Annual Student Research Poster Session

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  Adamts6 Function is Crucial for Skeletal Development in Mice

  Morgan Black

  ADAMTS (A Disintegrin-like and Metalloproteinase with Thrombospondin type 1 motifs) proteins are secreted, extracellular matrix (ECM)-associated metalloproteinases. There are 19 ADAMTS protein-coding genes in mammals. Among them is Adamts6, which is often referred to as an orphan enzyme. Interestingly, the Adamts6 mutant mice generated in our laboratory are associated with craniofacial and heart defects as well as significant skeletal anomalies. In this study, we attempted to uncover the molecular and cellular mechanisms underlying the morphological defects by examining the patterns of expression of known molecular markers of cartilage and bone development. We found that the skeletal developmental defects in Adamts6 mutant mouse embryos were associated with impairment of regional cell proliferation and differentiation.

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  The Best Studied Crab in Astronomy: Searching for Variability in VHE Emission from the Crab Nebula

  Christina Bourantas, Kate Cowger, and Avery Archer

  The Crab Nebula is the remnant of a powerful stellar explosion first observed in 1054 AD and has been extremely well studied for decades. previous very high energy (VHE); GeV) studies have observed no variability in the nebula flux making the Crab a standard reference tool for gamma-ray telescopes. As part of the VERITAS (Very Energetic Radiation Imaging Telescope Array System) collaboration, we continue monitoring the nebula’s flux to understand the VERITAS telescopes and physical processes occurring within the nebula. We are analyzing over 80 hours of data from 2017 and 2018 from VERITAS Collaboration, developing and adding to a light curve that includes data since 2007. Our analysis of the 2017-2018 combined dataset determined a spectral index of -2.324 plus or minus 0.005489 and fitting the light curve with a constant function yields a mean integrated flux above 200 GeV of, which is significantly lower than a 2007-2016 dataset.

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  Osmolyte Impact on Surfactant Bound Water Nanodroplets

  Luke Brake and David Cordero

  To investigate the impact of osmolytes on surfactant bound water nanodroplets, we studied reverse micelle systems involving anionic surfactant docusate sodium (AOT). David’s project focused on the effects of saccharide structure on reverse micelle stability as temperature decreased. David compared the effects of using glucose anhydride (the closed-form of glucose) and sorbitol (the open-chain form of glucose) in the reverse micelle system with varying concentrations of each. Using a temperature- dependent UV-vis spectrophotometer, the temperature of the AOT reverse micelles were decreased, and the stability of the reverse micelle systems were observed UV absorption. The data collected indicated that the stability of the reverse micelle system did appear to remain relatively more stable at some specific concentrations of saccharides, but structure of the saccharide did not appear to have a conclusive effect on the stability of the system. At the same time, Luke’s project centered on comparing systems with different polar molecules in the core. Luke compared reverse micelles containing formamide, N-methylformamide, and N,N-dimethylformamide. The data collected from UV-Vis absorption of methyl orange dye was used to determine the impact of the addition of formamide and its derivatives to the polar core. The data collected shows patterns of peak narrowing toward a higher energy level as the amount of water in the system decreases.

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  WWOOFing in Northern Europe: a Cross-Cultural Examination of Food, Farming, and Community

  Seth Brawner

  Industrial agriculture has changed the way Americans eat food. More food is available but many eat without knowing where the food came from, or the additives that were used to grow and preserve it. The implementation of this large-scale food system has caused many health issues among the American population. Large-scale agriculture systems, being primarily monocultures, are also the cause of many environmental problems affecting the United States such as deforestation, soil erosion, and the eutrophication of waterways. Small-scale, organic agriculture has the potential to combat these environmental issues while restoring local, more transparent food systems. This summer I spent two months in northern Europe working on two small- scale organic farms in the Netherlands and Norway. My goal was to learn about the small organic farm movement and food culture in places that were far from home so that I could compare the two region’s and America’s general philosophies regarding agriculture and food. This experience helped me to make connections between land stewardship and agricultural production firsthand.

