Biochemical and Biomolecular Engineering Commons^™

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 …

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 …

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 …

Design And Development Of Uio-67-Coated Pim-1-Based Composites And Demonstration Of Their Detoxification Performance, Sukanta K. Mondal, Peter O. Aina, Ali A. Rownaghi, Fateme Rezaei

Chemical and Biochemical Engineering Faculty Research & Creative Works

Polymer-supported MOF composites have emerged as versatile candidates for various separation and catalytic applications. In this study, we demonstrate design and development of UiO-67-coated Ce(OH)₄@PIM-1 composites via dip-coating, drop-casting, solid-phase coating, and supramolecular assembly, and assess their preparation-structure-performance relations. The catalytic performance of the composites was investigated through hydrolysis of dimethyl 4-nitrophenyl phosphate (DMNP), as a nerve agent simulant. The findings revealed that while dip-coating method was unable to achieve a thick and uniform coverage of the MOF layer on the Ce(OH)₄@PIM-1, the supramolecular assembly gave rise to 16 wt.% MOF loading and the composite prepared …

Examination And Improvement Of The Taguchi-Based Nanofluids Impact On Co2 Absorption Using Al2o3 Nanoparticles, Safa Waleed Shakir, Saif Saleh Hussein, Shaymaa Hasan Khazaal, Hyder Akram Al-Naseri, Ahmed Mohammed Ahmed, Rana Najah Hachim, Muthanna Hikmat Al-Dahhan

Chemical and Biochemical Engineering Faculty Research & Creative Works

In this study, a batch absorption reactor was used to evaluate the nanofluid of a binary aqueous solution of monoethanolamine and 2-amino-2-methyl-1-propanol (MEA/AMP) with nanoparticles of aluminium oxide (Al₂O₃) as a solvent used to remove carbon dioxide (CO₂) from simulated flue gas. Furthermore, the application of the Taguchi experiment design method determined the optimal conditions for the absorption process. This research focuses on the CO₂ absorption process and the optimal conditions related to nanoparticle addition. The main effects of using nanofluid were investigated. The concentration of nanoparticles, nanoparticle size, and stirrer speeds were …

Meteorological Data Mining And Synthesis For Supplementing On-Site Data For Regulatory Compliance, Ben Sonpon, Shoaib Usman, Joseph Smith, Sarah Kovaleski, Jason Wibbenmeyer

Nuclear Engineering and Radiation Science Faculty Research & Creative Works

Many regulatory requirements add significant delay in the licensing of new nuclear power stations. One area of particular interest is the environmental impact of potential atmospheric release. The purpose of this research is to demonstrate effectiveness of meteorological data mining and synthesis from offsite locations to reduce need for onsite data, hence allowing rapid licensing. The automated procedures tested for data mining and extraction of meteorological data from multiple offsite sources and the data analytic tool developed for data fusion are presented here. Three important meteorological parameters from regulatory compliance are considered for this analysis: wind velocity, wind direction, and …

Determination Of Binary Co2/H2 Adsorption Isotherms And Kinetics Over Porous Organic Cage Cc3 Via Zero-Length Column Technique, Jimmy D.L. Moreno, Kyle Newport, Ali A. Rownaghi, Fateme Rezaei

Chemical and Biochemical Engineering Faculty Research & Creative Works

Understanding the dynamics of mixed-gas adsorption is essential for industrial-scale adsorptive separations. Also, obtaining binary adsorption isotherms is essential to gain a better understanding of adsorbate-adsorbent interactions in multicomponent gas mixtures. Porous organic cages (POCs) are highly porous, crystalline materials, with a small average pore window that make them promising candidates for separation applications. In this work, we utilized zero-length column (ZLC) technique to not only determine the kinetics of CO₂/H₂ separation over CC3 but also obtain the binary adsorption isotherms. The ultra crystalline diffusivities of 1.49 x 10^–4 and 8.31 x 10^–5 cm^{2 …}

Dynamic Metabolic Flux Analysis Amidst Data Variability: Sphingolipid Biosynthesis Case Study In Arabidopsis Thaliana Cell Cultures, Abraham Boluwatife Osinuga

