Biological Engineering Commons^™

Analyzing Microalgae-Bacteria Population Changes In Response To Environmental Parameters For Improved Wastewater Treatment, Amanda M. Moravek

All Graduate Theses and Dissertations, Fall 2023 to Present

Microalgae are incredible organisms that have a variety of uses such as wastewater treatment, fertilizer, livestock feed, and bio-compound production. Microalgae require a light source and minimal nutrients space to proliferate, making them an environmentally friendly and sustainable option for such processes. The Sustainable Wastes-to-Bioproducts Engineering Center at Utah State University is developing and implementing a Rotating Algae Biofilm Reactor (RABR) to remove total nitrogen and phosphorous from the Central Valley Wastewater Reclamation Facility wastewater effluent. Harmful compounds such as nitrates and phosphates are metabolized by the microalgae and converted into useful bioproducts, resulting in a circular economy. These RABRs …

Uv-A Light And Heat-Activated Antimicrobial And Biodegradable Materials For Food Packaging And Preservation, Michael J. Bodily

All Graduate Theses and Dissertations, Fall 2023 to Present

Current food packaging materials are often non-biodegradable and harmful for ingestion, which poses a threat to the environment and public health. Thus far, the dangers of microbial contamination of food on human health have outweighed the risks associated with using these conventional packaging plastics. A possible solution to these issues is to use a combination of innovative materials and microbial inactivation methods that can potentially both reduce plastic waste and combat harmful microorganisms. In this study, two antimicrobial, biodegradable composites were developed and tested for their ability to inactivate two types of bacterium, Escherichia coli K12 and Listeria innocua, …

Computationally Guided Liquid Crystal-Based Competitive Binding Sensing Platform For Optical Detection Of Spike Protein, Homa Ghaiedi, Shubham Pandey, Sophia Ezendu, Tibor Szilvasi, Karthik Nayani

Chemical Engineering Faculty Publications and Presentations

A liquid crystal (LC)-based sensing platform for the rapid optical detection of SARS-CoV-2 ' s spike protein's receptor binding domain (RBD) domain is introduced. This platform utilizes a thermotropic LC, hosted on metal-cation decorated substrates, onto which the spike protein can competitively bind. Density functional theory (DFT) calculations guide the experiments that reveal a homeotropic-to-planar transition in the LCs upon exposure to SARS-CoV-2 spike-decorated yeast, providing a basis for sensitive virus detection. The sensor's reversibility/specificity is confirmed through antibody-induced orientation recovery of the LCs initial orientation. Strikingly, the sensor can detect approximate to 2000 copies of the spike protein per …

Design Of A Teleoperabletendon-Driven Robotic Hand, Zachary Giese, Joseph Gober, Samuel Grisham, Avery Mahan, Aspen White, Brayden May, Aspen White

ATU Scholars Symposium

This work presents the design, implementation, and validation of a 3D-printed tendon-driven robotic hand with a bi-directional wireless control system. The robotic hand emulates human anatomical principles, focusing on replicating flexion and extension mechanisms of the metacarpophalangeal (MCP), proximal interphalangeal (PIP), and distal interphalangeal (DIP) joints via a tendon-pulley system. Iterative prototyping resolved initial challenges in joint stiffness, tendon routing, and servo interference, culminating in a design where a single servo drives both flexion and extension for each joint using a bidirectional tendon control mechanism. A reliable bidirectional wireless communication framework, using Arduino Nano Every microcontrollers and NRF24L01 modules, enables …

Enhanced And Interpretable Prediction Of Multiple Cancer Types Using A Stacking Ensemble Approach With Shap Analysis, Shahid Mohammad Ganie, Pijush Kanti Dutta Pramanik, Zhongming Zhao

Faculty, Staff and Student Publications

Background: Cancer is a leading cause of death worldwide, and its early detection is crucial for improving patient outcomes. This study aimed to develop and evaluate ensemble learning models, specifically stacking, for the accurate prediction of lung, breast, and cervical cancers using lifestyle and clinical data.

Methods: 12 base learners were trained on datasets for lung, breast, and cervical cancer. Stacking ensemble models were then developed using these base learners. The models were evaluated for accuracy, precision, recall, F1-score, AUC-ROC, MCC, and kappa. An explainable AI technique, SHAP, was used to interpret model predictions.