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  The Effect of Osmolytes on Protein Folding

  Ellie Carlson and Quan Khuc

  Protein function is determined by the way that it folds. By studying how a protein folds we are able to examine how a protein interacts with its normal and abnormal environment. Because of the many different environmental conditions that exist within our bodies, proteins have developed a way to counteract stress conditions that may result in misfolding. This mechanism is the consumption of osmolytes. Osmolytes are known to stabilize protein structure so that aggregation or other consequences of misfolding do not occur. Although research has been done to show that osmolytes are stabilizing proteins, there are many ambiguities regarding the mechanisms of stabilization in terms of protein kinetics and thermodynamics. Therefore, we hypothesized that osmolytes help cells adapt to stress conditions by altering protein energy landscapes to prevent aggregation. Osmolytes are small organic solutes produced by cells in high stress situations to stabilize their macromolecules. In this study, we studied the effects of osmolytes on the rate of protein folding with chosen denaturant GdmCl and osmolyte Glycine Betaine (GB). A single domain protein SH3 was chosen because of its simple folding mechanism, which only has two steps – the least number of steps that protein folding process undertakes. Buffers were made with an increasing concentration of GB, starting with 1M GB, to stimulate different environments in which the designated protein unfolds and refolds. The results show that increasing concentration of GB in buffers helps to stabilize the protein. The cause of this behavior might include the crowding effect between GB and the protein and the effect of charges on GB. The crowding effect reduces spaces for protein to unfold. The charge effect potentially stabilizes charges on the protein. The results obtained in this study open new directions for future research into how concentration of osmolytes affects the rate of protein folding.

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  Examination of the effect of a Histidine tag and pH on the energy landscape of ACBP

  Karson Cecil and Papa Kobina Van Dyck

  A polyhistidine-tag is an amino acid motif in proteins that consists of at least six histidine (His) residues, often at the N- or C-terminus of the protein. While a 6 Histidine residue tag has multiple functions, it is often attached to the end of a protein for use in protein purification. It is important to determine if the His-tag has an effect on protein folding and stability. We use ACBP as our model because ACBP is a single-domain protein that is thought to fold in a two-state process. To characterize how the His-tag affects the protein energy landscape, we study the effects of ACBP stability and folding kinetics with and without a His-tag in different buffers with varying pHs of 5.3 and 7. At a pH of 5.3 Histidine is protonated and at 7 Histidine is deprotonated. We observed that there was a significant difference in the kinetics and thermodynamics of the C- Term His tagged ACBP. In a pH of 5.3, the C-Term His tagged ACBP was less stable whereas in a pH of 7 it was more stable. There was no significant difference in the thermodynamics or the kinetics of the N-term ACBP and the wild type ACBP.

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  Social Impacts through Environmentalism

  Peng Cheng

  Social impacts should not be merely planned, but implemented. Promotion of environmentalism plays a crucial part in environment conservation — the incorporation of such information and knowledge into the societal system can induce efficacious social changes. Over the past summer, I interned with Thirst, an NGO founded in Australia and based in Hong Kong, and worked to promote environmentalism through classroom lecture and discussion at elementary schools and middle schools, social events such as art gallery opening, and conservation program for endangered species. Our office also collaborated with real estate corporations and automobile companies and coordinated events such as RunningDry.

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  Acyl Substitution/Epoxide Opening Reaction

  Xi Chen and Rebecca Derringer

  Organic chemistry is a subdiscipline of chemistry that studies the structure, properties and reactions of organic compounds, which contain carbon in covalent bonding. In organic chemistry, we mostly study the elements of carbon, hydrogen, nitrogen and oxygen. This summer research we mainly focused on an area of organic chemistry called synthesis. In organic synthesis chemists build molecules which have a wide variety of potential uses. We specifically worked on building molecules from an epoxide molecule previously made by the Hansen group. From this molecule we used two different bases in an attempt to make two different products. Products are identified by using NMR spectroscopy. Once made the biological activity of the compounds will be determined using the brine shrimp lethality assay.

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  Assessing Tree Canopy Complexity in Northern Hardwood Forests

  Sarah Congress

  The composition and complexity of a forest’s canopy influences ecosystem functioning within the forest. Long-term Successional changes as well as short-term disturbance events and anthropogenic changes can cause canopy complexity to fluctuate over time. Ground-based LiDAR systems are being employed to gain a more in-depth understanding of the complexity of forest canopies. This study used a combination of ground-based LiDAR mapping and field-based data collection to begin to quantify the complexity of the forest canopy for northern hardwood forests. This study found that the successional stage of the forest was a driver of the differences in canopy composition and vegetation area index, but that fertilization treatments did not strongly affect canopy structure.