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Sphingolipids are pivotal for plant development and stress responses. Growing interest has been directed towards fully comprehending the regulatory mechanisms of the sphingolipid pathway. In this study, we explore its de novo biosynthesis and homeostasis in Arabidopsis thaliana cell cultures, shedding light on fundamental metabolic mechanisms. Employing ¹⁵N isotope labeling and quantitative dynamic modeling approach, we obtained data with notable variations and developed a regularized and constraint-based Dynamic Metabolic Flux Analysis (r-DMFA) framework to predict metabolic shifts due to enzymatic changes. Our analysis revealed key enzymes such as sphingoid-base hydroxylase (SBH) and long-chain-base kinase …

Induction Vacuum Swing Adsorption Over Magnetic Sorbent Monoliths And Extrudates For Ethylene/Ethane Separation, Khaled Baamran, Usman Shareef, Fateme Rezaei

Chemical and Biochemical Engineering Faculty Research & Creative Works

Electrification of adsorption processes is emerging as an adaptable solution for future gas separations. This study develops magnetic sorbent structures for use in induction vacuum swing adsorption (IVSA) process specifically designed for olefin/paraffin separation. Two sorbents, namely Fe₃O₄/ZIF-7 (ethane-selective) and Fe₃O₄/13X (ethylene-selective) were developed and formulated into extrudates (Fe₂₀/ZIF-7-P) and monoliths (Fe₂₀/13X-M), and tested under different regeneration scenarios, including simultaneous and subsequent induction-evacuation, induction only, and evacuation only. The dynamic adsorption results demonstrated that regeneration under subsequent induction-evacuation improves desorption rate and capability. Under this regeneration scenario, Fe …

Emulsion Liquid Membrane (Elm) Enhanced By Nanoparticles And Ionic Liquid For Extracting Vanadium Ions From Wastewater, Qusay Al-Obaidi, Nora Yehia Selem, Muthanna H. Al-Dahhan

Chemical and Biochemical Engineering Faculty Research & Creative Works

Emulsion liquid membrane (ELM) stands out as an extraction process that has drawn much attention due to its promising prospects in industrial wastewater treatment technology. Nevertheless, the pivotal challenge is to reach high membrane stability to overcome the obstacle of applying ELM at the industrial scale. In this study, ELM was boosted by using nanoparticles (superparamagnetic iron oxide (Fe₂O₃)) in the stripping phase (W1) and ionic liquid (1-methyl-3-octyl-imidazolium-hexafluorophosphate [OMIM][PF6) in the oil phase (O) for recovering/extracting vanadium from synthetic wastewater to near completion and at the same time enhancing emulsion stability to be appropriate for industrial …

Optimizing The Expression Of Polyethylene Terephtalate Hydrolase-Encoding Synthetic Gene In Escherichia Coli Arctic Express (De3), Jocelyn Nataniel, Maria Ulfah, Dini Achnafani, Niknik Nurhayati, Gabriela Christy Sabbathini, Sri Rezeki Wulandari, Abinawanto Abinawanto, Is Helianti

Makara Journal of Science

The waste of polyethylene terephthalate (PET) plastic waste in Indonesia is a pressing concern due to its slow degradation and potential environmental damage. One promising solution is to utilize polyethylene terephthalate hydrolase from Ideonella sakaiensis (IsPETase), an enzyme that specifically degrades PET. However, inducing the expression of IsPETase synthetic gene in Escherichia coli BL21 (DE3) has been challenging because much of it remains insoluble. This study aimed to express IsPETase in E. coli Arctic Express (DE3) and optimize the conditions to enhance its production. First, pET22b(+)pelB-IsPETase was inserted into E. coli Arctic Express (DE3). The …

A New Design Strategy For Sizes Of Polymer Gel Treatments Derived From A Comprehensive Assessment Of Their Case Histories, Munqith Aldhaheri, Abdullah Almansour, Na Zhang, Mingzhen Wei, Baojun Bai

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

The incentive to revive brownfield oil production extends the interest to apply polymer gel treatments in injection wells. Virtually, volumes of previous remediations implemented in similar reservoir types are used to size new jobs. Such an analogy-based design procedure imposes a need to evaluate the most frequent designs for each reservoir type based on a comprehensive field survey. This survey provides a new treatment sizing strategy for polyacrylamide-polymer bulk gels by reviewing their field applications in 653 injection wells. The new strategy proposes using the average and most frequent gel volumes per reservoir type as an initial estimate of the …

A New Design Strategy For Sizes Of Polymer Gel Treatments Derived From A Comprehensive Assessment Of Their Case Histories, Munqith Aldhaheri, Abdullah Almansour, Na Zhang, Mingzhen Wei, Baojun Bai

