Biochemical and Biomolecular Engineering Commons^™

Multiscale Network Modeling Of Native And Modified Photosynthetic Light-Harvesting Complexes, Zane E. Armijo

Chemical and Biological Engineering ETDs

Photosynthetic light-harvesting complexes harvest solar energy and direct electronic excitations toward reaction centers with exceptional efficiency. This dissertation models the Fenna--Matthews--Olson complex of green sulfur bacteria, coupled to the PscA1 reaction center, as a chromophoric network. Forster resonance energy transfer theory, validated against numerically exact hierarchical equations of motion, was implemented in kinetic Monte Carlo simulations to resolve fine-grained excitation-transport pathways. The predicted charge-transfer efficiency of 77\% agrees with experiment, with the FMO2 monomer and its gateway pigment governing interfacial transfer. Systematic single, multi, and symmetry-preserving site removals, interpreted through Mobius inversion, identify critical pigments and show that cooperative effects …

Transformation Efficiency And Gfp Expression In E. Coli, Jessica H. Hobbs

Honors Theses

Genetic transformation of bacteria is a foundational technique in molecular biology and biotechnology, enabling the introduction and expression of foreign genes for research, industrial, and educational applications. This thesis investigates the transformation efficiency and green fluorescent protein (GFP) expression in Escherichia coli using the pGLO plasmid system, with the primary objective of supporting the development of a graduate-level laboratory course focused on bioprocess engineering and molecular biotechnology. The pGLO plasmid contains a GFP reporter gene regulated by an arabinose-inducible promoter and an ampicillin resistance gene that allows for selective growth of transformed cells. Competent E. coli HB101 K-12 cells were …

Cultivation Of Arthrospira Platensis (Spirulina) In Food-Based Industrial Wastewater For High-Yield Phycocyanin Extraction, Pavithira Sathinathan

Student Works (2020-2029)

Arthrospira platensis (Spirulina) is a filamentous cyanobacterium valued for its nutritional profile, particularly the pigment–protein phycocyanin, with potent antioxidant and anti-inflammatory properties. Despite its industrial significance, large-scale commercialization remains constrained by high cultivation costs and inefficient extraction methods. This study investigated the use of food-based industrial wastewater as an alternative nutrient medium for Spirulina cultivation, aiming to reduce production costs, enhance phycocyanin yield, and support sustainable wastewater remediation. Three types of food-based wastewater with different nutrient composition (WW1, WW2, WW3) was diluted with Kosaric medium (1:1) and used for Spirulina cultivation. The highest biomass concentration was achieved in WW2 (1.93 …

Isolated Bacillus Licheniformis Sp01 From Daqing Oilfield In Reducing Chromium(Iii) Crosslinked Polymer Residue And Enhancing Oil Recovery, Xiao Hui

Student Works (2020-2029)

After polymer gel formation, the residual partially hydrolyzed polyacrylamide (HPAM) and the crosslinker (Cr3+) caused plugging and decreased oil recovery. Microorganisms can degrade HPAM to address the issues, but Cr³⁺ inhibits the process and reduces oil recovery. This study explores the underexamined biodegradation of HPAM and improved oil recovery in the presence of Cr³⁺, offering new perspectives for microbial enhanced oil recovery (MEOR) after polymer gel formation. HPAM and crude oil were innovatively used as the sole nitrogen(N) and carbon(C) sources to isolate the best-growing strain from Daqing Oilfield produced water, identified as Bacillus licheniformis SP01. The oil displacement potential …

Analysis Of Sessile Drop And Captive Bubble Contact Angle Measurements On Metallic And Hydrophobic Surfaces, Jack H. Darnell

Williams Honors College, Honors Research Projects

Contact angle measurements are widely used to characterize surface wettability and determine changes in surface energy, yet the choice of measurement technique can significantly influence the results. This study compares the sessile drop and captive bubble methods for measuring contact angles of sodium dodecyl sulfate (SDS) solutions on carbon steel, stainless steel, and a hydrophobic wafer. Additionally, the time‑dependent wetting behavior of water, SDS, polysorbate 20 (commercial name Tween 20), and rhamnolipids on a hydrophobic wafer was evaluated over a five‑minute period. Results show that the sessile drop method consistently produced higher contact angles than the captive bubble method on …

