Engineering

Jeremy Hunt, Brigham Young University Engineering Unnatural amino acid incorporation is a power tool in the synthetic biology toolbox that allows for unique residue chemistry to be incorporated into proteins. This technology has many promising applications in areas such as protein-protein interaction, biotherapeutics, biosensing, and biocatalysis. One challenge of uAA-incorporation is the current inability to properly predict the impact of the novel uAA-residue chemistry on proper protein folding and function. Therefore, a screening technology would be desirable to rapidly assess the viability of uAA-incorporation sites. Cell-free protein synthesis (CFPS) provides a promising basis for rapid screening technologies. The open environment of CFPS has a variety of advantages over conventional in vivo systems, such as direct monitoring, selective protein expression, and facile deployment of synthetic pathways. Another primary benefit CFPS has over in vivo expression is the ability to directly express proteins from PCR-generated products, known as linear expression templates (LETs). The use of LETs decreases the labor and time to expression of recombinant proteins. Thus, LET-based CFPS is a propitious system for rapid screening of uAA-incorporation. Here we demonstrate uAA-incorporation using LET-based CFPS and identify how this technology can significantly reduce time and labor to rapidly express proteins containing uAAs.

Braden Hancock, Brigham Young University Engineering In Evolutionary Multi-objective Optimization (EMO), the mechanism of epsilon-dominance has received a lot of attention because of its ability to guarantee convergence near the Pareto frontier and maintain diversity among solutions at a reasonable computational cost. The main weakness of this mechanism is its inability to also identify and exploit knee regions of the Pareto frontier, which are frequently the regions of the frontier that are most interesting to the user. Many attempts have been made to resolve this issue, but each has resulted in either decreased computational efficiency or slower convergence. We therefore propose a new mechanism – Lamé-dominance – as a replacement for epsilon-dominance in EMO. The geometry of the Lamé curve naturally supports a greater concentration of solutions in directions of high tradeoff between objectives. This adaptable resolution of solutions in knee regions of the Pareto frontier will result in significant savings in time and money for complex optimization routines in large n-objective design scenarios.

Raymond Bilodeau, Brigham Young University Engineering Extreme piezoresistivity was discovered in a silicone/nickel nanostrand (silicone/NiNs) nanocomposite. A quantum mechanical tunneling percolation model has been developed which bridges the gap between quantum effects at the nanoscopic scale and bulk material response at the macroscopic scale. To further improve on this theory, a measurement technique was adapted for use in measuring the average distance (in nm) between the NiNs in the silicone matrix. The measurements produced strong correlation to newly developed theories on the nature of the nickel-silicone interaction. The predictions of the previously developed model were also compared to these new experimental measurements and the model is being adapted to more accurately represent the real data.

David Lindell, Brigham Young University Engineering Current ion detector technologies require low pressures and temperatures to achieve high sensitivity. These extra constraints result in bulky or expensive ion detection units and make a highly-portable mass spectrometer difficult or impractical to produce. A new ion detector technology that is unhampered by such constraints would allow the construction of miniaturized mass spectrometers. Such devices would have a myriad of potential applications, including use in space probes, on-site chemical weapon analyses, and in-field forensics. This research has produced solid-state ion detection devices with detection levels in the hundreds-of-ions range. The detectors are produced on a printed circuit board, are inexpensive, and are functional at room temperature and pressure. Solid-state detection capabilities were realized by adopting concepts from modern non-volatile (flash) memory and using custom-made low capacitance MOSFETs. Detection occurs as ions impact a Faraday cup and charge the gate of a MOSFET, yielding a voltage change in the circuit. In addition to refinements made by incorporating low-capacitance MOSFETs, commercial MEMS switches (which have only recently become available) are used to produce ion counts at rates up to 30 kHz. Amplification and filtering circuitry has also been added to further increase sensitivity levels. Results of this research show that ion detectors can be reduced in size and complexity, making a portable mass spectrometer more viable.

Anthony Bennett, Brigham Young University Engineering Foot Mouth Disease is considered to be the greatest hindrance to livestock trade in the world. The disease is extremely contagious and can transmit via aerosol, food scraps, and through blood, and tears among other transmission routes [1]. Currently, technological challenges hinder eradication efforts due to a wide variety of FMD strains, high vaccine production costs, as well as limited efficacy of vaccines across strains [2]. The countries most affected by the disease also face economic, social, and political challenges to disease eradication. Based upon historical evidence disease eradication has proven to be possible as shown in the US, the UK, and other countries [3]. In this presentation, we highlight these challenges and propose various routes to eradication in order to open up economic opportunities to developing countries as well as eliminating the threat of a disease outbreak in countries currently free of the disease. Morgan, E.R., et al., Assessing risks of disease transmission between wildlife and livestock: The Saiga antelope as a case study. Biological Conservation, 2006. 131(2): p. 244-254. Parida, S., Vaccination against foot-and-mouth disease virus: strategies and effectiveness. 2009. Perry, B. and K. Sones, Poverty reduction through animal health. Science, 2007. 315.

