2017 Summer Undergraduate Research Projects

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You can browse the Summer 2017 descriptions of projects in Fine Arts, Humanities, Natural Sciences & Mathematics, Social Sciences and Interdisciplinary Studies.

FINE ARTS

Art and Art History

Peter Nelson - Digital Filmmaking
PROJECT SUMMARY:
How can digital filmmaking be used to construct a narrative, produce a documentary, or create an experimental artwork? How can the multifaceted elements of production — camera language, lighting, audio, and editing — be used to create something both visually and conceptually striking? In addition to working collaboratively with the professor on a project, students will conceive of and produce a short digital film together as a team.

Evan Weselmann  – In lieu of abstracts I have written artist statements pertaining to the work I have created this summer.

Real People Doing Real Things 

How does one negotiate the ever muddying waters of truth and reality and it’s relation to the world of film and cinema? When constructing a narrative one must assemble the pieces together into a situation that resembles a true, believable reality. But this in fact is not “real” in any true sense. It is wholly constructed and every detail of it has been executed and thought out. Real People Doing Real Things poses questions of truth and a film’s ability to document and subvert historical past through the use of animation, found footage, digital archives and historical truth At what point does one believe the narrator? Does the narrator stand in for a real person? Do these questions and conceptions of truthiness and bearing to a real true reality even matter or do they take a backseat to the constructed reality of the piece itself?

Abstract 2 – Kat Bluett 

This summer was dedicated to shooting a short documentary on my parents’ engagement story.Throughout the film, you are introduced to Jenny and Bill Bluett, who are the main storytellers. The film is a compilation of interviews I conducted with my parents, footage from their wedding, and video of the present. This short documentary is meant to capture a story of a radical events that occurred on November 25, 1991. Ultimately, the documentary is meant to explore the divine powers that lead to my parents marriage.

Dance

Anthony Roberts - Dance & Jeremy Loebach - Psychology - Scanning the Active Brain & Body: Revealing Connections Between the Art & Science of Movement
PROJECT SUMMARY:
The primary focus of this project is to record, process, and begin interpreting brain activity during the learning and execution/performance of short movement tasks/sequences ranging from ordinary, everyday to those imbued with an imagined intention. All project researchers will: 1) learn to use software and hardware that facilitate mobile transmission, recording, and processing of brain activity of moving subjects; 2) learn and execute/perform movement tasks/sequences that range from simple-to-complex (dance experience is NOT required), while wearing an EEG head cap.
Research participants will also review literature comparing artistic and scientific research practices and present their findings.
Sample research questions include:
1) What measurable brain activity occurs when a simple movement task/sequence is initially learned and executed/performed?
2) How does the introduction of an imagined intention to the learning and execution/performance of an ordinary task/sequence influence brain activity?
3) What changes in measurable brain activity occur when spatial, temporal, effort, interpersonal, or emotional parameters are varied within an existing task/sequence?
4) What changes in measurable brain activity occur when new variables are added to an existing task/sequence that has been learned and practiced over time?

Abstract 1 – Fiona Steen & Randal Rude – Comparing EEG Activity in the Motor Cortex Between Novice, Intermediate, and Professional Dancers

Generalist:

This research project measures and compares variations in brain activity of dancers with different experience levels using EEG (electroencephalogram) during the phases of creating, teaching, learning, and performing dance. Eight different locations on the right side of the brain were measured using one novice, one intermediate, and one professional dancer. We found the ‘creating’ phase produced the largest difference in brain activity as professional and intermediate dancers registered a positive slope and much higher values across all trials. This differed in the novice dancer who had higher values in the ‘learning’ stage, a mentally-fatiguing task for a beginning dancer. The results suggest future applications of enhancing teaching and learning strategies and improving proficiency through creative practice.

Field Specific:

This research project compares dancers of different levels of experience by measuring variations in brain activity using EEG during the phases of creating, teaching, learning, and performing dance. Eight electrode positions (Fp2, Fz, F4, F8, F10, C4, Cz, Pz) were studied working with one novice, one intermediate, and one professional dancer. We found the ‘creating’ phase produced the largest voltage variation in F8, where professional and intermediate dancers registered a positive slope and significantly higher voltages across all trials.. This differed in the novice dancer who had higher voltages in the ‘learning’ stage, a mental fatigue-inducing task for a beginner. The results suggest the professional and intermediate dancers registered more brain activity in F8 due to the challenge of implementing aesthetics to the movement, a task unfamiliar to novices, rather than lack of experience. Future applications include improving proficiency through creative practice and enhancing teaching and learning strategies.

Theatre

Dona Freeman & Todd Edwards - Integrating Film in Theater Performance
PROJECT SUMMARY:
We intend to use this summer process for two central purposes. 1) to investigate current uses of film in live theater performance, and 2) to create a film piece featured in one of next season’s St. Olaf Theater productions. This film product may serve a narrative function, such as filming scenes or characters, or a scenic function, such as creating environment, or both. Students working on this project will engage in both dramaturgical research of current global performance practices and practical elements of filmmaking in support of theater production.

Abstract 1 – Aaron Lauby and Chaz Mayo – Integrating Film in Theater Performance

Generalist:
With this project we investigated current uses of film in live theater and conducted an in-depth investigation of Brechtian theater practices, focusing on the “alienation effect” in which mid-century German playwright Bertolt Brecht sought to bring the audience out of the world of the play, to motivate a call to social and political action. Based on this work, we created media content that will be featured in the upcoming St. Olaf Theater production of Brecht’s Mother Courage and Her Children. Students engaged in the practical elements of filmmaking and the use of motion-media techniques. Weekly Skype meetings with the production’s composer rounded out the collaboration process.

Field-Specific:
With this project we investigated current uses of film in live theater and conducted an in- depth investigation of Brechtian theater practices, focusing on the “alienation effect” in which mid-century German playwright Bertolt Brecht sought to bring the audience out of
the world of the play, to motivate a call to social and political action. Based on this work, we created media content that will be featured in the upcoming St. Olaf Theater production of Brecht’s Mother Courage and Her Children. Using industry-standard resources including
Adobe After Effects and Premiere, students engaged in the practical elements of filmmaking and content creation. Postproduction processes included the creation of a 5 node render farm which improved production throughput by 800%. Weekly Skype meetings with the
production’s composer allowed for integration of media and audio that will be used in the November performance.

HUMANITIES

Music

Louis Epstein - The Musical Geography Project
PROJECT SUMMARY:
How can digital mapping help recreate the sound world of the past? By researching and visualizing the musical geographies of key times and places within music history, we will create pedagogical and scholarly resources that illustrate how music, musicians, and ideas about music have traveled. Maps have always been a useful tool for music historians, but our interactive, chronological maps – the first of their kind – will allow students, scholars and the general public to explore the riches of music history in new ways. To populate our map with musical events and objects, including premieres, manuscripts, letters, artworks, and editions, we’ll use digitized and archival primary sources. We’ll also curate a digital archive of primary source materials (accessible through our maps) and produce pieces of writing that will contextualize what users can see, hear, and manipulate when using the map. Depending on available funding, one student may be sent to Paris or the Library of Congress to work in archival collections. Students will gain skills in archival/primary source research, basic website design, database management, and historical and critical thinking. Ideal applicants include those with language skills (especially French and German, the languages of many important primary sources), expertise or interest in music history, and passion for historical inquiry. To learn more about the project and see what previous student researchers have contributed, please visit musicalgeography.org.

Abstract 1 – Juliette Emmanuel, Elizabeth Lacy & Anna Perkins 

Generalist:

The Musical Geography Project explores the intersections of time, space, and sound using digital mapping technologies. Our maps can be used as research tools to make arguments, illuminate unexpected spatial relationships and patterns, and inspire new research questions. In this paper, we use the concert performance and reception of the music of Darius Milhaud (1892-1974) as a case study to examine the interplay between the digital humanities and musicology. Through the curation of an extensive database of over 500 performances of Milhaud’s music between 1922 and 1933, we a series of maps that demonstrate several ways digital mapping and spatial history can enhance musicological research. Maps force us to reexamine received notions about concert programming and the reception of Modernist music during the interwar period. Mapping technology can make musicological work more accessible not only to scholars and students, but to the general public.

Field Specific:

The Musical Geography Project explores the intersections of time, space, and sound using digital mapping technologies. Our maps can be used as research tools to make arguments, illuminate unexpected spatial relationships and patterns, and inspire new research questions. We used the concert performances and reception of the music of composer Darius Milhaud (1892-1974) as a case study to examine the interplay between the digital humanities and musicology. Through the curation of an extensive database of over 500 performances of Milhaud’s music between 1922 and 1933, we’ve created a series of maps that demonstrate the ways digital mapping and spatial history can enhance musicological research. Mapping technology makes musicological work more accessible not only to scholars and students, but to the general public.

Kierkegaard Library

Gordon Marino & Eileen Shimota - Kierkegaard in the Present Age
PROJECT SUMMARY:
We live in an age in which anxiety and depression seem pandemic. Kierkegaard was a depth psychologist of the first order who grappled with and wrote extensively about these inner demons. What was his understanding of anxiety and depression? How might his understanding speak to current views about anxiety and depression? Might Kierkegaard be a resource for resuscitating the age-old distinction between psychological and spiritual disorders?

Abstract 1 – Anabel Kapelke & Linden Smith – Kierkegaard and Anxiety in the Present Age

Generalist:

This project investigates the relevance of Soren Kierkegaard’s writings to current medical and societal attitudes towards mental illness. Kierkegaard wrote extensively about anxiety and depression, but he described them psycho-spiritually instead of medically. Instead of pathologizing anxiety and depression, Kierkegaard considers them a necessary part of the human condition. For Kierkegaard, a human being is qualified as a spirit, or self. Specifically in regards to anxiety, he insists that it is an intrinsic aspect of each person’s self. His descriptions hint at a fundamentally different conception of wellness that diverges from a traditional understanding of health. In an age where diagnosis of mental illness is steadily increasing, we suggest that Kierkegaardian understandings of mental illness may enrich and improve our current medical model.

Field Specific:

This project critiques current conceptions of wellness using Soren Kierkegaard’s philosophical concepts. “Wellness” today is freedom from psychopathology as well as subjective feelings of wellbeing. Contrastingly, Kierkegaard had no conception of psychopathology, and little concern for subjective feeling. Kierkegaard’s chief concern is a person’s status as a spirit (or “self”). For Kierkegaard, anxiety is a necessary product of being a spirit. The more spirit or self a person is, the more anxiety they have. What medicine understands as an illness, Kierkegaard sees as affirmative of our humanity. Rather than dismissing anxiety as a medical affliction, Kierkegaard insists that people must look to their anxiety as a source of wisdom. However, it is only through faith that anxiety is educative. His idea of wellness hinges on self-knowledge and grounding oneself in relation to God. We suggest that Kierkegaard’s depth psychology can expand our contemporary, myopic vision of wellness.

NATURAL SCIENCES and MATHEMATICS

Biology

Sarah Amugongo - Impact of Maternal Prenatal Stress on Offspring Bone Development
PROJECT SUMMARY:
This project utilizes rats as a laboratory model to study the impacts of stress on mammalian fetus bone development. Fetal development is important for ensuring the future health of an individual. A number of studies have linked diseases of aging to harmful alterations that happen in critical periods during fetal development. During pregnancy some women experience daily stress, including depression, anxiety, anger, day-to-day challenges, sudden change of environment, social isolation, and disease states. The body typically responds to such stressors with elevation of cortisol hormone. Cortisol crosses the placenta and consequently influences various aspects of development in the human fetus. The effects of elevated cortisol levels on the fetus may vary from defective development to spontaneous abortion.
Rats are an ideal model for this research. First, their gestation period is short (twenty one days) and they reach sexual maturity within 4 months of birth, allowing my studies to be completed in a reasonable amount of time. Second and most important is that rats are mammals like humans, and bone development is highly conserved across mammals. The implications of stress on bone development we observe in rats provide insight about such effects in humans.

Abstract 1 – Cecelia Sagona & Toluwalope Toluhi – Genetic and Non-Genetic Risk Factors Associated with Breast Cancer in Costa Rica

According to the “Caja Costarricense de Seguro Social,” the incidence of breast cancer in Costa Rica more than doubled between 1999 and 2014. Various risk factors have been associated with the disease, including age of first pregnancy, estrogen–progestogen contraceptives, alcohol use, obesity, mutations in the genes BRCA1 and BRCA2, and more (Dumitrescu, R. G., & Cotarla, I., 2005). In this ongoing study, data is gathered through use of a questionnaire and genetic testing. The goal of the study is to identify BRCA1, BRCA2, and PALB2 mutations common to female breast cancer patients in Costa Rica and to determine other non-genetic risk factors characteristic to this population. Currently, 106 cases and 11 controls have participated in the study. Six mutations in BRCA2 and one mutation in PALB2 have been found among cases. Also, the majority of cases were found to be overweight or obese, increasing breast cancer risk. To further understand the factors associated with breast cancer in Costa Rica, comparisons must be drawn between cases and controls. Currently, emphasis is being placed on recruitment of controls.

Generalist:

Bacteriocins are antibacterial proteins secreted by lactic acid bacteria (LAB), commonly used to produce fermented foods, that target specific competing strains of bacteria in their environment. This offers the bacteria that produces them a competitive advantage. Bacteriocins use antibiotic pathways that are distinct from current clinically-used small-molecule antibiotics making them intriguing targets for use against antibiotic resistant bacteria as well as limiting potential side effects. The goal of our experiments is to isolate novel bacteriocins from LAB and to obtain their three-dimensional structure using nuclear magnetic resonance spectroscopy. By determining their structure, we can better understand their mechanism of action and use that information to aid in the development of new bio-preservatives and antibiotics.

Field Specific:

Lactic acid bacteria (LAB) produce bacteriocins, small peptides that function as antibiotics, in order to enhance their competitiveness in their environment. Many of these bacteriocins target food-borne pathogens and antibiotic resistant bacteria such as Listeria monocytogenes and Methicillin-resistant Staphylococcus aureus and can be used as bio-preservatives and novel clinical antibiotics. Structural characterization of bacteriocins would not only allow a better understanding of new antibiotic pathways, but also enables structural modifications to improve activity and stability. Cell-free supernatant (CFS) was obtained from L. plantarum, L. curvatus and P. acidilactici. Utilizing pH adjusted CFS subjected to cation exchange chromatography allowed for the isolation of putative bacteriocins followed by SDS-PAGE to visualize molecular weight of isolates. Spot-on-lawn assay tested antimicrobial activity of isolates. Structural data of isolated proteins 2-5 kDa was collected with 1D 1H NMR, 2D COSY, and 2D TOCSY spectra.

Diane Angell - Biodiversity and Resource Use of Small Prairie Mammals
PROJECT SUMMARY:
Prairies are one of our most endangered biomes and small mammals play crucial roles as predators, prey, seed dispersers and grazers. Next summer we will continue to explore the food resources that different species of small prairie mammals rely on by using stable isotope analysis of fur clippings. We have found quite different small mammal communities in native prairie remnants as compared with prairies planted on agricultural land. Examining the stable isotopes of carbon and nitrogen in fur can provide insight into the trophic systems in each of these kinds of prairies. We now have an extensive collection of fur from a large number of individuals of different species from different locations and years.
This research will also continue long term population monitoring of small mammal species diversity on prairies in and around Northfield. There are currently two species we are monitoring that are on the state’s list of species of special concern (prairie voles, Microtus ochrogaster and harvest mice, Reithrodontomys megalotis). Both have historically been found in the area and are currently declining in Minnesota. Understanding their distribution and changes in population density will inform conservation efforts by various agencies and institutions as they enact incentives to maintain and restore habitat in Minnesota. Preference will be given to students that have had Ecology and have some experience using R.

