Projects 2014

Haiyan Cheng, Assistant Professor of Computer ScienceCheng

Estimation of partially observable dynamic phenomena, such as weather or macroeconomic systems, is an important problem in the physical and social sciences.  We have complete solutions to simple versions of such problems, and a variety of incomplete solutions to the more complex types, when the chance elements of the phenomena do not follow the "bell-shaped" curve that captures the so-called normal statistical distribution. Depending on the area of application, the solutions are called data assimilation procedures, or filters, and come in various flavors such as ensemble filters, particle filters, and four-dimensional variational filters or methods.   

My current research project is to improve the function of particle filter method by tackling the particle degeneration problem. The outcome of the research will lead to improved nonlinear forecast simulation models. For this SCRP project, the participating students will start with critical literature reading to understand the background and research problem, followed by algorithm implementation and numerical simulations and analysis. The research activities will enhance students' programming proficiency and problem solving ability. Diverse fields of applications of the underlying algorithm such as geoscience, artificial intelligence, finance will provide students with motivation and perspective for future research career.

Emma Coddington, Assistant Professor of Biologycoddington

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Andrew Duncan, Associate Professor of Chemistryaduncan

Information to come...


Jason Duncan, Assistant Professor of Biologyjduncan

The transport of proteins, mRNA transcripts and organelles within a cell facilitates their localization to discrete cellular domains. This is especially critical in neurons: chemical messages synthesized in the cell body must be delivered through the axon to the distant synapse. This distance poses a significant challenge for the neuron, as the length of the axon is orders of magnitude the width of the cell body. The neuron employs a microtubule-based transport system to actively transport these chemical messages along its entire length. In Drosophila melanogaster larvae, the segmental nerve is ideal for studying axonal transport. Segmental nerve bundles emerge from the brain and bilaterally innervate the body wall musculature of each larval segment. They are easily accessible, narrow, extremely elongated and the microtubules within the axon are polarized, thus transport occurs in intrinsically defined directions. Research conducted in my lab will employ a genetics based approach in Drosophila to identify novel components of microtubule-based axonal transport. The identification of genes involved in axonal transport in Drosophila is facilitated by the fact that mutants defective in the process have a characteristic crawling defect in which the larval tail flips upwards, and transported synaptic vesicles accumulate as axonal clogs in the axons. Participation in this research will provide undergraduate students with a broad exposure to laboratory techniques in Genetics, Neurobiology and Molecular and Cell Biology.

Alison Fisher, Assistant Professor of Chemistryajfisher

Plants exchange hundreds, if not thousands, of diverse volatile (gaseous) organic compounds (VOCs) with the air around them. Although we generally can't see it, plants emit millions of tons of reactive organic carbon into the air each year, significantly impacting the chemistry of the lower atmosphere. As a result of the environmental impacts of VOC emissions from plants, the atmospheric processes these compounds participate in have been the subject of intense research for the last two decades. The biological questions surrounding these emissions have received less attention and, as a result, are less well understood. Students collaborating with me this summer will use classic biochemistry techniques combined with modern molecular genetic methods to answer some of the outstanding questions about plants and the volatile compounds they make.

1. How does the volatile hormone ethylene influence the timing of plant flowering?

Ethylene (ethane; C2H4) is a volatile plant hormone that affects virtually every developmental process in plants, from seed germination and root hair growth to fruit ripening and the senescence of leaves and flowers. Its role in the timing of plant flowering, the critical developmental switch from vegetative growth to reproductive growth, is not well understood. We are using reverse transcription coupled with quantitative polymerase chain reaction (RT-qPCR) to analyze ethylene's regulation of key flowering time genes in two model plants: Arabidopsis thaliana (thale cress) and Ipomoea nil ‘Violet' (Japanese morning glory). Furthermore, we are using chromatin immunoprecipitation (ChIP) assays to address the role of epigenetics in ethylene's regulation of flowering time in these model plants.

2. Why do plants make isoprene?

Isoprene is the most abundant reactive VOC produced by plants and, despite almost twenty years of research on isoprene production, why plants make it is still a matter of intense debate. With our collaborators at Portland State University, we are exploring the use of moss as a model system to better understand biogenic isoprene production. To this end, we are using classic protein chemistry methods and gas chromatography to isolate and characterize an isoprene-producing enzyme (isoprene synthase) from the model moss Campylopus introflexus (heath star moss).

