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Articles 1 - 28 of 28
Full-Text Articles in Engineering
Streamlined Extract Preparation For E. Coli-Based Cell-Free Protein Synthesis And Rapid Site-Specific Incorporation Of Unnatural Amino Acids In Proteins, Prashanta Shrestha
Streamlined Extract Preparation For E. Coli-Based Cell-Free Protein Synthesis And Rapid Site-Specific Incorporation Of Unnatural Amino Acids In Proteins, Prashanta Shrestha
Theses and Dissertations
This thesis reports the viability of E. coli cell extracts prepared using equipment that is both common to biotechnology laboratories and able to process small volume samples and expression of proteins containing unnatural amino acids (UAAs) at higher level using PCR amplified linear DNA templates (LETs) in cell-free protein synthesis (CFPS) system. E. coli-based cell extracts are a vital component of inexpensive and high-yielding CFPS reactions. However, effective preparation of E. coli cell extract is limited to high-pressure homogenizers (French press style or impinge-style) or bead mill homogenizers, which all require a significant capital investment. This work specifically assessed the …
Liquid-Liquid Equilibrium Of Biodiesel Components, Joseph C. Bell
Liquid-Liquid Equilibrium Of Biodiesel Components, Joseph C. Bell
Theses and Dissertations
Biodiesel is produced from vegetable oils through transesterification. Triglyceride mixtures extracted from oilseed feedstocks are upgraded by reaction with an alcohol in the presence of a catalyst to produce fatty acid esters. This reaction produces a mixture of esters, glycerin, alcohol, and catalyst. Separation of the fatty acid esters (biodiesel) and glycerin can be accomplished through liquid-liquid extraction by water addition. Designing liquid-liquid extraction with water as the solvent requires ternary liquid-liquid equilibrium data for mixtures of water, glycerin, and fatty acid esters. Ternary mixture LLE data have been experimentally measured for several of these systems. Those measured include mixtures …
Model Development And Application Of Molecular Simulations For The Study Of Proton Transport In Bulk Water And For The Prediction Of Dipole Moments Of Organic Compounds, Abhishek Asthana
Theses and Dissertations
The present work demonstrates the application of molecular simulations (MD) in two different areas: proton transport in bulk water and estimation of the dipole moment of polar organic compounds. In both areas, relatively few successful and robust methodologies exist. In the first part, a new polarizable water model is developed for MD simulations of the proton transport process. The model was parametrized from a combination of quantum chemical calculations and experimental water properties. The model was implemented in MD simulation studies of liquid water at room temperature, as well as with excess protons. For pure water the model gave good …
Site-Specific Metallization Of Multiple Metals On A Single Dna Origami Template, Bibek Uprety
Site-Specific Metallization Of Multiple Metals On A Single Dna Origami Template, Bibek Uprety
Theses and Dissertations
This work examines the selective deposition of two different metals on the same DNA origami template for nanofabrication. DNA, with adjustable size and shape serves as a suitable template for fabricating metal junctions in the nanometer domain via bottom-up assembly. Bottom-up assembly utilizes the recognition capability of molecules like DNA to self-assemble and form structures. In this regard, DNA origami provides a useful means for forming nanostructures by folding single-stranded DNA into different two and three dimensional shapes. Selective deposition of metal on specific locations of a DNA template is essential for making DNA-templated electronic circuits.Site-specific metallization of DNA origami …
Ultrasound-Induced Phase Change Of Emulsion Droplets For Targeted Gene And Drug Delivery, James R. Lattin
Ultrasound-Induced Phase Change Of Emulsion Droplets For Targeted Gene And Drug Delivery, James R. Lattin
Theses and Dissertations
