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Full-Text Articles in Engineering
The Effects Of Mismatches And Probe Tethering Configurations On The Stability Of Dna Duplexes On Surfaces, Kyle Evan Pratt
The Effects Of Mismatches And Probe Tethering Configurations On The Stability Of Dna Duplexes On Surfaces, Kyle Evan Pratt
Theses and Dissertations
DNA microarrays are chip-based, analysis tools which can perform hundreds of thousands of parallel assays to determine the identity of genes or gene expression levels present in a sample. They have been identified as a key technology in genomic sciences and emergent medical techniques; however, despite their abundant use in research laboratories, microarrays have not been used in the clinical setting to the fullest potential due to the difficulty of obtaining reproducible results. Microarrays work on the principle of DNA hybridization, and can only be as accurate as this process is robust. Fundamental, molecular-level understanding of hybridization on surfaces is …
Protein-Surface Interactions With Coarse-Grain Simulation Methods, Shuai Wei
Protein-Surface Interactions With Coarse-Grain Simulation Methods, Shuai Wei
Theses and Dissertations
The interaction of proteins with surfaces is a major process involved in protein microarrays. Understanding protein-surface interactions is key to improving the performance of protein microarrays, but current understanding of the behavior of proteins on surfaces is lacking. Prevailing theories on the subject, which suggest that proteins should be stabilized when tethered to surfaces, do not explain the experimentally observed fact that proteins are often denatured on surfaces. This document outlines several studies done to develop a model which is capable of predicting the stabilization and destabilization of proteins tethered to surfaces. As the start point of the research, part …
Multi-Processor Computation Of Thrombus Growth And Embolization In A Model Of Blood-Biomaterial Interaction Based On Fluid Dynamics, Brandon Thomas Andersen
Multi-Processor Computation Of Thrombus Growth And Embolization In A Model Of Blood-Biomaterial Interaction Based On Fluid Dynamics, Brandon Thomas Andersen
Theses and Dissertations
This work describes the development and testing of a real-time three-dimensional computational fluid dynamics simulation of thrombosis and embolization to be used in the design of blood-contacting devices. Features of the model include the adhesion and aggregation of blood platelets on device material surfaces, shear and chemical activation of blood platelets, and embolization of platelet aggregates due to shear forces. As thrombus develops, blood is diverted from its regular flow field. If shear forces on a thrombus are sufficient to overcome the strength of adhesion, the thrombus is dislodged from the wall. Development of the model included preparing thrombosis and …
The Structure And Stability Of Alpha-Helical, Orthogonal-Bundle Proteins On Surfaces, Shuai Wei
The Structure And Stability Of Alpha-Helical, Orthogonal-Bundle Proteins On Surfaces, Shuai Wei
Theses and Dissertations
The interaction of proteins with surfaces is a major problem involved in protein microarrays. Understanding protein/surface interactions is key to improving the performance of protein microarrays, but current understanding of the behavior of proteins on surfaces is lacking. Prevailing theories on the subject, which suggest that proteins should be stabilized when tethered to surfaces, do not explain the experimentally observed fact that proteins are often denatured on surfaces. In an attempt to develop some predictive capabilities with respect to protein/surface interactions, it was asked in previous works if the stabilization/destabilization of proteins on surfaces could be correlated to secondary structure …
Prediction Of Fluid Viscosity Through Transient Molecular Dynamic Simulations, Jason Christopher Thomas
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 …
A New Method For Treating Wells In Reservoir Simulation, Gregory M. Gessel
A New Method For Treating Wells In Reservoir Simulation, Gregory M. Gessel
Theses and Dissertations
A new method for formulating finite difference equations for reservoir simulation has been developed. It can be applied throughout the entire simulated reservoir or to local segments. When applied to cells containing vertical, fully penetrating, straight-line wells in a homogeneous reservoir, the resulting equations are equivalent to Peaceman's classical well equations used in most reservoir simulators today. However, when the new finite difference equations are applied to both the well-containing cells, and their neighbors, the accuracy of the simulation improves substantially. The method produces still better accuracy results when applied throughout the reservoir. Unlike the Peaceman correction, the new method …
A Finite Element Simulation Of Temperature And Material Flow In Fricton Stir Welding, Mark J. Lasley
A Finite Element Simulation Of Temperature And Material Flow In Fricton Stir Welding, Mark J. Lasley
Theses and Dissertations
The purpose of this research was to use the Transvalor S.A. product, Forge3, to develop a finite element simulation of the friction stir welding process that improves the predictability of temperature evolution and material flow within the plunge portion of the process. Previous modeling created more heating within the billet than experimental results, probably due to the simplification of the simulation with adiabatic boundary conditions. More realistic tooling temperatures were included in this model as these affect heat evolution which is a determining factor in microcrystalline growth. These results were validated by experimental efforts using a billet and tooling instrumented …
The Use Of Two Mixture Fractions To Treat Coal Combustion Products In Turbulent Pulverized-Coal Flames, Daniel V. Flores, Thomas H. Fletcher
The Use Of Two Mixture Fractions To Treat Coal Combustion Products In Turbulent Pulverized-Coal Flames, Daniel V. Flores, Thomas H. Fletcher
Faculty Publications
Previous coal combustion models using assumed-shape PDF's to treat turbulence-chemistry interactions have used only one progress variable to treat products from coal reactions. This assumes that the products of all coal reactions have the same composition. However. the composition of the combustion products of coal particles is known to vary with burnout, especially between devclatilization and char oxidation. In this work, two progress variables were implemented which distinguish between the products of devolatilization and those of char oxidation. This new approach requires as input the specified volatile content and elemental release during devolatilization. The values for these parameters were estimated …