2004 Rogers Science Program

Faculty Abstracts

Biology

Kellar Autumn, "Contact mechanics of natural and synthetic adhesive nanostructures"
Geckos climb using millions of adhesive setae. Our goal is to reveal how natural dry adhesives function, and how the performance of fabricated adhesives and climbing robots can be enhanced. Previously, we discovered that setae stick by van der Waals force. This summer we will study friction and adhesion mechanics in natural setae and use new artificial setae as a model system. This project has the potential for development of a synthetic adhesive that requires minimal attachment force, leaves no residue, detaches without measurable forces, is self-cleaning, directional, works underwater, in a vacuum, and on nearly every surface material and profile.
Prerequisites: Preference for students with courses in Physics. Solid quantitative skills required.

Paulette Bierzychudek, "Endangered butterflies, degraded habitats and diminishing returns for conservation? Developing a decision framework for when to 'give up' on restoring sites and species."
For over a decade, The Nature Conservancy has been attempting to restore a population of an endangered butterfly, the Oregon silverspot, at Cascade Head preserve. These efforts have not led to increased population numbers. One missing piece of information is how silverspot larvae respond to different densities of their violet hostplant. We will conduct greenhouse pilot studies of larval foraging, using larvae being captivity reared for release at Cascade Head. This information will allow us to make better estimates of the likelihood and probable cost of successful restoration, both of the Oregon silverspot and for other threatened species elsewhere.
Prerequisites: No course prerequisites

Greta Binford, "A phylogenic framework for studying the evolution of the toxic enzyme sphingomyelinase D in venom of brown spider (Loxosceles)"
Brown spider (Loxosceles) bites cause severe dermonecrotic lesions in human tissues. An enzyme in these venoms, sphingomyelinase D (SMD), is central to lesion formation. The genus Loxosceles includes 100 species from the Americas, Africa and Mediterranean Europe. Evolutionary relationships among these species are unknown. We will use molecular markers to estimate relationships among species of brown spiders and their relatives. Once relationships are known we will use this information for comparisons of venom characteristics among species. Results will help direct research toward understanding the evolutionary origin of the unique enzyme SMD, and improving treatment and diagnosis of bites.
Prerequisites: None

Ken Clifton, "Exploring the ecological consequences of gamete release by green seaweeds of coral reefs"
Tropical green seaweeds (Bryopsidales) release gametes directly into the water column during explosive pre-dawn bouts of sexual reproduction. Although these reproductive events presumably play an important ecological role within tropical marine communities, their causes and consequences remain poorly understood. An ongoing field study of these seaweeds examines the relationship between gamete concentration and fertilization as well as the fate of zygotes, once formed. Field-work will be conducted on algal populations in Caribbean Panama during from mid-May to late June. Follow up lab work will continue at Lewis& Clark through mid-July.
Prerequisites:Comfort with Spanish, snorkeling in the dark, working from small boats, and living under isolated, rustic conditions are necessary assets for this work.

Greg Hermann, "Genetic and molecular analysis of lysosome assembly and stability in C. elegans."
Lysosomes are membrane bound organelles that function as major degradative sites within cells. While much is known regarding the biochemical activities of lysosomes, the processes involved in their assembly and maintenance remain poorly understood. An understanding of these processes is important since the abnormal release of lysosomal contents is associated with a variety of human diseases including, Alzheimer, arthritis, and cancer. We are characterizing the function of three genes necessary for the assembly and stability of lysosomes in the model organism, Caenorhabditis elegans. Our work will focus on the genetic mapping and phenotypic characterization of these genes.
Prerequisites: Biology 200, 311/312 or 361

Gary Reiness, "Non-Classical Secretion of a Neurtrophic Protein"
To learn about mechanisms of protein secretion we study ciliary neurotrophic factor (CNTF), which is essential for development of the nervous system. Secreted proteins normally use the well-characterized “classical” pathway to exit from cells--moving sequentially through compartments called the endoplasmic reticulum, Golgi apparatus, and secretory vesicles before being released. A few secreted proteins, including CNTF, do not pass through this classical pathway. A better understanding of cellular communication requires a clearer picture of these “nonclassical” pathways. One student will use fluorescent microscopy of molecularly-tagged CNTF and markers of cellular organelles to identify the structures with which CNTF is associated. Another will study genetically modified versions of CNTF to identify the sequence of amino acids necessary for its secretion.
Prerequisites:Biology 200 is a minimum prerequisite. Preference will be given to students with advanced work in Molecular Biology (Bio 311/312), Cell Biology (Bio 361), or Biochemistry (Chem 330/335 and 336).

Chemistry

Niko Loening , "Methods Development for Nuclear Magnetic Resonance Spectroscopy"
Nuclear magnetic resonance (NMR) spectroscopy is a fundamental instrumental technique that has seen application to a wide range of problems, including chemical analysis, screening drug targets, the determination of protein structures, understanding fluid dynamics, and medicine (where it is known as magnetic resonance imaging). In comparison to other spectroscopic techniques, NMR has drawbacks in that it is relatively insensitive and advanced experiments can take a long time to complete. Our research this summer will focus on the development of techniques that can be used to reduce the experiment time and increase the sensitivity of NMR spectroscopy, including the design of new experiments, physical modifications of the instrument, and the study of advanced processing techniques for analyzing NMR data.