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  Bisexual Youth: Negative Health Outcomes in the United States

  Ashley Dapore and Naima Shifa

  Research over the past fifty years has suggested that although many legal and social changes have occurred in favor of LGBTQ individuals, members of this community still experience unfavorable mental health outcomes more frequently than their straight peers. Especially for bisexual teenagers, their social environment and response to risk behavior, including suicidal thoughts, is alarming in many states. An unwelcoming or unaccepting social and political environment surrounding them as they age may have a direct negative impact on their physical safety and mental health in victimization experiences such as bullying and the development of depression. We analyzed the Youth Risk Behavior Survey (YRBS) data collected by the Centers for Disease Control and Prevention (CDC) from high school students in twenty-four states to determine the rates of victimization of each sexual minority group. In seven of nine victimization experiences, bisexual youth had the highest prevalence of negative outcomes. Multiple Decision-Making Criteria was used to create a ranking of the best and worst states for positive outcomes for bisexual youth.

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  Short Chain Fatty Acid -butyrate Anti- IL-1 β Induced Intestinal Inflammation by Regulating the Intestinal Barrier Function Related Genes in Neonatal Mice

  Brittany Davis

  Necrotizing Enterocolitis (NEC) is a disease that causes excessive inflammatory necrosis within the intestines. It affects 10% of premature infants weighing under 1500 grams, and leads to increased morbidity and mortality, causing extensive expenditure of healthcare dollars. This disease triggers devastatingly painful symptoms within infants. Recent studies have shown that feeding infants breast milk rather than formula milk can help alleviate the painful inflammation of this disease.1 Moreover, supplementing a mother’s breast milk with probiotics has been shown to enhance this anti-inflammatory effect. Currently, the focus towards ameliorating NEC disease lies within determining the underlying mechanism of these findings. Seeing that short chain fatty acids (SCFAs) are a metabolite of breast milk, and have proven to help decrease inflammation within extant literature,2 this study focuses on the anti-inflammatory effects of short chain fatty acid-butyrate within the intestines of neonatal mice. Specifically, we used quantitative reverse transcription PCR (RT-qPCR) to explore the relationship between short chain fatty acid butyrate and intestinal barrier function genes. Intestinal genes were isolated and amplified from neonatal mice in order to perform gene analysis through transcription profiling. Preliminary results suggest potential relationships between anti-inflammatory effects of short chain fatty acid butyrate and increased expression of Olcn, Cldn4, Muc1, Muc2, Casp3, and Casp8 genes. If these findings can be replicated in human intestinal cells, further understanding gene regulation can ultimately provide more effective and efficient treatment to neonatal infants. [1] Gregory, K. E., Samuel, B. S., Houghteling, P., Shan, G., Ausubel, F. M., Sadreyev, R. I., & Walker, W. A. (2016, December 30). Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/28034306 2 Meng D, Zhu W, Shi HN, Lu L, Wijendran V, Xu W, Walker WA. The toll-like receptor - 4 in human and mouse colonic epithelium is developmentally regulated: a possible role in necrotizing enterocolits. Pediatr Res; 77,416-24 (2015).

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  Exploring Student Experiences in Science & Math to Address Underrepresentation in STEM

  Brittany Davis, Hira Ahmad, Berenice Contreras, Krista Kaleel, and Sydney Majka

  According to a 2018 publication by Higher Education Today, millions of dollars have been invested in recent years to promote diversity in science. Yet still, domestic students of color and first generation students are persisting in STEM at a lower rate than that of their similarly interested white or non-first-generation counterparts (Witham, Malcom-Piqueux, Dowd, & Bensimon, 2015). This state of underrepresentation is mirrored at our own university. To learn more about students’ experiences, we conducted a survey to gather insight on the experiences of first generation students, international students, and domestic students of color in science and math classes at DePauw. Our initial findings have shown that classroom climate, teaching styles, and peer relationships all affect the degree to which students negatively or positively evaluate their classroom experiences, and ultimately their decision to persist with or leave STEM departments.

