabyab, Isabella Lopez, Oluwatomisin Opaleye, Jessica Stone

Bioengineering Senior Theses

Membrane bioreactors (MBRs) are increasingly employed in biomanufacturing due to their ability to produce high-quality effluent and support complex biological processes. However, membrane fouling remains a critical operational challenge, driving increased energy consumption, frequent cleaning cycles, elevated transmembrane pressure (TMP), and accelerated membrane degradation. Conventional operator-driven cleaning strategies are reactive by nature and insufficient for managing the dynamic, nonlinear fouling behavior characteristic of full-scale MBR systems.

This study presents a data-driven machine learning pipeline for predicting TMP and fouling behavior in an industry-scale MBR system, with the goal of optimizing cleaning schedules and extending membrane lifespan. A Random Forest regression …

Bio-Payload Senior Design Report, Connor Bishop, Oliver Goodall, Marcus Kirk, Gabby Robles, Anish Shanmuganathan

Interdisciplinary Design Senior Theses

This project focuses on the design and development of an autonomous experimental platform capable of conducting cellular biology experiments in a well plate within a CubeSat environment. The system integrates microfluidics, robotics, and onboard sensors to remotely initiate experiments, monitor them, and collect data without human intervention. The objective is to create a platform for automated biological experimentation in microgravity, while reducing reliance on ground-based control and increasing mission efficiency and reproducibility. The team used Saccharomyces cerevisiae to assess the biocompatibility of the well plate and monitor changes in cell culture, including optical density and cell viability.

Engineering Exosome Delivery Systems For Targeted Cancer Therapeutics, Gerardo Aguayo Quezada, Mahika Arya, Eduardo Noyola Mojarro

Bioengineering Senior Theses

Treatments for glioblastoma (GBM) are limited, mainly because the blood-brain barrier (BBB) prevents large molecules like chemotherapeutic drugs from reaching brain cells, and other methods like brain surgery are incredibly invasive. Brain surgery is useful for large masses of tumors, but the surgery can’t always remove the entire tumor, which is where radiation can be used, but only in limited quantities to prevent neural damage. To circumvent these gaps in modern medicine, exosomes, which are naturally secreted nanoparticles, offer an exciting way to deliver treatments to diseased cells. Exosomes biologically cross the BBB and transport materials between cells. In our …

Ambulatory Monitoring Of Biomarkers For Enhanced Recovery, Lucas Abrahamian, Gurman Dhami

Bioengineering Senior Theses

Oxidative stress, an imbalance of reactive oxygen species and antioxidants, serves as both a marker and progressor of several chronic and degenerative diseases. These conditions create a major global health burden, accounting for significant cost and deaths. The prevalence of oxidative stress–driven diseases highlights the need for improved strategies to detect the imbalance before irreversible damage occurs. However, despite its major role in disease progression, oxidative stress is typically assessed using static, invasive, or laboratory methods. These approaches are poorly suited for continuous monitoring and fail to serve high-risk groups, such as patients with a family history of disease or …

Development Of In Vitro Hydrogel Blood Clots, Xiomara Garcia, Jasmine Urbina, Sapna Wolf

Bioengineering Senior Theses

Deep Vein Thrombosis (DVT) affects up to almost one million individuals in the United States annually and can lead to life-threatening complications, such as a pulmonary embolism. DVT occurs when a thrombus composed of platelets and fibrin forms within deep veins, obstructing blood flow. Current treatments include anticoagulants, thrombolytics, inferior vena cava filters, and balloon catheter procedures. However, the development and testing of these medical devices heavily rely on animal blood models due to physiological similarities in coagulation, raising ethical concerns and limitations related to cost, scalability, and sustainability. This project proposes a synthetic, in vitro alternative using agarose and …

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 …

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 …

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.

