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Opportunities in Science at Lewis & Clark

2017 Project Descriptions for Rogers Program

February 07, 2017

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Prerequisites must be completed by the end of spring semester 2017. 

Please review application instructions and forms here.
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Biology

1. The evolution of venom-expressed gene families in Synspermiata spiders

Principal Investigator: Greta J. Binford

Venoms are complex mixtures of peptides and proteins that include products of multiple gene families. The histories of the gene families in venoms typically include duplication of a gene that codes for a protein that does not have venomous function, change in expression patterns, and the evolution of differences in functional specificity. We are analyzing the histories of proteins in venoms of brown recluse spiders and their relatives. This work applies bioinformatics and molecular tools to analyze expression of members of gene families in venom glands and other tissues, and to infer the evolutionary histories of venom proteins.  

Prerequisites:
Comfort doing computation will be helpful. 

 
2. Arachnid biogeography in the Caribbean

Principal Investigator: Greta J. Binford

The Caribbean is a global biodiversity hotspot, yet historical influences on taxonomic diversity in the region are not well understood. An international group of arachnologists is undergoing a large-scale inventory of arachnids on the Caribbean. We are collecting multiple lineages and comparing their biogeographic histories to uncover shared patterns of divergence in space and time. This summer will involve taking high resolution images of arachnids to help delineate species that we have identified using molecular tools. With these images we will work to identify morphological characteristics associated with species boundaries.

Prerequisites:
Comfort doing computation will be helpful. 

 
3. Discovering how cell-type specific compartments are constructed

Principal Investigator: Greg Hermann

Lysosome related organelles (LROs) are compartments that carry out key functions within particular cells of an organism. While much is known regarding the functions of LROs (for example pigment formation in melanosomes and blood clotting by platelet dense granules), the processes involved in their construction remain poorly understood. Defects in these processes underlie a number of human genetic diseases.  We are discovering and analyzing the function of genes controlling the formation of LROs in the model organism, Caenorhabditis elegans, whose homologues function similarly in humans 

Prerequisites:
Required: BIO151 or AP equivalent.
Desired: BIO200, BIO311/312, BIO412 or BIO361

 
4. How seedling functional traits interact with environmental conditions to maintain forest diversity in an Amazonian rainforest

Principal Investigator: Margaret Metz

My research in the western Amazon examines the ecological mechanisms that influence the dynamics of tree seedlings in ways that promote or maintain tropical forest diversity. Many hypotheses about forest diversity invoke processes that occur at the seed and seedling stage, suggesting predictions for particular patterns of growth and mortality. Regeneration dynamics can thus create the template for future diversity of the forest canopy. As part of a long-term study of seedling dynamics, students will visit Ecuador to collect seedling functional trait data, quantify light availability above monitoring plots, and participate in an annual seedling census, with data analysis upon return to Lewis & Clark.

Prerequisites:

  • Course prerequisites: BIO 141 or equivalent. BIO 223 or 335 preferred. Spanish proficiency (fluency, preferred), esp. for taking detail-oriented data in Spanish and conversing with Spanish-speaking collaborators.
  • Valid passport and availability to travel in May immediately following the end of the semester.
  • Willingness to work under humid, muddy, buggy conditions with long days of strenuous hiking in a remote location with little to no communication to the outside world. Ability to remain focused on high quality, detail-oriented data throughout.
  • Experience working in rugged field conditions or traveling in remote locations will be very useful, as will a positive attitude, enthusiasm for learning, the ability to work as part of a team, and the interpersonal skills needed to work and live closely with other team members while far from home.
 
5. Seedling dynamics and the role of oomycete pathogens in maintaining diversity in an old growth forest

Principal Investigator: Margaret Metz

This project examines the seedling dynamics in an old growth forest near Portland and interactions with oomycetes, which may play a beneficial ecological role in the maintenance of forest diversity. Oomycetes, or water molds, are highly destructive fungus-like plant pathogens, best known for damage to agricultural crops. Native oomycetes are abundant in forested systems, and yet we know very little about their role in driving the dynamics or diversity of forests. This summer we will census a network of seedling monitoring plots in the Wind River Experimental Forest to assess the interactions between native tree performance at early life stages and interactions with pathogens.