Bradley Hackett, Utah Valley University Engineering The Arduino microcontroller is very robust and is capable of performing a wide variety of functions to fit the needs of almost countless different projects. Many robots that are being built use a microcontroller, and the Arduino microcontroller is a good fit for many robots. The microcontroller is also standardized so it can be learned easily, and maintained easily as well, especially in a team environment. The simplicity of the Arduino offers a much more accessible design and development environment. This environment allows for very complex projects such as robotics to be approached in a manageable way. The SERA Bot is a robot which is designed efficiently and yet still has complexity, using the Arduino microcontroller. The S.E.R.A Bot is an acronym which stands for Searching Exploring Roaming Autonomous robot. The first task this robot can do is to communicate over Bluetooth to an Android tablet or phone to remotely control the robot by driving the motors or sending command signals to the Arduino microcontroller. The next task it is capable of is to use Light Dependant Resistors or LDRs to follow a light source or find the most brightly illuminated area of a room. The third task is object avoidance which is implemented using a simple ultrasonic distance sensor to detect if there is an object close in front of the robot. The last function of this robot is the ability to locate a beacon which emits a loud detectable sound, and is implemented using three amplified condenser microphones. The purpose behind this project is mainly to incorporate many simple functions to one robot. Many robots do one simple task, but the focus is to create a versatile robot, with enough complexity to be useful, but simple enough to be efficient.

Zola Adjei, Brigham Young University Engineering The research project is aimed at developing a tool to monitor the progress of rehabilitation efforts in Lake Malheur in Harney count, Oregon. The application of remote sensing techniques, which will be used to detect chlorophyll-a distribution from water algae growth in the lake. Concentrations of chlorophyll-a act as an indicator for algal blooms, which compete for nutrients and oxygen and can have significant detrimental effects on a body of water. To better identify the trend in growth activities of algal colonies, remote sensing will be effective in developing a model to map the path and region of high activities of algal growth and subsequently monitoring fish habitation on the entire Malheur Lake. The method uses satellite images which measure the reflectance of pigment concentrations, which can then be quantified as concentrations of chlorophyll-a using appropriate software and algorithms. The algorithms are based on relationships between the chlorophyll-a concentration measured in-situ and the reflectance measured in the satellite images. The algorithm that would be tested relies on the ratio of suitable bands in the electromagnetic spectrum. The Oregon Fish and Wildlife services have set preliminary actions by taking chlorophyll measurements earlier this year that will be used to help draw the relationship between the measured and satellite derived chlorophyll-a concentrations. There exists a research group in the Civil and Environmental engineering department that have employed this process on the Deer Creek lake in Utah and other surrounding water bodies which has shown successful outcomes in monitoring these lake’s water quality parameters including chlorophyll-a to help support the survival of fishes, restore their habitats and preserve cultural history. There will be a comparison done to the performance of remote sensing models in a large, shallow lake in Oregon, compared to models developed in deep, narrow lakes.

Stephanie Mitts, Weber State University Engineering The recent development of rainwater harvesting (RWH) as a local government and individual property owner solution to stormwater management and water supply has led to a wide array of individual program implementations across the country. RWH involves collecting stormwater runoff, storing it and applying it for beneficial reuse or release at a controlled rate. Decreased need of freshwater withdrawals reduces hydrology based energy consumption and protects ecosystems, potentially making RWH a more sustainable and efficient practice than centralized water supply. The goal of this research project was to compile and analyze the national trends for local government urban rainwater harvesting program policy. A survey was created and administered to RWH managers across the country to collect U.S. policy information. This report contains information to be used as a guide for local governments and other institutions considering implementing a program to promote RWH.

Jake Seiter, University of Utah Engineering Mining has always been among the most hazardous of occupations, and with the increasing demand for coal and minerals, safety in mines assumes even greater importance. Worldwide, underground miners are being exposed to noise and respirable dust hazards associated with roof bolt drilling. These hazards are now being understood to cause irreparable damage to the health of miners.

