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Summer Research: 2013 Project Proposals Details

Application submission deadline: February 18, 2013

Biology projects

Bebej, Ryan, Biology
Project #1 A Whale of a Tale: The Origin of Tail-Powered Swimming in Early Cetaceans
Description:
Modern whales are aquatic mammals, but the fossil record indicates that they are descended from ancestors that lived on land. In recent decades, this strange and seemingly counterintuitive transition has become one of the most prominent examples of macroevolution, but many details remain to be elucidated. This project aims to explore one key aspect of this transition: the evolution of tail-powered swimming. Quantitative comparison of fossil skeletons with those of modern mammals will provide the framework for assessing the functional capabilities of these early whales, providing insight into how ancient whales became increasingly adapted for efficient modes of swimming. Research will involve trips to the University of Michigan Museums of Zoology and Paleontology, work with modern and fossil skeletal material, and learning how to analyze data using select multivariate statistical analyses.
Benefit to student: The student will be involved in helping to design the research, collect and analyze data, and present the results (in seminars and/or poster sessions at Calvin and other venues and via future preparation of a manuscript). This will provide the student with firsthand experience in the entire scientific process, from designing research to disseminating the results, which will provide them with an excellent foundation for future scientific endeavors at Calvin and beyond. Specifically, the student researcher will learn some basic approaches to studying morphology in an evolutionary context and gain experience working with modern and fossil skeletal material in a museum setting, collecting detailed morphological data from bones and photos, and analyzing that data using advanced statistical techniques.

Randall De Jong, Biology
Project #2 Genomic and niche characterization of bacteriophages in the microbial communities of the aquatic snails Biomphalaria and Helisoma
Description:
Most multicellular organisms rely on symbiotic relationships with prokaryotes (bacteria), especially within the digestive tract, where they assist in digestion and provide essential nutrients and energy. Even in the small guts of invertebrates, these bacterial communities can be robust, unique, and critical to survival. Gut bacteria play an important role in the host immune response, and have even been shown to alter disease transmission in invertebrates that vector pathogens. One aspect of invertebrate microbial communities that has been largely unexamined is the potential role of bacteriophage, which putatively could play a large role
in regulating community composition and function. We have isolated phages from the gut microbial fauna of aquatic Biomphalaria snails (which are the intermediate hosts for a human parasite, Schistosoma), Helisoma snails (local to campus), and sequenced their genomes. We have also begun to quantify the prevalence and abundance of phage in the snail gut using quantitative PCR. The student will begin and finalize existing genome annotations, perform quantitative assays of phage populations, continue characterization of the diverse bacterial communities from Helisoma, and implement new efforts to isolate novel phage.
Benefit to student: Student will finalize genomes that will be deposited in database and form basis of publication. Student will learn genomic analysis techniques. Student will learn quantitative PCR and other molecular techniques. Student will learn sterile technique.

David Dornbos and John Wertz, Biology
Project #2a Specificity of Frankia Bacteria in Symbiosis with Native Speckled Alder and Non-Native Autumn Olive
Description: Autumn olive (Elaeagnus umbellata) is a non-native invasive shrub from Asia that is increasingly problematic in much of the U.S. Midwest. Much of the competitiveness of autumn olive is due to its ability to fix atmospheric nitrogen in nutrient-poor soils. This nitrogen is used to optimize photosynthesis rates allowing autumn olive to grow significantly faster than native shrubs. Autumn olive engages in a symbiotic relationship with Frankia bacteria in root nodules, the location where nitrogen fixation occurs. Previous research has demonstrated that autumn olive is capable of high nitrogen fixation rates. This is surprising because symbiotic relationships among plant and bacterial species are often quite
specific. For example, Rhizobium japonicum has been developed specifically for soybean (Glycine max) and seed inoculation is required to optimize nitrogen fixation rates. Frankia also believed to interact with native alder species, notably speckled alder (Alnus incana). The objectives of this research program are to characterize the phylogenetic relationships among the Frankia bacteria responsible for nitrogen
fixation in autumn olive and speckled alder in comparison with the nitrogen fixation rates of these plant species.
Benefit to student: The student working on this project will develop a variety of research skills, including field sampling nodules of autumn olive and speckled alder, measurement of nitrogen fixation rates of these nodules using acetylene reduction bioassay via gas chromatography, isolation of the Frankia bacteria from representative nodules, proteomic characterization of Frankia using MALDI-TOF, preparation of DNA samples for genome sequencing.

Keith Grasman, Biology
Project #3 Effects of Pollutants on the Health of Colonial Waterbirds in Great Lakes Areas of Concern
Description:
Fish-eating birds are effective “sentinel species” for assessing toxic effects on the health of the Great Lakes ecosystem. Our previous studies have shown associations between pollutants and suppressed immune and hormonal functions in gulls, terns, and herons of the Great Lakes. The objective of the current study is to continue the assessment and monitoring of these health effects at contaminated sites around the Great Lakes. Specifically, this project is funded by the US Fish and Wildlife Service under the Great Lakes Restoration Initiative to measure the current health and population status of birds at specifically designated Areas of Concern. The data from this and other studies will help help the USFWS and other government agencies determine whether water quality at these sites has improved enough to remove them from the list of impaired sites, or whether they should remain designated as Areas of Concern. This project involves travel and boating for field work around the Great Lakes and follow-up laboratory work at Calvin. Students will have the opportunity to interact with USFWS scientists.
Benefit to student: Students will gain extensive experience in both ecological field studies and laboratory assays. They will benefit from interactions with other members of the Calvin research team (students and faculty) and with scientists in governmental wildlife agencies.

Keith Grasman, Biology
Project #4 Impact of Mercury on Immune Function in Common Loons of New York's Adirondack Park
Description: The deposition of airborne mercury into lakes in the northeastern US and Canada presents significant health risks to fish-eating wildlife such as common loons. This mercury comes primarily from coal-fired power plants and cement kilns. In a previous laboratory study, dietary mercury exposure suppressed immune function in young loons. Field studies conducted during the past 4 years suggest significant immunological effects in young wild loons but minimal effects in adults. This study will continue investigations into immunological effects in wild loons living in New York's Adirondack Park (and possibly other locations in North America such as New Brunswick, Wisconsin, Maine, and Michigan, depending on funding). Loons will be captured at night by spotlighting and netting them from boats and canoes. White blood cells will be isolated from blood samples and cryopreserved for transport back to the laboratory at Calvin. Immunological functions of these white blood cells will be assessed using cell culture assays in the laboratory. Students will have the opportunity to work with biologists, rangers, and veterinarians from the New York Department of Environmental Conservation, the Bronx Zoo, and the BioDiversity Research Institute.
Benefit to student: Students will gain extensive experience in both ecological field studies and laboratory assays. They will benefit from interactions with other members of the Calvin research team (students and faculty) and with scientists in governmental wildlife agencies.