C. Difficile Detection Method For First Responder Glove Application, Alli N. Senedak

Williams Honors College, Honors Research Projects

Clostridioides Difficile (C. diff) is a Anaerobic Gram-positive bacillus that is capable of spore formation, making it difficult to control its spread and duration in clinical environments. This phenomenon can provide danger to first responders, healthcare workers, and patients. The goal of this project is to create a biosensor capable of detecting C. diff in a clinical setting that can be applied to a glove apparatus. The project will involve the use of C. diff aptamers activated on the surface of an electrode. Once surface activation has been verified via surface analysis, the electrodes will be exposed to C. diff …

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 …

Calibration And Validation Of Cyclic Stretching Platform For Stiffness Testing Of Engineered Heart Tissue, Jillian Welsh

Chemical Engineering Undergraduate Honors Theses

Cardiac fibrosis (CF) is a major contributor to the high mortality rate of heart failure which affects over 23 million people worldwide. CF involves cardiac fibroblasts depositing extracellular matrix, made primarily of collagen type I, which stiffens the heart walls over time. As testing new drugs for CF is deterred by the high cost and time required for animal and clinical trials, this research helps to solve the problem by providing an in vitro platform to study fibrosis.

The work involved creating tissues containing human cardiac fibroblast (HCFB) cells. Spring testing was conducted to determine the force applied by the …

Purifying Circular Rna Therapeutics, Karen Guillen-Cuevas

All Dissertations

Circular RNA (circRNA) has emerged as a promising therapeutic modality due to its enhanced stability and resistance to exonuclease degradation compared with linear mRNA. However, its stability and functionality depend strongly on achieving high purity, and current methods such as size-exclusion chromatography suffer from peak overlap, low yields, and poor scalability. This dissertation addresses these limitations by developing ultrafiltration-based strategies to purify circRNA directly from in vitro transcription (IVT) and self-splicing (circularization) reactions. First, the feasibility of ultrafiltration was demonstrated using polyethersulfone membranes, where sieving coefficients and critical flux values of circRNA, precursor RNA, and nicked RNA were measured to …

Cultivation Of Botryococcus Braunii For The Production Of Hydrocarbons Suitable For Fuel Use, Bryan C. Carroll

All Theses

Energy security, rural poverty, and climate change are pressing issues of our time. Biofuels provide a solution to these issues, with a focus on sustainable aviation fuel, SAF, due to compatibility with aircraft infrastructure and energy density. This research aims to review and produce knowledge about a specific microalga, Botryococcus braunii, for its potential for SAF. First a literature review on the process was conducted followed by an experimental study on the impact of aqueous media and inorganic carbon its growth and hydrocarbon content. The literature review found the process consists of cultivation followed by lipid extraction or hydrothermal …

Impact Of Cysteine And Tyrosine Dipeptides On Cho Cell Performance In A Perfusion Mimic, Corrin L. Pruitt

All Theses

Perfusion cell cultures typically achieve higher cell densities and generate higher volumetric productivities than fed-batch cultures due to continuous nutrient supply and spent media removal. Despite these advantages, perfusion cell cultures remain underutilized for licensed product manufacturing, primarily due to the lack of small-scale perfusion models for high-throughput process development and the complexities involved in media formulation capable of supporting high cell densities during long-term continuous operation. To avoid nutrient limitation at high cell densities, current perfusion processes rely on using higher perfusion rates, which results in significant media wastage and downstream product dilution. Therefore, there has been an effort …

Interfacial Phenomena Of Plastics: From Surface Modifications To Environmental Impacts, Kennedy Guillot

LSU Doctoral Dissertations

Plastic is a ubiquitous part of everyday life since its introduction in the previous century. Global production continues to exponentially increase, establishing plastics as one of the most dominant materials in modern manufacturing. Within the scope of academia, plastic is essential due to its low cost and sterility, particularly for minimizing contamination. Beyond the laboratory, plastic use spans numerous industries, and its use and disposal has since raised many environmental concerns. Once valued for its durability, plastics now pollute the environment in landfills and natural ecosystems. In recent decades, the consequences of this pollution have been investigated, yet the full …

Adaptive Noise Estimation And Denoising With Deep Learning For Nmr Spectroscopy, Naveen Asokan

McKelvey School of Engineering Graduate Student Theses & Dissertations

Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful analytical technique widely used for molecular structure elucidation in chemistry, biology, and medicine. However, spectral accuracy is often degraded by noise—particularly in low acquisition time settings—resulting in reduced resolution and obscured chemical features. While traditional noise reduction techniques such as signal averaging can improve spectral quality, they require longer acquisition times, limiting their utility in real-time and high-throughput applications.