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  Mutagenicity of C8-Adenine DNA Adduct from the Environmental Carcinogen 6-Nitrochrysene in Escherichia coli and the Role of SOS Response in Mutagenesis

  Gina Federighi

  DNA is subjected to damage by a variety of exogenous and endogenous chemicals. If these damages are not repaired by DNA repair pathways before DNA replication occurs, these damages can cause mutations. These mutations have the potential to alter a cells life and function, which in some instances, is the initiation phase to the onset of cancer. 6-nitrochrysene (6-NC) is a known carcinogen found in gasoline and exhaust that can be metabolically activated in human cells to cause DNA damage. Cells are equipped with repair pathways that aid in bypassing or repairing damages of the DNA; E. coli responds to DNA damage by inducing the SOS response. The SOS response activates SOS genes that are involved in multiple DNA metabolism processes. The production of translesion synthesis (TLS) polymerases increases with the induction of the SOS Response which aid in bypassing DNA lesions in E. coli. This research studies the importance of the SOS Response in E. coli when the environmental carcinogen 6-NC forms a C8-adenine lesion site in the p53 tumor suppressor gene. Research found that when the SOS response was induced in E. coli, there was an increase in both survivability and number of mutations compared to the wild type cells studied. These results can be attributed to the increased production of low fidelity TLS polymerases with the induction of the SOS Response. Further work will include studying the role of specific TLS polymerases in bypassing the C8-Adenine adduct derived from 6-NC.

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  Trained but In-Senescent: Characterization of Alveolar Macrophages in Trained Immunity

  Anna Foley

  Alveolar Macrophages are the present in large quantities within airways and are necessary for maintaining homeostasis as well as helping initiate different types of inflammatory responses. These macrophages are necessary for protecting against acute respiratory infections such as Influenza, but have also been linked to processes promoting post infection inflammation. In addition, research has shown how multiple incidences of acute lung viral infections may aid in driving the development of chronic lung fibrosis. In this project, we investigated characteristics of highly upregulated genes SPP1 and IL-1β shown in mice memory-phenotype alveolar macrophages. In addition, we investigated gene markers of senescent cells such as p16, p21 and proliferation in these macrophages. Alveolar macrophages showed an increase in SPP1 and IL-1β expression and protein concentration in the PR8 influenza memory treatment. In addition, although the memory macrophages showed increase in p16 and p21 expression, there was no significant decrease in cell proliferation, showing that these cells are non-senescent like.

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  Nicotine-Seeking Behavior in Zebrafish

  Kaitlyn Gardner, Sabrina Krause, Andrew Tucker, and Lauren White

  The ultimate goal of our projects is to identify potential new pharmacotherapeutics for the treatment of nicotine dependence, the number one cause of preventable diseases in the U.S. Zebrafish are a stepping stone towards developing better medicines that help people quit smoking and vaping. Larval zebrafish have advantages for studying nicotine response behavior because of their small size, short developmental period, availability of zebrafish mutants, targeted gene-knockout methods, and simple drug- delivery methods. However, mechanisms of nicotine-seeking behavior in zebrafish are unknown. To explore nicotine-seeking behavior in larval zebrafish, we have established behavioral choice assays using a plus-maze and a gradient-maze. Individual larval zebrafish (6 to 8 days after fertilization) were videotaped before and after the start of local delivery of nicotine into a single compartment of a maze. Video tracking analysis using EthovisionXT (Noldus) software was employed to quantify nicotine-seeking behavior by measuring parameters such as the cumulative time larval zebrafish spent in a nicotine-containing compartment and frequency of entering a nicotine-containing compartment. Results of 468 tested larval zebrafish indicate that the assays can be used to distinguish nicotine-seeking from non-seeking larval zebrafish. Nicotine-seeking larval zebrafish occupy nicotine compartments for longer periods and enter the nicotine- containing compartments more frequently compared to non-seekers. About 20% (94 of 468) tested individual larval zebrafish were identified as nicotine-seekers. Patterns of nicotine-seeking behavior vary among identified nicotine-seekers. A color-plus maze, or rainbow maze was employed to explore conditioned place preference testing. Nicotine- seeking larval zebrafish will be raised to adult-hood for future genomic analysis and generation of a new zebrafish line of nicotine-seekers. Studies of a new nicotine-seeker zebrafish line could lead to a better understanding of the genomics and mechanisms of nicotine-seeking behavior in zebrafish and the identification of potential pharmacotherapeutics for smoking cessation therapy.