David Koetje, Biology; Herb Fynewever, Chemistry & Biochemistry
Project #5 Enhancing Learning Through Research in Biology 225
Description: Two students will join an interdisciplinary team of faculty seeking to strengthen student research projects in Biology 225, promote interdisciplinary STEM learning, and integrate assessments that support scientific teaching. The project will involve development and optimization of research methods, production of a new laboratory/field manual, and design of appropriate assessment instruments. There will also be opportunities in the fall of 2013 to assist with data collection and analyses that measure the effectiveness of these reforms as they are implemented.
Benefit to student: This project will provide invaluable experience for any student interested in pursuing an academic career involving a blend of research and teaching, a career in scientific writing, and/or a variety of educational vocations. The ideal candidates will have successfully completed Biology 225 and Math 143/145.

Darren Proppe and Dave Warners, Biology
Project #6 Avian and Water Quality Assessments along Plaster Creek
Description:
We are looking for two students to do research in the Plaster Creek Watershed collecting data on bird behavior and water quality. The objective of the bird project is to investigate whether human produced noise affects the foraging behavior of songbirds. Theoretically, if birds cannot hear predators they must spend more time looking for them. This could reduce the amount of food a bird is able to procure and thereby decrease their fitness. To assess whether noise is affecting foraging behavior we will set up bird feeders at multiple locations along Plaster Creek that are exposed to various levels of noise (primarily from roads) to assess whether foraging behavior is altered in noisy areas. This project will involve placement and maintenance of bird feeders, video recording of foraging behavior, and collecting behavioral data from the video recordings. As we do this work, we will also be generating a bird inventory for the Plaster Creek corridor.
The water quality project will continue research begun in the summer of 2012. We will be collecting data from multiple locations in the watershed throughout the summer. The primary focus will be to assess bacterial levels over time and space, as well as sediment, nutrient loading, pH, conductivity, and discharge volume. These data will be organized, processed, and compared among the different sites, and between this year and last year. Our objective is that these data will help identify the most problematic and dangerous sites in the stream, thereby informing the prioritization of restoration plans.
Benefit to student: Student will be involved in basic, field based data collection and processing with real world implications. This will be the first scientific assessment of the avian community in the Plaster Creek corridor. The water quality project will follow protocol developed by the Michigan Department of Environmental Quality, providing students with valuable preparation for graduate school or job applications.

Anding Shen, Biology
Project #7 The roles of endothelial cells on HIV infection and latency formation in resting T helper cells
Description:
In many patients with HIV-1 infection, highly active antiretroviral therapy (HAART) successfully suppresses viral loads and restores the immune system. However, a major latent reservoir identified in resting T helper cells (a type of white blood cells) poses a great barrier to viral eradication and ensures viral persistence in patients. A more complete understanding of the mechanisms contributing to the establishment of the reservoir will influence the strategies in battling viral persistence.Some recent studies demonstrated that endothelial cells increased the level of HIV infection in resting T helper cells and might play a significant role in latency formation in these cells. In this study, a replication incompetent pseudotyped virus system is used to investigate how endothelial cells interact with resting T helper cells to promote HIV infection and latency formation. Students who have taken Bio333 (Immunology Course) are preferred.
Benefit to student: Students will learn valuable research skills and will be trained in scientific reasoning and problem solving.

Randy Van Dragt, Biology
Project #8 Impacts of Fire on Insect Populations in Created Prairie
Description:
Prairie grasslands are maintained as biological communities largely through the regular occurrence of fire. Fire discourages the growth of woody plants and promotes a selection of grasses and wildflowers adapted to the prairie environment. Beyond the impact on plants, however, fire affects a range of other organisms, including insects. Half of the 20-acre created prairie at Calvin's Flat Iron Lake is burned each year, and this project will compare the two halves of the prairie to nearby unburned grasslands to identify the impacts that burning has on the species composition of the prairie insect community and the success of common species which compose that community. Since insects perform many essential functions on the prairie and in nearby ecosystems, it is important to understand the impacts of fire so that insect populations can be appropriately managed.
Benefit to student:
The student researcher will learn to use a variety of field techniques to sample the insect populations of the Flat Iron Lake prairie as well as techniques for the preservation of insect specimens. Further, the student will learn the fundamentals of insect taxonomy and strategies for identifying insect species.

Randy Van Dragt, Biology and Jeanette Henderson, Ecosystem Preserve
Project #9 Stewardship of the Calvin College Nature Preserves
Description:
Each summer three students serve for 12 weeks as stewards of the Ecosystem Preserve and the Flat Iron Lake Nature Preserve. The stewards are involved in a variety of land management, monitoring, and research projects. Land management activities include control of non-native species, restoration plantings, trail maintenance. Breeding birds, small mammal populations and vernal pool invertebrates are monitored annually, and current research projects are examining restoration strategies for different communities on both preserves. Work begins in late May and typically concludes in mid-August.
Benefit to student:
Students will be introduced to a variety of land management techniques and field investigation strategies.

Dave Warners, Biology; Michael Ryskamp, Program manager for Plaster Creek Stewards
Project #10 Restoring Native Habitats In Urban Landscapes
Description:
In this project, students will work in the greenhouse, nursery and at sites on and off campus investigating the reintroduction of native plants and native habitats into urban areas. Part of this work will involve assessing data from controlled experiments to elucidate optimal germination and growing conditions for a group of particularly desirable native species. These students will also become invested in a focused campus restoration project in which native short grass prairie will be established in place of lawn between DeVries Hall and Spoelhof Cafe, a project that will include replicated outplanting treatments and the generation of an extensive baseline dataset. Students interested in this project will be willing to work
outdoors in all kinds of weather and willing to invest in challenging physical labor.
Benefit to student: This project will give the student hands-on experience in restoration ecology and will also provide the student with opportunity to design, implement and evaluate a field-based, applied research experiment.

Dave Warners, Biology
Project #11 Plant Responses to Climate Change at Flat Iron Lake Preserve
Description:
This project will take place at Flat Iron Lake, during which time the student will be expected to live in a Calvin-owned house at Flat Iron Lake with one other student. This project is an ongoing flower phenology study, investigating the timing of flowering period for a variety of native prairie plants. The student who takes on this project will also evaluate a variety of planting strategies that were employed during a 2011 prairie restoration effort in a former feed plot located within the larger Flat Iron Lake prairie.
Benefit to student: This project will combine data collection and assessment with hands-on management. The student will become involved in an ongoing flower phenology study and will also help design a data collection strategy to evaluate an earlier prairie planting experiment.

