Physical Sciences and Mathematics Commons^™

Alzheimer’S Disease: A New Model Defining The Mechanism Of Iron- Catalyzed Radical Damage To Neurons, Richard Watt, Jonathan Wisco

Journal of Undergraduate Research

The MEG proposal focused on understanding how elevated homocysteine levels cause the inability of cells to control iron levels as a cause for Alzheimer’s disease. Iron is associated with the amyloid plaques and tau tangles that are proposed to cause damage to neurons. Dr. Wisco and I previously submitted an NIH R15 proposal that was viewed positively but was not funded due to a lack of preliminary data. Our goal was to use MEG funding to provide preliminary data supporting the hypothesis. We proposed that Homocysteine was a dangerous trigger for disrupting iron metabolism. Biochemical techniques, immunohistochemistry techniques and MRI …

Mentoring Undergraduates At The Intersection Of Organic Synthesis And Peptide Science, Steven L. Castle

Journal of Undergraduate Research

Our academic goals were threefold. First, we aimed to synthesize building blocks and begin assembling them to construct the anticancer peptide yaku’amide A (YA, Figure 1). Our purposes in synthesizing YA were to develop new chemical reactions suitable for efficiently preparing its unusual amino acids (shown in red and blue in Figure 1), and synthesize simplified analogues for use in studies designed to reveal its biological target and mode of action. Our second academic goal was derived from the first and involved investigating the ability of bulky dehydroamino acids (i.e., the amino acids of YA shown in blue in Figure …

Function Of Ric-8a In G Protein E+- Subunit Biogenesis, Barry Willardson

Journal of Undergraduate Research

1. Grant Ludlam. The MEG award helped support Grant’s work from January 2015 through August 2016. During this time Grant has worked on three projects. He investigated the role of Ric8A in the folding of the G protein a subunit and its assembly into the G protein heterotrimeric complex. Unfortunately, his results showed that deletion of Ric8A in the photoreceptor cells of mice did not affect G protein signaling. As a result, he changed his research focus to determining the structure of the BBSome core complex. He assisted a graduate student, Takuma Aoba, in this work. They used a combination of …

A Novel Approach To A Big Simulation Problem: Creating Efficient Dry Granular Material Simulations With Accurate Visual Detail And Behavior, Seth Holladay

Journal of Undergraduate Research

We received a MEG grant for researching the simulation of granular materials for computer graphics and animation. Materials such as sand and snow simulation is very expensive but necessary for productions, as well as hard to control the look, so I have been mentoring undergraduate and graduate students researching how to make sand simulations both efficient and art directable.

Calculating Music Similarity With Mobile Device Playlists, Jacob O'Bryant, Dennis Ng

Journal of Undergraduate Research

Music recommendation systems, such as Pandora and Spotify, help listeners to discover new music. The similarity of different songs is an important measure used in music recommendation. We have studied manually-created playlists on mobile devices to see if they can be used to accurately calculate song similarity. We collected playlists from 41 research subjects and used a co-occurrence model to calculate similarity between songs in the collection.

Using Frequency Noise Feedback To Satabilize Extended Cavity Diode Lasers For Use In Atomic Physics, Mckinley Pugh, Dallin Durfee

Journal of Undergraduate Research

Diode lasers in particular are useful in atomic physics because they are durable, compact, and relatively inexpensive. Unfortunately diode lasers also have linewidths that are much wider than atomic transitions. One common method to narrow the linewidth of diode lasers is to add a reflection grating outside the laser, creating an extended cavity diode laser (ECDL). While ECDLs are effective at narrowing the linewidth, they also introduce so many variables that affect the wavelength of the laser that small changes in the laser’s environment can cause the laser to mode hop, or jump to an entirely different wavelength.

A Photometric Approach To The Redshift Of Galaxies, John Bohman, Joseph Moody

Journal of Undergraduate Research

It is necessary to study the distribution of matter to better understand the universe. There are many difficulties associated with this task however, one of the most basic being that that the universe is an extremely large space, and it takes a lot of time and effort to observe faint objects. Multi fiber spectrometers have made this task much easier, and over 1.4 million spectroscopic redshifts have been obtained. While this is certainly impressive, much remains to be done. This project attempts to develop a survey method capable of detecting and finding the redshift of relatively close (meaning a redshift …

Weak Synchronization In Excitatory – Inhibitory Neuronal Networks, Joel Eliason, Benjamin Webb