Prerequisites:

  • Course prerequisites: BIO 141 or equivalent. BIO 223 or 335 preferred. Wilderness First Aid certification or willingness to obtain (wilderness first responder certification preferred)
  • Fieldwork will entail long days, strenuous hiking, and the ability to lift and hike with heavy backpacks on uneven terrain.
  • Experience working in rugged field conditions, and/or orienting in the back country will be very useful, as will a positive attitude, enthusiasm for learning, the ability to work as part of a team, and the interpersonal skills needed to work and live closely with other team members.
 
6. Effects of nicotine on Drosophila development: genes, neurotransmitters and toxicology

Principal Investigator: Norma A Velazquez Ulloa

Nicotine is the chemical in tobacco associated to addiction, yet little is known about the changes nicotine causes that produce addiction. My lab uses Drosophila, the common fruit fly, to discover the mechanisms for nicotine’s effects. Students working in this project will expose flies to nicotine, dissect brains, stain them, and use fluorescence and confocal microscopy to characterize nicotine’s effects on neurotransmitters and on proteins associated to nicotine metabolism. Students will also use molecular biology to identify genes involved in nicotine’s effects.

Prerequisites:
BIO151 or experience handling fruit flies and BIO200.

 
7. Investigating the role of thrombospondin in Drosophila development

Principal Investigator: Norma A. Velazquez Ulloa

Recently, it has been recognized that proteins of the extracellular matrix are important for nervous system and muscle development. Thrombospondins are glycoproteins that can interact with molecules in the extracellular matrix and also with proteins on the surface of cells. In mammals, thrombospondins have been shown to play in role in synapse formation in the central nervous system.  In the lab we are testing if thrombospondin has a role in synapse formation at the neuromuscular junction, in muscle development, and on behavior in Drosophila melanogaster. This research will expand our knowledge about extracellular matrix proteins on development.

Prerequisites:
BIO151 or experience handling fruit flies and BIO200.

 
8. Mapping neuronal development using multicolor imaging in Brainbow zebrafish

Principal Investigator: Tamily Weissman-Unni

Brain function relies upon the precise organization of neural circuits. The majority of neurons are born during early brain development, but there are many questions regarding how neuronal production is regulated. Our lab uses a multicolor fluorescence labeling approach (“Brainbow”) to label neuronal populations in many different colors within the living, developing zebrafish brain. Students will use embryonic microinjection techniques, express fluorescent proteins in zebrafish larvae, and use fluorescence microscopy to visualize neurons and dividing cells in vivo (in living fish). Our investigations will focus on mechanisms that regulate the dividing cells that generate neurons during brain development. There may also be an opportunity to work on an interactive, Brainbow-focused website. 

Prerequisites:
Bio 151 or equivalent; Neuroscience background and/or interest. (Bio 200 and/or additional background in cellular or molecular biology is ideal.)

 
9. Zebrafish to study cellular mechanisms of Parkinson’s Disease

Principal Investigator: Tamily Weissman-Unni

Parkinson’s Disease involves the abnormal aggregation of a protein called alpha-synuclein. Zebrafish is a useful model system for studying Parkinson’s Disease for two major reasons: 1) First, human forms of alpha‐synuclein are readily expressed in zebrafish, including forms that recapitulate human mutations in Parkinson’s Disease; 2) The developing zebrafish is optically transparent, allowing for clear visualization of expressed proteins. Students will use embryonic microinjection techniques, express fluorescent proteins in zebrafish larvae, and use fluorescence microscopy to visualize neurons and their connections in vivo. Our investigations will focus on the role of alpha‐synuclein aggregation in disease. There may also be an opportunity to work on an interactive, Brainbow-focused website.

Prerequisites: 
Bio 151 or equivalent; Neuroscience background and/or interest. (Bio 200 and/or additional background in cellular or molecular biology is ideal.)