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  Synthesis of Ether Alcohols with Varying Catalysts

  Hannah Grady, Frida Li, and Jeffrey A. Hansen

  It has previously been found that acids and bases are effective catalysts in the opening of epoxides into ether alcohols. Our first goal for this summer was to determine which of the acids and bases available were the most effective. After figuring out which of the acids and bases are the optimal catalysts, our second goal was producing ether alcohols in the shortest amount of time with higher yields. Our final goal was to see how biologically reactive the ether alcohols we produced were.

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  Automation of Karl Fischer Titration for Animal Pharmaceutical Product Testing at Elanco Animal Health

  Elizabeth L. Grubbs

  Ever wonder what doing research looks like in the context of working in industry? This summer I had the opportunity to work at Elanco Animal Health, the world’s third largest animal pharmaceutical company (and growing!) I worked in the Quality Control laboratories where products are tested before they are sent out the door. I did research to automate a process that checks for the water content of various animal health products. The water content of these products is important for many reasons including expiration dates and FDA requirements. The process that I automated is called Karl Fischer titration and is a widely used concept in food science, industry, quality control, and research. A lot of the work I did this summer is proprietary information, meaning that I will not be able to disclose specifics with a general audience in order to protect Elanco from competitors. The research that I was able to accomplish saved the company both time and money. Come see what research looks like in an industry setting!

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  Machine Learning to Support an Interactive Theorem Prover

  Salman Haider, Andy Le, Echo Wu, and Brian T. Howard

  An Interactive Theorem Prover (ITP) is a computer program that can assist a human in creating a proof of a mathematical theorem or the correctness of a piece of software. At each step in the proof, the human has the computer apply a chosen "tactic" to attempt to make progress toward the goal. We are exploring the possibility of using Machine Learning (ML) to assist in this tactic selection. Building on recent work at UC Berkeley and Princeton, where they adapted the Coq ITP so that it could interface with ML libraries via the Python scripting language, we have been evaluating strategies to encode the current proof state to try to improve the accuracy of tactic prediction.

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  Opening of an Epoxide Ring Using Azide to Form a Triazole

  Emily Hufnagel and Jeffrey A. Hansen

  The purpose of this research project is to identify and synthesize biologically active compounds that could potentially aid in pharmaceutical research. Once a compound is correctly identified and purified, the sample can be diluted and added to a Brine Shrimp Lethality Assay in order to determine the toxicity of the compound. This experiment was designed using an epoxide compound to form an azide that would eventually form a triazole. In carrying out this project, two main procedures were used in order to create two different compounds that would eventually create the final result. The triazole was not successful in the BSLA and the concentration was not able to be increased due to the solubility of the compound. With further research, the azide compound the azide compound can continue to be utilized in order to create other potentially biologically active compounds.

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  Visualizing the Mean and the Standard Deviation Using R/RStudio Shiny Package

  Rachel Hufnagel, Ziyi (Amy) Chen, and Mamunur Rashid

  Many of us have experienced an unpleasant situation in which only the mean and the standard deviation of a data set are reported, but we are expected to know everything about the dataset as if those two values were all we needed to know. We would learn so much more if there were easy ways to create and share graphical representations and interpretations of the entire raw data. Here we not only explain what the mean and the standard deviation tell us about a data set, but also describe how to include additional information on the data. We utilize the work of Sarkar and Rashid (2016) that introduced a geometric visualization of the sample mean based on the empirical cumulative distribution function of the raw data. They also extended the idea to visualize measures of spread such as the mean deviation, the root mean square deviation and the standard deviation. Our research involves creating interactive applications of these methods using R/RStudio Shiny, an open source package that provides an elegant and powerful web framework for building web applications. We hope, upon publication of these tools, users all over the world will use such interactive visualization methods for learning, teaching, and building more advanced tools.