Abstract 1 – Lindsey Kemp – Comparison of small mammal communities in restored and remnant prairies 

Generalist:

Very little of Minnesota’s original prairie remains due to agricultural land use. Some cropland has been replanted with native plants in restoration programs with the goal of achieving similar ecosystems to that of the original, remnant prairies. One way to compare these two prairie types is by observing the diversity and diets of mice and voles. These small mammals play important roles as seed dispersers and prey animals in the prairie ecosystem. This study surveyed species present in both remnant and restored prairies, comparing capture frequency and general diet trends of the small mammal communities. Significant differences were found between the two prairie types, suggesting that restored prairies are not an equivalent replacement of remnant prairies.

Field Specific:

Only 2% of Minnesota’s original prairie remains, mostly due to agricultural land use. Some cropland has been restored with native plants, often with the goal of achieving similar ecosystems to that of the remnant prairies. One way to compare these prairie types is by observing the diversity and diets of mice and voles. These small mammals play important roles as seed dispersers and prey animals in the prairie ecosystem. This study live-trapped in both remnant and restored prairies to measure species capture frequency. The study also analyzed stable isotopes in fur samples to examine general diet trends. Five species were targeted: R. megalotis, P. leucopus, M. ochrogaster, M. pennsylvanicus, and P. maniculatus. Significant differences were found between prairie types for species capture frequencies, δ13C, and δ15N. This suggests that restored and remnant prairies are not equivalent ecosystems and house distinct small mammal communities.

Eric Cole & Doug Beussman - Tetrahymena cell signaling
PROJECT SUMMARY:
We continue to explore how the single celled protozoan, Tetrahymena thermophila, initiates sexual reproduction. In particular we are searching for molecules that may serve as sex pheromones, and molecules that may serves as cell-adhesion proteins during early stages of conjugation.

Abstract 1 – Carl J. Chmelik – Screening for the bcd mutation in Tetrahymena thermophila: Identification and characterization of cortical and conjugal phenotypes

Generalist:

The unicellular protist Tetrahymena thermophila exhibits polarity and significant patterning on its outer surface, with structures such as the mouth, anus, and small openings called contractile vacuole pores developing in distinct locations. A recessive mutation known as bcd causes the surface regions that accommodate such features to expand, resulting in these structures being larger or multiplied. bcd also causes mating between T. thermophila cells to be blocked. Offspring resulting from the crossing of cells heterozygotic for the bcd mutation were screened for the structural features and mating failure typical of bcd cells via fluorescence microscopy. Multiple contractile vacuole pores were observed frequently, sometimes accompanied by enlarged or multiple mouths. In a strikingly non-Mendelian outcome, nearly 80% of the progeny cells were found to exhibit bcd characteristics. Select cells that appear to be bcd mutants will be used for comparative whole-genome sequencing, which should allow us to identify the gene affected by the bcd mutation and gain insight on how patterning is carried out and regulated on the surface of T. thermophila cells and other organisms demonstrating cellular polarity. Effects of Maternal Prenatal Stress on Offspring Bone Development Cecelia Sagona and Toluwalope Toluhi with Professor Sarah Amugongo

Bone is a dynamic structure throughout the life of an organism with three main types of bone cells tasked with maintaining a healthy balance between bone formation, resorption, and repair. This balance can be negatively impacted by external factors in the organism’s environment leading to bone weakening and conditions such as osteoporosis. Stress triggers a natural release of the hormone cortisol, which is healthy for an organism in small doses. Large doses have been shown to alter the balance of the bone cells causing more bone to be reabsorbed than is being made and repaired. In this study, pregnant rats were subjected to the stress of immobilization three times daily for a randomly assigned week. After birth, their pups were sacrificed at different stages of development. We are studying the bones of the pups to see if their mother’s stress altered their bone development.

Field-Specific:

The model ciliate Tetrahymena thermophila exhibits cellular polarity along three different axes and a high degree of cortical patterning, with organelles such as the oral apparatus, cytoproct and contractile vacuole pores developing in distinct locations on the cell cortex. A single-gene recessive mutation known as bcd causes the cortical regions that accommodate these organelles to expand, leading to enlarged or supernumerary organelles. bcd also induces pronuclear fusion failure, resulting in a conjugal block. Clone cultures generated by crossing bcd heterozygotes were screened for cortical and conjugal bcd phenotypes via immunolabeling and DAPI staining in conjunction with conventional fluorescence microscopy. Supernumerary contractile vacuole pores were observed frequently, sometimes accompanied by enlarged or multiple oral apparatuses. Immunolabeling has shown nearly 80% of the progeny clones to exhibit bcd phenotypes in a strikingly non-Mendelian distribution, an outcome that has so far been reinforced by analysis of conjugal features. Select clones that appear to be bcd mutants will be used for comparative whole-genome sequencing, which should allow us to identify the gene affected by the bcd mutation and gain insight on the molecular mechanisms behind cortical patterning in T. thermophila and other organisms.

Bone is a dynamic structure throughout the life of an organism with three main types of bone cells tasked with maintaining a healthy balance between bone formation, resorption, and repair. This balance can be negatively impacted by external factors in the organism’s environment leading to bone weakening and conditions such as osteoporosis. Stress triggers a natural release of the hormone cortisol, which is healthy for an organism in small doses. Large doses have been shown to alter the balance of the bone cells causing more bone to be reabsorbed than is being made and repaired. In this study, pregnant rats were subjected to the stress of immobilization three times daily for a randomly assigned week. After birth, their pups were sacrificed at different stages of development. We are studying the bones of the pups to see if their mother’s stress altered their bone development.

Abstract 2 – Jessica Choquette, Leigh Hahn & Vitaly Levlev – Intracellular Calcium and Pair Formation in Tetrahymena thermophila

Generalist:

Calcium is a common signal molecule within cells. It can either be taken in from outside the cell or released from internal stores. In the nucleus, one of calcium’s roles is to activate gene transcription for various cellular processes, including growth and reproduction. The single-celled ciliates, Tetrahymena thermophila, were mated with the addition of 0.1µM calcium ionophore A23187, which makes membranes more permeable to calcium, in order to investigate the effect of increased cytoplasmic calcium on the rate of pair formation, which is necessary for sexual reproduction. A23187 did not appear have an effect on the pair formation rate. This may indicate that increasing cytoplasmic calcium alone is not sufficient to accelerate the cellular process leading to conjugation.

Field Specific:

Calcium is a common second messenger molecule within cells. Our lab has seen elevations in intra-nuclear calcium associated with mating in Tetrahymena thermophila. In the nucleus, calcium can activate gene transcription for various cellular processes, including proliferation. We wanted to test whether elevated cytoplasmic calcium could trigger precocious mating in Tetrahymena. Cells of complementary mating types were mixed in a 1:1 ratio with the addition of 0.1µM calcium ionophore A23187 to investigate the effect of increased cytoplasmic calcium on the rate of pair formation during conjugation. A23187 did not appear have an effect on the pair formation rate, which may indicate that increasing cytoplasmic calcium alone is not sufficient to accelerate the cellular process leading to conjugation and that nuclear calcium may need to be targeted directly.

Abstract 3 – Wed Al-Nod – Creating a knockout construct to investigate the roles of ULP1 & ULP2 in the SUMO pathway of Tetrahymena thermophila

Generalist: 

SUMO, small ubiquitin like modifier, is a family of proteins known to play a role in post-translational modification of other proteins. So far, most of what is understood about the SUMO pathway comes from studies conducted in yeast. In this study we aimed to develop a better understanding of two genes in the SUMO pathway using the model organism Tetrahymena thermophila. To do this, we designed a plasmid containing the sequences flanking each gene. The plasmid was then introduced into Tetrahymena and used to knockout the genes through homologous recombination. By observing changes in growth rate, viability and cellular morphology in the absence of these functional genes, we hope to better understand what role they play in the SUMO pathway.

Field Specific:

SUMO, small ubiquitin like modifier, is a family of proteins known to play a role in post-translational modification of proteins, altering protein-protein interactions, and regulating cellular processes. So far, most of what is understood about the SUMO pathway comes from studies conducted in yeast. However, Tetrahymena thermophila possess complexity and diversity of cellular processes that are not present in yeast. In this study we aimed to develop a better understanding of two genes in the SUMO pathway using this complex model organism. To do this, we designed a construct by cloning in the sequences flanking each gene. The construct was then introduced into Tetrahymena and used to knockout the genes through homologous recombination. By observing changes in growth rate, viability and cellular morphology in the absence of these functional genes, we hope to better understand what role they play in the SUMO pathway.

Abstract 4 – Vitaly IevIev – Extracellular microvesicles – a factor secreted into conditioned media that stimulates Tetrahymena mating

Generalist:

Tetrahymena is a unicellular ciliated protozoan that lives in freshwater. Tetrahymena normally divides through binary fission, but when the cells are starved they conjugate by forming pairs with the opposite mating type. Starved tetrahymena produces some factor active in conjugation that was described by J.Wolfe and colleagues in 1980. However, the exact identity of this factor remains unknown. In this work, we propose that extracellular microvesicles – small, membrane bound packages with RNA and proteins – function as this factor. The isolated EMVs are able to restore the mating activity when the factor is depleted from the media. In addition, EMVs and the factor described by Wolfe et al. share a common unique property – they retain their activity after boiling.

Field Specific:

In the current work we propose extracellular microvesicles (EMVs) as a factor active in conjugation (FAC) in T. thermophila that Wolfe et al. first described in 1980. This factor appears to be necessary for sexual reproduction in Tetrahymena since the pairing is delayed when the starvation media – 10 mmolar Tris, in which Tetrahymena has been starved for 2-18 hours – is substituted with fresh Tris (Wolfe et al, 1980). We propose that T. thermophila conditions its media with EMVs which serve as proxies for intercellular contacts and prepare the cells for conjugation by triggering a cascade of events that lead to formation of the sticky junction. We suggest a molecular mechanism which is based on recycling of the sticky surface proteins and their selective redeposition into the area of the newly-forming sticky junction.

Abstract 5 – Leigh Hahn – Bacteria-protozoa predatory interactions drive fast evolution in Caulobacter crescentus

Generalist:

Caulobacter crescentus are bacteria that are able to change genetically and develop a skill, or an adaptation, to increase its survival in the environment it occupies. When Caulobacter encounters Tetrahymena for the first time, the Caulobacter density declines because Tetrahymena feeds on Caulobacter. Tetrahymena thermophila are protozoa that are bigger and more complicated microorganisms that eat Caulobacter. In order to evade the predation, Caulobacter has to develops adaptation(s) to improve its resistant to Tetrahymena. We hypothesis that in the presence of Tetrahymena, Caulobacter acquires adaptation(s) that helps it evade Tetrahymena predation and thus increase its survival rate in a short amount of time.

Field Specific:

The bacterium Caulobacter crescentus can show signs of adaptation after encountering Tetrahymena thermophila, a predatory ciliated protozoa, for its first time. Tetrahymena feed on Caulobacter, but Caulobacter do not have robust defense mechanisms against Tetrahymena. However, once cultured together in a closed environment, the population of Caulobacter show improved resistance to Tetrahymena predation. The acquired adaption(s) allow the Caulobacter to better survive the predator when encountering Tetrahymena again. This experiment supports our hypothesis that Caulobacter crescentus acquires an advantageous adaptation(s) after it encounters Tetrahymena for the first time, allowing it to evade the predation and improve its rate of growth.

Eric Cole & Jean Porterfield - Sea Cucumber Sex
PROJECT SUMMARY:
We will be exploring the reproductive life history and population genetics of a sea cucumber on the island of San Salvador in the Bahamas. Work involves wax-histology to examine sex and reproductive status, and PCR to examine genetic diversity of specimens collected in January.

Abstract 1 – Miranda Thackler – Natural History, Reproductive Histology, and Genetics of Synaptula hydriformis

Generalist:

Synaptula hydriformis (Lesueur, 1824) is a hermaphroditic self-fertilizing sea cucumber whose young undergo direct development inside the parent. A unique feature of this species is their ovo-testis and viviparous abilities. In past work, this organ was found to contain both sperm and eggs. Its autogamous and live-bearing abilities make it unique among other Synaptula who tend to release gametes into the water.

The individuals collected from Oyster Pond on Sal Salvador Island, Bahamas come in clear, brown, and striped varieties. While there, we developed a method for inducing both synchronous spawning and birthing. Subsequently, a successful technique for culturing juvenile sea cucumbers was established. While on the island we collected live samples to culture in our lab, and preserved specimens for DNA work and histology.

Field Specific:

Synaptula hydriformis (Lesueur, 1824) is a hermaphroditic self-fertilizing sea cucumber that undergoes brooding and matrophagy. A unique feature of this species is their ovo-testis and viviparous abilities. In past work, this organ was found to contain both sperm and eggs. Its autogamous and viviparous abilities make it unique among other Synaptula who tend to release gametes into the water.

Specimens are most commonly observed elsewhere as either red or green, but individuals from Oyster Pond on Sal Salvador Island, Bahamas come in clear, brown, and striped varieties. Oyster Pond contains one other species of sea cucumber, Chiridota rotifera.

We developed a method for inducing both synchronous spawning and birthing. Subsequently, a successful technique for culturing juvenile sea cucumbers was established. While on the island we collected live samples to culture in our lab, and preserved specimens for DNA work and histology.

Kevin Crisp - Cellular Mechanisms of Inflammation-Induced Microglia Accumulation
PROJECT SUMMARY:
Microglia are resident immune cells in the central nervous system (CNS) that phagocytize cellular debris and inactivate foreign cells and substances. In mammals, microglia undergo a characteristic activation and migration to sites of injury and inflammation in the CNS. Neuro-injury has also been shown to stimulate microglial accumulation in the invertebrate CNS through signaling mechanisms that depend on external ATP and nitric oxide. However, it is not known whether inflammation also induces microglial accumulation in the invertebrate CNS and what cellular signaling processes might be involved. The goal of this project is to determine whether an inflammatory agent such as lipopolysaccharides (LPS; a component of the cell wall of gram negative bacteria) can elicit a microglial response in leech nerves similar to that observed following neuro-injury.

Abstract 1 – Amber Juran, Aislinn Mayfield and Nicole Nothongkham – Microglial Response to LPS in the Leech Central Nervous System

Generalist:

Microglia are cells in the central nervous system which migrate along nerve cords to sites of inflammation and injury. At the site, they accumulate to devour debris, modulate the inflammatory response, and secrete repair molecules. This microglial response is known to be triggered by mechanical injury, but the response to bacterial infection has not been widely studied. In this study, we examine if LPS, a bacterial toxin, is capable of inducing microglial accumulation in leech nerve cords. To test a possible interaction between LPS and mechanical injury, we crushed nerve cords both with and without LPS present and compared microglial counts in the crushed regions. Results suggest LPS does not alter accumulation of microglia when coupled with a mechanical crush in leech nerve cords.