Ai Diagnostic Tool For Covid-19 Severity, Hunter Lau, Ryan Lang, Aidan Furuhashi

Bioengineering Senior Theses

With the advent of COVID-19 pandemic global, healthcare systems were challenged with resource constraints plaguing hospital environments around the world with consequences that presented weaknesses in our healthcare system. This demonstrated the importance of triage in unprecedented scenarios. This project presents an integrated AI-driven diagnostic tool to predict the severity of COVID-19 cases using length of stay as an analog. By using clinical data and radiographic chest images, this project integrates a XGBoost clinical data model with a Convolutional Neural Network (CNN) model utilizing chest CT images to create a comprehensive assessment of patient case severity through predicted length of …

Bilateral Gait Trainer For Transtibial Amputees, Desmond Greer, Odinachi Anene, Andrew Wallace, Noah Hill

Bioengineering Senior Theses

Lower limb amputation affects over 2.3 million individuals in the U.S., with peripheral vascular disease and diabetes as leading causes. Prosthetic rehabilitation is critical for restoring mobility, yet barriers like therapist shortages, cost, and inconsistent at-home training limit patient outcomes. This thesis presents the design, development, and testing of a bilateral gait training device that addresses these challenges by providing real-time haptic feedback and quantitative gait metrics for at-home rehabilitation. The device integrates force-sensitive resistors embedded in insoles to monitor plantar pressure distribution, haptic actuators (eccentric rotating mass motors) mounted on thigh straps to deliver corrective feedback, and an Arduino-based …

In Vitro Hydrogel Blood Clots Phantoms, Ethan Evans

Bioengineering Master's Theses

This thesis presents a mechanical and microstructural characterization of agarose-based hydrogels as synthetic thrombus analogs for balloon catheter testing. Agarose gels ranging from 0.25% to 1.0% (w/v) were fabricated and analyzed using dynamic shear rheometry, capillary flow porometry, and gas pycnometry. Rheological data showed a nonlinear increase in storage modulus (G′), from 110 ± 66 Pa at 0.25% agarose to 4,900 ± 1,600 Pa at 1.0%, effectively mimicking the viscoelastic spectrum of acute to chronic thrombi. Gas pycnometry measurements indicated that true density (P_true) increased modestly from 1.03 g/mL to 1.13 g/mL over the same concentration range. This …

In-Vitro Hydrogel Blood Clots, Ethan Evans, Khoi-Austin Ngo

Bioengineering Senior Theses

Creating a sustainable, ethical, and affordable substitute for animal blood in balloon catheter testing for Deep Vein Thrombosis (DVT) is important to take into consideration. This research utilizes agarose and dextran to develop hydrogel-based artificial blood clots. These hydro gels replicate the mechanical characteristics of human thrombi across acute, subacute, and chronic stages through their elastic and viscous moduli (G' and G") and phase angles. This project addresses extant testing protocols, including temperature regulation, agarose processing, and well plate size, and suggests efficient approaches to encounter these problems.

The hydrogels were characterized by means of a thorough literature review and …

Packed-Bed Reactor For Integrated Peritoneal Dialysis, Julia Appleget, Ally Kwong, Megan Moglia

Bioengineering Senior Theses

Patients with chronic kidney disease (CKD) have lost kidney function. 800,000 Americans have end-stage kidney disease resulting in one of the leading causes of mortality cross-listed with diabetes and heart disease. Over the past decade, the percentage of patients using peritoneal dialysis (PD) has nearly doubled. PD which is a portable treatment involves the insertion of a catheter into the selectively permeable peritoneal cavity infused with a hyperosmolar dialysis fluid drawing the toxins from capillary beds of the peritoneum and into a gravity fed waste solution with a reported clearance of 87%. In order to improve the clearance of the …

Novel Nano-Binders Treating Alzheimer’S Disease, Katie Ching, Sophie Criscione

Bioengineering Senior Theses

The objective of our project is to engineer exosomes to be an effective therapeutic agent as a possible new treatment option for the neurodegenerative disease, Alzheimer’s Disease (AD). Among the various causes of AD, we are focusing on treating the pathogenesis linked to the build-up of amyloid-beta plaques in the brain, which disrupts neural connections and ultimately kills nerve cells. Currently, the most widely available treatment options for AD only provide symptomatic relief and targeting amyloid plaques in the brain is a promising new therapeutic approach in the field. Even the partial clearance of plaques could significantly improve the prognosis …