Journal of Undergraduate Research

One ubiquitously observed dynamic phenomenon in the nervous system is that of weak synchronization or clustering, a behavior in which a large group of neurons in a population will all fire synchronously and then fall out of synchronization. When isolated to neurons that only form short-range connections, this behavior is typically referred to as “neuronal avalanches”, and is thought to be particularly important for robustness of information transmission as well as sensitivity to inputs. Given these potential computational benefits, avalanches have been a focus of theoretical biologists for the past 20 years. In particular, my project focused on the conditions, …

Identifying Binary Brown Dwarf Systems Using Model Point Spread Functions, Kyle Matt, Denise Stephens

Journal of Undergraduate Research

The purpose of this project was to improve upon a method for discovering binary brown dwarf systems, and create a program to speed up the implementation of that method. A Brown Dwarf (BD) is a celestial object that is not massive enough to undergo hydrogen fusion in its core, meaning it is too small to be a star, but is also too big to be a planet. BDs can form in low-mass binary pairs. A stellar object located many parsecs away will act as a point source of light for an observer on Earth, therefore the light from such an …

Machine Learning With Scattering Transforms, Jacob Hansen, Gus Hart

Journal of Undergraduate Research

Our goal was to implement scattering transforms as a mathematical representation of materials. The intention of this project was to build intuition on this technique using model data in one and two dimensions. The tools created here will be used as templates in further projects on real materials data. The intuition built during this project is crucial to the machine learning framework for materials design that we hope to build in the near future.

Characterizing Great Salt Lake Dust Relative Other Regional Dust Sources, Colin Hale, Carling Greg

Journal of Undergraduate Research

Dust storms occur frequently along the Wasatch Front. These dust events may have negative effects on human health and agriculture. To help understand dust events along the Wasatch Front, this study focuses on analyzing dust deposition to better locate dust emission sources. Understanding the source of dust events is important. This is important because Great Salt Lake water levels are dropping exposing lakebed. This newly expose lakebed may result in increased frequency and intensity of dust events. To understand if this lakebed is affecting the Wasatch Front and acting as an emission source.

Identifying Risk Factors For Interstate Crashes Using Spatial Statistics, Kaitlin Gibson, Matthew Heaton

Journal of Undergraduate Research

The goal of systemic highway safety improvement is to identify road characteristics, called risk factors, associated with a higher prevalence of crashes, so that the roads can be modified to avoid these characteristics. However, the statistical analyses these improvement projects are based on generally use methods which are not appropriate for the data. Our project implements novel spatial statistical methodology which is appropriate and state-of-the-art to identify these risk factors.

Utilizing The Power Of Graphical Processing For Dna Mapping: A Comparison Of Gnumap And Barracuda, Cole Lyman, Mark Clement

Journal of Undergraduate Research

Recent advances in genome sequencing technologies have resulted in a large increase in the amount of genetic data available. Large Genome Wide Association Studies (GWAS) have the potential to identify the causes of cancer, Alzheimer’s disease, heart failure and many other diseases if the large quantities of data that are becoming available can be analyzed effectively. Next-generation read mapping software, a crucial step in analyzing genetic data, is slow while trying to achieve high mapping accuracy. One approach to speeding up next-generation read mapping focuses on using Graphical Processing Units (GPUs). This project compared the effectiveness of two genome mappers, …

An Algorithm For Multiple Regression Variable Selection For Biochemical Oxygen Demand, Zach White, Dr. William Christensen

Journal of Undergraduate Research

Biochemical Oxygen Demand (BOD) is used to measure of the amount of oxygen required by aerobic bacteria and other microorganisms to stabilize decomposable organic matter. It is run as a laboratory based biodegradation test and relies upon the presence of a thriving microbial community that may be naturally present in the sample or artificially introduced by addition of a seed, commonly a known volume of sewage effluent of known BOD. A standard BOD test is run in the dark at a temperature of 20 degrees Celsius for 5 days. This is defined as a five-day BOD (BOD5), which is the …

Trace Element Analysis Of Quartz Grains In The Wah Wah Springs Tuff And Granodiorite Intrusion, Joel Barker, Dr. Eric Christiansen

Journal of Undergraduate Research

The Wah Wah Springs tuff and cogenetic granodiorite were part of the creation of the Indian Peak-Caliente Caldera Complex, which lies on the Nevada-Utah border (Skidmore, 2013). The complex formed during the middle Cenozoic (36-18 Ma) during an episode of explosive silicic activity (Best et al., 2013). Rollback of the subducting lithosphere likely caused the silicic activity, evidenced by the migration of magmatism southward (Best et al., 2013). The dehydration of the subducting oceanic lithosphere caused mafic magmas high in water to rise and fractionate in continental crust before eruption (Skidmore, 2013). Over twenty-four different ignimbrites have been found in …