This dissertation explores the potential of using perfluorocarbon emulsion droplets to add an ultrasound-sensitive element to drug delivery systems. These emulsion droplets may be induced to vaporize with ultrasound; during the rarefactional phase of an ultrasound wave, the pressure around the droplets may fall below the vapor pressure of the liquid forming the emulsion, providing a thermodynamic potential for vaporization. This ultrasound-induced phase change of the emulsion droplet could release therapeutics attached to the droplet surface or aid in drug delivery due to mechanical effects associated with vaporization and expansion, similar to the ability of cavitating bubbles to aid in …
Beyond Gel Electrophoresis: Microfluidic Separations, Fluorescence Burst Analysis, And Dna Stretching, Kevin D. Dorfman, Scott B. King, Daniel W. Olson, Joel D. P. Thomas, Douglas R. Tree
Beyond Gel Electrophoresis: Microfluidic Separations, Fluorescence Burst Analysis, And Dna Stretching, Kevin D. Dorfman, Scott B. King, Daniel W. Olson, Joel D. P. Thomas, Douglas R. Tree
Faculty Publications
This review addresses methods for obtaining sequence information directly from unamplified genomic length DNA. Our generic starting point is a large piece of DNA that contains many thousands of base pairs (kilobase pairs, kbp) or even millions of base pairs (megabase pairs, Mbp). We would like to determine the genomic distance between two repeats of a given sequence, indicated by the red dots on the coiled DNA molecule in Figure 1. Let us consider the case where these sequences are restriction sites, which can be selectively cut using proteins known as restriction enzymes. For decades, gel electrophoresis served as the …
Syngas Impurity Effects On Cell Growth, Enzymatic Activities And Ethanol Production Via Fermentation, Deshun Xu
Syngas Impurity Effects On Cell Growth, Enzymatic Activities And Ethanol Production Via Fermentation, Deshun Xu
Theses and Dissertations
A syngas compositional database with focus on trace impurities was established. For this work, ammonia (NH3) and benzene (C6H6) effects on cell growth, enzymatic activities of hydrogenase and alcohol dehydrogenase (ADH), and product formation were studied. NH3, after entering media, will be converted rapidly to NH4+, which will raise the total osmolarity of the media. NH3, as a common nutrient for the cell growth, is not the real culprit for cell growth inhibition. In essence, it is the high osmolarity resulting from the accumulation of NH4+ in the media which disrupts the normal regulation of the cells. It was concluded …
Thermodynamic Kinetics And Efficiency Analysis Of Methyl Viologen, Chang Chen
Thermodynamic Kinetics And Efficiency Analysis Of Methyl Viologen, Chang Chen
Theses and Dissertations
Methyl Viologen (MV) is an electron mediator that has great possibilities to be used with an electrode system in which the electrode system provides electrons towards reducing MV species. MV has three redox states and they can be converted to each other via redox reactions on the surface of the electrode. The concentration of the three species of MV was related to the voltage potential applied to the system through a thermodynamic model. With the thermodynamic model the concentration of the three species can be predicted with different applied voltage potentials towards providing guidance for controlling the redox state of …
Development Of A Method To Study Thromboembolism By Direct Observation In Blood-Contacting Microsystems Using High-Definition Video Microscopy, Yong Min Kim
Theses and Dissertations
A unique and novel method to study thromboembolism by direct observation was developed. High-definition videos of thrombus formation and embolization were successfully obtained in miniature flow cells using in-vitro, non-invasive, real-time techniques. Critical parameters of thromboembolism such as thrombus growth rate, thrombus growth direction, shear force on the thrombus at embolization, and adhesion strength of the thrombus to the foreign surface were determined. Thrombus growth was found predominantly in two locations: 1) in the flow recirculation zone just after the trailing edge of the small tubes (53%) and 2) at the leading edge of the small tubes (47%). In the …
Novel Iron Catalyst And Fixed-Bed Reactor Model For The Fischer-Tropsch Synthesis, Kyle Martin Brunner