Results: The stacking …

Evaluating The Effects Of Oxidative Stress On Primary Retinal Pigment Epithelial Cells, Sophia Hessami

Student Research Symposium

Introduction

Age-Related Macular Degeneration (AMD) is the leading cause of vision loss worldwide, affecting 200 million adults over the age of 40

• Affects subretinal layers: retinal pigment epithelium (RPE), Bruch’s membrane, and choroid (Fig. 1)

Problem: Early mechanisms of AMD are not well understood; oxidative stress is often cited as a key contributing factor to the development of AMD.3 Current studies neglect to use primary RPE cells when investigating oxidative stress.

Oxidative Stress occurs when there is an imbalance between reactive oxygen species (ROS) production and cellular antioxidant defenses

• Overabundance of ROS results in damage to tissue and …

Effects Of Uv Radiation On Algae Biofilms Of Rotating Algae Biofilm Reactors, Rebecca Sweeten

Student Research Symposium

Goal: Discover effects of UV-A and UV-B radiation on the biofilm production of algae using a Rotating Algae Biofilm Reactor (RABR)

Method: Expose 3 RABRs in triplicate to UV-A, UV-B, and PAR to identify differences in biomass, nutrient uptake and pH levels.

Results: RABR’s under UV-B light have the highest productivity

Induction Of Diabetic Cardiomyopathy In A Three-Dimensional Myocardial Model, Maelyn Andreasen

Student Research Symposium

Diabetic cardiomyopathy: Impairs and damages heart tissue through chronic exposure to hyperglycemia, or high blood sugar, in diabetic individuals

The Effects Of The Action Rate And Binding Density On Sensitivity In Lateral Flow, Mona Soroush

Student Research Symposium

Lateral Flow Assays (LFAs) offer rapid diagnostics, yet sensitivity remains a critical limitation. This study used a mathematical framework—the Convection-Diffusion-Reaction (CDR) equation—to optimize sensitivity by adjusting parameters such as flow velocity (U), association and dissociation rates (k_on and k_off), and nanoparticle valency. Our simulation results closely matched literature data (Berli & Kler, 2016), demonstrating significant enhancements in sensitivity with optimized parameters.

Preparing A Bioreactor For Avian Cell Culture, Joshua Bell, Taylor Davis, Payton Larsen, Abbie Smith, Joshua Thompson

Student Research Symposium

This project, in collaboration with Upside Foods and Thermo Fisher, focuses on optimizing a 50L bioreactor for avian cell growth. Thermo Fisher has assembled the bioreactor while Upside Foods has provided design specifications and avian specific growth media.

Effects Of Inhibitor Diffusion And Threshold Limits On Edge Detection With Reaction-Diffusion Equations, Zachary Hastings

Student Research Symposium

The purpose of this project is to model edge detection using the Nomura et al's¹ reaction-diffusion equation. Edge detection is an important visual processing tool for human sight, allowing for object detection and visual enhancement. This project explored the effects of inhibitor diffusion, D_i, and threshold limits, a, on edge detection in this model. This project also discovered the limit of Nomura et al's¹ model on the simultaneous detection of multiple edges in a step-wise intensity gradient and attempted to overcome that limitation.

Utilizing Enzymatic Microalgae Hydrolysates For Cellular Agriculture, Maelyn Andreasen, Sophia Hessami, Eli Sheley, Elise Barton

Student Research Symposium

UPSIDE Foods is working to produce chicken products to address the growing global food insecurity crisis.¹ Industrial scalability is limited due to the requirements of cell culture. Through collaboration with the company, we are working to supplement their existing media to drive costs down and improve cell viability.

Mathematical Modeling Of Color Perception Using Differential Equation, Siavash Pooretemad

Student Research Symposium

Color perception begins in the retina, where three cone types (L, M, S) detect light and initiate neural signals. These signals are processed by horizontal and bipolar cells to form opponent color channels: red-green (RG), yellow-blue (YB), and light-dark (LD). Perception is not solely based on physical input but also shaped by neural adaptation and context.

This project models color perception using a differential equation approach, simulating how color contrast and adaptation emerge from interactions between photoreceptors and lateral inhibition.