Field-Specific:

Microglia respond to damage caused by mechanical injury and bacterial infection in both vertebrate and invertebrate nervous systems. Unfortunately, not much is known about the effects of bacterial infection on the migration and accumulation of microglia. This study examines whether the gram negative bacterial antigen, LPS, affects microglial accumulation in leech nerve cords, and if LPS changes the microglial response in either healthy or damaged nerves. Medicinal leeches were dissected and their nerve cords were crushed, with or without LPS present, to examine these effects. Feulgen’s, propidium iodide and pen ink staining methods were used to view microglia nuclei and differentiate between other cell populations within the nerve cords. Finally, accumulation was quantified using hand and automatic counts from ImageJ and statistical analyses were conducted to compare accumulation across conditions. Results suggest LPS does not alter accumulation of microglia when coupled with a mechanical crush in leech nerve cords.

Jay Demas & Steve Freedberg - Linearly polarized light detection in the snapping turtle retina
PROJECT SUMMARY:
When freshwater turtles hatch, they must navigate solo from their nests on land to the water sources that will become their home. Studies of hatchling turtle navigation have established that light plays the key role in orienting hatchling marine and freshwater turtles so that they can find water. However, the environmental light cues that turtles use to navigate and retinal circuits that process these cues are not known. When light reflects off of water it is horizontally polarized. Behavioral data from my lab indicate that hatchling snapping turtles are especially attracted to horizontally polarized light. We wish to explore the retinal mechanisms that underlie the detection of polarized light in this vertebrate species.

Abstract 1 – Emily Lecy & Calisandra Larson

Generalist:

Hatchling turtles’ first objective in life is to navigate from their nest on land to refuge in water. Longer routes to water can increase the probability of being found by a predator or simply drying out. Hatchling turtles are able to find water with high rates of success using light, although the details of these sensory cues are poorly understood. When light hits a smooth non-metallic surface, such as a body of water, it becomes polarized. Our lab has previously shown that hatchling turtles prefer polarized light. We are testing whether or not polarization cues direct hatchling turtles to water. Because many man made structures are also strong polarizers of light, such as asphalt roads, this work may have important conservation implications.

Field Specific:

Hatchling turtles’ first objective in life is to navigate from the nest to the water. Circuitous routes to water elevate the risk desiccation and predation. Hatchling freshwater turtles are able to find water with high rates of success, primarily using light cues; however, the relevant light cues and neural circuits that process them are poorly understood. Sunlight is unpolarized, but can become significantly horizontally polarized after reflecting off water. As such, horizontally polarized light may be a cue for the presence of water. Indeed, we have found that hatchling snapping turtles, Chelydra serpentina, are attracted to horizontally polarized light in a Y-maze assay, but it is unclear whether or not polarization cues influence navigation in a natural setting. To investigate the importance of polarized light cues we have constructed helmets that block the turtles’ ability to detect polarized light and implemented fluorescent powder and arena release methods to track hatchling turtle navigation in natural settings.

Laura Listenberger - Lipid droplet form and function
PROJECT SUMMARY:
My lab studies the lipid droplet, the intracellular compartment for storage of excess fat. Current, ongoing projects in my laboratory aim to understand the mechanism that leads to lipid droplet accumulation in alcoholic fatty liver disease. Specifically, we explore how particular lipid droplet proteins contribute to the growth and function of lipid droplets in a cell culture model of this disease.

Abstract 1 – Olivia Paetz – Rab18 and Lanosterol Synthase Lipid Droplet Binding in Alcoholic Fatty Liver Disease

Generalist:

Alcoholic Fatty Liver Disease (AFLD) occurs when liver cells accumulate excess lipid in organelles called lipid droplets. Lipid droplets are encased in a membrane composed of phospholipids, predominately phosphatidylcholine and phosphatidylethanolamine. Proteins bind to the lipid droplet membrane, which affects the size and activity of the lipid droplet. It has been observed in animal studies of AFLD that lipid droplet membranes have a decreased ratio of PC:PE, which can contribute to altered protein binding. By culturing AML12 cells in Choline-deficient media and feeding them Oleate, an unsaturated fat, we are able to simulate the effects of AFLD. Using this model, I explored how Rab18 and Lanosterol Synthase bind during altered phospholipid conditions through Western blot analysis. Neither Rab18 nor Lanosterol Synthase had significantly different binding in choline deficient conditions as compared to choline sufficient conditions.

Field Specific:

Most people know that excessive consumption of alcohol leads to liver damage, but few know there is a reversible intermediate step called Alcoholic Fatty Liver Disease (AFLD). Our research aimed to better understand this intermediate step, which is characterized by fat accumulation in liver cells called lipid droplets. Lipid droplets are made of a core of fat surrounded by a layer of molecules called phospholipids. Because these lipid droplets are the main feature of AFLD, we study molecules called proteins that associate with the phospholipid layer. My research looked specifically at two proteins called Rab18 and Lanosterol Synthase. We used different techniques to isolate lipid droplet protein and analyze it. We did not observe a significant difference in protein binding of Rab18 or Lanosterol Synthase in AFLD conditions compared to our control.

Abstract 2 – Hannah Nilsson – Lipotoxicity: Elucidating the Cellular Pathway that Leads from Saturated Fatty Acid to Cell Death

Generalist:

Obesity-related health implications like heart disease and type 2 diabetes are caused in part by fat triggering cell death; however, the cellular pathway for this kind of cell death is not well understood. In this study, we sought to determine if stiffening of the cellular membranes caused cell death. The effects of saturated fat were measured with cell viability assays and fluorescence microscopy. Reducing the production of cellular membrane materials seemed to partially rescue cells from cell death and channel saturated fats into a more benign pathway. The results were ambiguous, however, so future studies should include a variety of cell viability assays that provide a clearer understanding of the cause of ER stress in cell death caused by fat.

Field Specific:

Obesity-related health implications like heart disease and type 2 diabetes are caused in part by lipotoxicity, cell dysfunction and death caused by an excess of saturated fat in cells; however, the lipotoxic pathway is not well understood. In this study, we sought to determine if the incorporation of saturated phospholipids into the ER membrane would trigger ER stress, leading to cell death. To understand the mechanisms of this pathway, cells were treated with the saturated fat palmitate in conditions that decreased phospholipid synthesis. The effects of palmitate treatment were measured with MTT assays, LDH assays, and fluorescence microscopy. Reducing phospholipid synthesis seemed to partially rescue cells from liptoxicity and channel saturated fat away from the lipotoxic pathway. The results were ambiguous, however, so future studies should include a variety of cell viability assays that provide a clearer understanding of the cause of ER stress in the lipotoxic response.

Abstract 3 – Sunny Vuong

Generalist:

Liver failure due to alcoholism is an underappreciated problem in the United States. Before liver failure, there is a stage where the liver accumulates fat in lipid droplets. We are interested in this stage because it indicates potential liver failure, yet is reversible if recognized before the disease progresses. We aim to determine what proteins are present on lipid droplets in a cell culture model for alcoholic fatty liver disease. As of now, not much is known about lipid droplet proteins and their functions. By determining what proteins are present in differing concentrations between control and alcoholic fatty liver cells, we can identify proteins of interest that may have a significant role in liver failure. We used a protein assay to determine the concentration of total protein in our samples and SDS-PAGE and western blotting to visualize the concentration of candidate lipid droplet proteins. We found that perilipin 1, perilipin 2, and CIDEC have shown up; however, we need to do further analysis. Ongoing work will assess the role that these proteins play in the development of alcoholic fatty liver disease.

Field Specific:

Liver failure due to alcoholism is an underappreciated problem in the United States. Before liver failure, there is a stage where the liver accumulates fat in lipid droplets. We are interested in this stage because it indicates potential liver failure, yet is reversible if recognized before the disease progresses. We aimed to identify proteins that are present on lipid droplets in a cell culture model. By determining what proteins are present in differing concentrations between control and AFL cells, we can identify proteins of interest that may have a significant role in the disease. We used a protein assay to determine the concentration of total protein in our samples. We used SDS-PAGE and western blotting to visualize the concentration of candidate lipid droplet proteins. Our work shows that three proteins perilipin 1, perilipin 2, and CIDEC are more prevalent under conditions that model AFLD. Future work will assess the role that these proteins play in the development of alcoholic fatty liver disease.

Emily Mohl - Milkweed Adaptation in a Changing World
PROJECT SUMMARY:
This research project aims to investigate patterns of adaptation in common milkweed, a plant that has and will experience significant changes due to human influence, especially relating to the dramatic decline of monarch butterfly populations. The project, based at St. Olaf, depends upon collaboration with researchers and their students at other institutions. We will build upon previous students’ work to investigate: 1. geographic variation in milkweed growth and tolerance to herbivory, and 2. whether milkweed populations are locally adapted to their region or habitat type, or whether certain milkweed genotypes perform better in multiple locations. In addition to research, the project will involve communicating about procedures and research with educators at various institutions participating in the project.
Students will use milkweed seeds collected from multiple sites in North America to begin to address these questions in both greenhouse and field settings. Students should be comfortable working with insects in these settings. They should also be comfortable presenting and leading groups, including educators, although support and guidance will be provided. Collaboration and communication will be critical for components of this project, but there is also potential for independent work. Students should have completed Bio150; backgrounds in statistics, ecology, and/or education are valued. Experience with video production may also be useful.

Abstract 1 – Kate Noel – Geographic Variation in Milkweed Growth and Tolerance

Generalist:

The recent decline in North American monarch butterfly populations corresponds to a decline in milkweed populations, the primary food source for monarch larvae. Climate change further threatens both species as it forces their populations to rapidly adapt to new environmental conditions. Identifying natural geographic clines in fitness-related traits can predict how successfully a species will respond to future variations in climate. Using seeds from 16 different sites, we conducted a greenhouse study to investigate the existence of a latitudinal cline in common milkweed growth patterns and tolerance. We identified significant geographic variation in growth and a marginally significant positive relationship between site longitude and tolerance. While the implications of future climate change on overall milkweed fitness remain uncertain with the finding that eastern ecotypes are more tolerant than western ecotypes, additional cline studies may provide insight into the species’ ability to endure changing environments and the uncertain future of the monarch butterfly.

Field Specific:

The recent decline in North American monarch butterfly populations corresponds to a decline in milkweed populations, the primary food source for monarch larvae. Climate change further threatens both species as it forces their populations to rapidly adapt to new environmental conditions. Understanding how certain traits naturally vary geographically can be useful for predicting how a species will respond to future climate change. Using seeds from 16 different sites, we conducted a greenhouse study to investigate common milkweed growth and tolerance across North America. We identified significant geographic variation in milkweed growth patterns and a potential geographic trend in tolerance. Further study may provide additional insight into the extent of milkweed’s ability to endure changing environments and the uncertain future of the monarch butterfly.

Abstract 2 – Dan Buchmeier – Local Adaptation of Common Milkweed (Asclepias syriaca)

Generalist:

Each year, a population of monarch butterflies migrates between overwintering grounds in Mexico and breeding grounds in North America. This population has been declining for years (Brower 2012). One potential explanation for this decline is the decline in the milkweed population due to farming practices (Pleasants and Oberhauser 2013). This has led to an increase in planting milkweed to create an environment for monarchs (USFWS 2017, NFWF 2017). Our goal is to determine whether milkweed displays signs of adaptation to their local environment and if it has any effect on restoring milkweed populations. Milkweed seeds were received from around the country and transplanted into plots at our experimental site. The methods were also designed to allow teachers to perform this experiment within their lesson plan and record data to be sent back to us. The effect of the place of origin was significant soon after transplanting, but lessened over time. This suggests that milkweed may have some adaptation to their local environment.

Jean Porterfield - Molecular Analysis of Soil Microbes
PROJECT SUMMARY:
What is the role of soil microbes in prairie restoration? We will collect soil samples from local (St. Olaf Natural Lands and Carleton Arboretum) prairie restoration plots. Then we will study the microbial DNA and RNA from these plots to see what effects different prairie restoration methods have on the soil microbial communities. While this project does include field collection of samples, most of the work is molecular in nature and will be done in Regents lab spaces. My research in general uses molecular genetic techniques to generate data that address bigger questions in evolution and ecology; the skills that students learn are transferable to many other fields of interest. Students who will have completed BIO 150 by Summer 2017 are encouraged to apply; completion of BIO 233 (Intermediate Genetics) is desirable but not required. Applicants must be comfortable with both independent and collaborative work.

Abstract 1 – Rebecca Ferrer & Laura Hurtado – The effects of controlled burns on the structure of the soil microbial community in the restored prairies of the St. Olaf Natural Lands

Generalist:

The St. Olaf Natural Lands include sections of restored prairies that are maintained in part by controlled burns conducted periodically. While this management technique is generally well-researched, less is known about the effects of burns on soil microbial communities. Soil bacteria and archaeans play crucial roles in most chemical reactions of the nitrogen cycle by using unique catalytic enzymes as part of their metabolism. As a result, these microbes influence large-scale ecological variables such as nitrogen availability to plants, nitrogen-based pollutants in water runoff, and production of the greenhouse gas nitrous oxide. In this study, we assessed the abundance of microbial genes encoding nitrogen-relevant enzymes in the soils of two St. Olaf Natural Lands restored prairie sections burned at different times. We extracted DNA from 30 soil samples taken from the two sections, used PCR to amplify six genes involved in the nitrogen cycle as well as the 16s rRNA gene, and measured the intensity of the PCR products as a proxy for gene abundance. There was no significant difference in 16s rRNA gene abundance between the two prairie sections, but most of the nitrogen-related genes had greater abundance in soil from the more recently burned section. Multivariate analyses suggested that gene abundance varied more widely in more recently burned soils. Overall, the two restored prairie sections did not markedly differ in microbial community structure as assessed by gene abundance at the time and scale studied.

Field Specific:

The St. Olaf Natural Lands include sections of restored prairies that are maintained in part by controlled burns conducted periodically. While this management technique is generally well-researched, less is known about the effects of burns on soil bacteria, many of which play crucial roles in the nitrogen cycle. These bacterial microbes have unique genes that help them process nitrogen for their own energy, thus influencing large-scale ecological variables such as nitrogen availability to plants, nitrogen-based pollutants in water runoff, and production of the greenhouse gas nitrous oxide. In this study, we assessed the abundance of nitrogen-relevant microbial genes in the soils of two St. Olaf Natural Lands restored prairie sections burned at different times. We extracted DNA from 30 soil samples taken from the two sections, and measured the abundance of six genes involved in the nitrogen cycle as well as a gene (called 16s) found in all bacteria. There was no significant difference in 16s gene abundance between the two prairie sections, but most of the nitrogen-related genes had greater abundance in soil from the more recently burned section. Analyses of all genes together suggested that gene abundance varied more widely in more recently burned soils. Overall, the two restored prairie sections did not markedly differ in microbial community structure as assessed by gene abundance at the time and scale studied.