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Chemistry

 
10. Surface Chemistry of Gold and Silver Nanoparticles

Principal Investigator: Anne Bentley

Gold nanoparticles (AuNPs) have the potential to be used in disease diagnosis, imaging, and treatment. They are favored for these applications because they are relatively chemically inert and their surfaces can be easily modified to affect their stability and/or transport desired medicines. As AuNPs advance from research lab to manufacture and use in applications, it is expected that they will be released to the environment, either intentionally or inadvertently. However, little is known about how the AuNPs will interact with the molecules found in natural environments, including other types of nanoparticles. This project will examine the stability of AuNPs under a variety of environmental conditions using UV-vis spectroscopy, dynamic light scattering, and transmission electron microscopy techniques.

Prerequisites:
Chem 120 or previous chemistry research experience

 
11. Electrochemical Growth of Manganese Oxide Supercapacitors

Principal Investigator: Anne Bentley

Manganese dioxide (MnO2) is a low cost and non-toxic supercapacitor that can store and release electrical charge more quickly than a battery. This project will focus on improving the electrochemical capacitance of MnO2 thin films by forming hybrid supercapacitor materials featuring TiO2, SiO2, AlOOH, and ZnO nanoparticle scaffolds supporting MnO2 thin films. Students will synthesize the ceramic oxide nanoparticles using sol gel methods and will coat them with polymeric ionic liquid (PIL) capping agents to enhance the charge transfer properties. Students will gain experience in nanoparticle synthesis, exchanging surface capping agents, and electrodeposition (applying an electrical potential to form a material on an electrode). Characterization tools will include dynamic light scattering, zeta potential measurements, cyclic voltammetry, powder X-ray diffraction, and electron microscopy.  

Prerequisites:
Chem 120 or previous chemistry research experience

 
12. Development of an immobilized ruthenium(II) chloride catalyst

Principal Investigator: Casey Jones

Ruthenium (li) chloride is a catalyst currently being used for the synthesis of pharmaceuticals and other compounds. However, ruthenium is also a toxic element for the human body and there are strict limits set on the amount of ruthenium that is found in pharmaceuticals. This project seeks to attach ruthenium chloride to the surface of aluminum metal so that it can (1) catalyze the desired reaction, (2) without leaching into the product, and (3) can be easily removed and reused in additional reactions. Students will explore and earn Surface modification and characterization, organic and organometallic chemistry, and green chemistry.

Prerequisites:
Organic Chemistry (Chem 220)

 
13. Designing a self-healing stent

Principal Investigator: Casey Jones

This project seeks to attach resveratrol, a compound found in red wine, to metal cardiovascular stents. Stents are used in patients with Coronary artery disease, but often fail from improper healing. Resveratrol has been shown to have the potential to improve cardiovascular healing. Our hypothesis is that a stent releasing resveratrol or analogues will improve healing, leading to device Success with less risk to patients. To accomplish this goal, we will (1) optimize the attachment of resveratrol and analogues to metal surfaces, (2) characterize the release of these molecules, and (3) evaluate the response of endothelia cells to the surfaces.

Prerequisites:
Organic Chemistry (Chem 220)

 
14. Organophosphate degradation with molybdenum oxo complexes

Principal Investigator: Louis Kuo

Sulfur oxidation (R2S → R2S(=O)) is key in the desulfurization chemistry of fossil fuels and in degrading organophosphate neurotoxins that include pesticides. To this end, we recently discovered several molybdenum oxo-peroxo compounds that carry out this oxidation under mild conditions. The organophosphate neurotoxins include sulfur-containing pesticides that are in current use. Both experimental and computational methods will be used to to elucidate a mechanistic route, and this effort informs the design of better reagents for sulfur oxidation that includes polymer-supported molybdenum complexes. The latter has the operational advantages of heterogeneous catalysis which yields new materials for remediation of these neurotoxins.

Prerequisites:
Chem 220
Chem 366 – preferred

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Environmental Studies

 
15. Cloud geometry observations for all-sky digital images

Principal Investigator: Jessica Kleiss

This project will develop novel measurements of shallow cumulus cloud geometry  – such as area, thickness, and spacing – from digital image analysis. Clouds can exert either a positive and negative feedback on climate depending on their shape, location, and composition. Shallow cumulus clouds have been challenging to measure due to their low elevation and transient nature. I’m looking for students interested in applying their skills in math, physics, or computer science to a real-world earth science application.

Prerequisites:
Students should have some computer programming experience, such as CS-171 or beyond. It is desirable to have taken at least one GEOL course. 