John Wertz, Biology; Serita Nelesen, Computer Science
Project #12 HTMAD: Software Design for MALDI-TOF Mass Spectrometry-Based Microbial Community Analysis
Description:
Scientific computing and the ability to write specific programs to analyze large datasets of biological information has become an increasingly important skill with regards to advancing biological research. DNA-based technologies to identify individual bacterial species and communities, place them phylogenetically, and compare them statistically are time-consuming and expensive. Our matrix-assisted laser desorption/ionization mass spectrometer (MALDI-TOF MS) can generate high-throughput, low cost protein-derived data of biological samples, and we are currently finalizing a novel software program (HTMAD) written in Python that is able to convert protein-derived data to answer questions previously reserved only for DNA-based methodologies. As we are now in the final stages of writing and testing the HTMAD program, research will be focused on using HTMAD to (i) statistically compare and de-replicate cultivated microbial communities (real and artificial) grown under different environmental conditions (ii) compare and de-replicate microbial communities without a priori cultivation and (iii) construct a database of microbial isolates to which future unknown bacteria can be compared and identified. Even in its nascent stages, this program has demonstrated it is a powerful tool that enhances the ability of microbiologists, microbial ecologists, and those interested in proteomics to do high-throughput experiments and gain
valuable data far more quickly and cheaply than ever before. The individual working on this project must have good knowledge computer science and programming but also an aptitude and interest for working with biological systems (i.e. proteomics, phylogenetics, bacterial cultivation and isolation).
Benefit to student: The student will benefit from collaboration with faculty and students from computer science and biology. The student will have the unique opportunity to continue our work on a novel computer program and test and refine it using biological data that is relevant to current research projects within both departments. The student will enhance their programming knowledge as well as refine the implementation, recording and troubleshooting of biological experiments using cutting edge equipment such as the MADLI-TOF mass spectrometer. The student will also learn how to report and present their results and interpretations scientifically - both informally as part of a research group as well as formally in a poster. The work done on this project previously has placed us on the cusp of submitting a peer-reviewed publication. Research this summer will focus on strengthening and repeating several experiments and performing additional control experiments necessary for manuscript submission by the end of the summer.

Amy Wilstermann, Biology
Project #13 Investigating the Dynamics of Bacterial Communities in the Female Reproductive Tract
Description:
A student working in my laboratory will have the opportunity to investigate the dynamics of bacterial communities found in the female reproductive tract. Normal flora, dominated by a variety of Lactobacillus species, serve to protect the vaginal tract from colonization by pathogenic species such as Gardnerella vaginalis that characterize an infected state known as bacterial vaginosis (BV). We are seeking to gain an understanding the factors that trigger a shift in this bacterial community from protective to pathogenic organisms. This shift is of particular importance in pregnant women since bacterial vaginosis is a risk factor for premature rupture of fetal membranes and resulting preterm births. This study aims to (i) determine whether pH changes in the reproductive tract trigger shifts in bacterial communities or are a result of such shifts and (ii) explore the differences that exist in the protective abilities of the Lactobacillus species that comprise the normal vaginal microflora.
Benefit to student: This project will benefit a student by providing them with the opportunity to participate in all aspects of a research project from conducting literature searches and designing and performing experiments to critically analyzing and discussing results with peers and mentors. The student will learn and utilize a variety of microbiological techniques including. The student will have the opportunity to present their results formally in a poster presentation and if successful, also have the opportunity to co-author a peer-reviewed publication.

Chemistry & Biochemistry projects

Carolyn Anderson, Chemistry & Biochemistry
Project #14 Organic Chemistry: Gold-catalyzed Rearrangement of N-Propargyloxypyridines
Description:
Organic synthesis is a powerful technique that allows access to a wide range of different structural motifs. In this project, we are working to advance a method for the synthesis of N-substituted pyridones; an interesting functional group found in a series of pharmacologically interesting compounds. To date, we have developed a new gold(III)-catalyzed method for accessing this motif by rearranging a related system. The student working in this area will be responsible for exploring and optimizing a related gold(I)-catalyzed rearrangement.
Benefit to student: The student will gain experience with synthetic organic chemistry techniques, including: running reactions, purification, organic spectroscopy, experimental design, and working under an inert atmosphere.

Carolyn Anderson, Chemistry & Biochemistry
Project #15 Organic Chemistry: Synthesis of N-Alkyl Pyridone Containing β- and γ-Amino Acids
Description:
Organic synthesis is a powerful technique that allows access to a wide range of different structural motifs. In this project, we are working to develop a method for the synthesis of N-alkyl pyridone containing β- and γ-amino acids – homologues of the natural amino acids, which contain an interesting functional group, found in a series of pharmacologically active compounds. To date, we have discovered an important intermediate in route to these species and have begun to optimize its synthesis. The students working in this area will continue to seek conditions for the preparation of this intermediate and its conversion into the desired amino acids.
Benefit to student: The students will gain experience with synthetic organic chemistry techniques, including: running reactions, purification, organic spectroscopy, and experimental design.

Eric Arnoys, Larry Louters, and Brendan Looyenga, Chemistry & Biochemistry
Project #16 Watching Membrane Proteins in Real Time
Description:
We will characterize the behavior of several membrane-bound proteins in living cells with state-of-the-art techniques to examine their cellular localization, mobility, and interactions with other proteins. Protein targets have been tagged with fluorescent proteins so that they can be viewed in living systems. We will also examine what effect extracellular signals have on the proteins' behavior. The student will serve as a research collaborator, learning both common and state-of-the-art biochemistry experimental techniques. In addition to learning about how research works, he or she will also gain valuable experience and will have the opportunity to serve as a co-author on research papers. No previous research experience or biochemistry coursework is required; a love of lab work and at least one college-level chemistry course are a must. First year science students interested in a multi-year research experience are strongly encouraged to apply.
Benefit to student: The student will serve as a research collaborator, learning both common and state-of-the-art biochemistry experimental techniques. In addition to learning about how research works, he or she will also gain valuable experience and will have the opportunity to serve as a co-author on research papers. Other students have already benefitted from this project, as it has provided independent projects for 20+ students in Chem 383 over the last few years.

Michael Barbachyn, Chemistry & Biochemistry
Project #17 Preparation of Bicyclo[1.1.1]pentyl Stannanes, Silanes and Trifluoroborates and Applications in Palladium-Catalyzed Cross Coupling Reactions
Description:
This research proposal focuses on the preparation of bicyclo[1.1.1]pentyl (BCP) stannanes, hypervalent silanes and trifluoroborates followed by an exploration of the palladium-mediated cross-coupling reactions of these substances. Initially, reliable synthetic protocols for the preparation of a range of BCP stannanes, silanes and trifluoroborates will be explored and optimized. The targeted BCP cross-coupled products are envisioned as useful intermediates for further synthetic transformations, leading to potential applications in a variety of distinct research areas. Of greatest interest is the incorporation of selected BCP subunits into known LpxC inhibitor scaffolds to yield antibacterial agents with potentially potent activity against multidrug-resistant Gram-negative bacteria such as Pseudomonas aeruginosa. LpxC [UDP-3-O-(R-3- hydroxymyristoyl)-GlcNAc deacetylase] is an essential metalloamidase that catalyzes the first committed step in the biosynthesis of the lipid A component of lipopolysaccharides in the bacterium's outer membrane. Any synthesized LpxC inhibitors will be evaluated for their antibacterial activity potential, potentially by a microbiologist at Calvin but most likely at the University of Notre Dame (Marvin Miller's lab).
Benefit to student: Undergraduate colleagues participating in this research will learn fundamental laboratory techniques associated with organic synthesis. These include handling air-sensitive reagents, running temperature controlled reactions, and learning extractive workup techniques and purification methods, especially column chromatography. Analytical methods, including spectral determinations (NMR, IR, MS) and HPLC purity assessments will also be experienced. The developed methodology, if successful, will allow the students to assist in the preparation of antibacterial agents of potential importance in the therapeutic clinical setting. Finally, publication of this work in peer-reviewed journals will provide the student with external visibility in the scientific community.