Kevin Potts - How does the social network of chimpanzees influence disease dynamics?
PROJECT SUMMARY:
Chimpanzees, our closest living relatives, are susceptible to many of the same pathogens that afflict humans, and particularly infectious strains can move quickly through a population, causing massive spikes in mortality. To understand how best to protect this endangered species from the effects of infectious disease outbreaks, we must know how a pathogen is likely to move through a population before an outbreak occurs. In this project, we will travel to Kibale National Park in southwestern Uganda to collect data on physical proximity networks, with physical proximity acting as an index for ease of pathogen transmission, within the largest community of chimpanzees in the world (the Ngogo community; currently approximately 200 individuals). We will then use this data to construct statistical models to explain how infectious diseases, in particular the Ebola virus, which has decimated chimpanzee populations elsewhere, might move through this community under various scenarios, with the long-term aim being to develop eventual vaccination strategies.

Kathleen Shea - Ecology of the St. Olaf Natural and Agricultural Lands
PROJECT SUMMARY:
Students working with me will study forest restoration, investigating questions about tree growth patterns, ecosystem services, such as carbon sequestration, and management goals. Trees in a 27-year-old restoration will be measured for diameter, height and mortality. New colonization will be documented. This information will be added to a long-term data set to determine the progress of the restoration. The effects of the likely arrival of the emerald ash borer on ash trees will be considered.
Students will also examine the effects of buffer strips and cover crops on corn and soybean agriculture with the goal of determining how to maintain healthy water and resources. Students will conduct research on working farms with the opportunity to help farmers make appropriate decisions about sustainable farming practices. Research will build on previous studies and examine changes in water and soil characteristics over time.

Abstract 1 – Kirsten Koerth & Robby Holmes – 27-Year Study of a Restored Maple-Basswood Forest in Southeastern Minnesota

Generalist:

In 1990, a 10-acre agriculture site on St. Olaf land was reseeded in order to return the land to a maple-basswood forest. The site has been measured every couple of years since 1990 in order to monitor the reforestation effort. Trees were measured for height and diameter, new and colonizing trees were recorded, and mortality rates were analyzed. In the original plantings, white ash, black walnut, bur oak, white oak, sugar maple, and red maple made up 90% of the trees. In 2017, the fastest colonizing species were white ash, black walnut, sugar maple, box elder, basswood, wild plum, and elm. We analyzed rates of tree mortality among species and overall by comparing the number of original trees planted with the ones that are still alive at each year. There was a 30% mortality rate for the first 9 years of growth but a 4% mortality rate after 10 years.

Field Specific:

In 1990, a 10-acre agriculture site on St. Olaf land was reseeded in order to return the land to a maple-basswood forest. The site has been measured every couple of years since 1990 in order to monitor the reforestation effort. Trees were measured for height and diameter, new and colonizing trees were recorded, and mortality rates were analyzed. In the original plantings, white ash, black walnut, bur oak, white oak, sugar maple, and red maple made up 90% of the trees. In 2017, the species that moved into the forest were white ash, black walnut, sugar maple, box elder, basswood, wild plum, and elm. We analyzed rates of tree mortality among species and overall by comparing the number of original trees planted with the ones that are still alive at each year.

Chemistry

Bob Hanson - Project 1 - Computational Material Science
PROJECT SUMMARY:
This research is in the area of computational materials science, a relatively new highly interdisciplinary field that involves physics, mathematics, and chemistry. AFLOW is an open-access database and high through-put computational service at Duke University that uses extreme computing to look for new materials with critically interesting properties. Our project aims to create an interactive web-based visualization of any structure in the AFLOW database that has associate band structure data in a way that allows novel simultaneous exploration of the crystal structure, electronic band structure, and “Brillouin zones”.

Abstract 1 – My Dan Nguyen, Jacob Packard, and Mingzhi Zhao 

Generalist:

AFLOW is an open-access database at Duke University that uses high-throughput computing to look for new materials with critically interesting properties. The research goal is to use Jmol and JavaScript to create an interactive web-based visualization of any crystal structures and their electronic band structures in the AFLOW database.

In order to achieve our goals, we have made many updates, which includes the report of wrong crystal structures, the development of the search tools in the landing page for the Brillouin zone website, and the improvement of user interactive capabilities with dynamically modified graphs in the website. See http://aflowlib.mems.duke.edu/users/jmolers/jmol/index.html to access the graphs and visualizations.

Field Specific:

AFLOW is an open-access database at Duke University that uses high-throughput computing to look for new materials with critically interesting properties. The research goal is to use Jmol and JavaScript to create an interactive web-based visualization of any crystal structures and their electronic band structures in the AFLOW database.

Over the period of the research, some crystal structures which have a discrepancy between the relaxed lattice variation and the one indicated in KPOINTS.bands have been found and reported to Duke University. The search function has been developed in order for users to filter through the inorganic compounds based on structure classification. The accessibility and visualization of the band structures in the AFLOW website have also been improved by incorporating dynamically changeable graphs. See http://aflowlib.mems.duke.edu/users/jmolers/jmol/index.html to access the graphs and visualizations.

Bob Hanson - Project 2 - SwingJS - A new Paradigm for Web-Based Applets
PROJECT  SUMMARY:
The SwingJS project (http://swingjs.sourceforge.net) was started in the spring of 2015 as an extension of the successful blended Java/JavaScript development of JSmol, the leading web-based application for the embedding of interactive molecular graphics on the web. The goal of the project is to develop a mechanism for the smooth transformation of a working Java applet or application into a working HTML5/JavaScript equivalent without having to do any extensive code rewriting. The problem we are trying to solve transcends any specific area of science. It is that Java applets — long an important part of the dynamic features of the web — are no longer able to be used. What we have are hundreds — thousands — of websites (mostly of an educational nature) that are no longer functional because their Java applets cannot be opened. It is a terrible loss of resources in physics, mathematics, chemistry, and many other areas. What we are developing allows the resurrection of these applets as JavaScript equivalents using technology that is unique and powerful and, as it turns out, developed entirely here at St. Olaf. The summer of 2016 was our first go at doing this, and it proved outstandingly successful, resulting in the resurrection of over 20 applets. Forty more were converted during the fall of 2016.

Abstract 1 -Tahir Ahsan, Andrew Lee, and Nikesh Yadav – The Essential Tool for Conversion of Java to Javascript

Generalist:

In the early 2000s, Java was the preferred programming language for researchers and educators seeking to integrate technology with their work. Thousands of web applets were made in Java to aid education and run simulations. However, in the early 2010s, it was discovered that running Java on a browser created security vulnerabilities, and internet browsers stopped supporting Java. As a result, thousands of applets from the past have died out. Creators needed a way to revive their applets without learning another language. SwingJS is a project that converts Java applets into native JavaScript, which can be run on web browsers just like the original applets. This can bring back thousands of research and education tools.

Field Specific:

In the early 2000s, Java was the preferred programming language for researchers and educators seeking to integrate technology with their work. Thousands of web applets were made in Java for education and simulations. However, in the early 2010s, it was discovered that running Java on a browser created security vulnerabilities, and internet browsers stopped supporting Java. SwingJS is the essential tool for converting Java applets into Javascript. It uses the Java2Script transpiler created by Zhou Renjian to convert Java to Javascript and recreates numerous features from the Swing GUI toolkit. We’ve made several improvements to Java2script such as addressing the issue of method overloading and overriding. Additionally, scripts for Mac, Windows and Linux have been created to facilitate the usage of SwingJS by installing Eclipse with the necessary plugins to transpile Java source code to Javascript. With SwingJS, previous Java developers are able to revive their outdated applets.

Dipannita Kalyani - Project 1 - Synthesis of Molecular Architectures Prevalent in Pharmaceuticals, Agrochemicals and Polymers using Palladium Catalysts
PROJECT SUMMARY:
The discovery of environmentally friendly methods for the construction of molecular architectures prevalent in fuels, pharmaceuticals, agrochemicals, polymers and commodity chemicals is very desirable. The goal of my research is the development of mild, and efficient methods for the formation of such compounds using palladium catalysts. The project will provide students experience with state of the art laboratory techniques and research methods for organic/organometallic chemistry. Students participating in the research will have opportunities to present their work at national chemistry conferences. The research experience will be invaluable for students considering graduate study in chemistry, a career in biomedical sciences or a job in the chemical industry.

Dipannita Kalyani - Project 2 - Transformation of Renewable Starting Materials to Compounds Relevant to the Pharmaceutical Industry
PROJECT SUMMARY:
Carbon–carbon bond forming reactions are extensively utilized for the assembly of compounds relevant to the pharmaceutical, industry. The goal of my research is the discovery of such reactions using inexpensive and/or renewable starting materials and earth- abundant nickel catalysts. Students participating in this project will benefit from a state-of-the-art experience in organometallic catalysis, a field that is extensively used in the synthesis of medicinal drugs and in biomedical applications. The research experience will be invaluable to students interested in graduate school in chemistry, careers at national labs or employment in the chemical/pharmaceutical industry. Students participating in the research will have opportunities to present their work at national chemistry conferences.

Laura Listenberger - Lipid droplet form and function
PROJECT SUMMARY:
My lab studies the lipid droplet, the intracellular compartment for storage of excess fat. Current, ongoing projects in my laboratory aim to understand the mechanism that leads to lipid droplet accumulation in alcoholic fatty liver disease. Specifically, we explore how particular lipid droplet proteins contribute to the growth and function of lipid droplets in a cell culture model of this disease.

Abstract 1 – Olivia Paetz – Rab18 and Lanosterol Synthase Lipid Droplet Binding in Alcoholic Fatty Liver Disease

Generalist:

Alcoholic Fatty Liver Disease (AFLD) occurs when liver cells accumulate excess lipid in organelles called lipid droplets. Lipid droplets are encased in a membrane composed of phospholipids, predominately phosphatidylcholine and phosphatidylethanolamine. Proteins bind to the lipid droplet membrane, which affects the size and activity of the lipid droplet. It has been observed in animal studies of AFLD that lipid droplet membranes have a decreased ratio of PC:PE, which can contribute to altered protein binding. By culturing AML12 cells in Choline-deficient media and feeding them Oleate, an unsaturated fat, we are able to simulate the effects of AFLD. Using this model, I explored how Rab18 and Lanosterol Synthase bind during altered phospholipid conditions through Western blot analysis. Neither Rab18 nor Lanosterol Synthase had significantly different binding in choline deficient conditions as compared to choline sufficient conditions.

Field Specific:

Most people know that excessive consumption of alcohol leads to liver damage, but few know there is a reversible intermediate step called Alcoholic Fatty Liver Disease (AFLD). Our research aimed to better understand this intermediate step, which is characterized by fat accumulation in liver cells called lipid droplets. Lipid droplets are made of a core of fat surrounded by a layer of molecules called phospholipids. Because these lipid droplets are the main feature of AFLD, we study molecules called proteins that associate with the phospholipid layer. My research looked specifically at two proteins called Rab18 and Lanosterol Synthase. We used different techniques to isolate lipid droplet protein and analyze it. We did not observe a significant difference in protein binding of Rab18 or Lanosterol Synthase in AFLD conditions compared to our control.

Abstract 2 – Hannah Nilsson – Lipotoxicity: Elucidating the Cellular Pathway that Leads from Saturated Fatty Acid to Cell Death

Generalist:

Obesity-related health implications like heart disease and type 2 diabetes are caused in part by fat triggering cell death; however, the cellular pathway for this kind of cell death is not well understood. In this study, we sought to determine if stiffening of the cellular membranes caused cell death. The effects of saturated fat were measured with cell viability assays and fluorescence microscopy. Reducing the production of cellular membrane materials seemed to partially rescue cells from cell death and channel saturated fats into a more benign pathway. The results were ambiguous, however, so future studies should include a variety of cell viability assays that provide a clearer understanding of the cause of ER stress in cell death caused by fat.

Field Specific:

Obesity-related health implications like heart disease and type 2 diabetes are caused in part by lipotoxicity, cell dysfunction and death caused by an excess of saturated fat in cells; however, the lipotoxic pathway is not well understood. In this study, we sought to determine if the incorporation of saturated phospholipids into the ER membrane would trigger ER stress, leading to cell death. To understand the mechanisms of this pathway, cells were treated with the saturated fat palmitate in conditions that decreased phospholipid synthesis. The effects of palmitate treatment were measured with MTT assays, LDH assays, and fluorescence microscopy. Reducing phospholipid synthesis seemed to partially rescue cells from liptoxicity and channel saturated fat away from the lipotoxic pathway. The results were ambiguous, however, so future studies should include a variety of cell viability assays that provide a clearer understanding of the cause of ER stress in the lipotoxic response.

Abstract 3 – Sunny Vuong

Generalist:

Liver failure due to alcoholism is an underappreciated problem in the United States. Before liver failure, there is a stage where the liver accumulates fat in lipid droplets. We are interested in this stage because it indicates potential liver failure, yet is reversible if recognized before the disease progresses. We aim to determine what proteins are present on lipid droplets in a cell culture model for alcoholic fatty liver disease. As of now, not much is known about lipid droplet proteins and their functions. By determining what proteins are present in differing concentrations between control and alcoholic fatty liver cells, we can identify proteins of interest that may have a significant role in liver failure. We used a protein assay to determine the concentration of total protein in our samples and SDS-PAGE and western blotting to visualize the concentration of candidate lipid droplet proteins. We found that perilipin 1, perilipin 2, and CIDEC have shown up; however, we need to do further analysis. Ongoing work will assess the role that these proteins play in the development of alcoholic fatty liver disease.

Field Specific:

Liver failure due to alcoholism is an underappreciated problem in the United States. Before liver failure, there is a stage where the liver accumulates fat in lipid droplets. We are interested in this stage because it indicates potential liver failure, yet is reversible if recognized before the disease progresses. We aimed to identify proteins that are present on lipid droplets in a cell culture model. By determining what proteins are present in differing concentrations between control and AFL cells, we can identify proteins of interest that may have a significant role in the disease. We used a protein assay to determine the concentration of total protein in our samples. We used SDS-PAGE and western blotting to visualize the concentration of candidate lipid droplet proteins. Our work shows that three proteins perilipin 1, perilipin 2, and CIDEC are more prevalent under conditions that model AFLD. Future work will assess the role that these proteins play in the development of alcoholic fatty liver disease.

Elodie Marlier - Development of first row transition catalysts using novel hybrid ligands
PROJECT SUMMARY:
This project aims to create a family of low-valent first-row transition metals complexes stabilized by novel hybrid N2P2 ligands and exploring their reactivity. Currently, most industrial processes use expensive second and third row transition metals as catalysts for a variety of transformations. This research aims to explore cheaper and more widely available first-row transition metals as replacements for these expensive metals. For this purpose, a family of N2P2 ligands will be prepared and reacted with first-row transition metals. The research will expose undergraduate students to organic and inorganic synthesis.

Abstract 1 – Andrew Reuter, Peder Johnson, and Jungoh Lee

Generalist:

Industrial catalysts are used to increase the speed and decrease the energy necessary to carry out chemical reactions. Current catalysts are not environmentally friendly and are expensive, often times utilizing palladium and platinum. The goal of this project is to create more sustainable and cost effective catalysts for a variety of uses. The process of making the catalyst has several steps and each step must be optimized to yield the maximum amount of final product. This summer’s efforts have focused on finding the best conditions for the first two steps of the catalyst production.

