Digital Commons Network^™

A Fundamental Study Of The Pcr Amplification Of Gc-Rich Dna Templates, T. G. Mamedov, Elsje Pienaar, Scott E. Whitney, Joel R. Termaat, G. Carvill, R. Goliath, Anuradha Subramanian, Hendrik J. Viljoen

Hendrik J. Viljoen Publications

A theoretical analysis is presented with experimental confirmation to conclusively demonstrate the critical role that annealing plays in efficient PCR amplification of GC-rich templates. The analysis is focused on the annealing of primers at alternative binding sites (competitive annealing) and the main result is a quantitative expression of the efficiency (η) of annealing as a function of temperature (T_A), annealing period (t_A), and template composition. The optimal efficiency lies in a narrow region of T_A and t_A for GC-rich templates and a much broader region for normal GC templates. To confirm the …

Monitoring Tissue Engineering Using Magnetic Resonance Imaging, Huihui Xu, Shadi F. Othman, Richard L. Magin

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Assessment of tissue regeneration is essential to optimize the stages of tissue engineering (cell proliferation, tissue development and implantation). Optical and X-ray imaging have been used in tissue engineering to provide useful information, but each has limitations: for example, poor depth penetration and radiation damage. Magnetic resonance imaging (MRI) largely overcomes these restrictions, exhibits high resolution (approximately 100 μm) and can be applied both in vitro and in vivo. Recently, MRI has been used in tissue engineering to generate spatial maps of tissue relaxation times (T₁, T₂), water diffusion coefficients, and the stiffness (shear moduli) of …

Quantitative Rrna-Targeted Solution-Based Hybridization Assay Using Peptide Nucleic Acid Molecular Beacons, Xu Li, Eberhard Morgenroth, Lutgarde Raskin

Department of Civil and Environmental Engineering: Faculty Publications

The potential of a solution-based hybridization assay using peptide nucleic acid (PNA) molecular beacon (MB) probes to quantify 16S rRNA of specific populations in RNA extracts of environmental samples was evaluated by designing PNA MB probes for the genera Dechloromonas and Dechlorosoma. In a kinetic study with 16S rRNA from pure cultures, the hybridization of PNA MB to target 16S rRNA exhibited a higher final hybridization signal and a lower apparent rate constant than the hybridizations to nontarget 16S rRNAs. A concentration of 10 mM NaCl in the hybridization buffer was found to be optimal for maximizing the difference between …

Biogeography-Based Optimization, Daniel J. Simon

Electrical and Computer Engineering Faculty Publications

Biogeography is the study of the geographical distribution of biological organisms. Mathematical equations that govern the distribution of organisms were first discovered and developed during the 1960s. The mindset of the engineer is that we can learn from nature. This motivates the application of biogeography to optimization problems. Just as the mathematics of biological genetics inspired the development of genetic algorithms (GAs), and the mathematics of biological neurons inspired the development of artificial neural networks, this paper considers the mathematics of biogeography as the basis for the development of a new field: biogeography-based optimization (BBO). We discuss natural biogeography and …

Circuit Modules For Six-Port Reflectometer On Chip, Chaojiang Li

All Theses

Broadband signal generator is an indispensable module for broadband Six-Port Reflectometer (SPR). To integrate a whole SPR system on a chip, the source must be compact. In this thesis, a three-stage voltage-controlled oscillator (VCO), using two parallel weak invertor-chain oscillators and sense amplifiers, is proposed and designed in a 0.13 µm CMOS process. These two parallel weak inverter-chain oscillators extend the low frequency operating range and the sense amplifiers expand the high frequency operation. The measurement results show that the oscillator can be tuned from 430 MHz to 12 GHz, which satisfies the targeted SPR operating frequency range.
In order …

Development And Characterization Of Moisture- And Heat- Activated Oxygen Scavenging Nanoparticle, Youngjae Byun

All Dissertations

Alpha-tocopherol and a transition metal, iron, mixture was evaluated as a possible oxygen scavenger. The effects of moisture, amount of transition metal, and thermal processing on oxygen scavenging capability were also investigated. Results showed that alpha-tocopherol and transition metal had 6.72 cc oxygen per gram of oxygen scavenging capacity and 0.11 cc oxygen per gram per day of oxygen scavenging rate.
Nanoencapsulation technology was adopted for the possible oxygen scavenging activation system. Alpha-tocopherol-loaded poly caprolactone (PCL) nanoparticles were prepared by oil in water (O/W) emulsion solvent evaporation with ultrasonification. The effects of PCL concentration, solvent in oil phase, and ultrasonification …