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  Acetal Formation from an Alcohol Epoxide

  Sarah Kelly

  Organic synthesis is the backbone for the discovery of new drugs. The goal of our lab is to create new organic, biologically active compounds to be used in pharmaceutical research. In our lab, we start with the creation of an epoxide molecule that we are able to make in large quantities. Each member of the research team started their reactions with the epoxide molecule and tried to combine it with an active nucleophile. For my experiment, I used an enolate and an enamine to attack the carbon of the epoxide ring. An enolate was generated using a cyclohexaone and kept under certain conditions. 1- pyrrolidino-1-cyclohexene was used as an enamine nucleophile. These two reactions were designed to create an acetal with the epoxide molecule. The chosen nucleophiles did not create the acetal as expected. Further research into the formation of an acetal includes looking into different nucleophiles and the addition of a protecting group.

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  Chronotropic Responses to Cardiomodulatory Agents in the Giant danio Heart

  Alyssa Koch and Emma Nelson

  The mammalian heart is regulated via both extrinsic and intrinsic nervous plexuses containing both sympathetic and parasympathetic nerve fibers. The physiological responses that are observed in mammalian hearts are facilitated by neurotransmitter and receptors that create either an inhibitory or an excitatory response in the cardiac cells. Previous studies in our lab have shown that the giant danio (D. Malabaricus) can be an important model for the study of cardiac developmental and regeneration. Whether the Giant danio can also serve as a model to study cardiac physiological control is not clear. The purpose of this study was to determine the chronotropic responses in the giant danio heart to various cardiomodulatory pharmacological agents. Using an ex vivo electrophysiological approach, we found that isoproterenol significantly increased heart rate, whereas muscarine and acetylcholine significantly decreased heart rate similar to that seen in mammalian and zebrafish hearts. However, in contrast to zebrafish, we found that treatment with nicotine varied, and did not have significant chronotropic effects. Our findings thus far suggest that cardiac physiology of the GD is comparable to that of mammals, and that the ex vivo GD heart preparation could serve as a model for investigations of comparative cardiac electrophysiology.

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  Droplet Rebound and Rupture

  Mason Lee and Alyssa Fisher

  Droplets of 1 cst silicone oil, with an initial velocity component tangent to the surface of a bath of the same fluid, will roll along the surface for hundreds of milliseconds, slowing exponentially until eventual coalescence. A rigid vertical wall, placed in the bath perpendicular to the path of the droplet, forces early coalescence either on the meniscus formed on the wall or after rebounding from the wall. By moving the wall along the line of motion of the droplet, a transition point is found in the droplet’s trajectory in which, at a fixed wall position, the droplet may either coalesce within less than one droplet diameters distance from the turning point or travel many droplet diameters. We find a clear bi-modal distribution in droplet travel distance at this transition point and present a physical model to explain this interaction.

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  Pyrrole Reaction Exploration and Development

  Mary Leonard

  The project “Exploration and Development of Pyrroles” was a subproject within Dr. Jeff Hansen’s research project “Diversity Oriented Synthesis of Biologically Active Compounds”. This specific project was comprised of conducting various organic synthesis reactions using ketone epoxide and several different aniline species all for the purpose of making pyrrole products. The goal for this project was to further investigate the making of several types of pyrrole products as well as learn more about how these reactions occur and how cleanly the reaction could produce pyrrole products depending on the type of aniline used. I also tested to learn if the products were biological activity which could indicate if a compound is pharmaceutically useful. In order to achieve this goal, I reacted several aniline species with ketone epoxide and analyzed the products. In addition, I used a Brine Shrimp Lethality Assay to test the biological activity of the certain pyrrole products. #30-42 OFF CAMPUS EXPERIENCES AND PRACTICUMS =Additional Poster authors but non-DPU related

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  Developing a Digital Simulation For Exploring the Thermodynamics of a Chemical Reaction

  Jingwei (Mike) Ling

  Shiny is a package used in the R programming environment to develop interactive applications without the need for a background in HTML, CSS, and/or JavaScript coding. Applications are run in a browser either remotely using shinyapps.io as a hosting service, or locally using a computer with R installed. The interactive nature of a Shiny application allows students to explore a (bio)chemical system in a manner that uses active-learning to promote critical thinking in the classroom. Work this summer focused on developing an application for Chem 260 that models the thermodynamic properties of a reaction, allowing students to explore how a change in temperature, enthalpy, entropy, and activation energy affects a reaction’s thermodynamic favorability and the reaction’s rate.