This thesis presents a deep learning-based denoising framework designed to enhance the quality of complex-valued NMR spectra. The proposed model, built upon a U-Net architecture, incorporates both real and imaginary components of the …

Binary Solid/Liquid Equilibrium Of Mixtures Of Thermally Robust Salts And Molecular Compounds For Use As Heat Transfer Fluids, Jared Ridge Mathews

Honors Theses

Fossil fuels, contributors to climate change that may bear catastrophic consequences, power the entire world. The human species is almost entirely dependent on fossil fuels for energy, but other sources of renewable and environmentally friendly energy must be developed. Concentrated solar power (CSP) is a promising source of renewable energy with hampered potential—better heat transfer fluids (HTFs) are needed for it to be economically feasible. Currently, the HTFs in industrial use are predominantly either synthetic oils or nitrate-based molten salts. Synthetic oils are only stable up to 400 °C, and molten salts often have high melting temperatures, making them prone …

Modeling Cell Buildup And Release In An Ultrafiltration Cartridge, Holiday B. Derosier

Chemical Engineering Undergraduate Honors Theses

While membrane filtration has improved greatly and has been incorporated into many modern practices, there isn’t much data on material exchange in and out of the lumen and how that effects the overall efficiency of the process. This data may help to accurately measure the reliability and efficiency of a filtration membrane system, which can lead to improvements in filtration sustainability, process lifespan, and product quality.

This project aims to model the material balance within a perfusion bioreactor ultrafiltration system in MATLAB, with a focus on bioreactors and cell buildup and release from the lumen. The results of this study …

Feasibility Of Liquid Carbon Sources For Algae Growth, Brady S. Jones

Chemical Engineering Undergraduate Honors Theses

This thesis explores the use of electrochemically produced aqueous bicarbonate as a novel liquid-phase carbon source for enhancing algal biomass productivity. Targeting the freshwater microalgae Chlorella Saccharophila, the study investigates its growth response to varying bicarbonate concentrations and compares the efficacy of liquid bicarbonate delivery with traditional gaseous CO₂ bubbling methods. Results demonstrate that Chlorella Saccharophila can sustain growth solely on bicarbonate, and that bicarbonate-fed cultures yielded higher biomass than those supplied with gaseous CO₂ or hybrid systems. These findings validate the potential of bicarbonate-based carbon delivery for scalable algae cultivation, offering key advantages such as gas-free operation, improved …

Composition And Rich/Lean Loading-Dependent Density Measurements Of A Series Of Aqueous Ionic Amines For Co2 Capture, Claudia Nguyen

Honors Theses

As climate change worsens worldwide, there is a drive to develop more efficient and sustainable methods to mitigate its impact through carbon capture methods like carbon dioxide scrubbing. Carbon scrubbing directly captures carbon dioxide (CO2) emissions from industries or power plants before they are released into the environment. The CO2 captured can be utilized for various applications or can be stored underground. However, this method faces numerous challenges, such as the degradation of the solvent or corrosion of equipment. As a result, research has expanded to find a better medium to overcome these issues. In particular, aqueous ionic amines (AIA) …

Development Of Translational Microscale Systems To Interrogate How Biophysical And Biochemical Cues Alter The Phenotype Of Hormone Positive Breast Cancer, Braulio Ortega Quesada

All Dissertations

Cancer is a complicated disease and one in every three diagnoses are women with breast cancer. Recent research shows that the progression of cancer depends strongly on interactions with other non-cancerous cells and non-cellular components. Metastasis, the spread of cancer to other parts of the body, is a key step in cancer progression and makes treatment harder, leading to poor response to treatments culminating in death in ~90% of patients. This dissertation focused on creating a series of microdevices as novel pre-clinical models of breast cancer. Two different devices were fabricated to (1) study how exposing cancer cells to the …