Michael Barbachyn, Chemistry & Biochemistry
Project #18 Synthesis of Novel QPT Antibacterial Agents Bearing Substitution at the Benzylic Position
Description:
The quinoline pyrimidinetriones (QPTs) are a novel class of bacterial topoisomerase inhibitors that were discovered in 2002 and subsequently reported in the open literature in 2008 (Miller, A.A.; et al. Antimicrob. Agents Chemother. 2008, 52, 2806-2812). The initial lead compound, PNU-286607, exhibited excellent in vitro activity and in vivo efficacy against problematic Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). This research project will focus on developing new synthetic methodology to synthesize QPT analogs substituted at the benzylic position, an area that has not been previously explored. Any synthesized analogs will be evaluated for their antibacterial activity potential, potentially by a microbiologist at Calvin but most likely at the University of Notre Dame (Marvin Miller's lab).
Benefit to student: Undergraduate colleagues participating in this research will learn fundamental laboratory techniques associated with organic synthesis. These include handling air-sensitive reagents, running temperature controlled reactions, and learning extractive workup techniques and purification methods, especially column chromatography. Analytical methods, including spectral determinations (NMR, IR, MS) and HPLC purity assessments will also be experienced. The developed methodology, if successful, will allow the students to assist in the preparation of antibacterial agents of potential therapeutic importance. Finally, publication of this work in peer-reviewed journals will provide the student with external visibility in the scientific community.

David Benson, Chemistry & Biochemistry
Project #19 Anti-Oxidant Nature of Tyrosine-Cysteine Crosslinks in BF4112
Description:
The covalent bond between tyrosine and cysteine amino acid sidechains in proteins could potentially provide anti-oxidant chemistry. This project will characterize how the covalent bond (crosslink) between a tyrosine and cysteine in an orphan protein (BF4112) occurs. Our research group found this crosslink for the first time, but we are using this protein to "test drive" a variety of formation chemistries. We are interested in copper, iron, and manganese-based oxidations that are biologically inspired.
Benefit to student:
Experience with protein production. Experience with basic biochemical characterization techniques. Experience with performing reactions in and out of oxygen.

David Benson, Chemistry & Biochemistry
Project #20 Anti-Oxidant Nature of Tyrosine-Cysteine Crosslinks in Cysteine Dioxygenase
Description:
The covalent bond between tyrosine and cysteine amino acid sidechains in proteins could potentially provide anti-oxidant chemistry. This project will characterize how the covalent bond (crosslink) between a tyrosine and cysteine in human cysteine dioxygenase (CDO) functions. Mammalian CDOs contain a tyrosine-cysteine crosslink where cysteine is oxidized but it is not clear if this crosslink contributes to the chemistry or if it contributes an additional function. We believe an additional anti-oxidant function in CDO controls how long the protein survives in the cell which is used to regulate cysteine concentrations in the cell. Some cysteine is necessary for protein production but too much cysteine contributes to neurological diseases.
Benefit to student:
Experience with protein production. Experience with basic biochemical characterization techniques. Experience with performing reactions in and out of oxygen.

David Benson, Chemistry & Biochemistry
Project #21 Analysis of Tyrosine-Cysteine Crosslinks Concentrations in Proteins
Description:
The covalent bond between tyrosine and cysteine amino acid sidechains in proteins could potentially provide anti-oxidant chemistry. To date, the most quantitative assay for tyrosine-cysteine crosslink concentration comes from a mobility shift assay in gel electrophoresis. A more quantitative assay needs to be developed. Our research group has explored absorbance, fluorescence, colorimetric, and electrochemical assays and has found encouraging results from a fluorescence assay. This project will collect the final data for calibration curve and apply this assay to BF4112, cysteine dioxygenase, and hemoglobin.
Benefit to student:
Experience with protein production. Experience with basic biochemical characterization techniques. Experience with fluorescence assays.

David Benson, Chemistry & Biochemistry
Project #22 Computational Analysis of Tyrosine-Cysteine Crosslinks in Proteins
Description:
The covalent bond between tyrosine and cysteine amino acid sidechains in proteins could potentially provide anti-oxidant chemistry. We have found at least one new tyrosine-cysteine crosslinked protein from a simplistic computational search of the protein databank (PDB), which houses all reported protein structures. Our research group is looking for better method to refine this list of potential proteins, and find additional proteins from the PDB, that might contain tyrosine-cysteine crosslinks. The work will involve running molecular dynamics calculations on Unix operating systems; which I have experience with.
Benefit to student:
Experience with protein structure and function. Experience with computational biochemistry.

David Benson and Chad Tatko, Chemistry & Biochemistry
Project #23 NMR Analysis of Tyrosine-Cysteine Crosslinks in Proteins
Description:
The covalent bond between tyrosine and cysteine amino acid sidechains in proteins could potentially provide anti-oxidant chemistry. To date, the only structural information for tyrosine-cysteine crosslink has been derived from X-ray crystallography. We are pursuing X-ray structure analysis of a new protein with a tyrosine-cysteine crosslink, but NMR can provide more rapid information. This work will use the 500 MHz NMR at Calvin to directly demonstrate formation of a tyrosine-cysteine crosslink within an intact protein and additional structural information.
Benefit to student:
Experience with protein production. Experience with basic biochemical characterization techniques. Experience with protein NMR.

Roger DeKock, Chemistry & Biochemistry
Project #24 Cooperativity in Hydrogen Bonding
Description:
For several years we have performed theoretical studies that relate to cooperativity in hydrogen bonding. For example, we examine molecular cubes with the formula NH3(H2O)7. We believe that these small cubes can serve as prototypes for cooperativity in hydrogen bonded networks in real chemical systems, such as ammonia, NH3, in water. We have completed similar studies on the thirty nine cubes of HF(H2O)7. Additional studies on these systems need to be completed. Those additional studies would be the focus of the summer 2013 work.
Benefit to student: The student will learn about computer modeling in chemistry. Specifically, he or she will learn something about the different theoretical techniques that can be employed to study minimum energy pathways in chemical systems. The student will learn about relative energies of reactants and products and of transition states; in other words they will learn about energy hypersurfaces. The student will also gain experience in reading the chemical literature related to the topic at hand, and in making written reports, oral reports, and preparation of posters for presentations. Most of our computational modeling has been done with Gaussian 09, but we also have deployed the Amsterdam Density Functional code, ADF.

