Digital Commons Network^™

Hybrid Dynamic Optimization Methods For Systems Biology With Efficient Sensitivities, Nicholas Lewis, John Hedengren, Eric Haseltine

Faculty Publications

In recent years, model optimization in the field of computational biology has become a prominent area for development of pharmaceutical drugs. The increased amount of experimental data leads to the increase in complexity of proposed models. With increased complexity comes a necessity for computational algorithms that are able to handle the large datasets that are used to fit model parameters. In this study the ability of simultaneous, hybrid simultaneous, and sequential algorithms are tested on two models representative of computational systems biology. The first case models the cells affected by a virus in a population and serves as a benchmark …

Rigidly Foldable Origami Gadgets And Tessellations, Thomas A. Evans, Robert J. Lang, Spencer P. Magleby, Larry L. Howell

Faculty Publications

Rigidly foldable origami allows for motion where all deflection occurs at the crease lines and facilitates the application of origami in materials other than paper. In this paper, we use a recently discovered method for determining rigid foldability to identify existing flat-foldable rigidly foldable tessellations, which are also categorized. We introduce rigidly foldable origami gadgets which may be used to modify existing tessellations or to create new tessellations. Several modified and new rigidly foldable tessellations are presented.

An Improved Statistical Analysis For Predicting The Critical Temperature And Critical Density With Gibbs Ensemble Monte Carlo Simulation, Richard A. Messerly, Richard L. Rowley, Thomas A. Knotts Iv, W Vincent Wilding

Faculty Publications

A rigorous statistical analysis is presented for Gibbs ensemble Monte Carlo simulations. This analysis reduces the uncertainty in the critical point estimate when compared with traditional methods found in the literature. Two different improvements are recommended due to the following results. First, the traditional propagation of error approach for estimating the standard deviations used in regression improperly weighs the terms in the objective function due to the inherent interdependence of the vapor and liquid densities. For this reason, an error model is developed to predict the standard deviations. Second, and most importantly, a rigorous algorithm for nonlinear regression is compared …

A Numerical Comparison Of Precipitating Turbulent Flows Between Large-Eddy Simulation And One-Dimensional Turbulence, Alex W. Abboud, Ben B. Schroeder, Tony Saad, Sean T. Smith, Derek D. Harris, David O. Lignell

Faculty Publications

This study presents the results of computational fluid dynamics simulations of a multiphase, reacting, turbulent mixing layer in an idealized geometry. The purpose is to compare large-eddy simulation (LES) to one-dimensional turbulence (ODT) and examine the trends of the flow under differing mixing conditions. Aqueous streams are mixed together to precipitate polymorphs of calcium carbonate. The polymorphs of calcium carbonate are tracked numerically using population balance equations (PBE). Each PBE contains all of the relevant physical models to track the particle evolution including nucleation, growth, and aggregation. A simple subgrid mixing model that is convenient for use with PBEs was …

Fast Inference For Interactive Models Of Text, Jeffrey A. Lund

Theses and Dissertations

Probabilistic models of text are a useful tool for enabling the analysis of large collections of digital text. For example, Latent Dirichlet Allocation can quickly produce topical summaries of large collections of text documents. Many important uses cases of such models include human interaction during the inference process for these models of text. For example, the Interactive Topic Model extends Latent Dirichlet Allocation to incorporate human expertiese during inference in order to produce topics which are better suited to individual user needs. However, interactive use cases of probabalistic models of text introduce new constraints on inference - the inference procedure …

An Approach For Designing Origami-Adapted Products With Aerospace Mechanism Examples, Jessica Morgan

Theses and Dissertations

The objective of this research is to develop a design process for origami-adapted products and demonstrate it using aerospace mechanism examples. Origami-adapted design is a type of origami-based design. Origami-based design ranges from abstract to concrete applications of origami to design and includes: origami-inspired design, origami-adapted design, and origami-applied design. Origami-adapted design adapts origami fold patterns into products while preserving functionality. Some of the desirable attributes of origami that are sought after in design include: 1) reduced number of parts, 2) stowability, 3) deployability, 4) transportability, 5) manufacturability from a flat sheet of material, 6) ease of miniaturization, 7) a …

Assessment Of The Immediate Impacts Of The 2013–2014 Drought On Ecosystems Of The California Central Coast, Christopher Potter

Western North American Naturalist

A methodology was developed to assess the impacts of the historic 2013–2014 drought on ecosystems of California’s Central Coast region, using a combination of satellite image analysis and in situ measurements of soil moisture in predominant vegetation types of the region. According to differences in Landsat drought indices for plant water stress and vegetation green cover (NDWI and NDVI, respectively), the geographic areas within the study region that were most severely impacted by the 2013 drought were the inland Carmel Valley in northern Monterey County and the coastal zones around San Simeon Point and Cambria in northern San Luis Obispo …

