Open Access. Powered by Scholars. Published by Universities.®

Digital Commons Network™

Open Access. Powered by Scholars. Published by Universities.®

Brigham Young University

Discipline
Keyword
Publication Year
Publication
Publication Type
File Type

Articles 6001 - 6030 of 8052

Full-Text Articles in Entire DC Network

Effects Of Gap Open And Gap Extension Penalties, Hyrum Carroll, Mark J. Clement, Perry Ridge, Quinn O. Snell Oct 2006

Effects Of Gap Open And Gap Extension Penalties, Hyrum Carroll, Mark J. Clement, Perry Ridge, Quinn O. Snell

Faculty Publications

Fundamental to multiple sequence alignment algorithms is modeling insertions and deletions (gaps). The most prevalent model is to use gap open and gap extension penalties. While gap open and gap extension penalties are well understood conceptually, their effects on multiple sequence alignment, and consequently on phylogeny scores are not as well understood. We use exhaustive phylogeny searching to explore the effects of varying the gap open and gap extension penalties for three nuclear ribosomal data sets. Particular attention is given to optimal phylogeny scores for 200 alignments of a range of gap open and gap extension penalties and their respective …

Go to article

Pharmacogenomics: Analyzing Snps In The Cyp2d6 Gene Using Amino Acid Properties, Wesley A. Beckstead, Mark J. Clement, Mark Ebbert, David Mcclellan, Timothy O'Connor Oct 2006

Pharmacogenomics: Analyzing Snps In The Cyp2d6 Gene Using Amino Acid Properties, Wesley A. Beckstead, Mark J. Clement, Mark Ebbert, David Mcclellan, Timothy O'Connor

Faculty Publications

Each year people suffer from complications of adverse drug reactions, but with pharmacogenomics there is hope to prevent thousands of these people from suffering or dying needlessly. The CYP2D6 gene is responsible for metabolizing a large portion of these drugs. Because of the gene’s importance, various approaches have been taken to analyze CYP2D6 and single nucleotide polymorphisms (SNPs) throughout its sequence. This study introduces a novel method to analyze the effects of SNPs on encoded protein complexes by focusing on the biochemical properties of each nonsynonymous substitution using the program TreeSAAP. We apply this technique to SNPs found in the …

Go to article

Performance Of Algebraic Multigrid For Parallelized Finite Element Dns/Les Solvers, Gregory James Larson Sep 2006

Performance Of Algebraic Multigrid For Parallelized Finite Element Dns/Les Solvers, Gregory James Larson

Theses and Dissertations

The implementation of a hybrid spectral/finite-element discretization on the unsteady, incompressible, Navier-Stokes equations with a semi-implicit time-stepping method, an explicit treatment of the advective terms, and an implicit treatment of the pressure and viscous terms leads to an algorithm capable of calculating 3D flows over complex 2D geometries. This also results in multiple Fourier mode linear systems which must be solved at every timestep, which naturally leads to two parallelization approaches: Fourier space partitioning, where each processor individually and simultaneously solves a linear system, and physical space partitioning, where all processors collectively solve each linear system, sequentially advancing through Fourier …

Go to article

Numerical Simulation Of Plasma-Based Actuator Vortex Control Of A Turbulent Cylinder Wake, Nathan Keith Mcmullin Sep 2006

Numerical Simulation Of Plasma-Based Actuator Vortex Control Of A Turbulent Cylinder Wake, Nathan Keith Mcmullin

Theses and Dissertations

A numerical study has been performed to investigate the mechanics of the turbulent wake of a circular cylinder that is controlled by a plasma actuator. The numerical investigation implements a straightforward moving wall boundary condition to model the actuator's effects on the flow. Validations of the moving wall for this simulation are set forth with the understanding that the moving wall can model the plasma actuator bulk flow effects at a distance downstream and not in a region near or on the plasma actuator. The moving wall boundary condition is then applied to a circular cylinder at a Reynolds number …