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Mathematical and Computer Science

 
16. Discretizations of boundary value problems

Principal Investigator: Paul T. Allen

Boundary value problems for differential equations arise in a number of common physical and mathematical contexts. In order to construct numerical approximations of solutions to boundary value problems, one must consider discrete approximations. In many common circumstances, the original differential equations problem has a mathematical property called the “Fredholm property.” If it is well-posed, the corresponding discrete approximation also has the Fredholm property. Since discretizations of boundary value problems are finite dimensional, establishing the Fredholm property involves only techniques from the linear algebra course. However, establishing the Fredholm property for differential equations is a much more technical matter. The purpose of this project is to investigate whether one can deduce the Fredholm property of certain boundary value problems from the Fredholm property of the corresponding discretization.

Prerequisites:

  • Prospective researchers are required to have completed Math 225 Linear Algebra and Math 341 Real Analysis.
  • Completion of Math 305 Calculus 4 and Math 442 Advanced Topics in Analysis and Topology is highly desirable.
 
17. Hitting Times for Generalized Ehrenfest Urn Models

Principal Investigator: Yung-Pin Chen

The original two-urn Ehrenfest model can be represented by a random walk on a graph for describing the diffusion of gas molecules between two isolated bodies.  For a random walk on a graph, the hitting time from node A to node B is the minimum number of steps the random walk takes to reach node B for the first time when the random walk initially starts at node A.  The expected hitting times associated with the two-urn model are well studied, but little work is known for the multiple-urn model.  This project is to investigate how to compute numerous expected hitting times under the generalized multiple-urn Ehrenfest models.  In particular, we will explore the electric network approach in our investigation.

Prerequisites:
Students are expected to have basic working knowledge of discrete mathematics, matrix algebra, and probability.  Computer skills (experiences in Mathematica or R) are a plus.

 
18. Machine Learning and Visual Analytics for Environmental Science

Principal Investigator: Peter Drake

Environmental science has entered the age of Big Data. Between elaborate sensor networks (both on satellites and at the Earth’s surface) and complex simulations, modern data sets sometimes contain billions of points. Each point associates many coordinates (three spatial, one temporal, plus simulation or policy parameters) with many values (temperature, pressure, moisture, density of plant and animal life, etc.). Using cutting-edge techniques from machine learning (e.g., deep convolutional neural networks) and data visualization, this project builds tools to help environmental scientists analyze these rich data sets and communicate their findings to community members and policymakers.

Prerequisites:

  • Required: Facility with the Python programming language and at least one programming course beyond CS 172.
  • Desired: Familiarity with the Python libraries NumPy, MatplotLib, and TensorFlow. Experience with software development techniques such as unit testing and version control (Git). Environmental science coursework or experience.
 
19. Capture-the-Flag Challenges that Enhance Cybersecurity Analysis Skills

Principal Investigator: Jens Mache

Cybersecurity analysis skills are of growing importance due to our increasing reliance on computers and networks. Current security exercises typically lack interactive, experiential components and configuration flexibility. This project seeks to develop a series of configurable cybersecurity scenarios, the infrastructure necessary for running them, and documentation that explains security implications. Scenarios may include capture the flag, web applications, malware analysis, data science, firewalls, buffer overflows, recover the network and intrusion detection.

Prerequisites:
CS-495 Cybersecurity and/or CS-393 Networks and Web Development

 
20. Mathematics of relativistic point particles

Principal Investigator: Iva Stavrov

It is somewhat common to treat a physical body as a cumulative effect of a big number of point particles. It might sound very surprising that such a line of reasoning is not commonly applied in the relativistic context. The reason for this is that the very idea of point particle is problematic in general relativity! Very roughly speaking, one cannot stuff a blob of mass into too tiny of a space without forming a black hole. This project will contribute to an ongoing effort of finding mathematical mechanisms for dealing with point particle limits in different physical contexts.

Prerequisites:
Students participating in the project will need to:

  • Be completely fluent in the language of multivariable calculus (MATH 233) and linear algebra (MATH 225).
  • Have exposure to the theory of (partial) differential equations through classes such as MATH 442: Advanced topics in topology and analysis and / or MATH 305: Calculus IV.

