Engineering Commons^™

Computational Modeling Of Biochemical Systems Using Cellular Automata, Advait Apte

Theses and Dissertations

Biological systems exhibit complex behaviors through coordinated responses of individual biological components. With the advent of genome-scale techniques, one focus has been to develop methods to model interactions between components to accurately describe intact system function. Mathematical modeling techniques such as constraint-based modeling, agent-based modeling, cellular automata (CA) modeling and differential equation modeling are employed as computational tools to study biological phenomenon. We have shown that cellular automata simulations can be used as a computational tool for 12 predicting the dynamics of biological systems with stochastic behavior. The basic premise for the research was the observations made during a study …

Investigation Of The Mechanical Properties Of Poly (Ethylene Glycol) Diacrylate By Nanoindentation Using Atomic Force Microscopy, Zouheir Drira

Theses and Dissertations

Poly (ethylene glycol) (PEG) hydrogel based polymers are among the most widely used synthetic materials for biomedical applications. Because of their biocompatibility, and ease of fabrication, hydrogels are highly suitable for use as constructs to engineer tissues as well as for cell transplantation. A critical parameter of importance for PEG hydrogels is their mechanical properties which are highly dependent on the environmental conditions. Properties of PEG-based hydrogels can be engineered to resemble scaffolds composed of extracellular matrix molecules, which provide structural support, adhesive sites and mechanical as well as biomechanical signals to most cells. The mechanical properties of these synthetic …

Prediction Of Fluid Viscosity Through Transient Molecular Dynamic Simulations, Jason Christopher Thomas

Theses and Dissertations

A novel method of calculating viscosity from molecular dynamics simulations is developed, benchmarked, and tested. The technique is a transient method which has the potential to reduce CPU requirements for many conditions. An initial sinusoidal velocity profile is overlaid upon the peculiar velocities of the individual molecules in an equilibrated simulation. The transient relaxation of this initial velocity profile is then compared to the corresponding analytical solution of the momentum equation by adjusting the viscosity-related parameters in the constitutive equation that relate the shear rate to the stress tensor. The newly developed Transient Molecular Dynamics (TMD) method was tested for …

Studies Of Coal Nitrogen Release Chemistry For Oxyfuel Combustion And Chemical Additives, John M. Sowa

Theses and Dissertations

Pollution is one of the greatest concerns with pulverized coal combustion. With tightening standards on pollution emissions, more information is needed to create better design models. Burner modifications are the most efficient changes that can be made to assure sufficient carbon burnout and low NOx emissions. Experiments were performed in the BYU Flat Flame Burner (FFB) lab, operating under fuel rich conditions for pyrolysis experiments and fuel lean conditions for char oxidation experiments. Effects of temperature, coal rank, residence time, and post flame oxygen content on mass release, nitrogen release, and reactivity were examined. Elemental and Inductively coupled plasma (ICP) …

Dilute Sulfuric Acid Pretreatment Of Switchgrass In Microwave Reactor For Biofuel Conversion: An Investigation Of Yields, Kinetics,, Oscar Martin

Theses and Dissertations

Lignocellulosic materials provide a raw material source for biofuel conversion and offer several advantages over fossil fuels- usage of a renewable resource, reduced greenhouse emissions, a decreased dependence on foreign oil, and stimulation of the agricultural sector. However, a primary technological challenge in converting lignocellulosic biomass into fuel is overcoming the recalcitrance of its matrix to enzymatic hydrolysis. To overcome these problems for chemical processing, naturally occurring cellulose biomass must be pretreated before it can be further processed using enzymatic hydrolysis or bioconversion. The goal of this work was to develop a model that predicts the glucose yield (pretreatment and …

Optimizing The Release And Methylation Of Bacterial Endospore Dipicolinic Acid, Aaron N. Nackos

Theses and Dissertations

Rapid, portable detection of biological threat agents such as Bacillus anthracis endospores (“spores”) is extremely important given the real and perceived threats of bioterrorism. Gas chromatography-mass spectrometry (GC-MS) is an excellent general means for chemical detection, although special sample preparation and specialized equipment are required to employ GC-MS for detecting biological agents such as spores in the field. A GC sample introduction probe consisting of a helical wire that can be retracted inside a syringe needle, called a coiled wire filament (CWF), was employed as a simple, passively-heated means to introduce the mixture of spores plus reagents for thermochemolysis methylation …