Go to article

Obstacle Avoidance For Small Unmanned Air Vehicles, Brandon R. Call Sep 2006

Obstacle Avoidance For Small Unmanned Air Vehicles, Brandon R. Call

Theses and Dissertations

Small UAVs are used for low altitude surveillance flights where unknown obstacles can be encountered. These UAVs can be given the capability to navigate in uncertain environments if obstacles are identified. This research presents an obstacle avoidance system for small UAVs. First, a mission waypoint path is created that avoids all known obstacles using a genetic algorithm. Then, while the UAV is in flight, obstacles are detected using a forward looking, onboard camera. Image features are found using the Harris Corner Detector and tracked through multiple video frames which provides three dimensional localization of the features. A sparse three dimensional …

Go to article

Studies On Cyclooxygenase-1, Its Structure And Splice Variants, And Modulation Of Cyclooxygenase-2 By Inducible Nitric Oxide Synthase And Novel Phytochemicals., Yibing Xu Sep 2006

Studies On Cyclooxygenase-1, Its Structure And Splice Variants, And Modulation Of Cyclooxygenase-2 By Inducible Nitric Oxide Synthase And Novel Phytochemicals., Yibing Xu

Theses and Dissertations

Cyclooxygenases (COXs) are of important therapeutic value as they are the target site of aspirin-like drugs. Here I report nine new COX-1 splice variants in chapter 1, which I characterized with regard to heme-binding and other properties. Inducible NO synthase (iNOS) and cyclooxygenase-2 (COX-2) are co-inducible in many tissues following mitogenic and proinflammatory stimulation. In chapter 2, I investigate the physical and enzymatic properties of human COX-2 and iNOS and demonstrate that, despite reports to the contrary by another laboratory, they do not interact. The only reported COX-1 splice variant to exhibit cyclooxygenase activity has been isolated from …

Go to article

Improving Error Discovery Using Guided Model Checking, Neha Shyam Rungta Sep 2006

Improving Error Discovery Using Guided Model Checking, Neha Shyam Rungta

Theses and Dissertations

State exploration in directed software model checking is guided using a heuristic function to move states near errors to the front of the search queue. Distance heuristic functions rank states based on the number of transitions needed to move the current program state into an error location. Lack of calling context information causes the heuristic function to underestimate the true distance to the error; however, inlining functions at call sites in the control flow graph to capture calling context leads to exponential growth in the computation. This paper presents a new algorithm that implicitly inlines functions at call sites to …

Go to article

Detection Of A Landslide Glide Plane Using Seismic Reflection Methods: Investigation At Little Valley Landslide In Draper, Utah, Brady E. Tingey Sep 2006

Detection Of A Landslide Glide Plane Using Seismic Reflection Methods: Investigation At Little Valley Landslide In Draper, Utah, Brady E. Tingey

Theses and Dissertations

An integration of geological and geophysical techniques has been used to characterize the internal structure of the Little Valley Landslide in Draper, Utah, USA. The Little Valley Landslide is a pre-historic landslide as old as 13ka B.P. It is found to consist of chaotic and disturbed weathered volcanic units derived from Tertiary age volcanics that comprise a great portion of the Wasatch Range. Geotechnical investigations that were integrated with the geophysical results included excavation of trenches and drilling of boreholes. Geophysical methods, in particular high-resolution seismic data, were used to provide a framework for interpreting the geotechnical observations. High-resolution seismic …

Go to article

Multiplatform Genome-Wide Identification And Modeling Of Functional Human Estrogen Receptor Binding Sites, Chin-Yo Lin, Vinsensius B. Vega, Koon Siew Lai, Li Say Kong, Min Xie, Xiaodi Su, Huey Fang The, Jane S. Thomsen, Ai Li Yeo, Wing Kin Sung, Guillaume Bourque, Edison T. Liu Sep 2006

Multiplatform Genome-Wide Identification And Modeling Of Functional Human Estrogen Receptor Binding Sites, Chin-Yo Lin, Vinsensius B. Vega, Koon Siew Lai, Li Say Kong, Min Xie, Xiaodi Su, Huey Fang The, Jane S. Thomsen, Ai Li Yeo, Wing Kin Sung, Guillaume Bourque, Edison T. Liu