Novel Iron Catalyst And Fixed-Bed Reactor Model For The Fischer-Tropsch Synthesis, Kyle Martin Brunner
Theses and Dissertations
This work investigates a novel iron Fischer-Tropsch (FT) catalyst preparation and describes the development of a trickle fixed-bed recycle reactor model (TFBRRM) for the FT synthesis applicable to both iron and cobalt catalysts. The iron catalyst preparation was developed using a novel solvent deficient precipitation reaction. Fifteen Fe/Cu/K/SiO2 catalysts were prepared to investigate key preparation variables including timing of promoter addition, washing or not washing after precipitation, and drying temperature. Adding promoters to starting materials before precipitation (1S) gives more uniform promoter distributions which gives higher water-gas shift activity and lower methane selectivity. Unwashed catalysts have smaller average pore and …
Understanding Noble Metal Addition In Cobalt Fischer Tropsch Catalysts, Kari Marie Cook
Understanding Noble Metal Addition In Cobalt Fischer Tropsch Catalysts, Kari Marie Cook
Theses and Dissertations
The effects of noble metal (NM) promotion and deposition order (co-deposition of NM with the final Co deposition [co-dep] or sequential deposition of NM after Co deposition [seq-dep]) on surface area, pore size, metal retention, crystallite size, noble metal distribution and bonding in Co Fischer Tropsch (FT) catalysts were studied as were the resulting Co reducibility and Fischer Tropsch activity/selectivity properties. Catalysts containing nominally 25wt% Co with either 0.3 wt% Ru, 0.58 wt% Pt, 0.55wt% Re, or no NM on a La-stabilized-Al2O3 support were prepared by wet deposition. The Co, Pt, and Re were uniformly dispersed, but Ru distribution and …
Homogeneous Viologens For Use As Catalysts In Direct Carbohydrate Fuel Cells, Dane C. Hansen
Homogeneous Viologens For Use As Catalysts In Direct Carbohydrate Fuel Cells, Dane C. Hansen
Theses and Dissertations
Deriving electrical energy from glucose and other carbohydrates under mild conditions is an important research objective because these biomolecules are abundant, renewable, and can provide 12 to 24 electrons per molecule, yielding substantial electrical power. It was previously observed that disubstituted viologens, salts of N,N'-disubstituted 4,4'-bipyridine, are able to oxidize glucose under alkaline conditions. Building on that initial result, the objective of this work was to understand and quantify the effectiveness and utility of viologens as catalysts for use in direct carbohydrate fuel cells.The extent that viologens oxidize carbohydrates, the conditions under which that oxidation occurs, and the mechanism for …
Constrained Control And Optimization Of Tubular Solid Oxide Fuel Cells For Extending Cell Lifetime, Ben Spivey, John Hedengren, Thomas F. Edgar
Constrained Control And Optimization Of Tubular Solid Oxide Fuel Cells For Extending Cell Lifetime, Ben Spivey, John Hedengren, Thomas F. Edgar
Faculty Publications
Extending fuel cell lifetime is a necessary objective for reducing fuel cell power generation cost of electricity. Capital costs comprise the most significant fraction of the cost of electricity. Reducing the frequency of fuel cell replacement can be achieved by implementing a control strategy that prevents excursions into operating regions causing failure. In this paper we implement a constrained MIMO model predictive controller (MPC) to avoid the failure modes relevant for a high-temperature tubular solid oxide fuel cell (SOFC) system while performing load-following. The primary causes of failure are catalyst poisoning, fuel or air starvation, carbon deposition, and microcracking. Prior …
Performance Characteristics Of Lithium Coin Cells For Use In Wireless Sensing Systems, Yin Zhang
Performance Characteristics Of Lithium Coin Cells For Use In Wireless Sensing Systems, Yin Zhang
Theses and Dissertations