Prereq: Not all projects require all of the following skills, but it would be useful for students to have/be:

• A background in quantum mechanics (chemistry 320, physics 321, or equivalent)

• Comfortable with learning mathematics (no courses required, but must be willing to learn)

• Experience with computer languages (preferably C/C++) Basic chemistry laboratory skills

Computer Science

Peter Drake, "Data structures and Algorithms for the Game of Go"
We will devise and implement data structures and algorithms for a computer program to play the classical Asian game of Go. Creating such a program is an open problem in the field of artificial intelligence. While more complex than the usual “toy problems,” Go is more precisely defined than real-world problems such as robot control.

A successful Go program must reason separately about each area of the board. The techniques we explore for tackling such a partially decomposable problem will have applications to other areas of artificial intelligence, including planning, resource allocation, attention, and reasoning under uncertainty.
Prerequisites: Necessary: skill in computer programming using a language such as Java or C; our CS 172 course or the equivalent.
Helpful: Go-playing experience; knowledge of artificial intelligence or object-oriented programming.


Jens Mache, "Computer security and Internet research"
The Internet, computer networks and distributed systems are fascinating topics. Many challenges remain, including security, grid services, peer-to-peer algorithms, distributed storage and streaming media. This summer, we will investigate important performance, scalability and robustness issues.
This internship includes studying existing systems, writing software and experimentation with various designs and algorithms.
Prerequisites: Computer Architecture (CS 377) and Algorithms (CS 383) are desired.

Math Sciences

Yung Pin Chen, "Assessing statistical significances of DNA sequence segmentation and alignment"

DNA sequences code the information of life. Compositionally homogeneous segments of DNA sequences may correspond to some units with specific biological functions. On the other hand, DNA sequences can show rich heterogeneities. We will investigate meaningful representations that help visualize the heterogeneities in the base composition of DNA sequences. One of our goals is to detect the boundaries of compositionally or functionally homogeneous DNA segments and statistically quantify their biological significances. We also want to build alternate statistical models and explore improving algorithms for sequence alignments that are used for evolutionary modeling.

Prerequsites: It is essential that a participant should have strong problem-solving skills. It is preferred to have some background in genetics (Bio 151), molecular biology (Bio 200 or 311), computer programming (CS 171) and statistics.

Physics

Tom Olsen, "Characterization and Control of Spatio-Temporally Chaotic Pattern Dynamics in Taylor Vortex Flow"

Chaotic Dynamics is deterministic motion that is unpredictable, very sensitive to slight changes of initial conditions or system parameters. Brief periods of periodic, predictable motion occur. Control algorithms extend these periods indefinitely by slight variations of system parameters. Our group has successfully controlled a particular chaotic fluid flow experimentally, and we are now considering systems with more than once center of activity. Previous students have modeled the control of analogous systems and measured the strength of their chaotic dynamics. We will continue to develop means of measuring the strength of chaos and learning what Reaction-Diffusion models imply for our system.

Prerequsites: This research requires mastery of mechanics at the level of Physics 151-2. Mathematics at the level of Differential Equations (235) and Linear Algebra (225) would be valuable. Familiarity with the Mathematica™ computing environment and/or Computer Science (171 and beyond) would also prove valuable. Methods of Experimental Physics (201) would be extremely useful for students wishing to work on data acquisition.

Tom Olsen, "Acquisition and Modeling of Light Curves for Short-Period Eclipsing Binary Star Systems"

Most stars are members of groups of two or more stars. Many stars are found in binary pairs. If the plane of a pair’s orbit intersects the position of the Earth, the stars will appear to eclipse each other. Some have orbital periods as short as six hours. We propose to continue and extend to other star systems a program of measuring the light curves from such pairs, a program of 40 years standing. Measurements of the variation in the light intensity received from these eclipsing stars, allow us to model the properties and evolution of these stars

Prerequsites: This project requires some experience in stargazing and astronomy. A course in astronomy, such as Physics 105, or preferably 205, would be extremely valuable. Participants must have some familiarity with computerized data acquisition, such as Methods of Experimental Physics 201 provides.

Steve Tufte, "High-Velocity Clouds and Their Role in the Evolution of the Milky Way Galaxy"

The interstellar medium of our galaxy consists of very dilute material filling the vast spaces between the stars. It is the material from which stars form and into which they vent their material when they (sometimes violently) expire. The project is to explore a mysterious sub-component of this medium: interstellar clouds moving at high and unexplained velocities. These high-velocity clouds (or HVCs) are mostly made of hydrogen, can be up to 10 million times the mass of the sun and 10,000 light years across, and are moving toward us at several hundred kilometers per second. We will explore these HVCs using a remotely operable observatory called the Wisconsin H-Alpha Mapper (WHAM). We have established a Remote Observing Laboratory at Lewis & Clark from where we can command the WHAM instrument, located on Kitt Peak in Arizona, to make spectroscopic observations. There is recent evidence that these high-velocity clouds may represent primordial material falling onto the galaxy as part of on on-going formation process (see the article "Our Growing, Breathing Galaxy" in the January 2004 issue of Scientific American for more information). The goal is to better understand HVCs and their role in galactic evolution.

Prerequsites: Computer skills desirable