The Extraction Of Cytochrome C And Dsred2 Into Reverse Micelles, Michelle Baker

Theses and Dissertations

Cytochrome c and DsRed2 were successfully extracted into reverse micelles by the contacting of an aqueous protein-containing phase with an organic phase. Two important properties that differentiate the extraction profiles of these proteins are pI and size. Cytochrome c is a relatively small, monomeric protein with a pI of 10.6. It was easily extracted into reverse micelles with the anionic surfactant AOT. DsRed2, however, is a large tetramer with a p1 of 6.3. It could not be extracted into AOT, but was extracted with the cationic surfactant CTAB, and with a wider error range than cytochrome c. CD data indicate …

Controlled Release Of Fluoride From Poly(Ethylene-Co-Vinyl Acetate) Films, Shadeed Khan

Theses and Dissertations

The development of aesthetically unattractive white spots is a concern for patients undergoing fixed orthodontic treatment. Due to poor oral hygiene during treatment, accumulation of plaque around orthodontic brackets causes bacterial fermentation reactions producing acids that dissolve the mineral enamel. Such dissolution results in white spot formation, an early sign of dental caries. In principal, to inhibit the appearance of these spots during treatment, fluoridated elastomeric o-rings might be employed. Once placed around brackets, these o-rings should release fluoride therapeutically for at least 30 days, after which the orthodontist may replace them. At the present time, such fluoride-releasing o-rings are …

Deposition Of Particulate From Coal-Derived Syngas On Gas Turbine Blades Near Film Cooling Holes, Weiguo Ai

Theses and Dissertations

Synfuel from gasification of coal, biomass, and/or petroleum coke is an alternative to natural gas in land-based industrial gas turbines. However, carryover fine particulate in the syngas may lead to a considerable amount of deposition on turbine blades, which reduces component life and system performance. Deposition experiments on film-cooled turbine components were performed in an accelerated test facility to examine the nature of flyash deposits near film cooling holes. Experimental results indicate that deposition capture efficiency decreased with increased blowing ratio. Shaped holes exhibited more span-wise coverage than cylindrical holes and effectively reduced deposition. The TBC layer increased surface temperature, …

Diesel Particulate Matter Quantification And Reduction Strategies For School Buses, David Martinez-Morett

Theses and Dissertations

This thesis evaluated the contributions of school bus self pollution from both the crankcase and the tailpipe emissions to in-cabin levels of fine and ultrafine particulate matter, and determined the effectiveness of commercially available retrofit technologies towards reducing levels of particulate matter inside the school bus passenger compartment. Mobile tests were conducted with a school bus powered by an International DT466E engine on an outdoor test track. Measurements of fine and ultrafine particle concentrations within the cabin of a school bus were performed with and without retrofit technologies.

The tests utilized a drive cycle using data from actual school bus …

Investigation Of Additives For Use In Electroless Plating Solutions For Fabrication Of Nanowires, Elliott J. Bird

Theses and Dissertations

This study focused on improvement of electroless plating methods by use of particular bath additives. The techniques developed here can enable us to plate very thin layers selectively on a nonconductive substrate and thus create metallized features on a nanoscale. Through the development of such bottom-up techniques this work contributes a key technology to achieving self-assembled nanocircuits. The use of additives in an electroless plating environment can modify the barriers to nucleation (or seeding) and growth. Two additives, namely 3-mercapto-1-propanesulfonic Acid (MPS) and 1,3-propanedisulfonic acid (PDS), notably increased the selectivity of electroless metallization on chemically modified surfaces, which can be …

Understanding Performance--Limiting Mechanisms In Li-Ion Batteries For High-Rate Applications, Indrajeet Vilasrao Thorat

Theses and Dissertations

This work presents novel modeling and experimental techniques that provide insight into liquid-phase mass transport and electron transfer processes in lithium-ion batteries. These included liquid-phase ionic mass transport (conduction and diffusion), lithium diffuion in the solid phase and electronic transport in the solid phase. Fundamental understanding of these processes is necessary to efficiently design and optimize lithium-ion batteries for different applications. To understand the effect of electrode structure on the electronic resistance of the cathode, we tested power performance of cathodes with combinations of three different carbon conductivity additives: vapor-grown carbon fibers (CF), carbon black (CB) and graphite (GR). With …

A Parallel Molecular Dynamics Program For Simulation Of Water In Ion Channels, Laxmi Mullapudi

Theses and Dissertations

With a modest beginning from developing a model of dynamics of hard liquid spheres (Alder et al., 1957), molecular dynamics (MD) simulations have come to a point where complex biomolecules can be simulated with precision close to reality (Noskov et al., 2007). In this context, a parallel molecular dynamics program for simulation of ion channels associated with cellular membranes has been developed. The parallel MD code developed is simple, efficient, and easily coupled to other codes such as the hybrid molecular dynamics/ brownian dynamics (MD/BD) code developed for the study of protein interactions (Ying et al., 2005). The Atom Decomposition …