The Problem Of Low Agreement Among Automated Indentification Programs For Acoustical Surverys Of Bats, Cliff Lemen, Patricia W. Freeman, Jeremy A. White, Brett R. Andersen

Western North American Naturalist

We compared 4 programs designed to identify species of bats from their echolocation calls (Bat Call ID, EchoClass, Kaleidoscope Pro, and SonoBat) using field data collected in Nebraska, USA (29,782 files). Although we did not know the true identity of these bats, we could still compare the pairwise agreement between software packages when identifying the same call sequences. If accuracy is high in these software packages, there should be high agreement in identification. Agreement in identification by species averaged approximately 40% and varied by software package, species, and data set. Our results are not consistent with the high accuracy often …

Improving Production Of Carbon Nanotube Composites, Dan Broadbent

Faculty Publications

Carbon nanotube (CNT) composites offer great promise for making lighter, thinner and stronger structures. Producing CNT composites, however, can be tricky. The focus of this work is to improve production yields of CNT composites by doing research and development in two areas:

• Research the relationship between ethylene gas concentrations used during CNT growth and yields of usable composite films produced.
• Develop furnace for growing larger CNT samples, which will enable larger sizes and quantities of research product.

Direct Search Algorithms For Nonlinear Optimization, Mark Abramson

BYU Research Development Office Research Networking Conference

Areas of Research • Increase efficiency by reducing the number of Poll points • Decomposition approaches for problems with more than 50 variables • Extending algorithm to problems with random noise • Extending to problems in which some derivative information is available • Extending to multifidelity problems • Applications to engineering problems

Analytical Chemistry Of Solids, Eric H. Christiansen

BYU Research Development Office Research Networking Conference

Demonstrating the use of various imaging technology (X-ray fluorescence spectrometry, laser ablation inductively coupled mass spectrometry, cathodoluminescence imaging) to analyze volcanic solids, areas, and tectonic processes.

Education Research In The Life Sciences, Jamie Jensen

BYU Research Development Office Research Networking Conference

Areas of Interest: The development and transferability of scientific reasoning skills; appropriate assessment techniques; effective strategies for constructivist teaching in the STEM classroom; strategies to enhance STEM retention

Speed/Research Networking, Conrad Monson, Kristen Kellems, Joann Ann Petrie

BYU Research Development Office Research Networking Conference

This is the fourth Speed Networking Event. One goal: faculty hear about research across the university. A second goal: foster collaborative/multidisciplinary/interdisciplinary research opportunities. A third goal: network.

Ribosome Component Turnover Kinetics Describes A Two-Pool Kinetic Model In Dietary Restriction That Suggests Rpl10 Is Exchanged During Ribosome Lifespan, Andrew David Mathis

Theses and Dissertations

The eukaryotic ribosome is a large molecular machine consisting of ~80 ribosomal proteins and 4 rRNAs. The 40S and 60S ribosomal subunits are assembled in the nucleolus by ~200 helper proteins then shipped into the cytoplasm or to the endoplasmic reticulum where protein translation takes place. Eventually ribosomes are removed from the cytoplasm and recycled through ribophagy, however, very is little is known about ribosomal protein exchange after assembly but before ribophagy. Using kinetic turnover measurements of ribosomal proteins and rRNA in vivo we determined ribosomal protein replacement rates are diverse suggesting ribosomal components may be replaced without destruction of …

Student Evaluation Of Mathematical Explanations In An Inquiry-Based Mathematics Classroom, Ashley Burgess Hulet

Theses and Dissertations

Students do not always evaluate explanations based on the mathematics despite their teacher's effort to be the guide-on-the-side and delegate evaluation to the students. This case study examined how the use of three features of the Discourse—authority, sociomathematical norms, and classroom mathematical practices—impacted students' evaluation and contributed to students' failure to evaluate. By studying three pre-service elementary school students' evaluation methods, it was found that the students applied different types of each of the features of the Discourse and employed them at different times. The way that the features of the Discourse were used contributed to some of the difficulties …

Teaching Leadership In Teaching And Mentoring, Denise M. Halverson, Alonzo Cook, Mike Diede

BYU Research Development Office Research Networking Conference

Leadership topics and the reasons to implement leadership practices in teaching and mentoring.