Inga Johnson, Associate Professor of MathematicsJohnson

Information to come...


Susan Kephart, Professor of Biologyskephart

   with Post-Doctoral Scholar, Dr. Kathryn Theiss

Plants show astounding diversity floral color, shape, and scent, so decoding these traits and their functions is like solving a good mystery! It is challenging yet essential to the practices applied daily in agriculture, conservation, and medicine. The undergraduate students who join our team will use novel approaches and discovery-driven hypotheses to compare the morphology, pollinators, and ecological niches of camas (Camassia) and rush lilies (Hastingsia). While conducting field work in several states, we will track flowering times, observe the responses of pollinators to experimentally manipulated and natural flowers, and design crossing experiments among species. Students must be prepared to work and hike under varied field conditions in wet or dry meadows and woodlands. Student effort typically spans a major part of the mid-May through mid-July field season, with some options negotiable.  There are also opportunities for split summer and academic year positions or to extend research through the academic year via a research thesis or other options. 

Student research associates join a multi-institutional collaborative team linked to undergraduates at two other universities nationwide. Your input is expected in developing the study, analyzing and interpreting data, and writing reports. You will work alongside peers, and faculty mentors as we learn and share the best practices of science, from poster design to talks & scientific writing. 

Broad goals: In addition to exploring species boundaries, we aim to extend understanding of the ecological and cultural value of plants today and for indigenous peoples, develop new keys for identifying rare and common plants, and contribute insights that will improve conservation efforts. 

 Michaela Kleinert, Assistant Professor of Physics kleinert

Ultrafast industrial laser system and ablation studies
Ultrafast lasers have become valuable tools in medicine, research, and industry. My research lab has recently received a generous donation of a picosecond pulsed laser system ("Duetto" by TimeBandwith) from Electro-Scientific Industries in Beaverton, OR. Together with a scan lens system (funded by a Hewlett grant in 2013), we are able to precisely move the laser beam over the work surface to systematically explore the effect that various laser parameters or drilling techniques have on a variety of samples. Samples are analyze using Willamette's Scanning Electron Microscope. 

Josh Laison, Associate Professor of Mathematicslaison

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Peter Otto, Associate Professor of Mathematics

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Chris Smith, Assistant Professor of Biology


Coevolution is a process of reciprocal evolutionary change, through which two or more species adapt to each other. Coevolution may be involved in an enormous variety of ecological interactions, from African gazelles trying to outrun cheetahs, to the origin of new flu strains each year. Work in our lab examines coevolution in an obligate pollination system - the interaction between the Joshua tree (Yucca brevifolia) and the yucca moths that are their exclusive pollinators. Both the moths and the trees are entirely dependent on one another for reproduction, and morphological features of the moths and the flowers that they pollinate fit together like a lock and key. Our lab seeks to understand whether and how reciprocal natural selection - as opposed to other, non-adaptive evolutionary processes - have produced the remarkable fit between this iconic desert plant and the insects on which it relies. We combine the traditional tools of field biology - field research in the Mojave Desert - with manipulative experiments, population genetics, and genome-wide-association studies to measure natural selection using both direct and indirect approaches.

Chuck Williamson, Professor of Chemistrywilliamson

In the Williamson research group, we use lasers to probe the chemical and physical properties of molecules. One major area of interest for us is the behavior of partially-miscible binary liquid mixtures. These are mixtures of two liquids, such as methanol and carbon disulfide, that are completely miscible above a certain critical temperature, but separate into two layers for certain composition ranges below that temperature. These separate layers, or phases, are also mixtures of the two liquids, but with differing compositions. We use elastic light scattering to make a map of the macroscopic behavior of binary liquid mixtures. This map is called a phase diagram, and shows the temperature boundary between one-phase and two-phase behavior as a function of composition. We use Raman spectroscopy, a type of inelastic light scattering, to probe the microscopic behavior of binary liquid mixtures. Raman spectroscopy provides a vibrational fingerprint of molecules, which in turn yields information about the spatial arrangement of molecules in the liquid. We record Raman spectra as a function of temperature and composition in the one-phase region, paying special attention to samples near the critical point. We have also used nuclear magnetic resonance spectroscopy as a third experimental method for probing liquid-liquid mixtures.