Jacob Robinson, Brigham Young University Mechanical Engineering Figure skating is a competitive sport that requires athletes to practice up to 5 days a week year round performing 50 to 100 jumps per day. This results in high, repetitive impact forces on the skater’s body which may lead to overuse injuries. While the negative effects of figure skating are well documented, the cause of these injuries is still unclear because the complexity of artistic figure skating limits current instrumentation from accurately measuring impact forces. This project has sought to fill this void by developing a force measurement system that will allow the figure skater to perform their jumps without any hindrance while accurately measuring the magnitude of the impact forces in the vertical and horizontal directions. Using strain gauges attached to the stanchions of the ice skate combined with a data collection system that attaches to the bottom of the boot, we have developed a prototype that accurately measures the forces produced in the ice skate. This will lead to a fully developed ice skate measurement system which will be used by researchers to investigate the impact forces generated in figure skating jumps and landings.

Connor George, Utah State University Electrical and Computer Engineering The SABER instrument, aboard the TIMED satellite, measures optical data regarding parameters of the Earth’s atmosphere with respect to altitude. Approximately once per minute, SABER performs a limb-scan measurement on the Earth’s atmosphere from which altitude emission profiles of key atmospheric gasses, including hydroxyl at wavelengths of 1.6 μm and 2.0 μm, are derived. Most hydroxyl profiles within the SABER dataset contain a single peak in the airglow altitude profile centered near an altitude of 87 km, but a significant portion of the profiles display two or more local maxima. MATLAB code was written to analyze the geophysical and temporal global distribution of the multiple-peak profiles. Graphs have been created which display relationships between the percentage of multiple-peak profiles and the local time, the cardinal orientation of the SABER device, and the latitude and longitude at which the atmospheric profile was measured. Patterns have been observed in multiple-peak profile distribution with respect to these variables. Possible causes of the multiple-peak occurrences in the hydroxyl altitude profiles include waves, geometrical effects of the SABER instrument, and/or chemistry of the atmosphere. In addition to graphing software, analysis software was written which counts the number of peaks present in any given altitude profile, and which ascertained the percentage of profiles displaying multiple-peak characteristics. A small (<1%) portion of hydroxyl altitude profiles were found to have abnormal distributions due to erroneous or noisy data collected by SABER. Software has also been written to remove such exceptions from the dataset. Additional investigation into the relationship between multiple-peak occurrences and cardinal direction orientation of the SABER device is required in order to further identify the causes for multiple peak profiles. An investigation into seasonal patterns for multiple-peak profiles is to be conducted. As the dataset grows, exception software will be updated to identify invalid altitude profiles. Also, ozone has been found to have multiple-peak altitude profiles similar to those of hydroxyl, and studies complementary to those performed on hydroxyl altitude profiles will be performed on ozone.

Derek Chang, University of Utah Bioengineering Atrial fibrillation (AF), the most common cardiac arrhythmia, is a rapid, irregular heart beat arising from uncontrolled and asynchronized electrical activation in the atria. This disruption of the normal electrical signaling hinders the contraction of the heart, leading to decreased blood flow, possible clot (thrombus) formation, and an increased risk of stroke. The left atrial appendage (LAA) is a small muscular pouch of highly variable anatomy within the left atrium. The LAA plays a prominent role in thrombus formation in patients with AF because of decreased blood flow within this structure. Thus, we hypothesized that the shape of the left atrial appendage is different in AF patients with a documented history of stroke. We used statistical shape analysis to determine which LAA shape variations contribute to stroke based on a cohort of AF patients who had both MRI and CT scans and a documented history of stroke. We manually delineated the boundaries of the LAA from each patient’s CT and MRI scans to analyze the resulting LAA segmentations for shape variations across imaging modalities and history of stroke. The results showed that patients who have AF and a history of stroke have an LAA with a narrower insertion site into the left atrium and are larger in size. In contrast, patients who have AF, but no history of stroke, have an LAA with a wider insertion site, which are smaller in size. By isolating specific LAA shape variants indicative of an underlying risk of stroke, we can use this shape classification scheme to better tailor AF therapies to each individual patient.

Autumn Pando, Brigham Young University Mechanical Engineering The wrist is one of the most common sites for joint injury. Over two-thirds of 75,000 annual repetitive joint injuries occur at the wrist. Excessive or abnormal wrist forces are thought to be one of the main contributing factors, yet no characterization of normal wrist forces exists. The purpose of this research is to fill this lack by creating a systematic, quantitative characterization of wrist forces and torques experienced in daily life. This database will aid further research in developing better and more personalized treatments as well as improving design considerations for human-machine interfaces. Ten healthy subjects participated in the experiment. Subjects performed 25 activities representative of daily life (e.g. hygiene maintenance, food preparation, using technology). Electromyographic (EMG) sensors recorded wrist muscle activity and electromagnetic motion sensors recorded wrist kinematics. Each subject performed a calibration task prior to the experimental protocol to determine the proportionality constant between EMG activity and torque. Wrist force and torque were determined from EMG activity using a constant of proportionality (identified by calibration), muscle length, and muscle velocity. Co-contraction was computed from torque. Wrist muscle usage, forces, torque magnitudes, torque angles, and percentage of co-contraction at varying levels of contraction were characterized. The results indicate muscle use, forces, and torques are unevenly distributed.