Field Specific:

Industrial catalysts are frequently unsustainable and expensive due to their use of 2nd and 3rd row transition metals. With the aim of using more abundant and inexpensive 1st row transition metals, a monoanionic tetradentate ligand has been synthesized. This ligand will provide the necessary environment for the stabilization of the reactive low oxidation state metal complexes. These highly reduced species can in turn be evaluated as potential catalysts for a variety of uses. To this end this summer’s efforts have focused on optimizing the first two steps of the ligand synthesis to maximize percent yield. Metallation of the ligand has been attempted with both zinc (II) chloride and nickel (II) chloride. Throughout the ligand synthesis and metallation, 1H and 31P NMR spectroscopy have been used to optimize the reactions and characterize each intermediate.

Rodrigo Sanchez-Gonzalez - Photophysics of toluene at low temperatures. Part I.
PROJECT SUMMARY:
Laser Induced Fluorescence (LIF) using organic molecular tracers is a technique commonly employed for flow visualization, heat transfer and fuel/air mixing studies, and for temperature determination in gaseous flows. Strong absorption cross sections at common wavelengths have made these molecules very attractive for the study of high-temperature environments using LIF. Molecular tracers such as acetone, toluene, 3-pentanote, and triethylamine can be excited using the fourth harmonic from a Nd:YAG laser at 266 nm. Tracers such as formaldehyde and poly-aromatic hydrocarbons (PAH) can be excited using the third harmonic at 355 nm. However, quantitative interpretation of LIF signals require knowing the photophysical properties of the tracers as well as of collisional quenching cross sections, both of which strongly depend on temperature. Information about photophysical properties and quenching cross-sections for these organic tracers is limited to temperatures above room temperature, and thus applicability of LIF at lower temperatures requires of additional experimental information. This project involves the design and functionalization of a cryogenic instrument and its use to measure photophysical properties and collisional quenching cross-sections of toluene at temperatures below 300 K. Self-motivated students interested in chemistry and physics are encouraged to apply.

Abstract 1 – Simon Broccard & Caroline Loe – Liquid Nitrogen Cryostat for Studies of Low Temperature Energy Transfer

Generalist:

In order to develop safe and reliable high speed flight, it is important to understand the behavior of gas flows under relevant conditions. It is possible to measure pressures, temperatures, and velocities in wind tunnel testing with the use of lasers. When a molecule is excited by a laser, it absorbs energy which is later released as a fluorescence signal. The intensity of this fluorescence signal can then be used to determine the temperature. This summer, we assembled and functionalized an instrument to study the fluorescence properties of toluene at low temperatures commonly found in high-speed wind tunnels. Computer programs were developed to control the instrument and acquire data, as well as to determine temperature from the fluorescence intensities.

Field Specific:

In order to develop safe and reliable high speed flight, it is important to understand flow behavior under a wide range of conditions. Using Laser Induced Fluorescence (LIF) methods, it is possible to determine the pressures, temperatures, and velocities in conditions relevant to high speed wind tunnel testing. In LIF, fluorophores such as nitric oxide and toluene emit fluorescence after being excited using ultraviolet lasers. Analysis of the images of fluorescence intensity distributions can provide a spatially resolved temperature measurement of the flow field under investigation. We have completed the assembly and functionalization of a liquid nitrogen cryostat to study photophysical properties of toluene – a potential seed fluorophore for high speed flows – to be used in LIF-based measurements. A LabVIEW program was designed to control the instrument and acquire data, and an image analysis MATLAB code was developed for quantitative instantaneous temperature determination from simultaneously acquired fluorescence signals.

Jeff Schwinefus - DNA and RNA Stability in Cosolute Solutions
PROJECT SUMMARY:
Have an interest in biochemistry or physical chemistry? If so, then I just may have a research project you would be interested in. My research project is appropriate for biology, chemistry, or physics students that have completed the Chem 121/123/126, Chem 125/126, or CH/BI 125/126/127 introductory course sequences. Cosolute Interactions with Nucleic Acids Biochemical reactions involving DNA, RNA, or proteins often involve large changes in the surface area of these biopolymers. Surface area changes expose (or bury) chemical functional groups that gain (or lose) interactions with the solvent and all its solute components. The thermodynamic favorability of the interactions between solvent and DNA, RNA, and protein surface areas can dramatically attenuate or enhance the rate of biochemical reactions. We can use the change in reaction rate constants (and equilibrium constants as well) to probe the chemical composition of surface area changes during DNA, RNA, and protein biochemical reactions and develop a general method to ascertain biopolymer structural changes.
For several years my research group has quantified the interaction of neutral organic molecules like urea or amino acids (which we generically call cosolutes) with the surface area of nucleic acids. We use a mix of uv-absorbance, differential scanning calorimetry, vapor pressure osmometry, solubility measurements, and molecular dynamics simulations to determine the excess (or deficiency) of these cosolutes near nucleic acid functional groups. If the interactions between cosolutes and the chemical functional groups in the newly exposed nucleic acid surface area after unfolding are thermodynamically favorable, the stability of the folded nucleic acid will be lower in aqueous cosolute solutions relative to water alone.
This summer, we plan to probe the stability of biologically relevant nucleic acid structures such as DNA G-quartet structures with urea, glycine betaine, and proline. We also plan to quantify the interactions of tetramethylamine formate with nucleobases and related compounds to develop this cosolute as a probe of nucleic acid surface areas.

Abstract 1 – Shutian Lu & Kaylyn Billmeyer – The Preferential Destabilization of GC-rich RNA Duplexes by Proline Explained

Generalist:

Solutes have the potential to probe biopolymer conformational changes during a biochemical reaction and provide a general method to map out the mechanistic steps in a reaction pathway. This work quantified the interactions of the solute L-proline with RNA surface areas of different guanine-cytosine content. Proline interactions with RNA became stronger at higher temperatures. When temperature was held constant, proline-RNA interactions were independent of RNA chemical composition. Therefore, proline interactions with RNA are dependent on temperature and negate comparison of experiments using L-proline as a probe of biopolymer surface area at different temperatures.

Field Specific:

To facilitate the use of L-proline as a probe of biopolymer conformational changes in vitro, proline interactions with RNA duplex surfaces exposed during unfolding were quantified using thermal and isothermal titration denaturation monitored by uv-absorbance. The m-values (our metric of proline-RNA interaction) from thermal denaturation decreased with increasing GC content, indicating increasingly favorable proline interactions with exposed RNA surface area. However, m-values from isothermal titration denaturation were independent of GC content and less negative than those from thermal denaturation. The m-value from isothermal titration denaturation of a 50% GC RNA duplex decreased as temperature increased and was in nearly exact agreement with the m-value from thermal denaturation. Therefore, the more favorable proline interactions with higher GC content duplex surface areas during thermal denaturation resulted from the temperature dependence of proline interactions rather than duplex GC content. Our results facilitate the use of proline as a probe of biopolymer conformational changes during biochemical reactions at different reaction temperatures.

W. Casey Solomon - Structural characterization of anti-listerial bacteriocins
PROJECT SUMMARY:
Bacteria exist in complex multi-species environments with extensive competition for space and resources. In order to secure their competitive advantage many bacteria produce small protein antibiotics that selectively target competing species. Lactobacillus bacteria generate a range of bacteriocins that target listeria monocytogenes, a potent human pathogen. Several of these anti-listerial peptides are currently in use in industrial food production as topical antibiotics. In order to better understand the structural and functional characteristics of anti-listerial bacteriocins we will pursue the structural characterization of these small peptides through muliti-dimensional NMR spectroscopy to be carried out both at Saint Olaf and at the MNMR Center at the University of Minnesota-Twin Cities. Understanding the physical structure of these bacteriocin proteins will provide insight into their mechanism of anti-listerial activity as well as a basis for rational design approaches to improve their efficacy and potency. Ultimately the goal of this project is to combine this new structural insight with in vitro protein synthesis to incorporated non-natural amino acids into the structures of these proteins resulting in increased resistance to inactivation by environmental factors.

Abstract 1 – Sydney Povilaitis & Xiaoping Zhang

Generalist:

Bacteriocins are antibacterial proteins secreted by lactic acid bacteria (LAB), commonly used to produce fermented foods, that target specific competing strains of bacteria in their environment. This offers the bacteria that produces them a competitive advantage. Bacteriocins use antibiotic pathways that are distinct from current clinically-used small molecule antibiotics making them intriguing targets for use against antibiotic resistant
bacteria as well as limiting potential side effects. The goal of our experiments is to isolate novel bacteriocins from LAB and to obtain their three-dimensional structure using nuclear magnetic resonance spectroscopy. By determining their structure, we can better understand their mechanism of action and use that information to aid in the development of new bio-preservatives and antibiotics.

Field Specific:

Lactic acid bacteria (LAB) produce bacteriocins, small peptides that function as antibiotics, in order to enhance their competitiveness in their environment. Many of these bacteriocins target food-borne pathogens and antibiotic resistant bacteria such as Listeria monocytogenes and Methicillin-resistant Staphylococcus aureus and can be used as bio-preservatives and novel clinical antibiotics. Structural characterization of
bacteriocins would not only allow a better understanding of new antibiotic pathways, but also enables structural modifications to improve activity and stability. Cell-free supernatant (CFS) was obtained from L. plantarum, L. curvatus and P. acidilactici. Utilizing pH adjusted CFS subjected to cation exchange chromatography allowed for the isolation of putative bacteriocins followed by SDS-PAGE to visualize molecular weight of isolates. Spot-on- lawn assay tested antimicrobial activity of isolates. Structural data of isolated proteins 2-5 kDa was collected with 1D 1 H NMR, 2D COSY, and 2D TOCSY spectra.

Mathematics, Statistics and Computer Science

Joe Benson - Symmetry preserving discretizations and their numerical implementations
PROJECT SUMMARY:
In solving differential equations numerically, a common technique is to use what is known as a finite difference approximation. These are discrete equations which approximate the given differential equation by difference quotients. In the event that a differential equation contains a symmetry, that is, a change of variables preserving solutions, it is possible to construct a finite difference approximation that inherits the symmetry of the differential equation. When this is done, the accuracy of the scheme improves greatly.
This project aims to construct some finite difference schemes for several differential equations (ordinary and partial) with symmetries, and investigate their accuracy, stability, consistency and convergence. Applicants should have a working knowledge Mathematica, Python, Matlab, or some other language in which to implement these numerical schemes.

Abstract 1 – Spencer Eanes & Shane Koseriadzki – Invariantizion of Multistep Methods and Buger’s Equation

Generalist:

Finding numerical solutions to differential equations is currently extremely desirable for many scientific fields. Any scheme can be made more accurate by increasing the density of independent variable data points, but doing so also increases the computational cost. New methods aim to increase accuracy for equivalent computational cost. We take traditional finite difference approximations for both ordinary and partial differential equations, and modify them to inherit the equations’ geometric properties. Doing this, we produce more accurate numerical approximations. Several different examples and numerical schemes were investigated in our work.

Field Specific:

Increasing accuracy for equivalent computational cost of numerical solutions to differential equations is extremely desirable in many scientific fields. To do this, we will exploit differential equations’ inherent geometric properties, called Lie symmetries, which encompass transformations that preserve solutions. These symmetries are an integral part of the equations that exhibit them, but are lost to traditional finite difference approximations. We will use the moving frame method so that the finite difference schemes inherit the differential equations’ symmetries, constructing corresponding invariant schemes. We will show that invariantization of multistep schemes on ordinary differential equations, and the of the Crank-Nicolson method applied to Burgers equation, a nonlinear partial differential equation, exhibit increased accuracy.

Adam Berliner - Combinatorial Matrix Theory
PROJECT SUMMARY:
In combinatorics, a graph is a collection of vertices (dots), some of which are connected by an edge (lines). Graphs have a natural correspondence to matrices, which are used to encode the adjacency or lack thereof between pairs of vertices. In this project, we seek to classify the possible sets of eigenvalues over the collection of matrices that represent particular classes of graphs. In particular, we will focus on the refined inertia of a matrix, which counts the number of eigenvalues of a matrix that have positive real part, those that have a negative real part, are zero, and are purely imaginary.
Students working on this project should be interested in and comfortable with linear algebra and, in particular, eigenvalues. Success in at least one proof-writing course (Math 244 or 252) is highly desirable, and coursework at the 300-level in mathematics may be beneficial. Exploration of examples will likely require the assistance of computational software such as Sage (python) or Mathematica, so students should be familiar with or readily able to work with computational software.

Abstract 1 – Deepak Shah & Derek DeBlieck – Refined Inertia for Sign Patterns

Generalist:

In this project, we tackle the linear algebraic problem of studying matrices where the sign of each entry is known but the value of the entries themselves are not. For example, in a predator-prey relationship, despite not knowing the exact population of the predator or prey, we can often predict if the rate of each population is increasing or decreasing. In our project, we study 3×3 matrices which have 0/ + /− entries (sign patterns) instead of numerical entries. We examine these sign patterns, looking for certain linear algebraic characteristics that make these patterns interesting to researchers in mathematical biology and dynamical systems. We then offer a theorem for the extension of our work beyond 3×3 sign patterns.

Field Specific:

Motivated primarily by the Inverse Eigenvalue Problem, the mathematical community has invested large amounts of time and energy into the study of the relation between matrices and their eigenvalues. We contribute to that study by examining which 3 × 3 sign patterns, matrices with non-numeric 0/+/- entries, allow certain types of eigenvalues. In particular, we are interested in patterns that allow refined inertia S3 = {(0, 3, 0, 0),(0, 2, 1, 0),(1, 2, 0, 0)}. In other words, we seek patterns that have one realization with all negative real-part eigenvalues, another with all negative real-part except for one zero eigenvalue, and a third with all negative real-part except for one positive real-part eigenvalue. The presence of this property is of particular interest, as it signals the presence of a saddle-node bifurcation in the study of dynamical systems. We classify all 19,683 3×3 sign patterns, and determine which of these patterns allow this specific set of eigenvalues. We also present a theorem for the extension of our work beyond 3×3 patterns.

Richard Brown - Project 1 - HiPerCic Collaborative Web Applications
PROJECT SUMMARY:
The HiPerCiC (High-Performance Computing in Context) initiative creates custom web applications to support professors in any field with their specific scholarly research and/or teaching. The creation of a convenient user interface and the potential of today’s high-performance computing combine to make it feasible to explore research possibilities in a given field that were impractical before now. Goals for this summer include: (1) extending and improving the core software used by all HiPerCiC applications; (2) continuing development of existing HiPerCiC apps, especially the Digital Humanities projects created in the HiPerCiC course ID 259 (Fall 2015); (3) creating new HiPerCiC apps in fields to be determined; and (4) preparing HiPerCiC training materials for the Fall 2017 offering of ID 259. Preparation: Minimum of CS 251 or comparable background in software development; qualifications that strengthen an application include ID 259 or other prior involvement with HiPerCiC, additional CS courses, or experience with web-app technologies.

Abstract 1 – Joe Peterson  Hugo Valent – Upgrading and Innovating Web Application Development at St. Olaf HiPerCiC 3

Generalist:

HiPerCiC (High Performance Computing in Context) has moved to using less custom technologies. We researched best practices in developing web applications and upgraded some applications to the new system. From
literature and online resources we found that Test-Driven Development, changes to the default project structure, and the Separation of Concerns philosophy enhance the security, performance, and ease of development
and maintenance. The new version of HiPerCiC uses the most up to date approaches and technologies such as containerization to isolate applications and Continuous Integration and Deployment. New training
materials were developed this summer that incorporate above findings so that we ensure that the new generation of HiPerCiC developers create web applications that are tested for failure and easily maintainable and
distributable in the future.

