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Professors Lynda Ellis, Department of Laboratory Medicine and Pathology, and Larry Wackett, Department of Biochemistry, Molecular Biology and Biophysics, both MSI Associate Fellows, have co-directed the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) since 1995. The UM-BBD, hosted at MSI, contains information on microbial biodegradation pathways, primarily for environmental pollutants. The UM-BBD Pathway Prediction System (UM-PPS) predicts microbial metabolic pathways, to help scientists determine how microbes may clean up an environment contaminated with new chemical compounds. The image at left is part of a visualization of a UM-PPS prediction for the microbial degradation of 2-bromo-1,1-dichloroethane.
It’s not easy being a plant. There are any number of pathogens just waiting to attack you, and, being a plant, you can’t run away. Fortunately, plants can defend themselves, and the research group of Associate Professor Fumiaki Katagiri, Department of Plant Biology and MSI Associate Fellow, is studying how. Their cross-disciplinary research, which involves molecular biology, biochemistry, genetics, reverse genetics, genomics, expression profiling, proteomics, structural biology, and computational biology, investigates how plants recognize the molecular signals of pathogen attack and how they then coordinate their defense responses. This work may lead to disease-control methods safer for humans and for the environment. The image at left is a method of visualizing relationships among mutant plants.
The use of massively parallel computing on powerful machines has been a great benefit to many scientific researchers. Among these are the astrophysicists, who deal with enormous datasets as they study cosmic phenomena. Professor Tom Jones, Department of Astronomy and Interim Director of the Supercomputing Institute, and his research group have successfully developed a fully parallel code that scales to several thousand cores. Using this code, the group is able to create simulations of galaxy jets. The simulation shown is a 2000x2000x500 mesh simulation of a "narrow angle tail” galactic jet, which is due to a relatively weak jet in a strong wind; the picture shows the jet’s vorticity in log scale. This computation was performed on a cluster running Microsoft HPC Server 2008.
The MSI Undergraduate Internship Program wrapped up its 19th summer last month. Twelve undergraduates from colleges and universities around the country worked on projects in chemistry, physics, geophysics, astronomy, biochemistry, medicinal chemistry, and drug design. In this annual program, undergraduate interns participate in the research groups of MSI Principal Investigators on projects using high-performance computing environments, especially visualization and computer gr aphics; they prepare a report and give a presentation about their work. The graphic at left, from the presentation of in tern Robin Weiss of Macalester College, depicts convection in the earth’s mantle. More information about the 2009 intern program can be found in the Summer 2009 issue of the MSI Research Bulletin. Information about the Summer 2010 intern program will be posted here later in the fall.
The new I-35W bridge, which replaces the one that collapsed in 2007, includes sensors to investigate its structural behavior. Professors Catherine French, Carol Shield, and Henryk Stolarski of the Department of Civil Engineering are using MSI resources for a key aspect of the data interpretation, which is the development of a detailed finite element model (FEM) to investigate the static and dynamic properties of the bridge, including time-dependent effects. Monitoring the bridge should lead to a better understanding of the behavior of post-tensioned concrete bridges in the state of Minnesota and potential improvements in the methods for analysis and design of these systems, as well as to recommendations for instrumentation of future bridges.