Faculty Publications

Transcription factor binding sites (TFBS) impart specificity to cellular transcriptional responses and have largely been defined by consensus motifs derived from a handful of validated sites. The low specificity of the computational predictions of TFBSs has been attributed to ubiquity of the motifs and the relaxed sequence requirements for binding. We posited that the inadequacy is due to limited input of empirically verified sites, and demonstrated a multiplatform approach to constructing a robust model. Results: Using the TFBS for the estrogen receptor (ER)alpha (estrogen response element [ERE]) as a model system, we extracted EREs from multiple molecular and genomic platforms …

Go to article

Design And Fabrication Of Rotationally Tristable Compliant Mechanisms, Tyler M. Pendleton Sep 2006

Design And Fabrication Of Rotationally Tristable Compliant Mechanisms, Tyler M. Pendleton

Theses and Dissertations

The purpose of this research is to develop the tools necessary to create tristable compliant mechanisms; the work presents the creation of models and concepts for design and a demonstration of the feasibility of the designs through the fabrication of tristable compliant mechanism prototypes on the macro scale. Prior methods to achieve tristable mechanisms rely on detents, friction, or power input; disadvantages to these methods include a high number of parts, the necessity for lubrication, and wear. A compliant tristable mechanism accomplishes tristability through strain energy storage. These mechanisms would be preferable because of increased performance and cost savings due …

Go to article

Digital Roots Of Human Relations: Enabling Technologies For Family History And Genealogical Research, William Barrett Sep 2006

Digital Roots Of Human Relations: Enabling Technologies For Family History And Genealogical Research, William Barrett

BYU Family Historian

No abstract provided.

Go to article

Design Of Piezoresistive Mems Force And Displacement Sensors, Tyler Lane Waterfall Sep 2006

Design Of Piezoresistive Mems Force And Displacement Sensors, Tyler Lane Waterfall

Theses and Dissertations

MEMS (MicroElectroMechanical Systems) sensors are used in acceleration, flow, pressure and force sensing applications on the micro and macro levels. Much research has focused on improving sensor precision, range, reliability, and ease of manufacture and operation. One exciting possibility for improving the capability of micro sensors lies in exploiting the piezoresistive properties of silicon, the material of choice in many MEMS fabrication processes. Piezoresistivity—the change of electrical resistance due to an applied strain—is a valuable material property of silicon due to its potential for high signal output and on-chip and feedback-control possibilities. However, successful design of piezoresistive micro sensors requires …

Go to article

Vol 5 Fall 2006 The Byu Family Historian, The Byu Family Historian Sep 2006

Vol 5 Fall 2006 The Byu Family Historian, The Byu Family Historian

BYU Family Historian

No abstract provided.

Go to article

About The Authors, The Byu Family Historian Sep 2006

About The Authors, The Byu Family Historian

BYU Family Historian

No abstract provided.

Go to article

Fourier Spectroscopy Of Ultrashort Laser Pulses, Scott D. Bergeson, Justin Peatross Sep 2006

Fourier Spectroscopy Of Ultrashort Laser Pulses, Scott D. Bergeson, Justin Peatross

Faculty Publications

We describe a Fourier-transform spectrometer appropriate for use in an undergraduate optics laboratory. The modular design, which uses off-the-shelf equipment, is suitable for determining the spectra of ultrashort pulsed and continuous light sources. The spectrometer does not require equal step sizes for the motion of the mirror. An algorithm interpolates the phase of both a reference and an unknown light beam at equal intervals before performing the Fourier transform. The interferometer scan and the phase and spectral analysis are performed in a few seconds, making the apparatus a useful tool for teaching concepts of temporal coherence and Fourier spectroscopy.