Ecm Stabilization Strategies For Bioprosthetic Heart Valves For Improved Durability, Devanathan Raghavan

All Dissertations

Abstract
Approximately 85,000 heart valve replacement surgeries are performed every year in United States and about 300,000 surgeries worldwide. It is estimated that half of them are mechanical valve replacements and the other half bioprosthetic valve replacements. The use of bioprosthetic heart valves is slowly increasing. Bioprosthetic heart valves are made from porcine aortic valves or bovine pericardium. Commercially these bioprostheses are currently crosslinked using glutaraldehyde (GLUT) to prevent tissue degradation and reduce tissue antigenicity. GLUT crosslinks these bioprostheses by stabilizing the collagen present in the tissue via a Schiff base reaction of the aldehyde with the hydroxylysine / lysine …

High Speed Wavelength Tuning Of Sgdbr Lasers For Optical Coherence Tomography Applications, Benjamin Maher

Master's Theses

The application of Sample Grated Distributed Bragg Reflector (SGDBR) wavelength tunable lasers for swept-wavelength Optical Coherence Tomography (OCT) is explored. OCT is a method of measuring reflectivity versus distance into samples under test with a focused infrared light source. Swept wavelength OCT requires a laser light source that is capable of sweeping its wavelength quickly over the entire wavelength range of the tunable laser. Fast sweeping of the laser's wavelength enables real-time imaging of a wide surface area of the surface under test. This thesis will show that SGDBR lasers can be designed to meet the fast wavelength ramp speeds …

Nano-Raman Spectroscopy And Surface Nanostructuring Using Near-Field Optics, Kaijun Yi

Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research

To satisfy the development of nanoscience and nanotechnology, techniques to characterize and fabricate nanostructures and nanodevices are in great demand. Laser, as a unique monochromatic and coherent light source, meets the needs because it exhibits the potential to reveal some vital information of the materials. However, the applications of laser technology to nanoscience and nanotechnology are facing a severe challenge: the spatial resolution cannot be further enhanced to achieve nanometer scales due to the optical diffraction limit associated with conventional optics. In response to this challenge, near-field optics has been emerging as a new scientific area to deal with optical …

Characterization Of Vascular Smooth Muscle Cell Mechanical And Frictional Properties Using Atomic Force Microscopy, Jason Hemmer

All Dissertations

A working hypothesis within the Laboratory of Vascular Research is that mechanical loading on vascular smooth muscle cells (VSMCs), especially due to solid contact from endovascular devices, contributes to the development of restenosis. In order to better understand the role of mechanical loading on VSMCs in vascular disease development, it is imperative to understand the mechanical properties of VSMCs themselves. To measure the viscoelastic and frictional properties of living VSMCs in an in vitro setting, an atomic force microscope (AFM) was utilized, thereby allowing for mechanical testing of living cells in a fluid environment. In the first phase of research, …

Human Microvasculature Fabrication Using Thermal Inkjet Printing Technology, Xiaofeng Cui

All Dissertations

The current tissue engineering paradigm is that successfully engineered thick tissues must include vasculature. As biological approaches alone such as VGEF have fallen short of their promises, one may look for an engineering approach to build microvasculature. With the advent of cell printing, one may be able to build precise human microvasculature with suitable bio-ink. Human Microvascular Endothelial Cells (HMVEC) and fibrin were studied as bio-ink for microvasculature construction. Endothelial cells are the only cells to compose the human capillaries and also the major cells of blood vessel intima layer. Fibrin has been already widely recognized as tissue engineering scaffold …

Modeling And Control Of Piezoactive Micro And Nano Systems, Saeid Bashash

All Dissertations

Piezoelectrically-driven (piezoactive) systems such as nanopositioning platforms, scanning probe microscopes, and nanomechanical cantilever probes are advantageous devices enabling molecular-level imaging, manipulation, and characterization in disciplines ranging from materials science to physics and biology. Such emerging applications require precise modeling, control and manipulation of objects, components and subsystems ranging in sizes from few nanometers to micrometers. This dissertation presents a comprehensive modeling and control framework for piezoactive micro and nano systems utilized in various applications.
The development of a precise memory-based hysteresis model for feedforward tracking as well as a Lyapunov-based robust-adaptive controller for feedback tracking control of nanopositioning stages are …