We hypothesize that a system of differential equations can model how retinal cone cells respond to and process light intensity, …

Laparoscopic Articulating Arm: In Collaboration With The Xenocor Saberscope, Zac Hastings, Lizbeth Pugliese, Rebecca Sweeten, Dallin Thomas, Dallin Treasure-Areno

Student Research Symposium

• Laparoscopy a minimally invasive procedure performed through small incisions using a laparoscope, a camera-equipped instrument, along with specialized tools.

• Laparotomy or "open" surgery, requires a large incision to perform an abdominal operation.

Metabolite Analysis To Understand Factors Limiting Microbial Fermentation At High Substrate Concentrations, Bishal D. Sharma

Dartmouth College Ph.D Dissertations

Clostridium thermocellum, a thermophilic anaerobic bacterium, holds promise as a biocatalyst for conversion of lignocellulosic biomass into biofuels. This microbe has been subjected to various metabolic engineering strategies, including the deletion of genes encoding secondary fermentation products such as H₂, formate, acetate, and lactate, as well as the expression of heterologous genes to redirect carbon flux toward ethanol production. Despite these efforts, achieving economically viable ethanol titers remains a challenge. We hypothesized that studying how intracellular metabolite concentrations change as fermentation stops could reveal metabolic bottlenecks or regulatory mechanisms limiting ethanol production at high titers. However, metabolomics studies at …

Dataset: Compositional Analysis And Hydrothermal Liquefaction Of A High-Ash Microalgae Biofilm, Jacob Watkins, Hamza Abdellaoui, Elise Barton, Clayton Lords, Ronald C. Sims

Biological Engineering Student Research

This dataset contains biochemical composition data and hydrothermal liquefaction (HTL) yield results for a high-ash microalgae biofilm which was cultivated in effluent from a mesophilic anaerobic digester using polyethylene rotating algae biofilm reactors (RABRs). These data were originally collected for use in a techno-economic analysis of biocrude, biodiesel, and bioplastic production from algae that was cultivated using RABRs for municipal wastewater reclamation.

Biochemical data for the microalgae biomass includes bulk protein, measured both using the Bradford protein assay and by multiplying total N; carbohydrate content, measured using a 3-methyl-2-benzothiazolinone hydrazone / dithiothreitol (MBTH/DTT) assay; total lipid content, measured using a …

Stable Heteroclinic Channels As A Decision-Making Model: Overcoming Low Signal-To-Noise Ratio With Mutual Inhibition, Natasha A. Rouse

Faculty Scholarship

Bio-inspired robot controllers are becoming more complex as we strive to make them more robust to, and flexible in, noisy, real-world environments. A stable heteroclinic network (SHN) is a dynamical system that produces cyclical state transitions using noisy input. SHN-based robot controllers enable sensory input to be integrated at the phase-space level of the controller, thus simplifying sensor-integrated, robot control methods. In this work, we investigate the mechanism that drives branching state trajectories in SHNs. We liken the branching state trajectories to decision-splits imposed into the system, which opens the door for more sophisticated controls-all driven by sensory input. This …

Recent Developments In Heterologous Expression Of Cellulases Using The Pichia Pastoris Expression System: A Comprehensive Literature Review, Nazish Muzaffar, Abdur Raziq, Muhammad Waseem Khan, Niaz Muhammad Khan, Bushra Shahid, Anbareen Gul, Hayat Ullah

Biological Engineering Student Research

Cellulosic biomass is considered an important and sustainable source of renewable energy, which needs a complex mixture of different enzymes for its degradation. After amylase, cellulases are the second most important enzymes, gain more importance due to their broad range of applications at the industrial level, and are considered more economical and environmentally friendly; researchers have focused more on the production of cellulase with its higher expression rate and low cost. Pichia pastoris, a methylotrophic yeast strain, has a more effective and well-established system for the production of heterologous proteins, particularly for industrial enzymes. Moreover, its readily achievable high-density …

Strategies For Enhanced Meg Data Analysis In Clinical Practice And Emerging Frontiers, Pegah Askari

Bioengineering Dissertations - Archive

Epilepsy and dementia are debilitating neurological disorders that pose substantial challenges for patients, caregivers, and healthcare systems. Advances in magnetoencephalography (MEG) and signal processing offer new opportunities to improve diagnostic accuracy, surgical planning, and treatment monitoring. This dissertation presents a unified body of work comprising artifact removal, automated event detection, and deep learning-based biomarker discovery. These approaches collectively enhance the clinical utility of MEG for diverse patient populations.