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 …

Quantifying The Effectiveness Of Rhamnolipid As A Biocide: Assessing Comparability Of A Modified Solution, Rosemary Sterling

Williams Honors College, Honors Research Projects

The CO2 induced corrosion of carbon steel in oil and gas pipelines, exacerbated by sulfate-reducing bacteria (SRB), poses a serious threat to infrastructure. This study evaluates the effectiveness of rhamnolipid (RhL), a biosurfactant, as a corrosion inhibitor and potential SRB biocide in simulated pipeline environments. Using a Postgate-C Modified Produced Water Simulant, which demonstrated electrochemical behavior comparable to industry-standard solutions while sustaining SRB, corrosion trials were conducted with and without RhL. Mass loss and electrochemical data revealed that RhL significantly reduced corrosion rates—by 85% on average and up to 99% instantaneously in a 4-day trial. Visual and analytical results from …

Magnetic Resonance Imaging Trackable Pathology-Triggered Polymersomes Toward Enzyme Replacement Theranostics For Gm1 Gangliosidosis, Dorian Foster

All Dissertations

This dissertation investigates the development and optimization of pathology-responsive polymersomes for simultaneous enhanced magnetic resonance imaging (MRI) and enzyme replacement therapy (ERT) in the treatment of GM1 gangliosidosis (GM1). While therapeutic strategies exist for similar, non-neuropathic lysosomal storage disorders, implementation towards GM1 faces significant challenges due to the blood-brain barrier.

Herein, we developed and characterized a range of low molecular weight hyaluronic acid-b-polylactic acid (HA-PLA) polymersomes (PSs) capable of encapsulating therapeutic enzymes in their hydrophilic core. These polymersomes exhibit pathophysiology-triggered responsiveness, degrading in the presence of acidic conditions, which is characteristic of lysosomes, and enzymes such as hexosaminidase A, which …

The Design And Implementation Of A Modular Tissue Engineering Test Bed To Pursue An Alternate Pathway Of Cell Culture Based Research, Ryley Patrick Griffin

Theses and Dissertations

The development of a Modular Automated Tissue Engineering Test Bed (MATETB) is the next step in the development of cheap and easily available in vitro cell regulatory systems for both academic and industrial purposes. This project outlined the framework and requirements for a device that could automatically regulate and collect data on a cell culture through the manipulation of its liquid environment. From this framework, a prototype was built. The device would fulfill cell culture needs while collecting data automatically and allowing for live viewing and imaging of cells. The device was comprised of a mechanical skeleton (MS), an environmental …

Biocargos: Capture And Release Gels For Room Temperature Cell Storage., Justin Jacobson

Electronic Theses and Dissertations

Currently, cryovials on dry ice or liquid nitrogen vapor transportation vessels are primary ways utilized to transport mammalian cells from one location to another. Due to the safety concerns of dry ice and liquid nitrogen, associated costly shipping charges, and limitations of proper packaging and labeling of materials, these conventional shipping techniques are unacceptable. It is urgent to develop a safe and environmentally friendly protocol to preserve and ship the biological samples from one place to another. In this research, a method was developed for an ecofriendly and safe protocol to preserve cancer cells. The cell viability of cell line …

Enhancing Ammonium And Bicarbonate Tolerance In Chlorella Sorokiniana Through Ems-Induced Mutagenesis, Wentao Yang

McKelvey School of Engineering Graduate Student Theses & Dissertations

This study explores the enhancement of ammonium and bicarbonate tolerance in Chlorella sorokiniana via EMS-induced mutagenesis, aimed at improving the microalgae's resilience and growth under high-stress conditions of elevated NH4+ and HCO3 concentrations. By mutating C. sorokiniana using EMS, we developed mutant strains capable of thriving in conditions that are inhibitory to the wild type strain. The successful adaptation of these strains demonstrates a significant increase in biomass production and tolerance to environmental stressors, highlighting the potential of EMS mutagenesis in industrial algal applications for sustainable biofuel production and environmental remediation.