Synthesis And Characterization Of Macromolecular Layers Grafted To Polymer Surfaces, Oleksandr Burtovyy

All Dissertations

The composition and behavior of surfaces and interfaces play a pivotal role in dictating the overall efficiency of the majority of polymeric materials and devices. Surface properties of the materials can be altered using surface modification techniques. It is necessary to highlight that successful methods of surface modification should affect only the upper layer of the polymer material without changing bulk properties. The processes must introduce new functionalities to the surface, optimize surface roughness, lubrication, hydrophobicity, hydrophilicity, adhesion, conductivity, and/or biocompatibility.
Research presented in this dissertation is dedicated to the synthesis, characterization, and application of thin macromolecular layers anchored to …

Vascular Tissue Engineering: The Creation Of Living, Non-Thrombogenic, Functional Blood Vessels Based On Elastin Scaffolds, Aditee Kurane

All Dissertations

Cardiovascular diseases are the leading cause of death worldwide. Blood vessel replacement is a common treatment for vascular diseases such as atherosclerosis, restenosis and aneurysm, with over 300,000 bypass procedures performed each year. However, vein grafts are limited due to their availability. Although synthetic vascular replacements have been successful for large diameter arteries, they have shown minimal success in arteries with diameters <6mm. This is because most synthetic materials induce thrombus formation which, within a few months of implantation, causes failure of the vascular graft due to occlusion. Tissue engineering is a promising approach to the fabrication of non-thrombogenic vascular grafts, but a reliable and expandable cell source for tissue-engineered vascular graft (TEVG) has not been established.
The work presented here is motivated by the current unavailability of an ideal tissue engineered blood vessel replacement. Our overall goal is to create a living tissue engineered vascular graft that is biodegradable, non-thromobogenic, presents low antigenicity and …

Measuring And Modeling Of Plant Root Uptake Of Organic Chemicals, Erik Dettenmaier

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Determining the root uptake of xenobiotic organic chemicals into plants is critical for assessing the human and ecological health risks associated with the consumption of plants growing in contaminated environments. Root uptake of xenobiotic organics occurs passively in conjunction with transpiration and the transport from root to shoot is ultimately controlled by passage through one or more lipid root membranes. The transpiration stream concentration factor (TSCF), the ratio between the concentration of a chemical in the xylem to that in the solution used by the roots, is used to describe the relative ability of an organic chemical to be passively …

Particle Characterization And Concentration Using Aerodynamic Vectoring, Zac Humes

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

An experimental demonstration of a new, non-contact particle characterization technique called Aerodynamic Vectoring Particle Sorting (AVPS) is presented. AVPS uses secondary blowing and suction control flows-flows that are a fraction of the jet flow rate-to sharply change the direction of a planar, particle-laden jet. As the jet is vectored, particles present in the flow experience a resultant drag force, dependent upon their size, that balances inertia. Since this balance determines the particle's trajectory, vectoring the flow leads to a separation of particles downstream. This simple, low-pressure-drop sorting technique classifies particles with less risk of damage or contamination than currently available …

Hydrogen Production Using Geothermal Energy, Theodore Wayne Hand

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

With an ever-increasing need to find alternative fuels to curb the use of oil in the world, many sources have been identified as alternative fuels. One of these sources is hydrogen. Hydrogen can be produced through an electro-chemical process. The objective of this report is to model an electrochemical process and determine gains and or losses in efficiency of the process by increasing or decreasing the temperature of the feed water. In order to make the process environmentally conscience, electricity from a geothermal plant will be used to power the electrolyzer. Using the renewable energy makes the process of producing …

Dechlorinating And Iron Reducing Bacteria Distribution In A Trichloroethene Contaminated Aquifer, Carmen Lourdes Yupanqui Zaa