Field Specific:

Porting and Best Practices in Developing HiPerCiC 3 Applications
HiPerCiC (High Performance Computing in Context) is moving to its third major version. Every new HiPerCiC application now gets its own Django project and is placed inside of a Docker container. We researched and
implemented Separation of Concerns and other adjustments to the default Django project structure, as well as security measures for privacy and attack protection. We applied these to some applications to test the
findings. Docker is combined with a Heroku-like system called Dokku that allows for easy deployment from development to production. Every container has its own Gunicorn web server and reverse proxy. White Noise takes care of serving static files for persistence and PostgreSQL runs in its own container to ensure that the web server container does not get slowdown. We adopt Test-Driven Development along with Continuous Integration which code is tested on deployment. New training materials were also developed to put these findings into practice.

Richard Brown - Project 2 - Interactive text materials for teaching parallel and distributed computing through programming languages
PROJECT SUMMARY:
This project will develop a dynamic user interface for an online, interactive textbook segment for introducing parallel and distributed computing (PDC) to undergraduate computer science students, through the viewpoint of programming languages. This online resource would be a proof of concept enabling students to learn through hands-on experience with actual PDC resources, conveniently and ubiquitously available through a browser, with immediate feedback. Our programming-language approach to introducing PDC is novel, and could be presented as a three-week unit in a programming languages course, or early in a PDC course as an alternative to standard approaches such as message passing or shared memory. The user interface developed this summer will connect with a “backend” multi-language computational platform to be completed in a subsequent project.

Richard Brown - Project 3 - New Frontiers in Teaching Parallel and Distributed Computing
PROJECT SUMMARY:
Nowadays, nearly all computer hardware uses multicore parallelism and “big data” computation has an impact on everyone’s daily life through the web services industry and more.  This project will explore emerging hardware and software technologies in order to make them more accessible to researchers on campus (in CS and other fields) and to make them available to undergraduate CS students at St. Olaf and elsewhere. Specifically, we will explore two or more of the following initiatives: (1) developing WebMapReduce software, a convenient web-based user interface for big-data computations using Hadoop or Phoenix; (2) exploring a new software-based approaches to teaching parallel and distributed computing (PDC) at all levels, such as the Thread-Safe Graphics Library for visualizing parallel computations and/or a programming-languages based approach to introducing PDC; (3) high-performance computing capabilities, taking advantage of St. Olaf’s CS-managed specialized servers and networking up to 40Gb/sec; and (4) microclusters and embedded computing/Internet of Things with single-board computers. Educational materials will be posted on CSinParallel.org. Preparation: Minimum of CS 251; CS 300 (PDC), CS 273 (OS) or equivalent knowledge of parallel computing and/or systems is an asset, as are other CS courses.

Abstract 1 – Bidi Sharma 

Generalist:

In 2016, a project of installing 10-gigabit network infrastructure started with the support of National Science Foundation and it was extended to certain servers and lab machines in the initial stage. In the summer of 2017, it was
extended into other CS-managed computing resources. A massive 208-terabyte storage server was also introduced into the infrastructure and deployed after multiple tests and benchmarking with different software and hardware configurations, thus enabling centralized storage over the network. Along with these hardware- and network- related enhancements, many software and application server upgrades were performed such as the upgrade of StoGit—our primary source code version control service, to include features such as Continuous Integration to facilitate courses and research.

Field Specific:

In 2016, a project of installing and switching to a 10-gigabit network infrastructure started with the support of National Science Foundation and was extended to some servers and the MistRider cluster, a high-performance
cluster that runs on lab machines in the initial stage. In the summer of 2017, 10-gigabit ethernet was extended to other CS-managed computing resources: infrastructure servers, general purpose servers, clusters and HPC
resources. The 10-gigabit network serves as a foundation of the newer, more performant network infrastructure that remains independent from St. Olaf’s network and continues to be managed autonomously by the team of Cluster Managers. A massive 208-terabyte storage server was also introduced into the infrastructure and deployed after multiple tests and benchmarking with different RAID schemes, enabling centralized storage over the network. Along with these, software and application server upgrades were performed such as the upgrade of StoGit—our web based Git collaborative hub, to include features such as Continuous Integration to facilitate courses and research.

Abstract 2 – Syver Johansen – Protein Sequence Alignment and RCR on Intel ® Xeon Phis TM

Generalist:

This research project examined the replicability–the capability for other researchers to replicate scientific results–of a previous study that used Xeon Phi-equipped computers to compare a given protein sequence against a database of sequences. The underlying algorithm, called the Smith-Waterman algorithm, aligns protein sequences and then identifies regions of similarity between them. We discovered that the original researchers
were correct in concluding that the Xeon Phis allowed the code to run much quicker, but that they inaccurately coded the algorithm. Our study suggests a new role for undergraduate research in investigating the scientific replicability of computing research results.

Field Specific:

This research examined software produced by a team of Chinese researchers that was supposed to run protein sequence alignments using the Smith-Waterman algorithm. If accurate, the program should take a query sequence and perform alignments with it and every sequence in the 2013 version of the TrEMBL sequence database. We investigated whether this code calculated the alignments accurately, and whether the performance of
the code on a Xeon Phi cluster was indeed faster than a prior GPU implementation of the algorithm. We found that the performance and runtime results produced by the original researchers was accurate and that the Xeon Phi cluster did have better performance than the GPU implementation, but that the code incorrectly calculated the sequence alignments. Our study suggests a new role for undergraduate research in investigating the scientific replicability of computing research results.

Olaf Hall-Holt & Ryota Matsuura - Learning Mathematics on Mobile Devices II
PROJECT SUMMARY:
This project will involve (1) continuing development of a mobile device application and supporting materials for learning algebraic concepts and related numeric fundamentals and (2) research on the effectiveness of the device with elementary and middle school students. The mobile device is a game from which students can learn a variety of topics starting with operations on the number line and leading into the evaluation of algebraic expressions, backwards reasoning to solve simple equations, and minimization of algebraic functions. “Playing” the game will entail solving a series of problems intended to guide students as they learn and make sense of mathematics through their own doing of mathematics. The device will conduct real-time assessment and provide dynamic scaffolding, adjusting the level of difficulty according to how students play the game. It also has a team-player mode, allowing students to play the game (even across the globe!) and learn mathematics together.  Students interested in this project should have either (1) experience with the learning and teaching of early mathematics topics, or (2)
experience with mobile device or web development with (preferably) an interest in the learning of mathematics, or (3) possibly both.  The project will involve a close collaboration between students with these varying backgrounds.

Abstract 1 – Jacquie Hanson, Mazon Abu-Sharkh, Nathan Swan, Katheryn Wolff & Elizabeth Clement – The Suuji Project

Generalist:

Many students struggle with the numeric and symbolic aspects of learning mathematics. Our goal is to develop stronger foundations for high-level mathematics by appealing to the visual-spatial intuitions of elementary schoolers. We’ve developed a 3-week curriculum alongside a suite of physical manipulatives and digital applications (apps) and games that focus on enhancing students’ intuitions, representing numbers with lengths. Using both environments allows students to make more connections and enhances their understanding. We investigated the effectiveness of our product with feedback from a small group of students from Prairie Creek Elementary School. We call this curriculum the Suuji Project after the Japanese word for number.

Field Specific:

Many students struggle with the numeric and symbolic aspects of learning mathematics. Non-integer numbers, ratios and proportions, functions, algorithms, and calculus are common road bumps for students. Our goal is to develop stronger foundations for high-level mathematics by appealing to the visual-spatial intuitions of elementary schoolers to decrease the likelihood of these road bumps. We’ve developed a 3-week 2nd and 3rd grade curriculum alongside a suite of physical manipulatives and digital applications (apps) and games that focus on enhancing students’ intuitions, representing numbers with lengths – values are shown on an exact, stretchable number line. Using both environments allows students to make more connections and enhances their understanding. We investigated the effectiveness of our product with feedback from a small group of students from Prairie Creek Elementary School. We call this curriculum the Suuji Project after the Japanese word for number.

Bruce Pell - Data-Based Mathematical Modeling of Oncolytic Tumor Therapy
PROJECT SUMMARY:
Applied mathematics and computation have become extremely useful tools for understanding complex systems that arise in the study and treatment of tumors. An oncolytic virus is a virus that preferentially infects and kills cancer cells. In this project, students will explore and formulate mathematical models to answer some of the many questions arising in using viral therapy to treat cancer. Professor Bruce Pell will be advising the project. Professor Pell is a specialist in mathematical biology and has research experience in mathematical modeling of within-host viral dynamics. Students are expected to be highly self-motivated. Meetings are expected to occur at least once a week, with additional meetings scheduled as necessary.
This project is well suited for students interested in applied mathematics, computational mathematics and/or mathematical biology. Calculus II and Linear Algebra are minimum requirements. Differential Equations would be great, but not required. Strong computational skills in MatLab, R or Python will be extremely beneficial. Having a biological background in oncolytic viruses is not required, but motivation to learn the fundamentals is important.

Abstract 1 – Marlyne Hakizimana & Sawyer Jacobson – Mathematical Modeling of Oncolytic Virotherapy

Generalist:

An oncolytic virus is designed to specifically target and kill cancer cells while leaving normal cells alone. Oncolytic Virotherapy uses oncolytic viruses as a form of therapy to treat cancer. This new form of therapy can be used in combination with other forms of cancer treatment to potentially create an effective form of treatment. Using data collected from a previous study and modifying a previously created mathematical model, a new model was fit to this data to be able to predict the outcome of treatment in different scenarios. This model was created by implementing biological mechanisms in hopes of generating a better understanding of the cancer treatment dynamics.

Field Specific:

An oncolytic virus is designed to specifically target and kill cancer cells while leaving normal cells alone. Oncolytic Virotherapy uses oncolytic viruses as a form of therapy to treat cancer. Previous models have used ordinary differential equations in their modeling process. Our model implements a system of delay differential equations to incorporate the time delay in the adaptive immune system. The model assumes that the adaptive immune system is completely dependent on infected tumor cells created by timed injections of an oncolytic adenovirus. The model was fit to data obtained from Zhang et al. (2011) using the statistical program R-studio. A univariate local sensitivity analysis was performed to see which parameters were most sensitive to a slight perturbation. It is hoped that the model can be used in clinical trials to help determine the best course of treatment for individual patients.

Matthew Wright - Topological Data Analysis
PROJECT SUMMARY:
Persistent homology is a popular tool in the area of topological data analysis and has been the subject of much research in the past decade. Multidimensional persistent homology shows particular promise for discerning the structure of complex geometric data. The software program RIVET for computing and visualizing multidimensional persistent homology has been developed in the past three years by Matthew Wright (St. Olaf) and Mike Lesnick (Princeton). RIVET is now available to use in the analysis of real-world data.
In this project, students will explore the question, “What insights can multidimensional persistent homology provide into real-world data?” Students will use RIVET to analyze data arising from areas such as neuroscience, computer science, and biology. Students will consider the practical and statistical significance of their findings, and will contribute to the development of statistical techniques for the multidimensional persistent homology.
Students interested in working on this project should have strong background in math, statistics, and programming. Prior experience in topology is not required, but would be helpful. Due to the interdisciplinary nature of this project, a student should not expect to have prior knowledge of all topics relevant to the success of the project. Instead, students will work collaboratively together and with the research mentor, and will gain knowledge of the relevant background material during the first weeks of the summer.

Abstract 1 – So Mang Han – Topological Data Analysis on Network of Thrones

Generalist:

Topological data analysis (TDA) is a collection of the methods that find the shape of data. TDA is especially useful to extract information of high dimensional and noisy data, which poses challenges for quantitative analysis for detecting data structures. Persistent Homology is a main tool for TDA to bridge ideas between geometry and topology. Using RIVET, an interactive visualization software for two-parameter persistent homology, the shape of a network map of Game of Thrones was analyzed. Throughout the change of values of parameters, different structures (ex. connected components and holes) of the map were observed. The information provided by RIVET gives a better understanding of the entire picture of data and the contribution of each character on the network map.

Field Specific:

Topological data analysis (TDA) is a collection of the methods that finds the shape of data. TDA is especially useful to extract information of high dimensional and noisy data, which can be challenging for a geometric approach to analyze the structure of data. Persistent Homology is a main tool for TDA to bridge ideas between geometry and topology. Using RIVET, an interactive visualization software for two-parameter persistent homology, the structure of a network map of Game of Thrones was analyzed. RIVET detects structures of sub-graphs of the final network graph and provides detailed information that users can understand what is happening at each level. Throughout the filtration process, different numbers of structures (ex. connected components and holes) of the map were observed, and it gives a better understanding of the entire picture of data and the contribution of each character on the network map.

Abstract 2 – Xiaojun Zheng – Topological Data Analysis on Simple English Wikipedia Articles

Generalist:

Persistent homology is an algebraic method to detect the topological features (such as connected components and holes) of high-dimensional data. In this poster, we use persistent homology to analyze the structure of a point cloud produced from a semantic analysis of Simple English Wikipedia articles. Specifically, the semantic algorithm converts each article to a 200-dimensional vector. We use the two-parameter persistent homology software RIVET to distinguish the Wikipedia point cloud from a point cloud of similar random vectors. We also compare the topological similarity of Wikipedia articles for major cities using semantic distance and geographic distance between the cities. In addition to analyzing the RIVET plots, we apply statistical tests to the topological differences between the data sets to confirm our conclusions.

Field Specific:

Persistent homology is an algebraic method to detect the topological features (such as connected components and holes) of high-dimensional data. In this poster, we use persistent homology to analyze the structure of a point cloud produced from a semantic analysis of Simple English Wikipedia articles. Specifically, the semantic algorithm converts each article to a 200-dimensional vector. We use the two-parameter persistent homology software RIVET to distinguish the Wikipedia point cloud from a point cloud of similar random vectors. We also compare the topological similarity of Wikipedia articles for major cities using semantic distance and geographic distance between the cities. In addition to analyzing the RIVET plots, we apply statistical tests to the topological differences between the data sets to confirm our conclusions.

Physics

Prabal Adhikari - Scattering in low-energy QCD
PROJECT SUMMARY:
Nucleon-nucleon scattering is an incredibly interesting problem, yet very difficult to solve. The difficulty arises from the fact that protons and neutrons are composite particles with constituent quarks and gluons that all interact via strong interactions. The standard approach for solving scattering problems involves perturbative methods, where many-body interactions can be systematically ignored, eg. electron-electron scattering. However, there are theories of strong interactions, i.e. Quantum Chromodynamics (QCD), where it is possible to study nucleon-nucleon scattering and nucleon-pion scattering systematically. In this project, we will consider two versions of QCD: 1) two colors and fundamental quarks and 2) a large number of colors with adjoint quarks and study the scattering cross-section and differential cross-section when two nucleons or a nucleon and pion are fired at each other. There is a probability that the nucleon will scatter in some direction but the result is not random.
The project is most suitable for students who have learned special relativity and the basics of quantum mechanics. Knowledge of Quantum Mechanics at the level of 376 may be useful but not necessary.