Genetically-Encoded Optical Barcodes For Single-Cell Analysis, Daniel Pritko

All Theses

Cell barcodes are capable of being used to answer many different biological questions. They have been used to track the lineage of cells to identifying the function of a gene. While there are multiple different methods to creating cell barcodes, they are limited in their scalability and application. In a previous publication we propose and computationally prove an optical single-cell barcoding method that bridges fast and scalable readouts with the benefits of genetic encoding. In this approach fluorescent proteins (fps) are combined to form fluorescent barcodes that can then be analyzed using a spectral flow cytometer. Here, we test the …

Investigating The Detection And Transport Of Low Molecular Weight Species To Better Understand Their Impact On Disease Pathology And Treatment, Haley Michelle Duncan

Graduate Theses and Dissertations

Due to the drastic differences in the projects involved, this dissertation will be split into two sections: Alzheimer’s disease and chronic kidney disease. Each chapter will contain an introduction, materials and methods section, results and discussion, conclusions, and works cited section. The Alzheimer’s disease chapter will also have a supplemental figures section containing the polyacrylamide gels that were silver stained and quantified via ImageJ. The presence of elevated levels of amyloid beta oligomeric species in the brain has been related to the pathology of Alzheimer’s disease. As these oligomeric species are transient in nature, their kinetics pose a challenge to …

Fabrication And Characterization Of Lignin–Pva Hydrogels With Tunable Network Structures, Keturah Bethel

All Dissertations

The ability to directly tune the crosslinked network structure of hydrogels is crucial for their functional applications in various fields, such as water filtration, protein separation, and tissue engineering. By controlling the crosslink density of the hydrogel, one can directly alter the mesh size – i.e., the end-to-end distance between crosslink junctions – and, subsequently, directly alter the hydrogel performance. This work discusses the fabrication and characterization of soft composites containing the biopolymer, lignin, are discussed. Precisely, physically-crosslinked composite lignin–Poly(vinyl alcohol) (PVA) hydrogels were fabricated via the freeze-thaw (F/T) pathway, whereby solutions containing specified amounts of PVA and lignin were …

Analysis Of The Relationship Between Flow Patterns In The Post-Stenotic Region Of Model Arteries And Stenosis Severity., Michael Laroche

Electronic Theses and Dissertations

In this study, contour fields of mean age and turbulence kinetic energy (TKE) in the post-stenotic region of model arteries were analyzed to explore their correlation with FFR. While both high and low FFR cases exhibited similarities with an inner low-age region and an outer high-age region, low FFR cases displayed asymmetry in their low-age regions due to eccentric stenosis. Moreover, gradients of age across the artery diameter were more pronounced for low FFR cases. Additionally, low FFR cases demonstrated significantly higher TKE in the post-stenotic blood jet stream compared to high FFR cases that are reflected in low-age boundary …

Constant-Ph Molecular Dynamics At Inorganic Interfaces: Adding A New Dimension To Simulations Of Interfacial Phenomena., Ted Kalbfleisch

Electronic Theses and Dissertations

This dissertation explores the application of novel molecular dynamics simulation methods to better understand complex systems, with a particular focus on silica materials and protein interactions. Silica materials, known for their versatile surface and solution chemistries, play critical roles in catalysis, chromatography, and wastewater treatment. Despite their widespread use, the molecular-level interactions between silica surfaces and their environments remain poorly understood. To address this knowledge gap, we employed λ-dynamics enabled constant pH molecular dynamics to dynamically model protonation and deprotonation events on silica surfaces. Traditional experimental techniques such as x-ray crystallography, NMR, and cryo-EM are inadequate for probing structures in …

Fundamental Study Of Nonlinear Electrophoresis, Joseph Armakan Bentor

All Dissertations

Classical electrophoretic theory describes the linear response of particles suspended in Newtonian fluids under weak electric fields. When the electric field exceeds this weak limit, a nonlinear response arises due to non-uniform surface conduction over the curved particles. This nonlinear behavior introduces dependencies on fluid and particle properties not considered in the classical theory, offering potential advantages for microfluidic particle manipulation. While this phenomenon has been extensively studied theoretically and numerically in Newtonian fluids, experimental investigations have been relatively limited.

Fluid rheology can significantly alter particle dynamics under applied electric fields. Rheological properties like shear-thinning and elasticity which are not …