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A group of MSI researchers from several departments are combining their expertise and making exciting new contributions in the field of biomedicine. These collaborators, highlighted in the Fall 2010 issue of the MSI Research Bulletin, are from the Interactive Visualization Lab in the computer science and engineering department, St. Anthony Falls Laboratory, and the Medical Devices Center. The group uses MSI resources to create computational models to study fluid flow and to design medical devices. The image above shows simulated flow through a synthetic heart valve as it opens and closes with the beat of the heart inside of a patient-specific model of the left ventricle and aorta . A poster about this work was a finalist in the 2010 MSI Research Exhibition.
Computational chemists apply chemistry, mathematics, and computing to interesting chemical problems. Using efficient computer codes and fast, powerful machines, computational chemists can generate the properties of molecules and simulate experimental results. Highlights of the work of three computational chemists using MSI---Professors and MSI Fellows Chris Cramer, Jiali Gao, and Don Truhlar---appear in MSI's Annual Research Highlights 2010. The figure is an illustration detail from the Cramer group's research description. Because of the complexity of the problems, supercomputers are important to this branch of chemistry. Professor Cramer recently told us that the new Itasca system has increased his group's productivity several-fold.
AFTOL: Resolving the Evolutionary History of the Fungi is a project that involves researchers at ten universities and many collaborators in the mycological community. It will contribute to understanding the lineage of fungi---fungi phylogeny---at multiple levels and will promote training and education in fungal biology. In support of this project, the research group of Professor David J. McLaughlin (Plant Biology) is coordinating analysis of subcellular characters as well as studying molecular phylogenetics of selected species. Part of this project includes the development of a Structural and Biochemical Database. This database will become a major resource for the scientific community, managing and providing morphological and biochemical information on fungi and serving as a phyloinformatics tool.
The MSI Undergraduate Internship Program wrapped up its 20th summer last month. Eleven undergraduates from colleges and universities around the country worked on projects in chemistry, physics, geophysics, medicinal chemistry, biomedical engineering, astronomy, biochemistry, and chemical engineering. 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 graphics. They prepare a report and give a presentation about their work. The image above shows a docking simulation with the compound cephalosporin C, from the presentation of Aatif Mansoor, who worked with Assistant Professor Elizabeth Amin (Medicinal Chemistry, MSI Associate Fellow). Information about the Summer 2011 intern program will be posted on our website later in the fall.
MSI hosted two courses for graduate students and postdoctoral researchers during Summer 2010 in association with the Virtual School of Computational Science and Engineering (VSCSE). The VSCSE is a national virtual organization whose goal is to develop and deliver a computational science curriculum that accelerates the ability of faculty, staff, and students to use emerging computational resources to advance science and engineering. The Petascale Programming Environments and Tools course was held July 6-9. Graduate students Jagan Jayaraj and Pei-Hung Lin presented their experience scaling a gas-dynamics code up to 100,000 cores (picture above) during this course. The Big Data for Science course was held July 26-30.