Design, Fabrication, And Optimization Of Miniaturized Devices For Bioanalytical Applications, Suresh Kumar

Theses and Dissertations

My dissertation work integrates the techniques of microfabrication, micro/nanofluidics, and bioanalytical chemistry to develop miniaturized devices for healthcare applications. Semiconductor processing techniques including photolithography, physical and chemical vapor deposition, and wet etching are used to build these devices in silicon and polymeric materials. On-chip micro-/nanochannels, pumps, and valves are used to manipulate the flow of fluid in these devices. Analytical techniques such as size-based filtration, solid-phase extraction (SPE), sample enrichment, on-chip labeling, microchip electrophoresis (µCE), and laser induced fluorescence (LIF) are utilized to analyze biomolecules. Such miniaturized devices offer the advantages of rapid analysis, low cost, and lab-on-a-chip scale integration …

A Nonabelian Landau-Ginzburg B-Model Construction, Ryan Thor Sandberg

Theses and Dissertations

The Landau-Ginzburg (LG) B-Model is a significant feature of singularity theory and mirror symmetry. Krawitz in 2010, guided by work of Kaufmann, provided an explicit construction for the LG B-model when using diagonal symmetries of a quasihomogeneous, nondegenerate polynomial. In this thesis we discuss aspects of how to generalize the LG B-model construction to allow for nondiagonal symmetries of a polynomial, and hence nonabelian symmetry groups. The construction is generalized to the level of graded vector space and the multiplication developed up to an unknown factor. We present complete examples of nonabelian LG B-models for the polynomials x^2y + y^3, …

A Method For Using Pre-Computed Scenarios Of Physically-Based Spatially-Distributed Hydrologic Models In Flood Forecasting Systems, Herman Guillermo Dolder

Theses and Dissertations

Every year floods are responsible of a significant number of human losses, many of which could be avoided with a broader implementation of flood forecasting systems. Nevertheless, there are still some technological and economic limitations that impede the creation of these systems in many parts of the world. At the core of many flood forecasting systems is a hydrologic model that transforms the weather forecast into a flow forecast. Using real-time modeling for potential floods poses a series of problems: if the model is complex, the computational power required can be significant, and consequently expensive, and if the model is …

Peroxy Radical - Water Complexes: Their Role In The Atmosphere, Sambhav Rajendra Kumbhani

Theses and Dissertations

The importance of radical-water complexes in the atmosphere is explored in this dissertation. Radicals, although present in small concentrations in the atmosphere, play a significant role in creating and removing atmospheric pollution. As the atmosphere warms and consequently gets wetter, it is essential to understand the effects of water vapor on radical chemistry. This dissertation reports studies on the effects of water vapor on the kinetics of the self-reaction of β-hydroxyethyl peroxy radical (β-HEP), a prominent organic peroxy radical in the atmosphere. Both experimental and computational studies have been performed to examine the effects of water vapor on the kinetics …

Big Data: Challenges And Opportunities For Digital Libraries, Richard Hacken

Faculty Publications

Presented as a Keynote Address to the International Conference on Computing in Engineering and the Sciences in Istanbul, Turkey, on July 30, 2015.

This is an abstract of the speech:

Thanks to technological progress, thanks to the copious Internet, thanks to geometrically burgeoning social media and to quickly proliferating sensors, the flood of data available to us is surging larger and larger, faster and faster. Paradigms for management and analysis are at the core of data-driven businesses and institutions, fueling the velocity of scientific research and development. The phrase “Big Data” was itself coined by scientists as they manipulated exploding …

Comparing Theory And Experiment For Analyte Transport In The First Vacuum Stage Of The Inductively Coupled Plasma Mass Spectrometer, Matthew R. Zachreson

Theses and Dissertations

The inductively coupled plasma mass spectrometer (ICP-MS) has been used in laboratories for many years. The majority of the improvements to the instrument have been done empirically through trial and error. A few fluid models have been made, which have given a general description of the flow through the mass spectrometer interface. However, due to long mean free path effects and other factors, it is very difficult to simulate the flow details well enough to predict how changing the interface design will change the formation of the ion beam. Towards this end, Spencer et al. developed FENIX, a direct simulation …

The Synthesis And Characterization Of Ferritin Bio Minerals For Photovoltaic, Nanobattery, And Bio-Nano Propellant Applications, Trevor Jamison Smith

Theses and Dissertations

Material science is an interdisciplinary area of research, which in part, designs and characterizes new materials. Research is concerned with synthesis, structure, properties, and performance of materials. Discoveries in materials science have significant impact on future technologies, especially in nano-scale applications where the physical properties of nanomaterials are significantly different than their bulk counterparts. The work presented here discusses the use of ferritin, a hollow sphere-like biomolecule, which forms metal oxo-hydride nanoparticles inside its protein shell for uses as a bio-inorganic material.Ferritin is capable of forming and sequestering 8 nm metal-oxide nanoparticles within its 2 nm thick protein shell. A …