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

The incentive to revive brownfield oil production extends the interest to apply polymer gel treatments in injection wells. Virtually, volumes of previous remediations implemented in similar reservoir types are used to size new jobs. Such an analogy-Based design procedure imposes a need to evaluate the most frequent designs for each reservoir type based on a comprehensive field survey. This survey provides a new treatment sizing strategy for polyacrylamide-polymer bulk gels by reviewing their field applications in 653 injection wells. the new strategy proposes using the average and most frequent gel volumes per reservoir type as an initial estimate of the …

Experimental Investigation Of Liquid Holdup In A Co-Current Gas–Liquid Upflow Moving Packed Bed Reactor With Porous Catalyst Using Gamma-Ray Densitometry, Ali Toukan, Ahmed Jasim, Vineet Alexander, Hamza Albazzaz, Muthanna H. Al-Dahhan

Chemical and Biochemical Engineering Faculty Research & Creative Works

This study explores the dynamics of liquid holdup in a lab-scale co-current two-phase up flow moving packed bed reactor, specifically examining how superficial gas velocity influences the line average external liquid holdup at a fixed superficial liquid velocity. Utilizing gamma-ray densitometry (GRD) for precise measurements, this research extends to determining line average internal porosity within catalyst particles. Conducted with an air–water system within a bed packed with 3 mm porous particles, the study presents a novel methodology using Beer–Lambert's law to calculate liquid, gas, and solid holdups and catalyst porosity that is equivalent to the internal liquid holdup that fills …

Targeted Drug Delivery: Investigating Protein Corona Behavior, Atharva Markale

Theses

Due to high specificity and less toxicity, nanoparticles have become promising for targeted drug delivery against cancer, although they face challenges when they enter the bloodstream, making their behavior unpredictable. The deposition of proteins on nanoparticles, the protein corona, changes their biosignature, affecting their circulation, drug release potency, targeting ability, and immunogenicity. The continuous exchange of protein layers on a nanoscale is complex to analyze.

Nanoparticle tracking analysis (NTA) is a method to characterize nanoparticles in blood plasma by combining principles of light scattering microscopy and Brownian motion. In this work, time-dependent experiments with plasma were conducted to analyze the …

Kinetic Studies Of Liquid Phase Hydrogenation Of Acetylene For Ethylene Production Using A Selective Solvent Over A Commercial Palladium/Alumina Catalyst, Humayun Shariff, Muthanna H. Al-Dahhan

Chemical and Biochemical Engineering Faculty Research & Creative Works

The Kinetics of Selective Hydrogenation of Acetylene in the Liquid Phase over a Commercial 0.5 Wt % Pd/Al2O3 Spherical Catalyst Was Investigated in a Stirred-Tank Basket Reactor. the Liquid Phase Was Acetylene Gas Absorbed in a Selective Solvent, N-Methylpyrrolidone (NMP). the Reactor Was Operated at a Pressure Range of 15-250 Psig with Temperature Varying from 60 to 100 °C using Different Catalyst Loadings to Identify the Suitable Operating Conditions. the Kinetic Experiments Were Conducted in the Absence of External Mass Transfer Resistances with the Liquid Phase in Batch Mode and the Gas Phase Being Continuous. the Initial Rates Varied Linearly …

Development Of Agar-Based Preformed Particle Gel For Water Control In High-Salinity Reservoirs, Ahmed Ben Ali, Reem Elaf, Abdulaziz A. Almakimi, Mohammed Saad, Ibnelwaleed A. Hussein, Baojun Bai

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

Oil Extraction Faces Challenges in Cost and Complexity Due to Excessive Water Production, Leading to Diminished Hydrocarbon Recovery. Preformed Particle Gels (PPGs) Hold Promise for Enhancing Oil Recovery and Sealing High-Permeability or Fractured Zones. However, Current PPGs Encounter Limitations in High-Temperature Reservoirs, Including Salt Sensitivity and Potential Hazards. to Address These Issues, We Propose Eco-Friendly PPGs Utilizing Agar Polysaccharides. Agar Backbones Grafted with Acrylamide (AM) and AM/N,N′-Methylenebis(AM) (MBA) Via Microwave-Assisted Techniques Resulted in Polyacrylamide Grafted Agar (Ag/PAM) and Cross-Linked Polyacrylamide Grafted Agar (Ag/PAMBA). Various Sizes (75 Μm to 1.18 Mm) Were Prepared to Accommodate Diverse Reservoir Porosities and Ensure Effective …