Roger DeKock, Chemistry & Biochemistry
Project #25 Sequential Ionization Energies of Atoms
Description:
For several years we have performed theoretical studies in order to obtain insight into the electronic structure of atoms. Specifically we aim to provide a theoretical underpinning as to why the sequential ionization energies of atoms roughly follow an arithmetic progression. We employ the GAMESS software, and the Restricted Open Shell Hartree Fock model within GAMESS (General Atomic and Molecular Electronic Structure System).
Benefit to student: The student will learn about computer modeling in chemistry. Specifically, the student will learn about Restricted Open Shell Hartree Fock theory, and how it is implemented in GAMESS (General Atomic and Molecular Electronic Structure System). The student will also learn much about reading the literature in the field, and preparing written, oral, and poster reports on the project.

Herb Fynewever, Chemistry & Biochemistry
Project #26 Faculty approaches to student interaction in teaching science, math, and engineering
Description: Usually when students are learning science, math, and engineering they reveal their thinking to the instructor and the instructor uses this information to give feedback to the students. Often, however, this two-way communication is limited to formal assessments such as quizzes and exams, which happen after most of the learning has happened. Research has shown that there are many effective ways to better integrate this communication into the learning process (e.g. interactive classroom delivery and activity) realizing significant gains in student learning. Further research is needed to determine what the barriers are to two-way communication and to devise strategies to remedy these barriers. In this research, students will analyze data from classroom observations and interviews with faculty and students to detect and classify these barriers.
Benefit to student: Students participating in this research will learn about techniques of education research including thematic analysis of transcripts, conducting interviews, and technical writing. Experience in these skills will serve the students well. Students pursuing advanced degrees in the large and growing field of science, math, and engineering education have a significant advantage over peers when they are mentored in research during their undergraduate years. As educational research and policy work is more visible and relied upon, an increasing number of students apply for graduate research fellowships. And even though there have been significant increases recently in federal funding for educational research, receiving the best fellowships can make a significant difference in viability of finishing graduate work and in securing future employment.

Brendan Looyenga, Chemistry & Biochemistry
Project #27
Description:
Benefit to student:


Larry Louters, Chemistry & Biochemistry
Project #28 Detection of oligomers of GLUT1 and its relationship to the activity of the transporter
Description:
One model to explain the activation of GLUT1 is that it becomes more active if the transporter aggregates, likely as a tetramer. We will use two techniques to try to isolate GLUT1 tetramers and determine if the concentration of these tetramers changes when glucose uptake is activate. The first method is called blue native PAGE, which, in contrast to SDS-PAGE, is an electrophoretic technique capable of isolating membrane protein complexes intact. The second method will be using chemical crosslinking reagents that covalently link the GLUT1 proteins together, which can be then separated and sized by SDS-PAGE.
Benefit to student: One model to explain the activation of GLUT1 is that it becomes more active if the transporter aggregates, likely as a tetramer. We will use two techniques to try to isolate GLUT1 tetramers and determine if the concentration of these tetramers changes when glucose uptake is activate. The first method is called blue native PAGE, which, in contrast to SDS-PAGE, is an electrophoretic technique capable of isolating membrane protein complexes intact. The second method will be using chemical crosslinking reagents that covalently link the GLUT1 proteins together, which can be then separated and sized by SDS-PAGE.

Larry Louters and Brendan Looyenga, Chemistry & Biochemistry
Project #29 Relationship of GLUT1 tethering to the cytoskeleton and its influence on its activity
Description:
GLUT1, like many membrane proteins, can be tethered to the cell cytoskeleton by connector proteins. Typically this tethering is involve in the recycling of the protein to and from the membrane surface. We will measure the fraction of GLUT1 tethered to the cytoskeleton and determine if that fraction changes when GLUT1 is activated.
Benefit to student: Students will learn research techniques including reading the literature, planning experiments, and interpreting data.

Mark Muyskens, Chemistry & Biochemistry
Project #30 Photochemistry: Research in Fluorescence in Sycamore Wood and Photoelimination in Acetylacetone
Description:
There are two areas of photochemistry that will be investigated. One area is to investigate the chemical structure of the highly fluorescent components of the aqueous extract of sycamore wood. This project continues an effort to identify the fluorescent compounds from sycamore wood. The work involves liquid chromatography for separation and fluorescence spectroscopy. The other project will use computational tools to model the kinetic and molecular structural details of a gas-phase photochemical reaction. My research has experimental results from the ultraviolet laser photoelimination of hydrogen fluoride from fluorine containing acetylacetone in the gas phase. The work will be greatly assisted by developing models related to the data.
Benefit to student: The student will either gain experience in separation and molecular structure identification techniques, or will gain experience in using computational tools to understand molecular structure and chemical reactions. The work will directly support ongoing research projects. Both projects, with sufficient progress, will lead to publication.

Kumar Sinniah, Chemistry & Biochemistry
Project #31 Investigating the Binding of Insulin with G-Quadruplex DNA
Description:
G-quadruplexes are noncanonical DNA structures formed from guanine-rich DNA sequences in the presence of monovalent cations such as potassium or sodium ions. These structures are of significant interest due to their role in biological processes. The human genome contains hundreds of thousands of sequences that have the potential to form quadruplexes. Proteins that bind to G-quadruplex DNA are likely to provide a clue to the role of G-quadruplex DNA in biology. Our group is currently studying the biophysical interactions between the protein insulin and the various sequences of G-quadruplex DNA found in the insulin linked polymorphic region. This project is suitable for a student interested in biochemistry, chemistry, or biology.
Benefit to students: Students will be trained in research methodologies, learn critical thinking skills and get to do hands-on scientific research.

Kumar Sinniah, Chemistry & Biochemistry
Project #32 Characterizing Riboflavin Conjugated Nanoparticles for Targeted Drug Delivery in Cancer Therapy
Description:
Riboflavin (RF) receptors have been found to overexpress in prostate and breast cancer cells. RF receptors can be targeted for selective delivery of anticancer drug molecules. Our group has characterized RF conjugated dendrimer series for targeting the RF receptor. We determined that one series of dendrimer conjugates based on the orientation of RF attachment to the dendrimer performed better at binding to the RF receptor. This summer we hope to extend this work to study both monovalent and multivalent interactions between RF and its receptor using single molecule and bulk ensemble methods. This project is suitable for a student interested in biomedicine / biochemistry / chemistry /
biology / bioengineering.
Benefit to student: This is a biomedical research project which involves collaboration with a team of scientists in the biomedical sciences program at the University of Michigan. The students will have the opportunity to interact with a number of scientists, learn from them, and also be involved in multi-disciplinary research. The benefit to the students will be significant.

Chad Tatko, Chemistry & Biochemistry
Project #33 Perturbation of Acidity via Noncovalent Interactions
Description:
A structured environment or lipid association can result in a significant alteration. This project will construct a series of folded peptides into a beta-hairpin conformation. This co-localizes a queried amino acid proximal to an acid. Through NMR methods the pKa of the acid will be determined to elaborate the noncovalent impact of the neighbor.
Benefit to student: Students will benefit from an interdisciplinary project with significant instrumentation use.