Understanding the pulsed discharge behavior of low-rate lithium coin cells in wireless sensing systems is critical to prolong the operating life and/or reduce the size of battery-powered WSs. This dissertation presents the battery transient analysis for a sensor duty cycle, experimental studies for sustained pulse discharge cycling, and investigation on recharge strategies for a battery/power harvesting hybrid system for WSs. The transient behavior of the lithium coin cells during pulse discharge and subsequent relaxation was investigated with single-pulse experiments and theoretical analysis. The voltage response for a pulsed discharge had two parts: a region of rapid voltage change and a …
Determination Of Phase Equilibria And The Critical Point Using Two-Phase Molecular Dynamics Simulations With Monte Carlo Sampling, Sonal Patel
Theses and Dissertations
The two-phase MD technique employed in this work determines the liquid and vapor phase densities from a histogram of molecular densities within phase clusters in the simulation cell using a new Monte Carlo (MC) sampling method. These equilibrium densities are then fitted in conjunction with known critical-point scaling laws to obtain the critical temperature, and the critical density. This MC post-processing method was found to be more easily implemented in code, and it is efficient and easily applied to complex, structured molecules. This method has been successfully applied and benchmarked for a simple Lennard-Jones (LJ) fluid and a structured molecule, …
Chemical Potential Perturbation: A Method To Predict Chemical Potential Using Molecular Simulations, Stan G. Moore
Chemical Potential Perturbation: A Method To Predict Chemical Potential Using Molecular Simulations, Stan G. Moore
Theses and Dissertations
A new method, called chemical potential perturbation (CPP), has been developed to predict the chemical potential as a function of composition in molecular simulations. The CPP method applies a spatially varying external potential to the simulation, causing the composition to depend upon position in the simulation cell. Following equilibration, the homogeneous chemical potential as a function of composition can be determined relative to some reference state after correcting for the effects of the inhomogeneity of the system. The CPP method allows one to predict chemical potential for a wide range of composition points using a single simulation and works for …
Fiber Optic Monitoring Of Subsea Equipment, David Brower, John Hedengren, Cory Loegering, Alexis Brower, Karl Witherow, Karl Winter
Fiber Optic Monitoring Of Subsea Equipment, David Brower, John Hedengren, Cory Loegering, Alexis Brower, Karl Witherow, Karl Winter
Faculty Publications
Bass Lite deepwater field in the Gulf of Mexico, at water depths of approximately 2,050 m (6,750 feet), commenced operation in February 2008. Natural gas is produced from Bass Lite via a 90-km (56-mile) subsea tieback to the Devils Tower Spar. This project involved several innovations, one of which was the incorporation of a fiber optic sensing system that measures realtime temperature, pressure and strain along the pipeline length. This is a first of its kind innovation that is in actual operation.
Mobility Of A Semiflexible Chain Confined In A Nanochannel, Douglas R. Tree, Yanwei Wang, Kevin D. Dorfman
Mobility Of A Semiflexible Chain Confined In A Nanochannel, Douglas R. Tree, Yanwei Wang, Kevin D. Dorfman
Faculty Publications
The classic results of de Gennes and Odijk describe the mobility of a semiflexible chain confined in a nanochannel only in the limits of very weak and very strong confinement, respectively. Using Monte Carlo sampling of the Kirkwood diffusivity with full hydrodynamic interactions, we show that the mobility of a semiflexible chain exhibits a broad plateau as a function of extension before transitioning to an Odijk regime, and that the width of the plateau depends on the anisotropy of the monomers. For the particular case of DNA in a high ionic strength buffer, which has highly anisotropic monomers, we predict …
Uv Visible Spectra Analysis Of High Temperature Water Gas Shift Catalysts Made From Iron, Lanthanum, Copper, And Chromium Oxides, Jared C. Brown
Uv Visible Spectra Analysis Of High Temperature Water Gas Shift Catalysts Made From Iron, Lanthanum, Copper, And Chromium Oxides, Jared C. Brown
Theses and Dissertations