The first study addresses a significant technical obstacle in the management of drug-resistant epilepsy. Patients receiving responsive neurostimulation (RNS) have historically been excluded from MEG as the data is contaminated by device-related …

Novel Electrophysiological Biomarkers In Pediatric Drug Resistant Epilepsy And Genetic Epilepsy Syndromes, Sakar Rijal

Bioengineering Dissertations - Archive

Pediatric epilepsies, particularly those that are drug-resistant or genetically driven, represent some of the most complex neurological disorders encountered in childhood. Central to their pathophysiology is a disruption in the delicate balance between cortical excitation and inhibition (E/I), often resulting from impaired GABAergic interneuron function. This imbalance manifests as aberrant network dynamics and altered neural oscillations, giving rise to seizures and long-term cognitive impairments. In this thesis, we developed a translational framework to identify electrophysiological biomarkers that (i) assess cortical E/I imbalance and (ii) map epileptogenic zones, with the aim of enhancing diagnosis, guiding surgical planning, and informing therapeutic monitoring …

Vendor-Independent B0 Shimming Framework With Application To Metabolic Mri In Human Gliomas, Mahrshi Jani

Bioengineering Dissertations - Archive

High and ultra-high field MRI and MRSI offer markedly improved signal-to-noise ratio and spectral dispersion, enabling in-vivo characterization of tumor metabolism with unprecedented detail. However, these benefits are tightly coupled to high demands on static magnetic field (B₀) homogeneity, particularly in the brain where susceptibility interfaces near the skull base and paranasal sinuses generate complex, higher-order field perturbations. In glioma patients, additional susceptibility variations arise from surgical cavities, hemorrhage, calcifications, and cystic components, further degrading B₀ homogeneity. As a result, shimming often become the main bottleneck limiting robust, whole-brain spectroscopic imaging and, consequently, our ability to map metabolic …

Simplified Molecular Diagnostics Methods For Environmental Testing Of Pathogens And Other Applications, Mohammad Dehghan Banadaki

Theses and Dissertations--Mechanical and Aerospace Engineering

Environmental Surveillance (ES) has emerged as a powerful tool to monitor the emergence and persistence of a pathogen within a facility or community using wastewater/water analysis. Over the past four years, implementation of ES has experienced an explosive acceleration, driven by efforts to monitor the spread of SARS-CoV-2, which has made ES a routinely used public health tool in many locations. We can now use ES to measure the emergence/presence/abundance of different viruses (e.g., SARS-CoV-2, influenza, mpox), bacteria (e.g., E. coli, V. cholerae, antibiotic-resistant strains), fungi (e.g., C. auris), and other biological markers indicative of infectious diseases. However, its broad …

Direct Numerical Simulation Of Pulsating Flow In Curved Pipes: Insights Into Aortic Dissection In Humans, Gokul Anugrah Gopakumar

Theses and Dissertations--Mechanical and Aerospace Engineering

This dissertation investigates the hemodynamics of pulsating blood flow in curved vessels through direct numerical simulations (DNS), with the overarching aim of uncovering fluid dynamic mechanisms linked to the onset and progression of aortic dissection in humans. The work is structured in two parts: (i) fundamental studies in idealized geometries and (ii) preliminary investigations in patient-specific anatomies. In the first part, curved pipe models representing the aortic arch are used to isolate the effects of pulsation frequency, amplitude ratio, and curvature ratio on transitional and turbulent flow dynamics. The simulations reveal that curvature-driven centrifugal forces shift the peak velocity toward …

Influence Of Agrochemical Mixtures On Nitrogen Transformations In Floating Treatment Wetlands, Matthew Russell

Theses and Dissertations--Biosystems and Agricultural Engineering

Controlling losses of nitrate-N from agricultural fields to ground and surface water environments is one of the most pressing water resources problems today. Increasing levels of nitrate-N pollution in surface and groundwater is a critical threat to human and environmental health across the globe. To mediate nitrate-N losses, natural and constructed wetlands have been increasingly used as nutrient mitigation technologies and strategies. The use of wetlands as a treatment approach for nitrogen in runoff is a common practice in agroecosystems, however, nitrate-N is not the sole constituent present in agricultural runoff, and other biologically active contaminants have the potential to …

Learning From Leads: A 1d Dilated Resnet For Ecg Chagas Disease Screening, Somesh Saini, Matheus Lima Diniz Araujo

Student Scholarship

No abstract provided.