Douglas Vander Griend, Chemistry & Biochemistry
Project #34 Nanomolecular Building Projects
Description:
Understanding and controlling the synthesis of supramolecules is a key goal of nanotechnology. Students working on this project will use UV-vis spectroscopy and mass spectrometry to investigate the solution chemistry of various inorganic and biochemical systems in which individual molecules associate in solution to form larger structures. Students may also get involved with computer programming and modeling if so desired.
Benefit to students: I anticipate that the students will not only get ample hands on experience with making up solutions and mastering several analytical devices, but also have a chance to interact in a collaborative effort with other research labs. It is ideal for first or second year students.
Note: Professor Vander Griend is out of the country. Contact him about this project by e-mail.

Computer Science projects

Serita Nelesen, Computer Science; John Wertz, Biology
Project #35 HTMAD: Software for Analyzing MALDI-TOF Data
Description:
The ability to write programs to analyze large datasets of empirically gathered data has become an increasingly important skill with regards to advancing research in biology, chemistry, and physics. A student working on this project will continue the development of a program (HTMAD) to analyze data from the MALDI-TOF mass spectrometer. The current version of HTMAD needs to be prepared for publication and distribution, and there are several extensions we would also like to implement. Previous programming experience is required (ideally CS 112, but perhaps not required).
Benefit to student: The student will benefit from collaboration with faculty and students from computer science, biology and chemistry. The student will have the unique opportunity to continue work on a prototype of a novel computer program (adding features, testing and refining existing algorithms) using biological and chemical data that is relevant to current research projects within multiple departments. The students will enhance their programming knowledge and software distribution skills, and the students will also learn how to report and present their results and interpretations scientifically - both informally as part of a research group as well as formally in a poster. If experiments are successful, the students will also have an opportunity for co-authorship on a peer-reviewed publication.

Engineering projects

Yoon Kim, Engineering
Project #36 Development of portable battery-operated wireless devices for environmental monitoring
Description:
This project is to develop palm-size wireless computing devices for environmental monitoring. The device measures environmental factors, such as noise, temperature, relative humidity, atmospheric pressure, and soil moisture through sensors and performs logging data for a month-long period without recharging a battery. Although a conventional automated recording system could record data, one needs to bring the system to a lab to retrieve its data. This method is not only cumbersome, but also invasive to nature if repeated. There is more work that needs to be done to retrieve data conveniently. Using the proposed device, the saved data could be retrieved remotely through a wireless link. It reduces human intervention, and therefore, it would be less-invasive to nature and be more environmental friendly. Having a microphone and camera embedded, it can also stream a live audio and video of wildlife without disturbing nature. This project involves literature search, data measurements, designing of computer hardware and analog electronics, programming, system integration, and testing.
Benefit to student: The project would benefit students in understanding Christian stewardship. As Christian caretakers, we are called to sustain God's wonderful creation. It also provides students with an opportunity to apply their knowledge in science and technology to solve a real-world problem. Students will learn how to integrate several components, such as sensors, electronics, microprocessors, and software modules. Students will learn overall design processes ranging from a literature search to realization with realistic constraints.

David Wunder, Engineering
Project #37 Removal of Fluoride in Bagasse Charcoal
Description:
Wood charcoal (WC) is broadly used in developing global regions (DGR) for heating and cooking. In many regions, WC production contributes to deforestation which can exacerbate global climate change and increase the adverse effects of soil erosion and flooding. Bagasse, the sugarcane residual from processing, is an alternative and sustainable source for charcoal. Although studied as a fuel source, bagasse charcoal (BC) also has potential value for water treatment. Treating water of DGR has focused largely on biological pathogens. However, there remains a need to develop novel and sustainable methods for removing non-biological contaminants. This work focuses on BC column studies of the removal of fluoride from water supplies.
Benefit to student: This project will benefit students by given them hands-on research experience with novel and sustainable approaches for treating water in developing global regions. Students will learn more about how to do research, how to design simple treatment processes, and about cultural factors that impact the sustainability of engineering solutions.

David Wunder, Engineering
Project #38 Fate and Impact of Antibiotics in Denitrifying Biofilters
Description:
Nitrate contamination of water supplies is caused by widespread use of fertilizers, erosion due to changes in land use, and leaching. One of the most cost effective and environmentally responsible processes used to remove nitrates from groundwater is fixed-film biological denitrification. A possible concern with this process is the presence of antibiotics at in water supplies and their impact on dentrifying biofilm bacteria and their ability to reduce nitrate. . Interestingly, recent work has shown that some antibiotics that might impede the activity of denitrifying bacteria may also be abiotically transformed in reducing conditions necessary for biological denitrification. This research attempts to understand whether grouped antibiotics at environmentally-relevant concentrations will impact the activity and community structure of denitrifying biofilm bacteria, and whether the response of individual antibiotics to reducing environmental conditions will partially mitigate their impact(s). Using substrate utilization kinetic studies, a continuous-feed rotating annular bioreactor would be used to better understand the fate and impact of grouped antibiotics ondenitrifying biofilm bacteria used for water treatment.
Benefit to student: Students will gain hands-on research experience. As part of their experience, students will be involved in the design of experiments and experimental systems. From this experience students will be deriving new knowledge that addresses real challenges associated with medicine, engineering, and a healthy society.

Geology, Geography & Environmental Studies projects

Deanna Van Dijk, Geology, Geography & Environmental Studies
Project #39 How does human activity affect coastal dune activity?
Description:
This project will investigate how human impacts and management strategies affect the geomorphic activity of Lake Michigan coastal dunes. At North Beach dune and Mt. Pisgah in Ottawa County, the investigation will build on preliminary results from First-Year Research in Earth Sciences (FYRES) research students showing that management efforts are stabilizing these dunes. This summer, we will collect and analyze data to see whether it is possible to determine the relative contributions of different management strategies to the overall stabilization of the two dunes. We will also generate a list of promising research questions for future FYRES projects by exploring other dune sites for interactions between dune activity and human impacts and/or management strategies.
Benefit to student: The students will gain valuable research experience by carrying out the investigation from start to finish, including reviewing relevant literature and previous study results, designing a data-collection plan to measure management effort contributions to dune stabilization, analyzing the study results, and working towards a manuscript on the study for a scientific journal. The end result of the research project is expected to be a presentation at an academic conference such as the Michigan Academy meeting and co-authorship on a future journal article.

Jason VanHorn, Geology, Geography & Environmental Studies; Dave Warners, Biology; Gail Heffner, Director of Community Engagement
Project #40 GIS and Remote Sensing of Plaster Creek Watershed
Description:
Over the course of 10 weeks, we will engage in the development of a more sophisticated GIS system than is currently available for the Plaster Creek watershed. Gathering and developing a variety of spatial layers for the watershed and collecting an historical view of the watershed through aerial imagery will be the primary goal. Adding this GIS data to the existing watershed GIS @ gis.calvin.edu and developing new tools for the online application will be a secondary goal. Lastly, we will build a series of technical briefs to assist individuals interested in conducting spatial analysis using the layers we add to the GIS Server at Calvin College as an outreach to the Calvin Community.
Benefit to student: You will learn:
1. New GIS skills;
2. Experience with online GIS server application;
3. Deepen knowledge of the Plaster Creek;
4. Assist in a larger project;
5. Produce technical briefs for educational purposes.