Go to article

Digital Roots Of Human Relations: Enabling Technologies For Family History And Genealogical Research, William A. Barrett Sep 2006

Digital Roots Of Human Relations: Enabling Technologies For Family History And Genealogical Research, William A. Barrett

Faculty Publications

Flowing out of a Computer Science research lab on the third floor of the Talmage Building is a wellspring of enabling technologies for family history and genealogical research. Here, computer science students, working under the direction of Dr. Tom Sederberg and Dr. Bill Barrett are creating software tools to help individuals with their family history research so that people everywhere can seek out their ancestors and perform vital ordinances in their behalf, as desired. These tools include visualization of an entire pedigree on a single (large) sheet of paper, the ability to automatically calculate if and how two or more …

Go to article

Detection Of Proteins By Two-Photon Excitation Of Native Fluorescence, Li Li Aug 2006

Detection Of Proteins By Two-Photon Excitation Of Native Fluorescence, Li Li

Theses and Dissertations

Proteins are of primary importance to the structure and function of all living cells. Study of proteins relies on the ability to separate a complex mixture so that individual proteins can be more easily processed by other techniques. Since protein samples often exist at low concentration in a small volume, the trend in chemical analysis is toward micro total analysis systems (µTAS) or lab-on-a-chip devices. Among µTAS separation methods, the relatively new electric field gradient focusing (EFGF) technique has shown potential. It focuses and separates analytes based on their electrophoretic migration in an opposing hydrodynamic flow. The detection principles that …

Go to article

Sound Absorption And Sound Power Measurements In Reverberation Chambers Using Energy Density Methods, David B. Nutter Aug 2006

Sound Absorption And Sound Power Measurements In Reverberation Chambers Using Energy Density Methods, David B. Nutter

Theses and Dissertations

Measurements in a reverberation chamber use spatially averaged squared pressure to calculate sound absorption, sound power, and other sound measurements. While a reverberation chamber provides an approximation of a diffuse sound field, variations in the measurements introduce uncertainty in measurement results. Room qualification procedures require a sufficient number of source-receiver locations to obtain suitable measurements. The total acoustic energy density provides greater spatial uniformity than squared pressure, which requires fewer source-receiver positions to produce similar or better accuracy in measurement results. This paper explores the possibility of using energy density in place of squared pressure, using methods outlined in current …

Go to article

Experimental And Modeling Investigations Of Biomass Particle Combustion, Hong Lu Aug 2006

Experimental And Modeling Investigations Of Biomass Particle Combustion, Hong Lu

Theses and Dissertations

This investigation provides a comprehensive analysis of entrained-flow biomass combustion processes. Experimental and theoretical investigations indicate how particle shape and size influence biomass combustion rates. Experimental samples include flake-like, cylinder-like, and equant (nearly spherical) shapes with similar particle masses and volumes but different surface areas. Samples of small (less than 500 µm) particles were passed through a laboratory entrained-flow reactor in a nitrogen/air atmosphere and a maximum reactor wall temperature of 1600 K, while large samples were reacted in suspension in a single particle furnace operated at similar conditions as the entrained-flow reactor. A separately developed computer and image analysis …

Go to article

Recovering Grain Boundary Inclination Parameters Through Oblique Double-Sectioning, Eric Richards Homer Aug 2006

Recovering Grain Boundary Inclination Parameters Through Oblique Double-Sectioning, Eric Richards Homer

Theses and Dissertations

A method for the retrieval of grain boundary inclination parameters of the grain boundary character distribution by oblique double-sectioning is proposed. The method, which is similar to the recovery of the orientation distributions from sets of incomplete pole-figures, is described along with a framework for implementation. The method directly measures grain boundary inclinations in a manner similar to serial sectioning while statistically sampling the microstructure comparably to stereological methods. Computer simulations of the method were used to confirm the mathematical framework. Additional simulations, where the grain boundary normal distributions were recovered by both oblique double-sectioning and stereological methods, showed that …

Go to article

Feedback Applications In Active Noise Control For Small Axial Cooling Fans, Matthew J. Green Aug 2006

Feedback Applications In Active Noise Control For Small Axial Cooling Fans, Matthew J. Green

Theses and Dissertations

Feedback active noise control (ANC) has been applied as a means of attenuating broadband noise from a small axial cooling fan. Such fans are used to maintain thermal stability inside of computers, projectors, and other office equipment and home appliances. The type of low-level noise radiated from axial cooling fans has been classified as harmful to productivity and human well being. Previous research has successfully implemented feed-forward ANC, targeting specific narrow-band fan noise content related to the blade passage frequency (BPF) of the fan. The reference signal required for a feed-forward algorithm limits its ability to attenuate much of the …