Skin Phantom Development For Electrophysiological Wearable Device Testing, Rohan Sodha, Kiet Vu, Jonathan Nguy

Bioengineering Senior Theses

This senior design project aimed to develop a skin phantom suitable for testing electrophysiological wearable devices. Our skin phantom consisted of a porous paper PDMS as the epithelial layer, initially paired with agarose gel as the tissue layer, and later with gelatin based on comparative analysis. Through rigorous experimentation and leveraging data from the IT’IS Foundation’s interactive database, we identified that gelatin exhibited superior electrical properties compared to agarose, making it a more effective medium for replicating human tissue. Our work not only validated the use of paper PDMS with both agarose and gelatin but also demonstrated that gelatin's lower …

Impact-Reducing Prosthetic Liner With Variable Volume & Integrated Haptic Feedback, Luke Brothers, Gigi Schaefer, Zoe Straughn

Bioengineering Senior Theses

Transtibial amputees face challenges such as loss of proprioception and fluctuations in the size and composition of their residual limb, which can compromise comfort and mobility. This project aims to create a transtibial impact-reducing liner combined with integrated haptic feedback to enhance comfort and restore proprioceptive senses. The impact-reducing liner includes impact reduction over pressure-intolerant regions, impact redistribution over pressure-tolerant regions, and a variable volume system that dynamically adjusts to changes in the residual limb’s volume throughout the day. The haptic feedback system employs force-sensitive resistors located on various regions of the prosthetic foot. These sensors transmit via Bluetooth to …

Dreamtemp: A Platform For Sleep Monitoring And Improvement, Michelle Lim, Kyle Pedersen, Will Cockrum

Interdisciplinary Design Senior Theses

With 70 million Americans suffering from chronic sleep disorders and only 7500 board-certified sleep physicians, a clear logistical problem exists that technological solutions may be able to address. The proliferation of IoT devices in homes and on our person presents a unique opportunity to improve sleep quality by leveraging the data they produce, and the control they provide to us over our everyday lives. DreamTemp is a platform for sleep monitoring and improvement that aims to improve an individual’s quality of sleep by dynamically adjusting the room temperature based on the user’s sleep cycle using a smart wearable and thermostat. …

Rhea Breast Pump: Implementation Of Biomimicry Technology, Harper Daniels, Leanne James, Laini Reynolds, Courtney Rowe, Julia Yaklich

Interdisciplinary Design Senior Theses

Rhea Breast Pump is an innovative breast pump that implements biomimicry informed technology for a more efficient and comfortable breastfeeding experience. Our design implements a tongue actuator in conjunction with vacuum to mimic the suckling motion of a baby’s mouth, a heating element for pain alleviation, and a soft flange to maximize comfort. The development of this device is motivated by the goal of empowering women, specifically nursing mothers, to maintain their independence and individuality while raising a family. Our team, consisting of all female engineers, strongly believes in and supports the notion that women can and should have the …

Screening Of Microorganism Mutations Using Microbial Fuel Cell Activity, Grant Gini, Joshua Chansky

Bioengineering Senior Theses

Microbial fuel cells (MFC) are a rapidly growing field of interest with potential for clean energy production, effluent/waste capture and purification. Drawbacks associated with MFCs is the short duration of the peak current, discouraging integration into emerging nanogrids, as well as the operational cost associated with the infrastructure, offsetting the net cost of power generation. With the objective of quantifying the success of genetic mutations using the MFC to address the above-mentioned problem-solving opportunities, the following specific aims were formulated in this study: 1) To measure current as a metric for growth/catalytic activity for microencapsulated microorganisms, and, 2) To optimize …