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The Operable Unit 5 (OU 5) area of Hill Air Force Base currently has two trichloroethene-contaminated groundwater plumes underneath residential areas in Sunset and Clinton, Utah. Bioremediation by biological reductive dechlorination can be an important mechanism for the removal of chlorinated compounds from the plumes. The presence of suitable bacteria to carry on reductive dechlorination is the key in the bioremediation process. The goal of this study was to determine the distribution and population density of the 16S rRNA genes of Bacteria, Dehalococcoides ethenogenes, Desulfuromonas michiganensis, Geobacter spp and Rhodoferax ferrireducens-like bacteria, as well as the functional genes trichloroethene reductive …

A Three-Dimensional, Time-Dependent Circulation Model Of Utah Lake, Eric V. Callister

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Spatial and temporal variations of Utah Lake’s flow field were modeled using the Estuary Lake and Computer Model from the Centre for Water Research (CWR-ELCOM) at the University of Western Australia as part of an effort to increase understanding of the lake’s natural processes in order to restore the lake to its pristine, clear-water state and preserve the habitat of the June sucker, an endangered species. The model was validated using temperature measurements taken by sensors in 2007. The water temperature was a strong function of air temperature and incident short wave radiation, and was influenced to a lesser degree …

Rank-Data Distribution Method (R-D Method) For Daily Time-Series Bayesian Networks And Total Maximum Daily Load Estimation, Joon-Hee Lee

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Daily time series-based models are required to estimate the higher frequency fluctuations of nutrient loads and concentrations. Some mechanistic mathematical models can provide daily time series outputs of nutrient concentrations but it is difficult to incorporate non-numerical data, such as management scenarios, to mechanistic mathematical models. Bayesian networks (BNs) were designed to accept and process inputs of varied types of both numerical and non-numerical inputs.

A Rank-Data distribution method (R-D method) was developed to provide large time series of daily predicted flows and Total Phosphorus (TP) loads to BNs driving daily time series estimates of T-P concentrations into Hyrum and …

Application Of Structural Control For Civil Engineering Structures, Abdollah Shafieezadeh

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This study presents the application of control methods in seismic mitigation of structural responses. The study consists of two parts. In the first section, fractional order filters are utilized to enhance the performance of the conventional LQR method for optimal robust control of a simple civil structure. The introduced filters modify the state variables fed back to the constant gain controller. Four combinations of fractional order filter and LQR are considered and optimized based on a new performance criterion defined in the paper. Introducing fractional order filters is shown to improve the results considerably for both the artificially generated ground …

Uptake And Release Kinetics Of Sulfolane By Cattail Plants, Tiffany Leo

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Sulfolane (tetrahydrothiophene 1,1-dioxide, C₄H₈O₂S) is a highly water-soluble, non-ionizable, organic compound used along with diisopropanolamine in the Sulfinol™️ process to remove hydrogen sulfide from natural gas. Sulfolane has been identified in wetland vegetation near a sour gas processing facility in Alberta, Canada, and extensive uptake of sulfolane by cattails has also been demonstrated in a laboratory environment. Consequently, it has been suggested that plants could play an important role in the natural attenuation of sulfolane in contaminated wetlands. This assumes that the sulfolane is metabolized and/or sequestered in the plant and not released back …

Volatilization Of Trichloroethylene From Shallow Subsurface Environments: Trees And Soil, Rachel Melanie Winters

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Results from two previous studies conducted at Operable Unit 2 (OU2) of Hill Air Force Base, Utah indicate that the phytovolatilization (volatilization from leaves and trunk) of TCE by indigenous trees as well as soil surface flux may play a significant role in the removal of TCE from shallow groundwater plumes around the base. Previous studies investigated late summer and early autumn TCE leaf volatilization but no attempt was made to examine potential TCE volatilization seasonal variability and the volatilization of TCE directly from tree trunks. Whole tree transpiration rates were also not directly measured. To address those limitations and …

Integrating Surface And Sub Surface Flow Models Of Different Spatial And Temporal Scales Using Potential Coupling Interfaces, Alphonce Chenjerayi Guzha

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The main objective of this research was to develop and utilize a coupled surface water groundwater model to simulate hydrological responses of watersheds. This was achieved by coupling the U.S. Geological Survey (USGS) groundwater flow model, MODFLOW, and the rainfall runoff model, TOPMODEL, in one case study and coupling MODFLOW with a networked version of TOPMODEL called TOPNET in another case study. The model coupling was achieved using the InCouple approach, which utilizes Potential Coupling Interfaces (PCIs) that are abstractions from model flow diagrams that expose only those aspects of a model relevant to coupling. Coupling the rainfall-runoff models to …