The Bacteriostatic, Regenerative, And Immunomodulatory Properties Of Extracellular Matrix Particles For Lung Injury, Keera P. Rhoads

Theses and Dissertations

Acute respiratory distress syndrome (ARDS) is a prevalent, life-threatening lung condition, affecting nearly 200,000 Americans annually, with a 40% international mortality rate. There is no cure for ARDS, and current pharmacological treatments have limited effectiveness. Symptoms can be mitigated with mechanical ventilation, though this often leads to ventilator-induced lung injuries (VILI) and puts critically ill patients at risk of infections, including ventilator-associated pneumonia (VAP). A promising therapeutic is the extracellular matrix (ECM), a complex network of structural proteins and bioactive molecules that has been shown to have anti-inflammatory properties and prevent fibrosis. We aim to utilize the regenerative and immunomodulatory …

Design And Control Of Reversible Adhesion: Switchable Adhesive Molecules And Electrochemical Approaches, Kan Wang

Dissertations, Master's Theses and Master's Reports

Smart adhesives are materials that can reversibly gain or lose adhesion in response to external stimuli such as temperature, pH, electric fields, or light. Their switchable and temporary adhesion makes them highly promising for applications in wound healing, manufacturing, and robotic locomotion. Among them, catechol-based polymers have been widely studied for pH- and electro-responsive adhesion, due to their reversible non-covalent crosslinking. However, their performance is limited by irreversible covalent crosslinking reactions and the need for conductive surfaces in electrochemical systems. While boronic acid has been used to protect catechol, its reversibility remains limited. Therefore, new adhesive molecules and system designs …

Effects Of Invigorating And Relaxing Music On Heart Rate, Blood Pressure, And Heart Rate Variability, Matthew Joshua Faur

Honors Undergraduate Theses

Heart-rate variability (HRV) has been documented to correlate with several health measures, including autonomic nervous system longevity and athletic performance (Zulfiqar, 2010). While increasing age does not affect heart rate, there is a steady decline in HRV, which is a biological marker of aging and the decline of autonomic nervous system function. Furthermore, men who exercise regularly tend to have increased HRV, suggesting a mitigation of the typical age-dependent loss of HRV (Kristal-Boneh et al., 1995). Previous studies have suggested that music may have a physiological effect (e.g., fluctuating vitals, emotional changes) on cardiovascular parameters. However, little is known about …

Generation And Characterization Of Human Blood-Brain Barrier Models For Investigating Neuropsychiatric Disorders And Tumor Metastasis, Yunfei Li

Dissertations and Theses

The blood–brain barrier (BBB) is important in the normal function of the central nervous system (CNS). An altered BBB has been described in various neuropsychiatric disorders. The brain-specific microvascular endothelial cell (BMEC) is an essential structural component of the BBB. To test if integrity of the BBB formed by BMECs is compromised in 22q11.2 deletion syndrome (also called DiGeorge syndrome), which is one of the validated genetic risk factors for schizophrenia, a 2D iBBB (induced BBB) on a Transwell filter was generated from human microvascular endothelial cells (HBMECs) derived from the induced pluripotent stem cells (iPSCs) out of patients with …

Characterization Of Nanoplastic-Induced Exacerbation Of Asthmatic Pathophysiology In A Murine In Vivo Model, Keith Li

Theses and Dissertations

As global plastic production increases, so does the environmental and biological presence of nanoplastics (NPs), raising growing concerns about their potential impact on human health. These particles have been detected in various organs, including the lungs, yet their role in respiratory inflammation remains largely unexplored. Emerging evidence suggests that NP exposure may influence immune responses in the lungs, particularly in individuals with preexisting conditions such as asthma. However, the specific ways in which these particles interact with allergen driven inflammation are still unclear.

In this study, a murine model of allergic airway inflammation was used to investigate how surface modified …