Microneedles For Wound Healing, Maya Matheny, Maggie Dubus, Lily Eribes

Bioengineering Senior Theses

Microneedles are a virtually painless and minimally invasive transdermal delivery system comprised of an array of micron-sized needles that can be used to deliver cells, drugs, proteins, and vaccines. However, a major challenge to this delivery method is controlling puncture depth. To advance the microneedle landscape, our project aims to identify and characterize the biomechanical cues between a microneedle puncture and a hydrogel skin phantom for pre-clinical testing A stopper microneedle design that controlled puncture depth into the phantom skin model patch to 150μm was tested on millimeter-thick mold-casted alginate slabs. The hysteresis loop differs in the presence and absence …

Thermometer Servo Loop For Actuating Marine Permaculture, Anna Gabriele, Connor Grady, Jeremiah Rufus, Illan Vargas

Interdisciplinary Design Senior Theses

This project aimed to develop a system to improve the Climate Foundation’s (CF) existing Marine Permaculture (MP) technology in the Philippines. MP is the cultivation of seaweeds and other macroalgae on submerged structures in offshore ocean waters to support food security, carbon sequestration, ecosystem restoration, and more. Current MP arrays feature a circular platform with substrate for seaweeds to grow on, manually raised and lowered by a winch on the above-surface control platform. The team designed the system to provide real-time temperature and pressure data sensing at depth, real-time platform-to-surface data transfer, real-time winch actuation, and data storage. The team …

Neurogen: Eeg And Near-Infrared Light Stimulation Control System, Arnold Nieto, Jaylinn Solis, Matthew Tamanaha

Interdisciplinary Design Senior Theses

Light stimulation or transcranial photobiomodulation (tPBM) therapy has been shown to be effective when treating patients suffering neurodegenerative diseases such as Alzheimer’s and Parkinson’s disease. While there is currently no cure, light stimulation can help alleviate symptoms for those patient’s suffering from these diseases. With this in mind, the senior design team from last year began a prototype hybrid electroencephalography (EEG) and tPBM device. They implemented a specific wavelength of 810 nanometer (nm) near-infrared (NIR) light emitting diodes (LEDs), with a 16 channel EEG headset from OpenBCI. The device was intended to serve as a potential research tool, with a …

Minimally Invasive 3d Printed Microneedles For Glucose Monitoring, Eduardo Quintero, Justin Wong

Bioengineering Senior Theses

Continuous glucose monitoring (CGM) provides an instantaneous real-time display of glucose level, rate of change of glucose, alerts, and alarms for actual or impending hypo- and hyperglycemia. Continuous glucose monitors are able to stay implanted on the patient anywhere from 7-14 days, giving patients and doctors valuable information to help improve patient care for diabetics, and providing them with a way to continuously monitor their blood glucose level concentration throughout the day.

Conventional methods of glucose detection such as blood glucose meters require the patient to gather frequent blood samples to generate instantaneous results that are only accurate as of …

Towards Targeted Delivery To Cns Neurons By Conquering The Bbb, David G.A. Bengford

Bioengineering Master's Theses

Brain cancer treatments have long been restricted by the blood-brain barrier (BBB). Semi-permeable in the most selective way, this barrier may be crossed by one of three methods: membrane integrity disruption, passive transport, or active transport. The third option offers the opportunity for many medically relevant cargoes, such as proteins and nucleic acids, to be shuttled into the brain. The concept of a therapeutic “Trojan horse” builds on this capability by employing engineered nanovesicles—in this work, engineered exosomes—whose surfaces are studded with ligands functioning as the keys to crossing the BBB. Exosomes are a powerful methodology for this approach because …

Immuno-Anti-Infective Drug Design Using Bioai, Cathy Chen, Vivian Zhang

Bioengineering Senior Theses

According to the World Health Organization, antibiotic resistance is one of the biggest threats to global health, food security, and development today. A growing number of infections, like Methicillin-resistant Staphylococcus aureus, are becoming harder to treat as the antibiotics used to treat them become less effective. As a result, the primary concern for infections in the hospital setting is due to the S. aureus’s growing resistance to antibiotics. Therefore, in response to this global health threat, our project focuses on furthering the research in developing a drug that S. aureus will not develop resistance to. In this paper, we assess …