Gene Expression Analysis Of Immobilized Saccharomyces Cerevisiae, Ryan Michael Summers

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Immobilization is an effective method to increase ethanol production, as proven by previous research. Results almost exclusively demonstrate an increase in ethanol production by and decrease in reproduction rate of immobilized Saccharomyces cerevisiae cells. Recently, research has been conducted to determine the cause of this change. The extreme variance in results due to lack of technology makes it difficult to determine the cellular changes induced by immobilization. With the advent of new technology, specifically gene expression analysis, the RNA content of cells can be easily and rapidly analyzed.

S. cerevisiae cells were immobilized in 3% (w/v) calcium alginate beads and …

The Effect Of Climate Change On The Hydrology Of A Mountainous Catchment In The Western United States: A Case Study At Reynolds Creek, Idaho, Anurag Nayak

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This research is focused on understanding the sensitivity of a hydrologic regime at the Reynolds Creek Experimental Watershed (RCEW), a snowmelt dominated semi-arid mountain basin located in southwest Idaho, to climate warming.

Climate data, collected during 1962 to 2006 at many locations in the RCEW, was carefully checked, preprocessed, and corrected for errors and noise signals introduced by the instrument malfunctioning and extreme weather conditions. An Automated Precipitation Correction Program (APCP) was developed to remove mechanical errors from the weighing-recording bucket type precipitation gauge measurements. APCP produces comparable results to the manual techniques but a degree faster (few minutes against …

Estimating Total Phosphorus And Total Suspended Solids Loads From High Frequency Data, Amber Spackman Jones

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Frequently measured turbidity was examined as a surrogate for total phosphorus (TP) and total suspended solids (TSS) loads at two locations in the Little Bear River, Utah, USA. Using regression techniques, equations were developed for TP and TSS as functions of turbidity. The equations accounted for censored data, and additional explanatory variables to represent hydrological conditions were considered for inclusion in the equations. By using the resulting surrogate relationships with high frequency turbidity measurements, high frequency estimates of TP and TSS concentrations were calculated. To examine the effect of sampling frequency, reference loads were determined from the concentration records for …

Hydrogen Production By Anaerobic Fermentation Using Agricultural And Food Processing Wastes Utilizing A Two-Stage Digestion System, Reese S. Thompson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Hydrogen production by means of anaerobic fermentation was researched utilizing three different substrates. Synthetic wastewater, dairy manure, and cheese whey were combined together at different concentrations under batch anaerobic conditions to determine the optimal hydrogen producing potential and waste treatment of each. Cheese whey at a concentration of 55% was combined with dairy manure at a concentration of 45% to produce 1.53 liters of hydrogen per liter of substrate. These results are significant because the control, synthetic wastewater, which was a glucose-based substrate, produced less hydrogen, 1.34 liters per liter of substrate, than the mixture of cheese whey and dairy …

Distributed Control For Robotic Swarms Using Centroidal Voronoi Tessellations, Shelley Rounds

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This thesis introduces a design combining an emerging area in robotics with a well established mathematical research topic: swarm intelligence and Voronoi tessellations, respectively. The main objective for this research is to design an economical and robust swarm system to achieve distributed control. This research combines swarm intelligence with Voronoi tessellations to localize a source and create formations. Extensive software coding must be implemented for this design, such as the development of a discrete centroidal Voronoi tessellation (CVT) algorithm.

The ultimate purpose of this research is to advance the existing Mobile Actuator and Sensor Network (MASnet) platform to eventually develop …

Student Achievement And Affective Traits In Electrical Engineering Laboratories Using Traditional And Computer-Based Instrumentation, Matthew D. Lammi

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Distance education has the ability to transcend distance and time, reaching students anywhere at any time, particularly those underrepresented in engineering. Engineering is a practice-oriented profession requiring an interweaving of scientific theory and applied hands-on activities. Despite the need for distance education in engineering, few studies have systematically investigated the impact of student achievement and attitude in distance engineering laboratories. This quasi-experimental research addressed that need by studying the cognitive and affective domains of achievement in engineering laboratories while employing computer-based and traditional oscilloscopes. The students from two courses, electrical engineering for nonmajors and electronic fundamentals, were randomly assigned into …