Brian Borovsky - Two-dimensional materials and the physics of friction
PROJECT SUMMARY:
Graphene and other two-dimensional materials have gained enormous interest in the scientific community recently due to their extreme mechanical strength, high electrical conductivity and many other useful properties. The simple mechanical exfoliation (i.e. sticky tape) method of preparing clean atomically-thin layers, famously used in the Nobel prize winning study of 2010, has only increased their charm.
These materials also show great promise as lubricating layers for sliding contacts. Several studies have shown ultralow friction at the atomic level, and others have suggested ways to extend this performance to macroscale contacts.
This summer, the Borovsky research group will begin a new collaboration with Prof. David Burris, a faculty member in Mechanical Engineering at the University of Delaware. Prof. Burris is pursuing a project funded by the National Science Foundation whose goal is to understand the frictional behavior of molybdenum disulfide across many length scales, from nanometers to centimeters. This unique multiscale study of a 2D material will use both commercially available and custom-built tribometers (friction testers). Prof. Borovsky’s group will contribute to this study using the St. Olaf microtribometer. This apparatus is distinctive for its ability to perform measurements in the high-speed sliding regime relevant to practical devices (~ 1 m/s), in contrast to the lower speeds accessed by some of the most widely used friction testing methods.

Abstract 1 – Gabe McAndrews & Raymond Wieser – Frictional properties of molybdenum disulfide: Understanding the forces inside high speed, microscopic contacts

Generalist:

Tribology, the study of friction, has endless applications and impacts everyday life. Scholars estimate that up to $200 billion per year in the US alone can be saved with improved friction reduction practices. In collaboration with the University of Delaware we seek to create a unified model across all size regimes while probing deeper into the characteristics of 2D materials. The weak bonding between layers of these materials, specifically molybdenum disulfide, allows for their use as lubricants. Our experimental setup allows us to measure friction at realistic contact speeds. We developed a procedure to reliably attach thin films of molybdenum disulfide to our instrument. By varying the load applied to the film of molybdenum disulfide we quantified its frictional characteristics.

Field Specific:

Tribology, the study of friction, has endless applications and impacts everyday life. Scholars have estimated that up to $200 billion per year in the US alone can be saved with improved friction reduction practices. In collaboration with the University of Delaware we seek to create a unified model across all size regimes while probing deeper into the characteristics of 2D materials. The weak bonding between layers of these materials, specifically molybdenum disulfide, allows for their macroscopic use as dry lubricants. Our Quartz Crystal Microbalance with a nano-indenter can achieve realistic contact speeds between the micro and macro length scales. We developed a procedure to reliably attach thin films of MoS2 to the crystal while probing with a 1mm sapphire tip (Al2O3). By varying the load applied to the film of MoS2 we quantified its frictional characteristics with classical models.

Jay Demas & Steve Freedberg - Linearly polarized light detection in the snapping turtle retina
PROJECT SUMMARY:
When freshwater turtles hatch, they must navigate solo from their nests on land to the water sources that will become their home. Studies of hatchling turtle navigation have established that light plays the key role in orienting hatchling marine and freshwater turtles so that they can find water. However, the environmental light cues that turtles use to navigate and retinal circuits that process these cues are not known. When light reflects off of water it is horizontally polarized. Behavioral data from my lab indicate that hatchling snapping turtles are especially attracted to horizontally polarized light. We wish to explore the retinal mechanisms that underlie the detection of polarized light in this vertebrate species.

Abstract 1 – Emily Lecy & Calisandra Larson

Generalist:

Hatchling turtles’ first objective in life is to navigate from their nest on land to refuge in water. Longer routes to water can increase the probability of being found by a predator or simply drying out. Hatchling turtles are able to find water with high rates of success using light, although the details of these sensory cues are poorly understood. When light hits a smooth non-metallic surface, such as a body of water, it becomes polarized. Our lab has previously shown that hatchling turtles prefer polarized light. We are testing whether or not polarization cues direct hatchling turtles to water. Because many man made structures are also strong polarizers of light, such as asphalt roads, this work may have important conservation implications.

Field Specific:

Hatchling turtles’ first objective in life is to navigate from the nest to the water. Circuitous routes to water elevate the risk desiccation and predation. Hatchling freshwater turtles are able to find water with high rates of success, primarily using light cues; however, the relevant light cues and neural circuits that process them are poorly understood. Sunlight is unpolarized, but can become significantly horizontally polarized after reflecting off water. As such, horizontally polarized light may be a cue for the presence of water. Indeed, we have found that hatchling snapping turtles, Chelydra serpentina, are attracted to horizontally polarized light in a Y-maze assay, but it is unclear whether or not polarization cues influence navigation in a natural setting. To investigate the importance of polarized light cues we have constructed helmets that block the turtles’ ability to detect polarized light and implemented fluorescent powder and arena release methods to track hatchling turtle navigation in natural settings.

David Nitz - Spectroscopy of Rare Earth Ions
PROJECT SUMMARY:
This project is in the area of atomic physics known as emission spectroscopy. Historically, measurements of the different wavelengths of light emitted by excited state atoms produced in an electrical discharge (“spectral lines”) provided the information necessary to discern the energy level structure of the elements in their neutral and ionic forms (something you can look up for any given species by going to the Atomic Spectra Database maintained by the National Institute of Standards and Technology). Another important (and generally more difficult to measure) property of a spectral line is its intensity, which carries information about the relative probability of the various state-to-state transitions which the atom can make. For scientists who study high temperature gas phase environments like the atmosphere of a star, knowledge of these “transition probabilities” is crucial to interpreting the spectrum of the star to gain insight about its composition and dynamic behavior. As it turns out, the fraction of cataloged spectral lines whose transition probabilities have been measured is surprisingly small. The goal of this project is to determine transition probabilities for atomic transitions in a pair of spectrally-complex rare earth ions (cerium (Ce+) and gadolinium (Gd+)), expanding the data base of measured lines available for astrophysical applications. We will be following up on and taking advantage of techniques developed in recent studies of neutral cerium and gadolinium. Depending on the rate of progress made, the project has the potential for eventual publication of results in a peer-reviewed scientific journal.
The project is most suitable for students interested in learning fundamentals of atomic physics and applying them to the analysis of spectra.

Abstract 1 – Ian Sutherland – Boltzmann Analysis of Gadolinium II Spectra

Generalist:

Spectroscopy studies the wavelengths of light emitted by elements to determine atomic properties that are used to help astrophysicists model stars and increase the efficiency of industrial lighting, among other things. Gadolinium II has a complex pattern of light emission, and increased data aid in understanding systems containing it. In this project, spectroscopic data of Gadolinium obtained from the digital archives of the National Solar Observatory in Kitt Peak, Arizona was analyzed using custom software. Combining this analysis with previously published results for Gadolinium II, a model known as the Boltzmann distribution was fitted to the data points. Data for two of the studied spectra yielded fits accurate enough to serve as a basis for future analysis.

Field Specific:

New atomic data, particularly transition probabilities, are needed for Rare-Earth elements to increase reliability of spectral modeling used for analysis of stars as well as advances in industrial lighting. In this project, four Gadolinium spectra from the digital archives of the National Solar Observatory in Kitt Peak, Arizona were analyzed to determine the excited state population distributions of the emission sources. The intensities of approximately 400 emission lines were determined by numerical integrated using custom software and, in combination with published atomic transition probability data, fitted to a Boltzmann distribution. Of the four spectra, two show acceptable Boltzmann fits, another does not, and the fourth lacks adequate data points for a statistically meaningful answer. The fact that the population levels in the first two spectra were found to follow a Boltzmann distribution implies that these spectra can be used to measure new transition probabilities in a continuation of this project.

Brianna Thomas - Wave function propagation in 2D quantum percolation with nonzero binary hopping integrals
PROJECT SUMMARY:
Quantum percolation (QP) is a statistical model for disordered systems and is closely related to the study of metal-insulator transitions in condensed matter physics. The model can be imagined as creating a maze with infinite-potential walls through which a quantum particle travels. It has been found that, unlike other models, QP in two dimensions exhibits delocalized (ie conducting) phases at low disorder. Recently, I discovered that the essential characteristics of the QP model in 2D are surprisingly stable even when tunneling is allowed, that is, the infinite-potential walls become finite (PRE 94, 042141(2016)). From our current knowledge of the model and its characteristics we can infer possible reasons for this stability, but we have not explicitly checked our inferences. For this project, we would examine the quantum particle’s wave function on a handful of representative model realizations (ie “maze” setups) as tunneling is “turned on” from zero to maximum, in order to gain a clearer picture of how tunneling affects the particle’s transmission at an individual level and how that relates to the macroscopic behavior we have previously observed. Students should have at least an introductory knowledge of quantum mechanics (on the level of Physics 244) and linear algebra, and at least an introductory working knowledge of computer programming (especially of a dynamic scripting language such as Matlab, Python, or Javascript, though knowledge of any programming language is usually transferable).

Abstract 1 – Zhifei Yang – Wave function propagation in 2D quantum percolation with nonzero binary hopping integrals

Generalist:

Quantum Percolation (QP) models a quantum particle in a disordered system by disconnecting sites on the lattice the particle moves through; its three phases indicate how freely the particle moves. Modified QP allows partial connections to “disconnected” sites; previous work in 2D seems to show the particle’s wave function unchanged for weak connections. To verify this, we calculate various wave function properties on 105×105 square lattices at an energy E=1.6 and a dilution in each phase (2%, 20%, and 35%) on 53 disorder configurations each for different connection strengths. For 2% and 35% dilution, we find most wave function properties unchanged for weak connections; individual configurations behave like the average. For 20% dilution, the behavior as connection strength changes is less predictable.

Field Specific:

The Quantum Percolation model in two dimensions exhibits delocalized, weakly localized, and strongly localized phases as disorder is increased from 0%. Recent work shows that these phases are stable even when tunneling to diluted sites is allowed by increasing the hopping energy w, and suggests that the wave function occupies the same sites for w<0.1. To better understand the behavior previously observed, we examine 105×105 square lattices at an energy E=1.6 and a dilution in each phase (2%, 20%, and 35%) on a representative sample of 53 disorder realizations for hopping energies 0<w<1. We calculate the wave function amplitude and phase, transmission, and inverse participation ratio to characterize these realizations. For 2% and 35% dilution, we find that most wave function properties are unchanged for w<0.1 and individual realizations behave like the average. For 20% dilution, the behavior as hopping energy changes is less predictable.

Psychology

Jeremy Loebach - Auditory Cognitive Abilities and Cochlear Implants
PROJECT SUMMARY:
In this project, students will assist in a number of ongoing experiments in the Speech and Cognition Lab.
1. We have designed a battery to assess auditory cognitive abilities in normal hearing listeners, hearing impaired individuals, and cochlear implant users. This portion of the project will continue this work, require additional data collection, and get into a higher level of data processing and modeling to better understand how auditory cognitive abilities contribute to perceptual abilities.
2. We are ready to release the high variability online training program for CI users (HiVOlT-CI). This adaptive, online program is designed to teach new CI users how to hear with their devices and is unique in its scope and design. In this part of the project, students will help make additional recordings, normalize the new stimuli, and help program the online module so that a critical mass of stimuli will be ready for the release of the program. Here, students will also work with running the program and data analysis.
3. We continue to work with the SoLoArc, a device designed to test sound localization in the horizontal and vertical planes. This part of the project will involve designing instrumentation for the arc, developing protocols for testing and analysis, and involve some coding.
All students must have a passion for research. Research methods experience and statistical training is desirable, but not necessary.

Abstract 1 – Brock Carlson and Elaine Grafelman – DIY Pupillometry Measurement of Auditory Cognitive Effort 

Generalist:

It is likely that cochlear implant (CI) user performance is dependent on cognitive abilities such as auditory working memory, listening effort, encoding, and personality characteristics. These factors influence CI user performance both before and after they receive their implants. We hypothesize that the influence of these auditory cognitive “X-Factor(s)” can explain variability in outcome across CI users. To find the “X-Factor(s),” we refined our experimental protocol for use with older adults and redesigned our approach to pupillometry (measurement of pupil dilation as a physiological measure of auditory cognitive processing and load). For more robust data collection, we built, tested and implemented a new open source eye tracking system using a retrofitted webcam mounted onto a 3D-printed glasses frame and Pupil Labs software. Pupil Labs software provides a cost-effective, dynamic, and fully mobile capability to collect data in real time.

Field-Specific:

Etiological and post-surgical factors cannot account for all variability in cochlear implant (CI) user performance. It is likely that domains of extant auditory cognitive abilities such as auditory working memory, listening effort, encoding, and personality characteristics influence CI user performance both pre- and post-implantation. We hypothesize that the influence of these auditory cognitive “X-Factor(s)” can explain variability in outcome across CI users. To find the “X-Factor(s),” we refined a previously designed experimental protocol for use in older adults and reconfigured our approach to pupillometry (pupil dilation as a physiological measure of auditory cognitive processing and load). For more robust data collection, we built, tested and implemented a new open source eye tracking system using a Microsoft HD 6000 webcam and Pupil Labs software. We de-cased the commercial housing on the webcam, desoldered redundant components, and soldered on infrared LEDs. The retrofitted webcam mounts onto a 3D-printed glasses frame. Pupil Labs software provides a cost-effective, dynamic, and fully mobile capability to collect data in real time.

Jessica Petok - Effect of genetics on reward learning and generalization of associations in aging
PROJECT SUMMARY:
People acquire new information from feedback about the consequences of their choices and then use these experiences to predict future outcomes in novel environments. This ability to learn from experience and apply that knowledge to new situations is critical for making decisions that can affect our lives throughout adulthood, including social interactions (deciding whom to date), business choices (weight what to buy) or financial transactions (choosing what to invest in). Therefore, this summer project will examine the effects of aging on such reward-based associative learning and generalization. Further, we will examine how these relationships vary by common genetic polymorphisms, exploring whether genetics can contribute to variability in cognitive function across the adult lifespan.
The identification of cognitively relevant genes, and the age-related differences therein, brings promise to refine knowledge about neurobiological mechanisms of cognition and may help to explain heterogeneity of cognitive function in old age. This understanding, in turn, may ultimately inform cognitive training programs aimed at maximizing cognitive functioning in old age – a goal that is becoming increasingly important with the rising number of older adults in society.
Students will be trained to test college-aged, middle-aged and older adults, and will learn more about how age and genotype can contribute to our cognitive phenotype. Students should have strong communication skills and interest in working with middle-aged and older adults. Students should have completed courses relevant to this work (for example, Research Methods in Psychology, Developmental Psych, Statistics, Cognition, Biopsychology, Genetics, etc); however, strong interest in research (even without these recommended courses) among strong underclassmen is appealing. Because we may work on designing/developing new tasks, interest in simple computer programing would be valuable. Finally, students will help with recruiting college-aged and older adults for participation in research studies, which will include outreach into the Northfield community (especially the Northfield Senior Center).