Go to article

Vision-Based Rendering: Using Computational Stereo To Actualize Ibr View Synthesis, Kevin L. Steele Aug 2006

Vision-Based Rendering: Using Computational Stereo To Actualize Ibr View Synthesis, Kevin L. Steele

Theses and Dissertations

Computer graphics imagery (CGI) has enabled many useful applications in training, defense, and entertainment. One such application, CGI simulation, is a real-time system that allows users to navigate through and interact with a virtual rendition of an existing environment. Creating such systems is difficult, but particularly burdensome is the task of designing and constructing the internal representation of the simulation content. Authoring this content on a computer usually requires great expertise and many man-hours of labor. Computational stereo and image-based rendering offer possibilities to automatically create simulation content without user assistance. However, these technologies have largely been limited to creating …

Go to article

Mesoscopic Domain Average Engineering Simulations Of Ferroelectric Perovskites Compared With Multidomain Group Theoretical Predictions, Brandon J. Keith, Dorian M. Hatch Aug 2006

Mesoscopic Domain Average Engineering Simulations Of Ferroelectric Perovskites Compared With Multidomain Group Theoretical Predictions, Brandon J. Keith, Dorian M. Hatch

Faculty Publications

Engineered, multidomain ferroelectrics are of current interest for mechatronic and optical applications. Previously [D. M. Hatch et al., J. Appl. Phys. 94, 5220 (2003)], we presented a set of tables/symmetry rules showing all possible domain average engineered multidomain structures arising from [100]-, [110]-, and [111]-ordering ferroelectric transitions from a Pm[overline 3]m perovskite structure. In this work we test those predictions against three-dimensional mesoscopic fast quench simulations under various electric/stress field combinations and find excellent agreement with multidomain group theory. These simulations use a Langevin strain-displacement/polarization evolution strategy and are important to developing processing conditions for materials with precise domain structures.

Go to article

Understanding Dc-Bias Sputtered Thorium Oxide Thin Films Useful In Euv Optics, William R. Evans, Sarah C. Barton, Michael Clemens, David D. Allred Aug 2006

Understanding Dc-Bias Sputtered Thorium Oxide Thin Films Useful In Euv Optics, William R. Evans, Sarah C. Barton, Michael Clemens, David D. Allred

Faculty Publications

We use spectroscopic ellipsometry to determine the optical constants of seven thin-film ThO2 samples deposited by radio-frequency sputtering, thickness ranging between 24 and 578 nm, for the spectral range of 1.2 to 6.5. We used a hollow-cathode light source and vacuum monochromator to measure constants at 10.2 eV. None of the deposition parameters studied including DC-bias voltages successfully increased the n of (that is, densify) thoria films. The value of n at 3.0 eV is 1.86 ± 0.04. We find compelling evidence to conclude that the direct bad gap is at ~5.9 eV, clarifying the results of others, some of …

Go to article

Sources Of Variability In A Proteomic Experiment, Scott Daniel Crawford Aug 2006

Sources Of Variability In A Proteomic Experiment, Scott Daniel Crawford

Theses and Dissertations

The study of proteomics holds the hope for detecting serious diseases earlier than is currently possible by analyzing blood samples in a mass spectrometer. Unfortunately, the statistics involved in comparing a control group to a diseased group are not trivial, and these difficulties have led others to incorrect decisions in the past. This paper considers a nested design that was used to quantify and identify the sources of variation in the mass spectrometer at BYU, so that correct conclusions can be drawn from blood samples analyzed in proteomics. Algorithms were developed which detect, align, correct, and cluster the peaks in …

Go to article

Effects Of Anthropogenic Land Use On Odonata In Playas Of The Southern High Plains, K. M. Hernandez, B. A. Reece, N. E. Mcintyre Aug 2006

Effects Of Anthropogenic Land Use On Odonata In Playas Of The Southern High Plains, K. M. Hernandez, B. A. Reece, N. E. Mcintyre