Laser Levitation Of Solid Particles For Combustion And Gasification Applications, Skigh E. Lewis

Theses and Dissertations

This dissertation details theoretical and experimental work in the development of a novel combustion diagnostic: laser levitation of solid particles. Theoretical analyses of the forces involved in the suspension of solid particles in a laser beam provide a comprehensive description of the levitation mechanism. Experimental work provides extensive observations and data that describe each of the forces involved, including results from detailed models. Theoretical models establish that a free-convective drag force, light scattering, photon momentum, and other minor forces contribute to the trapping mechanism. The theory quantitatively predicts particle temperature and magnitudes of each of the forces involved. Experimental measurements …

Effects Of Prior Aging At 316°C In Argon On Inelastic Deformation Behavior Of Pmr-15 Polymer At 316°C: Experiment And Modeling, Ozgur Ozmen

Theses and Dissertations

The inelastic deformation behavior of PMR-15 neat resin, a high-temperature polymer, was investigated at 316 deg C. The experimental program was designed to explore the influence of strain rate on tensile loading, unloading, and strain recovery behaviors. In addition, the effect of the prior strain rate on the relaxation response of the material, as well as on the creep behavior following strain controlled loading were examined. The material exhibits positive, nonlinear strain rate sensitivity in monotonic loading and unloading. Early failures occur in the inelastic regime. The recovery of strain at zero stress and creep response are strongly affected by …

Binding Studies Of Epidermal Growth Factor Receptor Targeted Compounds Using Surface Plasmon Resonance, Spandana Kankanala

Theses and Dissertations

The study of binding kinetics of proteins plays an important role in understanding molecular mechanisms that drive biological processes. The binding rate constants reflect the dynamics of the system and associated biological activity measurements of the association and dissociation rate constants make it possible to compare different interactions in a standardized manner and help elucidate a mechanistic understanding of binding events. In our study, we used Surface Plasmon Resonance (SPR) technology (Biacore) to study the binding kinetics of the antibodies EGF, Cetuximab and a candidate drug P-13 with the receptor EGFR. The candidate drug P-13 was synthesized and tested on …

A New Model For Aqueous Electrolyte Solutions Near The Critical Point Of Water Incorporating Aqueous Reaction Equilibria, Craig J. Peterson

Theses and Dissertations

Aqueous electrolyte solutions at temperature and pressure conditions near the critical point of water are difficult to describe using traditional equations of state based upon the excess Gibbs energy. Models based upon the residual Helmholtz energy have proven more effective. Anderko and Pitzer1 developed a residual Helmholtz energy model (AP) for aqueous electrolyte solutions in which the electrolyte is assumed to be fully associated. The model has been effectively used in describing densities and vapor-liquid equilibria for simple electrolyte systems. The model is less effective for describing enthalpic properties such as heats of dilution. Oscarson and coworkers2, 3 modified the …

Redox, Pressure And Mass Transfer Effects On Syngas Fermentation, Allyson White Frankman

Theses and Dissertations

The fermentation of syngas (a mixture of CO, CO2 and H2) to produce ethanol is of interest as an alternative fuel. Clostridium carboxidivorans, has been found to produce higher than average amounts of ethanol and butanol from CO-rich mixtures. This project sought to determine the effects of the redox level in the solution, partial pressures in the headspace and mass transfer limitations on the products obtained through fermentation of syngas. It was determined that cysteine sulfide has a greater effect on the redox level of the media used to grow bacteria, than does the gas composition. Therefore, changing gas …

The Developmental Effect Of Human Embryoid Bodies (Heb) Under Dynamic Culturing Conditions Using A Perfusion Based Slow Turning Lateral Vessel (Stlv) Bioreactor, Claiborne Collier

Theses and Dissertations

Human embryonic stem cells (hESCs) can provide a unique approach for novel tissue engineering applications. Previous groups have shown that hESCs can differentiate into specialized cell types through the generation of human embryoid bodies (hEBs). These multi-cellular constructs are then subjected to suspension culture for several weeks. Traditional hESC differentiation techniques have yielded non-homogeneous EBs derived in standard static cultures providing an inefficient platform for cellular viability and embryonic modeling. Here, our study aimed at systematically comparing the formation, growth, and differentiation capabilities of hESC-derived hEBs in dynamic and static suspension cultures. We used a continuous flow perfusion slow turning …