Mathematics & Statistics projects

Michael Bolt, Mathematics & Statistics
Project #41 Analytic functions of a generalized complex variable
Description:
This is a continuation of a program in which students have participated since 2008 and which already has resulted in five publications with students as coauthors. This year's effort will center around properties shared and not shared by analytic functions of a complex variable with analytic functions of a dual or double variable. In general, the variable has form z = x + e y where e^2 = -1 for a complex variable, = 0 for a dual variable, and = +1 for a double variable. The applied math component is reflected in the recent appearance of double numbers in the study of nonlinear dynamics; students will be expected to gain familiarity with this application. The line of inquiry most closely resembles the work done by two students in summer 2011. Depending on student interest, it is expected that just one of my proposed projects will run in 2013.
Benefit to student: The primary goal is to provide students with a high-quality research experience in mathematics. A pair (or group) of students will be presented with a problem very early in the summer and they will take responsibility for seeing the project through to completion. As adviser, I'll offer suggestions for how to approach the problem and identify errors as they arise. Students will present their work in colloquium and will be expected to help prepare a written report. At the end of the project, it is anticipated that students will participate in MathFest 2013 in Hartford, CT.

Michael Bolt, Mathematics & Statistics
Project #42 Numerical Schwarz-Christoffel mapping
Description:
This project represents a second effort at computing angle-preserving (conformal) maps from a prescribed two-dimensional region to a fixed region such as a half-plane. For the case of polygons, the Schwarz-Christoffel formula represents the map explicitly using an integral formula. The goal will be to develop the numerics needed to compute the maps and to implement the methods in an environment like that of the CAS Sage. The applied math component is reflected in the historical application of conformal mapping methods to the solution of Dirichlet problem. The line of inquiry most closely resembles the work done by two students in summer 2009. Depending on student interest, it is expected that just one of my proposed projects will run in 2013.
Benefit to student:
The primary goal is to provide students with a high-quality research experience in mathematics. A pair (or group) of students will be presented with a problem very early in the summer and they will take responsibility for seeing the project through to completion. As adviser, I'll offer suggestions for how to approach the problem and identify errors as they arise. Students will present their work in colloquium and will be expected to help prepare a written report. At the end of the project, it is anticipated that students will participate in MathFest 2013 in Hartford, CT.

Todd Kapitula, Mathematics & Statistics
Project #43 The Krein function - a new characteristic polynomial
Description:
It is well-known that the eigenvalues of a matrix are found by determining the zeros of the characteristic polynomial. In many problems of physical/mathematical interest the goal is to not find all of the eigenvalues, but only those few that have some special significance. The Krein function is a different type of characteristic function - no longer a polynomial - which accomplishes precisely this task. The Krein function can be constructed in many different ways. The student researchers will explore the various ways of creating the Krein function, and attempt to determine a criteria which says which one is "best" for solving a particular problem.
Benefit to student: Will synthesize previously learned material in linear algebra and calculus. Will gain an appreciation of how seemingly different mathematical subjects "talk" to each other in ways that allow one to solve interesting and relevant problems.

James Turner, Mathematics & Statistics
Project #44 Utilizing algebra to address problems in the geometry of polynomials
Description: Certain problems in geometry can be studied through hypersurfaces, that arise as the zeroes of multivariable polynomials, as well as their intersections. Such problems can often be resolved through knowledge of the dimension of such intersections. A device that facilitates the computation of such a dimension is the Hilbert function. The aim this summer will be to explore one or both of the following:
1. Use Hilbert functions to measure the extent a planar graph is rigid. A first step would involve giving an algebraic proof of Laman's theorem for characterizing rigid planar graphs.
2. Associated to a Hilbert function is its Hilbert series. Such a series has a lower bound and a conjecture of Froberg indicates when the Hilbert series is this lower bound. We will examine the next open case.
Benefit to student: The study of polynomials in several variables is at the basis of several areas of higher mathematics. Thus, this gives students the sense of the foundations of certain areas of advanced mathematics they would encounter in graduate studies. Also, for students pursuing secondary education, polynomials give important insight to the understanding of algebra, geometry, and calculus.

Nursing projects

Adejoke Ayoola and Gail Zandee, Nursing
Project #45 Preconception reproductive knowledge promotion (PREKNOP)
Description:
Unplanned pregnancy continues to be an ongoing public health problem in the United States which has a relatively higher rate than other developed countries. The social and economic cost of unplanned pregnancy and its associated adverse health outcomes on individuals and the society is enormous. Unplanned pregnancy rates and their adverse effects are even worse among minority and low-income women. The long-term objective of this research is to promote women’s reproductive health and positive pregnancy outcomes by examining the effectiveness of the “Preconception Reproductive Knowledge Promotion (PREKNOP)”, an intervention to increase women’s knowledge of their body, while reducing the risk of unplanned pregnancy and delayed pregnancy recognition. The social cognitive theory and the health promotion model guide this study. Based on a community-based participatory research approach, this study builds on residents’ reported concerns and recommendations as well as a longstanding partnership between the Calvin College nursing department and three racially diverse medically underserved low-income communities in southwest Michigan. The hypothesis is that the PREKNOP program will reduce the risk of unplanned pregnancy and improve women’s ability to manage their reproductive health. A sample of 120 women, 18-44 years old will be randomly assigned into two groups, one control and one intervention at the time of recruitment. A pre-intervention survey will be conducted to establish a baseline. The PREKNOP intervention will consist of 8 home visits during which women will receive information on the female reproductive system and the expected monthly cyclical changes. Teams of nursing students and community health workers will administer the 12 month intervention and surveys in face-to-face interviews. The PREKNOP intervention will consist of 6 ovulation test kits (participants can request refills at any time), a 12 month menstrual calendar, a digital thermometer, and educational brochures covering: the female reproductive anatomy, hormones and menstrual cycle, how to recognize ovulation period, various methods of birth control and how they work, early pregnancy symptoms, and how to confirm pregnancy symptoms. Women of childbearing age, especially minorities and the medically underserved, need continuous monitoring and on-going educational approach to reduce disparity in health and improve pregnancy outcomes. Promoting better understanding of the reproductive changes in their bodies and actively involving women in their own care is a logical place to start.
Benefit to student:
During the first year of the project, in the spring 2013 semester nursing student/CHW teams would conduct the pre-test, provide PREKNOP education to the experimental group and general education to the control group, conduct follow-up visits during month two and three, and complete the 3-month study follow-up in the 4th month. Four nursing student research assistants will be hired the first year to complete home visits that are needed outside of clinical hours (during the semester) and after the semester ends. Nursing student research assistant/CHW teams will provide monthly home visits during the 5th and 6th month, and conduct the 6-month study follow-up visit to those in the experimental and control group during the 7th month when there will be no regular academic session. These students will also be involved in recruiting with the CHWs, and entering study data. The Center for Social Research will provide training for the nursing research assistants in survey data entry and direct student-to-student support for database and methodological issues. This involvement will provide opportunities to develop students’ knowledge in evidence-based practice, especially in the area of maternal/child health nursing.