Carlo Veltri - MMPI-2-RF Meta-Analysis - Phase 2
PROJECT SUMMARY:
The Minnesota Multiphasic Personality Inventory – 2 – Restructured Form (MMPI-2-RF) is the latest iteration of the most commonly used clinical measure of personality and psychopathology in North America. Since its publication in 2008, well over 150 articles have been published examining the test’s utility in such tasks as predicting who is likely to complete a batterer’s intervention program, identifying respondents who have exaggerated symptoms of mental illness, predicting which patients are likely to experience complications from bariatric surgery, and differentially diagnosing Bipolar Disorder from Major Depressive Disorder. I’m interested in systematically examining the strengths and limitations of the test in order to better guide psychologists who use it in their day-to-day work.
Our aim with this project is to use meta-analytic techniques to provide a picture of what we currently know about a subset of the MMPI-2-RF’s validity scales. The scales I’m interested in were designed to identify when a test-taker is likely over- or under-reporting symptoms (i.e. exaggerating, feigning, minimizing, or denying psychological problems). We will look for any systematic differences in the performance of these scales across the settings or populations in which the instrument is used as well as identify areas of application in need of additional empirical investigation.
Students applying for this project should demonstrate a strong interest in the assessment of personality/psychopathology, psychometrics, or both. Ideal candidates will have relevant coursework in psychology as well as advanced courses in statistics.

Abstract 1 – Erik Kuehl & Agnesa Sejdijaj – A Meta-Analysis of the MMPI-2-RF Validity Scales: Phase 2

Generalist:

The Minnesota Multiphasic Personality Inventory 2 Restructured Form (MMPI-2-RF) is the most recent iteration in the MMPI family, which is the most widely used assessment of personality and mental disorders worldwide. One of the most significant features of the MMPI-2-RF are the validity scales that detect over-reporting (fake more symptoms than they have) and under-reporting of symptoms. As such, it is used widely in North America in different settings such as child custody, where parents tend to under-report their symptoms to show they are competent for custody. In our research we conducted a meta-analysis study, which is a study of studies. To this end, we created a coding sheet and coded the most important information from these studies. Specifically we focused on the setting and how did people from a particular setting performed on the validity scales. Therefore, we aim to reach a conclusion about how the average person from different settings and motivations score on the MMPI-2-RF, in order to help clinicians and evaluators to have a better interpretation of their patients’ scores.

Field-Specific:

The Minnesota Multiphasic Personality Inventory 2 Restructured Form (MMPI-2-RF) is the most recent iteration of the most widely used and studied inventory of personality and psychopathology worldwide. It features 10 validity scales which are used to detect underreporting, over-reporting and general malingering in people taking the inventory.  For the purposes of this meta-analysis, a coding sheet was utilized by two coders to assess individual studies for crucial variables such as sample setting and participant instructions.  As such, its use in a large variety of settings leads to its widespread use and acceptance. The purpose of the present meta-analysis therefore, is two-fold.  First, we wish to review and add to the literature surrounding this tool in order to broaden understanding of its merits and potential uses.  Second, through this meta-analysis, we hope to identify crucial differences in the expected validity scale scores across clinical and forensic settings compared to the normative sample. This will hopefully lead to improved use and understanding of the tool and the scores derived therefrom.

SOCIAL SCIENCE

Political Science and English

Anthony Pahnke & Carlos Gallego - The Rise of Trump: Nationalism, Capitalist Development, and the 2016 Presidential Election
PROJECT SUMMARY:
How did Trump win? This deceptively basic question conceals a more complex one – how did a candidate of a major political party generate the support of millions of people and win the Presidency of the United States while expounding a general campaign discourse rooted in racially-offensive language, religious intolerance, and the dismissal of basic American institutions, such as freedom of the press and the integrity of the electoral process?
We seek to answer these questions by analyzing the 2016 US Presidential election in a historical and comparative context. While some scholars and commentators consider Donald Trump’s election an aberration, we consider his electoral success as quite normal, even predictable. More specifically, we hypothesize that his ability to retain the support of millions of followers is rooted in a variety of long-standing characteristics specific to nationalism and capitalist development, such as the tendency to create economic inequality and instability, as well as the combination of racial and national identity as a political platform to oppose those deemed “outsiders.” Stated differently, we theorize that Trump’s victory was the product, not the cause, of the combination of generalized economic-political inequities and their accompanying anxieties.
To verify our hypothesis, we seek students with a general knowledge and interest in critical theory, an ability to work with complicated theoretical texts, an understanding of political institutions and processes in the United States, and a desire to work in teams. We expect to assemble a group of students (approximately three) who will work with two faculty members.

Abstract 1 – Leidy Rogers & Hoda Al-Haddad – The Rise of Trump: Nationalism, Capitalist Development, and the 2016 Presidential Election

Generalist:

How did Trump win? This seemingly simple question conceals a more complex one- how did a candidate whose campaign was rooted in racially-offensive language, religious intolerance, and the dismissal of basic American institutions manage to win the Presidency? Our research examines the political environment that enabled Trump to succeed, looking at factors ranging from changes in pre-existing political power bases to new techniques for campaigning, such as Twitter and other social media platforms. We also examine similar political events in other countries such as Brazil, Italy, and South Africa, while also engaging in a genealogical study of modern far-right-wing political theory. Our research hopes to show that Trump’s elections was not a unforeseen possibility, but rather the product of inevitable political forces.

Field-Specific:

How did Trump win? This deceptively basic question conceals a more complex one – how did a candidate of a major party generate the support of millions and win the Presidency while expounding a campaign discourse rooted in racially-offensive language, religious intolerance, and the dismissal of American institutions, namely freedom of the press and the integrity of the electoral process? We seek to answer these questions by analyzing the 2016 US Presidential election in a historical, comparative context. While some scholars consider Donald Trump’s election an aberration, we consider his electoral success quite normal, even predictable. More specifically, we hypothesize that his ability to retain the support of millions of followers is rooted in a variety of long-standing characteristics specific to nationalism and capitalist development, such as the tendency to create inequality and instability, as well as the combination of racial and national identity as a political platform to oppose “outsiders.” Stated differently, we theorize that Trump’s victory was the product of the combination of generalized economic-political inequities and their accompanying anxieties.

Political Science

Chris Chapp - Voter turnout in low-income communities: The role of electoral institutions
PROJECT SUMMARY:
This project will help disentangle the complex relationship between socioeconomic status and voter turnout. While a good deal is known about why some people vote and others do not, research struggles to account for the turnout gap between wealthy and poor voters. Moreover, many of the public policies thought to increase turnout (like early voting) are actually relatively ineffective at mobilizing voters with lower socioeconomic status. This project will use quantitative and qualitative methods to examine and explain the turnout gap. Students will analyze an original voter turnout database, assist in constructing and piloting an original survey, and conduct and code qualitative interviews with community members and government officials responsible for promoting voter turnout in their communities. Through this project, students will generate and test original hypotheses about the causes of political participation, and learn how to improve voter turnout in the U.S. The project will examine turnout broadly, but will have a specific emphasis on how state and county electoral institutions help facilitate turnout. Students should have had coursework and/or experience with quantitative and qualitative research methods in the social sciences, including experience working with statistics. Student applications should also indicate if they have any language skills other than English.

Abstract 1 – Hoda Al-Haddad, Angela Fusselman & Leidy Rogers – The Role of County Political Party Spending in Voter Turnout

Generalist:

This study analyzes the relationship between political party expenditures and voter turnout at the county level in Maine, New Mexico, and Wisconsin. First, we correct existing voter turnout estimates by accounting for disenfranchised populations. Second, we code county party expenditures to examine how varied categories of spending are related to voter turnout in these three states. Specifically, we test whether expenditures dedicated to direct contact with voters such as community events and canvassing are related to higher turnout, and whether this relationship interacts with community socioeconomic status. We find that in Maine and Wisconsin, high county party contact expenditures are associated with higher turnout, particularly in low income communities. The data also suggests that differences in state registration laws incentivize different contact strategies.

Field Specific:

This study analyzes the relationship between political party expenditures and voter turnout at the county level in Maine, New Mexico, and Wisconsin. First, we correct existing voter turnout estimates by accounting for disenfranchised populations. Second, we code county party expenditures to examine how varied categories of spending are related to voter turnout in these three states. Specifically, we test whether expenditures dedicated to direct contact with voters such as community events and canvassing are related to higher turnout, and whether this relationship is moderated by community socioeconomic status. We find that in Maine and Wisconsin, high county party contact expenditures are associated with higher turnout, particularly in low income communities. The data also suggests that differences in state registration laws incentivize different contact strategies.

INTERDISCIPLINARY and GENERAL STUDIES

Asian Studies

Ito Rika - Language ideologies in Japanese popular media
                                                                                                              PROJECT SUMMARY:                                                                                                                                                                                                                       This project investigates how stereotypes are constructed, reproduced, and contested in Japanese pop-culture (such as anime) by using visual images and language as resources. In particular, we will examine the following:
• How are foreign characters and Japanese who speak English represented in various Japanese anime?
• What are the roles that these characters play in the anime program?
• What are the common features that are used to construct these characters?
• What do these representations inform us about language ideologies in Japan?
The CURI students will read scholarly work on language ideologies at the beginning of the summer; students will identify various anime programs that include foreigners and Japanese who speak English target characters, watch these programs as data, identify common features used to constructed these characters, and analyze its social meaning.
Students must have solid background in Japanese and some knowledge in linguistics.

Abstract 1 – Megan Bisila – Amazing!: A construction of foreigner stereotypes in Japanese anime

Generalist:

Similar to Disney, Japanese anime is a huge forerunner in animated media. While seemingly innocent, the way in which animators decide to represent certain nationalities is actually a way for them to reaffirm a dominant culture over subordinate cultures (Lippi-Green 2012). This study examines how the language used by foreign (non-Japanese) characters in anime aligns with the concept of Japanese nationality by analyzing 17 shows. We recorded the nationality (if possible), visual representation, and linguistic features of each foreign character. We also divided the shows between many foreign characters and few foreign characters. Visually, a staggering amount of the characters were white and/or male. Linguistically, it was more common for the characters to speak non-standard Japanese.

Field Specific:

The concept of a “mediatized childhood” is reflected in Disney by associating linguistic features with a certain type of character, leading to the construction of racist stereotypes that are then naturalized (Lippi-Green 2012). While the theory of Japaneseness (Nihonjinron) has been refuted in academia, it is still circulated through popular media (Jackson and Kennett 2013).  In this study, we examine the patterns of language use by foreign characters in anime by assessing each character’s speech and how it is associated to non-Japaneseness. Out of 17 shows, we recorded the nationality (if possible), visual representation, and linguistic features of each foreign character. Visually, a staggering amount of the characters were white and/or male. Linguistically, it was more common for non-Asian characters to speak non-standard Japanese. Similar to Disney, mediatization in Japanese anime perpetuates the ideals established by the concept of “Nihonjinron,” and has led to the formation of racist ideologies of foreigners.

Environmental Studies

Seth Binder - Population, Technology and Environmental Limits
PROJECT SUMMARY:
The ultimate goal of this project is to develop a new set of global sustainability indicators. We will begin by asking an extreme question: What would be the maximum sustainable human population on Earth if society were actually organized to pursue that objective and had at its disposal “perfect” technology? In this context, perfect technology implies that human population is only constrained by biological requirements, the availability of key environmental resources (e.g., water, oxygen, phosphorous, sunlight) and the laws of physics. By developing a model to answer this extreme question, we will be able to identify several key sustainability benchmarks. Most obviously, we will identify the absolute maximum equilibrium human population that Earth can support, which can be compared to our current population to see if we are already unambiguously “overshooting” our limits.
This project is highly transdisciplinary. Applicants should have a strong background in the natural sciences. Basic proficiency with GIS tools is highly desirable. Experience with mathematical modeling software such as Mathematica, Matlab or STELLA, is a plus.

Abstract 1 – Ly Trinh & John Smith Population, Technology, and Environmental Limits: Modeling Long-run Human Population Potential

Generalist:

Estimates of the maximum long-term human population that Earth could sustain vary widely and assume, rather than solve for, binding constraints. We consider a scenario in which human technology is limited by only what is physically possible and investigate the maximum long-run human population. In our model, humans exist in equilibrium with plants optimized for maximum oxygen and calorie production. The two populations require a given percentage of Earth’s stock of nutrient resources and support each other via resource transfer through photosynthesis and respiration. We find that oxygen and calorie production constrain population before nutrients become limiting. Sunlight usable for photosynthesis limits oxygen and calorie production, and constrains human population to a long-run maximum of 3.174*1014 individuals.

Field Specific:

Estimates of Earth’s human carrying capacity vary widely and assume, rather than solve for, binding constraints. We consider a scenario in which human technology is limited only by basic laws of physics and investigate the maximum possible long-run human population. In our model, humans exist in equilibrium with a population of plants optimized for maximum photosynthetic efficiency and nutrient content. The two populations require fixed percentages of the global stock of nutrient resources and support each other via resource transfer through photosynthesis and respiration. However, we find that the photosynthetic production of oxygen and calories constrains population before nutrients become limiting. Total available photosynthetically active radiation (PAR) limits photosynthesis. PAR therefore constrains human carrying capacity to 3.174*1014 individuals.

Writing

Bridget Draxler - Jane Austen in Community
PROJECT SUMMARY:
How are digital archives changing the way we can conduct and publish primary research? This project will introduce students to methods in digital research and digital publishing, within the context of the 200th anniversary of Jane Austen’s death and the posthumous publication of her final two novels. Participants will design and conduct research on Jane Austen and her novels, drawing on digital archives that give researchers access to primary historical documents. The research will be published in the form of interactive, multimedia digital timelines.
Students will also use this research to host a series of community lunch discussions, which will include both student research presentations to provide context for the novels and student-led discussion of Austen’s final two works.

Abstract 1 – Sarah Hindman, Joey Putnam & Elissa Temme

Generalist:

The Jane Austen in Community project aims to place Austen’s novel Northanger Abbey in two different kinds of communities. The archival research projects on this website contextualize the novel in the early 19th century and display how Austen engaged with the literary, social, and political communities of her time. The second part of this project integrates that contextual information with reading guides and discussion questions for the community reading groups we will be hosting in summer 2017. In addition to offering new ways of reading Austen within her contemporary community, we hope these conversations will also help us reflect critically on our own cultural moment.

Field Specific:

How are digital archives changing the way we can conduct and publish primary research? This project introduced us to methods in digital research and digital publishing, within the context of the 200th anniversary of Jane Austen’s death and the posthumous publication of her first and last novel, Northanger Abbey. We designed and conducted research on Jane Austen, Northanger Abbey, and the time period and cultural moment in which it was written. Our research draws heavily on digital archives that give researchers access to primary historical documents. Our work is published in the form of digital projects intended for a general audience. We also used this research to host a series of community reading groups, which included both student research presentations to provide context for the novel and student-­led discussion of Austen’s Northanger Abbey.

History

Timothy Howe - Photogrammetry at the Jeffers Petroglyphs: Protecting Cultural Heritage
PROJECT SUMMARY:
Jeffers Petroglyph Project will worth with indigenous Dakota communities to use the emerging 3D Photogrammetric technologies of RTI (Reflectance transformation Imaging) and PhotoScan to document and analyze the over 15,000 known examples of Native American rock art. The project will involve: (1) taking multiple still photographs (70-90) of each object, (2) processing those digital photos to produce a finished image, (3) organizing the images according to site-specific metadata, and (4) interpreting the historical and cultural significance of each finished image. Students are needed who have experience in photography, photographic manipulation (Adobe Photoshop, Adobe Lightroom), GIS, and metadata to perform tasks 1-3 and begin task 4.