Preference will be given to students who are familiar with the content of MATH 490: Curvature of Space and Time. Sophomores with interest in both math and physics are particularly encouraged to apply.

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Physics

 
21. Strings in compactified gauge theories

Principal Investigator: Mohamed Anber

The strong nuclear force is responsible for confining the quarks inside the nucleons. However, we still do not fully understand why confinement happens, thanks to the complexity of the mathematics that describes this force. One of the ways to simplify the mathematical description is to compactify one of the spatial dimensions over a circle. This enables us to analytically compute various physical observables that are otherwise very complicated to compute. The purpose of this project is to study the nature of the confining flux tube (string) between two quarks in compactified theories.

Prerequisites:

  • PHYS 252 (Thermal Physics)
  • PHYS 380 (Field Theory)
  • Strong programming skills
 
22. Investigations of the Acoustics of the Mandolin

Principal Investigator: Stephen Tufte

We continue a broad-based experimental study of the acoustics of the mandolin. We will further investigate the complex coupling of the motions of the doubled strings using high-speed video and the musical implications of these interactions will be elucidated. Measurements of the sound spectrum and bridge impedance combine to characterize the transfer of mechanical energy from string motions through the bridge to the motions of the instrument body that ultimately produce sound. Experiments to understand in detail the connection between the mechanical properties of the bridge and the resulting sound spectrum aim to identify potential improvements in bridge design. Details of the resulting body motions, the modes of vibration, will be studied using holographic interferometry.  

Prerequisites:

  • Preference for students equipped with skills learned in Physics 201: Experimental Methods in the Physical Sciences
  • Other useful experience: computer skills, optics, differential equations, Physics 451.

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Psychology

 
23. Psychophysiological Responses to Racial Passing Behavior

Principal Investigator: Diana J. Leonard

Racial passing–presenting oneself as a race other than one’s own–is often viewed negatively (Dawkins, 2012), but the reason is unclear. Thus far, our lab has shown that passing as a member of a lower status racial group (i.e., as Black) is more morally condemned than the reverse (i.e., passing as White). We have also demonstrated that people who endorse Colorblind ideology judge racial passing more harshly, perhaps because it threatens their core beliefs. In our next step, we will measure stress and cognitive depletion to examine why people find racial passing to be morally condemnable under these circumstances.

Prerequisites:
Psy 200 (Stats) and 300 (Research Methods) are highly recommended; Psy 260 (Social Psychology) is preferred.

 
25. Motivating Walking through Social Referencing and Data Visualization with Activity Trackers.

Principal Investigator: Erik Nilsen

We are developing a web-based app that uses fit-bit activity trackers and a google map-based competition to motivate people to maintain a healthy level of physical activity.  Teams of LC community members will create self-designed Google-Map based competitions using fitbit activity trackers! Last summer we found that using the app with the full feature set and an experimenter-defined competition increased activity by 27% over baseline.  The study this summer continues to explore the impact of social referencing while extending the customizability of the app to allow users to set up their own routes, participants, and motivators to increase their level of engagement.

Prerequisites:
Experience in either Behavioral Research and/or computer Programming.  This can be met through coursework (Psy 300 or CS 171/172) or other experience.

 
25. Relating Eating “Styles” and Cognitive Control Over High- and Low-Calorie Food Cues in College-Aged Adults and Young Children

Principal Investigator: Todd D. Watson

We will relate potentially healthy and unhealthy eating habits (“styles”) with cognitive/behavioral responses to food-cues in two populations. In adults, we will explore interrelationships between eating styles, responses to high- and-low calorie food-cues during two cognitive control paradigms, and food consumption during a post-test snack. Separately, we will explore interrelationships between young children’s performance on a simplified food-cue task and their eating styles, physical risk-taking, and parents’ feeding habits. In all, we hope to determine if healthy eating styles are linked to better cognitive control over distracting food-cues, and if the opposite pattern is found for potentially unhealthy eating styles.

Prerequisites:
It is highly preferred (but not required) that students have previous experience with cognitive/neuropsychological testing, task development/programming, and/or experience working with young children (ages ≈ 3-6 years).

 

For more information:

Amy Timmins
Administrative Coordinator
timmins@lclark.edu