Seeing The World Through New Eyes: Implementing Map-Based Mobile Apps In Field Trips And Research, Mariah Chambers, Ron Harris

Journal of Undergraduate Research

Mobile apps are a resource that can aid in field trip instruction and enhance students’ learning. Because the specific location of the field trip is often an important element in overall understanding, map-based learning materials can be used to integrate information with the place, providing context for the concepts that will be learned on the field trip. The purpose of this project was twofold. One purpose was to provide professors with information and instructions for using map-based mobile apps to prepare students for, and provide resources during, field trips and study abroad experiences. A second purpose was to implement the …

Characterizing The Design Space Of Oscillatory Biological Networks, Leanne Lunsford, Denise Stephens, Eric Hintz

Journal of Undergraduate Research

Characterizing the relevant parameters of a design space in order to satisfy a specific behavior criterion is an important problem throughout all of science and engineering. In this project we proposed to apply model reduction to the case of biological oscillations involving Michaelis-Menten reactions. By removing irrelevant parameters from a fully connected network we were able to reduce a known problem in systems biology to a more general model. Furthermore, significant progress has been made in applying Manifold Boundary Approximation Method (MBAM) to oscillatory models in systems biology.

Right Now Is The Wrong Time: And Other Considerations When Presenting Security Warnings, Brock Johanson, Bonnie Anderson

Journal of Undergraduate Research

Neuro Information Security (NeuroIS) focuses on the use of neurological measurements to improve the security of information systems. The BYU NeuroIS lab uses neurological tools and measurements to examine factors that affect security outcomes. Previous work has focused on various factors such as dual task interference (DTI), threat assessment, as well as factors such as habituation and generalization, which have become focus streams of research. The primary point of failure in most security related incidents tends to be users themselves. As such, anything that can be used to overcome neurobiological phenomenon such as those listed above can ultimately lead in …

Fabrication Of Dye Sensitized Solar Cells Using Native And Non-Native Nanocrystals In Ferritin As The Dye, Alessandro Perego, John Colton

Journal of Undergraduate Research

Dye-sensitized solar cells (DSSCs) present a valuable and sustainable alternative to silicon solar cells. These cells present numerous advantages compered to inorganic photovoltaic systems, such as ability of absorb more sunlight per surface area than standard silicon-based solar panels, DSSCs are also able to work even in low-light conditions such as non-direct sunlight and cloudy skies. Finally, they are economical, easy to manufacture and constructed from abundant and stable resource materials. This makes DSSCs an attractive replacement for current photovoltaic technology. Ferritin (FTN) is a 12 nm diameter spherical protein with an 8 nm hollow interior, which naturally contains iron …

Mobile Hands: What Your Phone Use Says About You, Parker Williams, Jeff Jenkins

Journal of Undergraduate Research

The percentage of individuals using mobile phones to respond to online applications, forms, and surveys is predicted to rapidly increase in the future. As of June 2, 2015, there were an estimated 2.6 billion smartphones in use in the world; by 2020 there will be 6.1 billion smartphones in use. Smartphones will account for roughly 80% of all mobile driven data traffic by 2020 (Lunden, 2015). With the proliferation of smartphones, measuring the fidelity of information gathered from and about the user becomes extremely important. Smartphones are a rich source of behavioral and biometric information, gathering data about how the …

Intelligent Stitching: Transforming Offline Stroke Extraction For Online Handwriting Recognition, Curtis Wigington, William Barrett

Journal of Undergraduate Research

Images of historical documents are being collected and archived much faster than volunteers can possibly index them alone. Improvements in offline handwriting recognition could greatly accelerate the work of indexing by FamilySearch. Offline handwriting recognition has already been shown to be effective in assisting indexers and automating the transcription of historical documents into searchable texts. As documents are collected from all around the world, generalized techniques that are robust to damage and noise are needed. Effective stroke extraction and processing is an important tool in improving current recognition techniques.

Reverse-Engineering Gene Networks That Can Remember Using The Manifold Boundary Approximation Method, Andrew White, Mark Transtrum

Journal of Undergraduate Research

Observable biological behaviors result from the interactions of microscopic elements, which form complex systems that we can model mathematically. Ideally, mechanistic models should predict a biological system’s behavior without misrepresenting the system’s biochemistry. The method of model reduction known as the Manifold Boundary Approximation Method (MBAM) [2, 3] can help us identify which parts of a model are relevant for explaining a particular behavior. This project applies MBAM to gene transcription networks that exhibit a behavior known as “memory,” the ability to retain cellular decisions to activate or silence genes. We hypothesize that MBAM can help us model the behaviors …