Hydrogen is a vital component in several different chemical reactions as well as a potential fuel source for the future. The water gas shift (WGS) reaction converts CO and water to hydrogen and CO2. The objective of this work is to first, characterize the potential benefits of the addition of lanthanum oxide (lanthana) to the iron-chromium-copper (Fe-Cr-Cu) oxide catalysts industrially used in high temperature water gas shift processes, and second, analyze these catalysts using in-situ UV-Visible spectroscopy. The benefits of each component in the catalyst are discussed as well as potential benefits from the addition of lanthana. Lanthana is a …
Chemical Potential Perturbation: Extension Of The Method To Lattice Sum Treatment Of Intermolecular Potentials, Stan G. Moore, Dean R. Wheeler
Chemical Potential Perturbation: Extension Of The Method To Lattice Sum Treatment Of Intermolecular Potentials, Stan G. Moore, Dean R. Wheeler
Faculty Publications
The recently developed chemical potential perturbation (CPP) method [S. G. Moore and D. R. Wheeler, J. Chem. Phys. 134, 114514 (2011) https://doi.org/10.1063/1.3561865.] is extended to the lattice (Ewald) sum treatment of intermolecular potentials. The CPP method predicts chemical potentials for a range of composition points using the local (position-dependent) pressure tensor of an inhomogeneous system. When computing the local pressure tensor, one can use the Irving-Kirkwood (IK) or Harasima (H) contours of distributing the pressure. We compare these two contours and show that for a planar interface, the homogeneous pressure and resulting chemical potential can be approximated with …
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 …
Simulations Of Controlled Fires Using The One-Dimensional Turbulence Model With Application To Fire Spread In Wildland Fires, Elizabeth Ida Monson
Simulations Of Controlled Fires Using The One-Dimensional Turbulence Model With Application To Fire Spread In Wildland Fires, Elizabeth Ida Monson
Theses and Dissertations
The mechanism of flame propagation in fuel beds of wildland fires is important to understand and quantify fire spread rates. Fires spread by radiative and convective heating and often require direct flame contact to achieve ignition. The flame interface in an advancing fire is unsteady and turbulent, making study of intermittent flames in complex fuels difficult. This thesis applies the one-dimensional turbulence (ODT) model to a study of flame propagation by simulating a lab-scale fire representative of the flame interface in a fuel bed and incorporating solid fuel particles into the ODT code. The ODT model is able to resolve …
Resolution Limit For Dna Barcodes In The Odijk Regime, Yanwei Wang, Wes F. Reinhart, Douglas R. Tree, Kevin D. Dorfman
Resolution Limit For Dna Barcodes In The Odijk Regime, Yanwei Wang, Wes F. Reinhart, Douglas R. Tree, Kevin D. Dorfman
Faculty Publications
We develop an approximation for the probability of optically resolving two fluorescent labels on the backbone of a DNA molecule confined in a nanochannel in the Odijk regime as a function of the fluorescence wavelength, channel size, and the properties of the DNA (persistence length and effective width). The theoretical predictions agree well with equivalent data produced by Monte Carlo simulations of a touching wormlike bead model of DNA in a high ionic strength buffer. Although the theory is only strictly valid in the limit where the effective width of the nanochannel is small compared with the persistence length of …
Effect Of Hole Spacing On Deposition Of Fine Coal Flyash Near Film Cooling Holes, Weiguo Ai, Nathan Murray, Thomas H. Fletcher, Spencer Harding, Elizabeth Bonsignore, Jeffrey P. Bons
Effect Of Hole Spacing On Deposition Of Fine Coal Flyash Near Film Cooling Holes, Weiguo Ai, Nathan Murray, Thomas H. Fletcher, Spencer Harding, Elizabeth Bonsignore, Jeffrey P. Bons
Faculty Publications
Particulate deposition experiments were performed in a turbine accelerated deposition facility to examine the nature of flyash deposits near film cooling holes. Deposition on both bare metal and thermal barrier coating (TBC) coupons was studied, with hole spacing (s/d) of 2.25, 3.375, and 4.5. Sub-bituminous coal ash particles (mass mean diameter of 13 microns) were accelerated to a combustor exit flow Mach number of 0.25 and heated to 1183°C before impinging on a target coupon. The particle loading in the 1 h tests was 310 ppmw. Blowing ratios were varied in these experiments from 0 to 4.0 with the density …