Principal Learning-Centered Leadership And Faculty Trust In The Principal, Shane Justin Farnsworth

Theses and Dissertations

Principals are increasingly held accountable for student achievement outcomes. Existing research has found principal leadership indirectly affects student achievement (Leithwood, Louis, Anderson, & Wahlstrom, 2004). Principals face a problem when they are accountable for achievement outcomes and are dependent upon others and other variables to achieve those outcomes. Consequently, principals will benefit from a richer understanding of how their leadership indirectly affects student achievement. Using the Vanderbilt Assessment of Leadership in Education (VAL-ED) measurement of principal learning-centered leadership (Goldring, Porter, Murphy, Elliot, & Cravens, 2009) and the Omnibus T-Scale measurement of faculty trust in the principal (Hoy & Tschannen-Moran, 2003), …

A Mexican Woman's Journey In Becoming A Successful American Educator, Lucy Ordaz Sanchez

Theses and Dissertations

This self-study explores the question of "What factors in my life shaped my journey in earning an American college degree and becoming a successful educator in the U.S.?" This question is explored in the context of my own lived experiences. Results contribute to the field of immigrant studies and may encourage others who wish to transition from first generation immigrant to successful professional educator in the U.S. This study employed hermeneutic phenomenology to answer the research question. It used in-depth narrative interviews to elicit my responses to lived experiences from growing up in Mexico to my current teaching position. Thematic …

Analytical Approaches In Investigating The Kinetics Of Water-Molecule Complexes In Tropospheric Reactions, William J. Keeton

Theses and Dissertations

Ozone is a heavily monitored pollutant. Ozone is not directly emitted into the atmosphere, but rather the product of chemical reactions. Ground level ozone occurs when nitrogen oxides (NOx) and volatile organic compounds (VOCs) react with each other in the presence of sunlight. The primary precursors of ozone are anthropogenically emitted, and as a result, tropospheric ozone has cost millions of dollars in damages and has hurt the health of countless people. This dissertation is a collection of work that aims to provide insight into atmospheric reactions that result in tropospheric ozone and the instrumentation to study such reactions. While …

Vector Intensity And Holography-Based Acoustic Source Characterization Of A Military Jet Aircraft, Trevor Alden Stout

Theses and Dissertations

The scientific community has employed multiple methods to analyze and describe the jet noise emanating from the turbulent exhaust flow from modern military aircraft engines, with the goal that better characterization of the sound radiation will improve noise reduction efforts. This thesis utilizes three different approaches to characterize the noise source region from a static F-22A Raptor. First, the energy flow field along planes near the aircraft and along an arc is measured using a multidimensional vector intensity probe. The resulting vector intensity maps give a clear indication of the directionality of the noise as a function of frequency at …

An Improved Classifier Chain Ensemble For Multi-Dimensionalclassification With Conditional Dependence, Joseph Ethan Heydorn

Theses and Dissertations

We focus on multi-dimensional classification (MDC) problems with conditional dependence, which we call multiple output dependence (MOD) problems. MDC is the task of predicting a vector of categorical outputs for each input. Conditional dependence in MDC means that the choice for one output value affects the choice for others, so it is not desirable to predict outputs independently. We show that conditional dependence in MDC implies that a single input can map to multiple correct output vectors. This means it is desirable to find multiple correct output vectors per input. Current solutions for MOD problems are not sufficient because they …

Glimpses Of World War Ii In Denmark: Memory And History In Frayn's Copenhagen And Sibbern's Resistance Scrapbook, Adriana Pinegar

Theses and Dissertations

The relationship between history and memory is long and complex. While some theorists argue that they are at odds with one another, this thesis explores the necessary relationship between the two. Using Michael Frayn's 1998 play, Copenhagen, and the scrapbook of a Danish police officer and resistance fighter during World War II, the author posits the central role of uncertainty in the negotiation of individual memory and history. The position of the observer or witness to history affects the way the past is remembered and recorded. Individual witnesses, even and perhaps especially where they stray from the accepted historical narrative, …

Correlation Of Fluorescence Spectroscopy And Biochemical Oxygen Demand (Bod5) Using Regression Analysis, Alexander Tetteh Narteh

Theses and Dissertations

This research uses Regression analysis of fluorescence spectroscopy results to correlate with Biochemical Oxygen Demand (BOD5). Fluorescence spectroscopy was applied to samples taken from seven sample sites in the Provo and Orem waste water treatment plants found in Utah County. A total of 161 samples were collected for this research. 23 samples each were taken from four sites in the Provo waste water treatment plant namely Provo head works, aeration basin, primary filter settlement basin and the Provo effluent basin. The Orem head works, the clarifier and the Orem effluent basin were the three sample sites in the Orem waste …