Western North American Naturalist

Playas are ephemeral wetlands that are the only source of aboveground freshwater in the southern Great Plains, making them of vital importance to aquatic and amphibious animals. Playas are also highly threatened from anthropogenic land use (chiefly agriculture, which decreases hydroperiod through increased sedimentation). We examined community structure of adult odonates (dragonflies and damselflies) in playas differing in the 2 main regional forms of surrounding land use (cropland vs. grassland). Analysis of odonate diversity revealed high overlap between cropland and grassland playas. Traditional species-area theory did not fit observed patterns, as there appears to be a threshold playa size that …

Go to article

Methane Conversion In Pulsed Corona Discharge Reactors, Morris D. Argyle, Gui-Bing Zhao, Sanil John, Ji-Jun Zhang, Linna Wang, Suresh S. Muknahallipatna, Jerry C. Hamann, John F. Ackerman, Ovid A. Plumb Aug 2006

Methane Conversion In Pulsed Corona Discharge Reactors, Morris D. Argyle, Gui-Bing Zhao, Sanil John, Ji-Jun Zhang, Linna Wang, Suresh S. Muknahallipatna, Jerry C. Hamann, John F. Ackerman, Ovid A. Plumb

Faculty Publications

This work reports the effect of capacitance, cathode material, gas flow rate and specific energy input on methane conversion, energy efficiency and product selectivity in a co-axial cylinder pulsed corona discharge reactor. Ethan and acetylene appear to be formed from dimerization of CH3 radicals and CH radicals, respectively, while ethylene is formed mainly from the dehydrogenation of ethane. At a given power input, low capacitance with high pulse frequency results in higher methane conversion and energy efficiency than operation at high capacitance with low pulse frequency. Platinum coated stainless steel cathodes slightly enhance methane conversion relative to stainless steel cathodes, …

Go to article

Ferritin: Mechanistic Studies And Electron Transfer Properties, Bo Zhang Aug 2006

Ferritin: Mechanistic Studies And Electron Transfer Properties, Bo Zhang

Theses and Dissertations

Ferritins are ubiquitous iron storage proteins in living systems. Although much is known about the iron deposition process in ferritin and a mechanism has been developed, several important issues still remain unknown. One lingering question is the less than stoichiometric quantities of hydrogen peroxide detected in previous studies on animal ferritins. Extensive experimental data on identifying the species in competition for peroxide equivalents point to a surprising conclusion that H2O2 generated in the ferroxidase reaction is consumed by amine buffers that are commonly employed in in vitro ferritin studies, while non-nitrogen containing buffers, such as acetate, phosphate, and carbonate, do …

Go to article

Adaptive Control Of Micro Air Vehicles, Joshua Stephen Matthews Aug 2006

Adaptive Control Of Micro Air Vehicles, Joshua Stephen Matthews

Theses and Dissertations

Although PID controllers work well on Miniature Air Vehicles (MAVs), they require tuning for each MAV. Also, they quickly lose performance in the presence of actuator failures or changes in the MAV dynamics. Adaptive control algorithms that self tune to each MAV and compensate for changes in the MAV during flight are explored. However, because the autopilots on MAVs are small, many of the adaptive control algorithms like those that employ least squares estimation may take too much code space, memory, and/or computing power. In this thesis we develop several Lyapunov-based model reference adaptive control (MRAC) schemes that are both …

Go to article

Improved State Estimation For Miniature Air Vehicles, Andrew Mark Eldredge Aug 2006

Improved State Estimation For Miniature Air Vehicles, Andrew Mark Eldredge

Theses and Dissertations

Research in Unmanned Air Vehicles (UAV's) continues to push the limitations of size and weight. As technical advances have made UAV's smaller and less expensive, they have become more flexible and extensive in their roles. To continue using smaller and less expensive components while retaining and even enhancing performance requires more sophisticated processing of sensor data in order for the UAV to accurately determine its state and thereby allow the use of feedback in controlling the aircraft automatically. This work presents a three-stage state-estimation scheme for the class of UAV's know as Miniature Air Vehicles (MAV's). The first stage estimates …

Go to article

First Prev Next Last