Physics & Astronomy projects

Loren Haarsma, Physics & Astronomy; Serita Nelesen, Computer Science
Project #46 Developing a computer model of evolution of interlocking complexity in biology
Description:
We have developed and are expanding a computer model which investigates one possible strategy for the gradual evolution of increasing interlocking complexity in biological systems. Artificial organisms called Pykaryotes gather resources from their environment, move, and build proteins and protein complexes based on their genetic code. Through mutation and selection their genetic code gradually becomes more complex. While the focus of the project is biological, some of the model's details are also relevant to questions of self-organized complexity in other fields. A student will work with professors in biophysics and computer science to run the computer program, modify the program, and evaluate how the model performs.
Benefit to student: The student will gain knowledge of and experience with computer modeling methods. The student will both write the computer code and work with the professors in evaluating the performance of the model. The model will be based on agentinteraction and artificial life forms. While this project models some aspects of evolutionary biology, features of this project are relevant to questions of self-organized complexity in other fields of natural and social sciences. Thus, many of the modeling
skills learned in this project should be transferable to other research. We will also write a paper based on the results for submission to a professional journal.

Loren Haarsma, Physics & Astronomy; Becky Haney, Economics; Vic Norman, Computer Science
Project #47 Programming and optimizing an agent-based computer simulation of a self-organized, interdependent economy
Description:
Over the last three summers, Calvin undergraduates have programmed an “agent-based” computer simulation similar to computer games such as SimCity and Life. In this simulation, computer agents gather resources, invent tools and trade with other agents. Over time a complex network of interdependencies develops among the agents. This is a model of the
development of economic relationships that exist in modern, technologically-advanced economies. The purpose of this model is to investigate the variables which affect wealth and inequality within an economy. This summer, a student will work with professors in economics, computer science, and physics to add functionality to the existing computer model by adding human virtues and vices to agent behavior and social institutions to the trading scenarios. The programming project will also include “parallelizing” the code, to vastly reduce runtime. Students should know or be able to quickly learn the C++ programming language. Students having had at least one economics course are preferred.
Benefit to student: The student will gain knowledge of and experience with computer modeling methods. The student will both write computer code and work with the professors in evaluating the performance of the model. The model will be based on agent-interaction, and features of this computer model are inspired by economics and evolutionary biology. Thus, many of the skills learned in this project should be transferable to other computer modeling projects in the natural and social sciences. We will also write a paper based on the results for submission to a professional journal.

Paul Harper, Physics & Astronomy
Project #48 DSC and Temperature Jump Studies of Lipid Phase Transitions
Description:
Lipid phase transitions among the many types of lipid phases are highly relevant to understanding the behavior of membrane proteins and the cellular processes of pore formation, division, fusion, and infection. Likewise, sugars play a key role in stabilizing membranes against freezing and dehydration. Last summer, we found that the disaccharide sucrose appears to be excluded from the surface of the frozen lamellar and hexagonal phases of the lipid SOPE, but partially included in the surface of the fluid lamellar phase. Over the fall, we started to study the lipid monoolein and sucrose, which forms exotic minimal surface based phases. In monoolein, we’ve seen the greatest phase transition shifts yet. This summer, we’ll use DSC, differential scanning calorimetry, to investigate effects of other sugars, such as glucose, trehalose, and raffinose. Concurrently, we’ll also build a temperature jump apparatus that will use optical methods to monitor the phase transitions.
Benefit to student: Students will benefit by performing original research on lipid kinetics, constructing samples, taking and analyzing data, and devising models of the observed behavior. Potentially, their results will be presented at the national Biophysical Society Meeting and published.

Larry Molnar, Physics & Astronomy
Project #49 Asteroid Collisions
Description:
To a remarkable degree, the history of our solar system is recorded in the details of the orbits of the numerous small bodies that are left over: the asteroids. In the last few years, we have developed new techniques to read this history, especially in identifying the age and membership of asteroidal collisional families. One key parameter in models of the collisional history of the asteroid belt is the impact energy required to disrupt an asteroid. Theoretical estimates of this parameter vary widely. The main goal of this summer's work is to establish this parameter observationally by careful study of the collisions that have occurred in the Koronis zone, an isolated region in the outer portion of the main asteroid belt. Towards this end we have written software to compute collisional speeds and probabilities along with software to combine several catalogs of asteroid information. This summer we will put these together to get a final answer.
Benefit to student:

Steven Steenwyk and Larry Molnar, Physics & Astronomy
Project #50 Modeling Fast and Unusual Binary Stars
Description:
Though they often appear as a single star, even when magnified, binary stars are two stars held in mutual orbit around one another by gravity. Contact binary stars are so close together that their atmospheres touch as they rapidly orbit one another. While these so called “W UMa” systems are not uncommon, many aspects of their life cycle remain poorly understood, from formation to final state. They are identified by characteristic shapes of the light curves obtained with Calvin's telescopes. Using powerful search and analysis software, student researchers have already found and typed many new variable stars over the last two years. Several of these are quite extraordinary and thus of significant interest to the astronomical community. One is one of the fastest contact binaries known that we call V0811+3119. Another is a complex system consisting of a contact binary that is itself orbited by a third star (V859 Cyg). While fast contact binaries remain the primary interest, the proposed ten week project will also follow up on a very rare blue sub dwarf in an eclipsing orbit with a red dwarf star (V2008-1753). Finally continued follow up is needed on a contact binary we call V0738+2950 that exhibits extraordinary variations in the shape and period of its light curve. This behavior may be due to activity of monstrous starspots or even presage a catastrophic stellar merger.
Benefit to student: This project builds essential skills in many aspects of observational astronomy, from technical matters of optics, atmospheric effects, and precise planning of observations to the fitting of light curves with physical models using available computer resources. It is accessible to undergraduates, yet rich with nuanced physical understanding as a student progresses. It is well suited to someone with strong interests in both astronomy and computer modeling using both established software and original computer programming.

Matthew Walhout, Physics & Astronomy
Project #51 Experiments with trapped krypton atoms
Description
: We will use laser light to trap a small cloud of atoms, and then we will use various tools to study atomic collisions in the cloud. The goal is to understand the collisional dynamics in terms of diatomic molecular potentials that characterize the pairwise interactions between atoms. The work will involve optics, electronics, vacuum equipment, and computer programs for data acquisition and molecular modeling.
Benefit to student: Students will become familiar with several techniques and various kinds of equipment that are common in state-of-the-art research laboratories worldwide. There may also be opportunities to read and write scientific papers, to attend scientific meetings, and to become acquainted with exciting recent developments in experimental atomic physics. This will be great preparation for any student who hopes to pursue a graduate degree physics.

 


 

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Past funding

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