Mitchell Dabling, Utah State University Civil and Environmental Engineering Water management and flood control are essential elements of civilization. Linear weirs (e.g. ogee crest, sharp crested, and broad crested weirs) are often used in irrigation channels or reservoir spillways to regulate the discharge and upstream water level during flood flows. As hydrologic data sets increase in size and accuracy, the highest probable maximum flood (PMF) discharge is becoming increasingly more accurate, and in many cases much larger than previous estimates. Because of this, an older weir may need to be rehabilitated to ensure it can pass the updated PMF discharge safely without upstream flooding. A nonlinear weir (e.g. labyrinth or piano key weir) can replace a linear weir in a channel or spillway to pass significantly more discharge without requiring increased channel width. The Utah Water Research Laboratory at Utah State University, with the help of Utah Mineral Lease Funds, has developed and published design data for multiple configurations of nonlinear weirs. In 2012, the Utah Division of Water Resources used this data to design a labyrinth-style nonlinear weir that will replace the spillway currently in use at Millsite Reservoir in Emery County. This rehabilitation project will significantly decrease the flooding potential of the surrounding area.

Kay (Beau) Freckleton, University of Utah Mechanical Engineering Current quad-rotors provide excellent maneuverability and opportunity for data collection in large scale areas such as agriculture, but lack the capability to maintain flight for an extended period of time. This is due primarily to a lack of energy supply, requiring operators to replace the battery source before the quad-rotor completes its designated purpose [1]. In this paper, we introduce a mechanism to enable flying robotic rotorcraft, such as quadrotors and helicopters which utilize vertical takeoff and landing, to perch similar to a bird. The mechanism is passive, using only the weight of the rotorcraft for actuation. Such a mechanism will dispel the need for multiple batteries by allowing the quadrotor to perch amid its designated flight course, recharge using solar energy, and complete data collection over large scale areas in less time. In previous research to this same end, biomimetic approaches were pursued, resulting in designs that looked similar to the legs and feet of birds. The design in this paper utilizes a Sarrus mechanism to convert rotorcraft weight into perch grip. We began by designing the mechanism for a range of cylindrical perch sizes. Using MATLAB, we developed a program to optimize the various mechanism dimensions needed to perch within this range while also maximizing the mechanical advantage of grip force. Using SolidWorks, a 3-dimensional model was created and manufactured with these dimensions. In testing, the mechanism successfully allowed a small RC helicopter to perch on a 4cm diameter rod with some resistance to external forces. However, in crash tests, the mechanism was unable to withstand certain moment forces and developed large fractures. Further research will focus on decreasing these moment forces’ ability to weaken the mechanism while optimizing perching capability.

Kimberly Uchida, University of Utah Bioengineering and Oncological Sciences Programmed cell death 4 (PDCD4) loses its function as a tumor suppressor when co-expressed with a specific binding partner, protein arginine methyltransferase-5 (PRMT5). A better understanding of the regulation of PDCD4-PRMT5 interaction may lead to cancer therapies targeted at restoring the tumor suppressive function of PDCD4. Using Xenopus laevis (frog) eggs to generate extract trapped in either interphase or mitosis, we found that PDCD4-PRMT5 interaction is regulated by the cell cycle. Full-length PDCD4 bound PRMT5 more robustly in interphase than in mitosis. However, a truncated version of PDCD4, that retained the PRMT5 binding site, bound PRMT5 equally in interphase and mitosis. These results indicate that there may be a component of full-length PDCD4 that occludes the PRMT5 binding site in mitosis. Furthermore, we found that both full-length and the truncated PDCD4 are preferentially phosphorylated in mitosis, but preferentially methylated in interphase. From these results we speculate that phosphorylation of PDCD4 in mitosis allows PDCD4 to fold upon itself and effectively block the PRMT5 binding site. Additionally, phosphorylation may prevent methylation even when PRMT5 can bind PDCD4, explaining the lack of PDCD4 methylation in mitosis. Such an inhibitory mechanism may be useful in therapeutically restoring the tumor suppressive function of PDCD4. Future research will be aimed towards completing our understanding of PDCD4-PRMT5 interaction in the cell cycle, such as proving our model in human cells.

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