Computational Analysis Of Conjugate Heat Transfer And Particulate Deposition On A High Pressure Turbine Vane, Weiguo Ai, Thomas H. Fletcher
Computational Analysis Of Conjugate Heat Transfer And Particulate Deposition On A High Pressure Turbine Vane, Weiguo Ai, Thomas H. Fletcher
Faculty Publications
Numerical computations were conducted to simulate flash deposition experiments on gas turbine disk samples with internal impingement and film cooling using a computational fluid dynamics (CFD) code (FLUENT). The standard k-epsilon turbulence model and Reynoldsaveraged Navier–Stokes were employed to compute the flow field and heat transfer. The boundary conditions were specified to be in agreement with the conditions measured in experiments performed in the BYU turbine accelerated deposition facility (TADF). A Lagrangian particle method was utilized to predict the ash particulate deposition. Userdefined subroutines were linked with FLUENT to build the deposition model. The model includes particle sticking/rebounding and particle …
Deposition Near Film Cooling Holes On A High Pressure Turbine Vane, Weiguo Ai, Nathan Murray, Thomas H. Fletcher, Spencer Harding, Scott Lewis, Jeffrey P. Bons
Deposition Near Film Cooling Holes On A High Pressure Turbine Vane, Weiguo Ai, Nathan Murray, Thomas H. Fletcher, Spencer Harding, Scott Lewis, Jeffrey P. Bons
Faculty Publications
Deposition on film-cooled turbine components was studied in an accelerated test facility. The accelerated deposition facility seeds a natural-gas burning combustor with finely ground coal ash particulate at 1180 C and 180 m/s (M=0.25). Both cylindrical and shaped holes, with and without thermal barrier coating, were studied over a range of blowing ratios from 0.5 to 4.0. Coolant density ratios were maintained at values from 2.1 to 2.4. Deposition patterns generated with the cylindrical film cooling holes indicated regions of low deposition in the path of the coolant with heightened deposition between film holes. This distinctive pattern was more accentuated …
Coal Swelling Model For Pressurized High Particle Heating Rate Pyrolysis Applications, Randy C. Shurtz, Joseph W. Hogge, Kade C. Fowers, Gregory S. Sorensen, Thomas H. Fletcher
Coal Swelling Model For Pressurized High Particle Heating Rate Pyrolysis Applications, Randy C. Shurtz, Joseph W. Hogge, Kade C. Fowers, Gregory S. Sorensen, Thomas H. Fletcher
Faculty Publications
A model was previously developed to describe the decrease in swelling during coal pyrolysis at atmospheric pressure when maximum particle heating rates increase from 104 K/s to 105 K/s. That model included effects of coal type using chemical structure properties. This paper presents results of new experiments to study the effects of elevated pressure and high heating rates on coal pyrolysis. A pressurized flat-flame burner (PFFB) was designed and built to conduct these studies. The pyrolysis experiments reported in this paper were conducted at particle heating rates of ∼105 K/s and maximum gas temperatures of 1700 to 1900 …
Prediction Of Tar And Light Gas During Pyrolysis Of Black Liquor And Biomass, Thomas H. Fletcher, Harland R. Pond, Jarom Webster, Judson Wooters, Larry L. Baxter
Prediction Of Tar And Light Gas During Pyrolysis Of Black Liquor And Biomass, Thomas H. Fletcher, Harland R. Pond, Jarom Webster, Judson Wooters, Larry L. Baxter
Faculty Publications
A generalized model for describing the pyrolysis behavior of low-grade fuels is being developed for incorporation into larger combustion simulation models. Light gas and tar yields from black liquor or biomass pyrolysis can be predicted using the chemical percolation devolatilization (CPD) model originally developed for coal. The initial approach is to measure the average chemical structures in a black liquor sample using 13C NMR spectroscopy. These chemical structures are then used in pyrolysis model predictions. With few changes from the coal-derived kinetic parameters, the model describes the organic pyrolysis behavior of black liquor samples obtained in a nitrogen-purged furnace. It …