Supercomputing Institute Research Bulletin Newsletter of the University of Minnesota Supercomputing Institute Volume 13 Number 4 Spring 1997

In This Issue: 1997 Summer Undergraduate Intern Program Rational Drug Design Workshop Rayleigh-Taylor Instability How Alumina Phases Impact the Ruby Scale Turbulent Flow and Hypersonic Vehicles Origin 2000 Arrives Seminar Synopses Research Reports 1997 Summer Undergraduate Intern Program This June, students from around the country arrived at the University of Minnesota Supercomputing Institute to begin 10-week summer internships in biophysical computing and computational dynamics. The twelve interns, who were selected from a pool of 143 applicants, work closely with University of Minnesota faculty members on various research projects. During the summer, interns work full-time, immersing themselves in high-performance computing research as it relates to their fields of interest. The internship program, which is in its seventh year, is sponsored by the Institute and the National Science Foundation's Research Experiences for Undergraduates program. Intern Projects Chris Hart, a junior from Siena College in Loudonville, N.Y., is a mathematics major working with Professor William Gleason in the Department of Laboratory Medicine and Pathology. Hart is working on homology modeling studies of the GLUT-1 glucose transport system. He is helping to investigate two proposed structural models for this important transport system. The first is a classical membrane-spanning helix arrangement, and the second involves a beta-sheet configuration. Understanding such systems is important for designing drugs that may cross the blood/brain barrier. Ben Anderson, a junior from Gustavus Adolphus College in St. Peter, Minn., is a computer science major working with Professor William Gleason. Anderson's project is directed at understanding how sulfated and sulfonated materials interact with proteins. One application of this research is in understanding anticoagulant activities of heparin. Numerous other important physiological events, such as neurite outgrowth, wound healing, and tumor metastasis involve the interaction of sulfated carbohydrate derivatives with proteins. Some promising AIDS drugs, also, are sulfonated materials. Anderson is helping investigate the molecular mechanism for these diverse activities, with the aim of determining how to model them. Elijah Newren, a University of Utah junior, is a mathematics and computer science major who is working with Professor David Thomas in the Department of Biochemistry (Medical School). Newren is receiving training in large-scale computing with the Cray C90 computer, including programming, communications, data analysis, and graphics. His project is to examine the molecular (protein) motions that produce force in muscle contraction and that can be detected by spectroscopic probes. Analysis of this data requires the simulation of the spectroscopy experiment by solving numerically (and iteratively) a large system of differential equations. Andrew Howard, a Massachusetts Institute of Technology junior, is a physics major working with Professor J. Woods Halley in the Department of Physics and Astronomy. His project is to examine the scattering of atoms from very dilute Bose-condensed gases. Howard is helping to calculate the scattering rate of atoms in order to analyze the expected results of a new kind of experiment on the recently discovered Bose-condensed alkali gas. Matt Anderson and Eric Johnson are both working on a project with Professor George Wilcox of the Department of Pharmacology. Anderson, a computer science major, is a junior from Gustavus Adolphus College in St. Peter, Minn. Johnson, a biology and computer science major, is a junior from Augsburg College in Minneapolis, Minn. The two are working on simulation and graphic visualization of a realistic neuronal model, using both vector (Cray C90) and parallel supercomputers (Cray T3E). Models of both individual and interconnected neurons will provide an unprecedented level of structural and functional detail and complexity. The group is extending previous modeling efforts by other researchers by breaking each neuron into smaller membrane elements and by including active, nonlinear conductances and long-term biochemical processes in the model. Jeffrey Chu, a Boston University freshman, is a biomedical engineering major working with Professor Edward Egelman in the Department of Cell Biology and Neuroanatomy. Chu is using three-dimensional reconstructions from electron micrographs to understand molecular motions in protein polymers. The Egelman laboratory has been concentrating on two biologically important protein polymers-actin and RecA. The research is generating a wealth of structural information that is advancing the understanding of the function of these molecular assemblies. Brian Zaugg, a senior from Brigham Young University in Provo, Utah, is a computer science major working with Professor Leonard Banaszak of the Department of Biochemistry (Medical School). He is working on computer-assisted interpretation of X-ray diffraction data in protein crystallography. Proteins are biological macromolecules containing thousands of atoms. Their biological function-or sometimes malfunction-is determined by their three-dimensional structure. Therefore, protein structural data is important to all aspects of molecular biology, especially the area of computer-assisted drug design. Dana Goodman, a University of Minnesota junior, is a mathematics major working with Professor David Yuen of the Department of Geology and Geophysics. She is working on determining the fractal dimensions of deformed line boundaries in turbulent convection. She is calculating fractal dimension as a function of time for the deformed boundaries. This will yield valuable information concerning the style of mixing in thermal convection with complicated rheologies. Darrell Hurt, a Brigham Young University junior, is a chemistry major working with Professor Donald Truhlar of the Department of Chemistry and visiting research associate Professor Laura Coitiño. The group is developing new computational chemistry software for direct dynamics calculations. Their goal is to develop an interface between the GAUSSIAN and POLYRATE programs that will allow researchers to include electron correlation effects in a localized part of a large reactant molecule at all points along a reaction path. This will allow the determination of variational transition states and multidimensional tunneling probabilities more accurately than in conventional methods. Jason Lang, a University of Minnesota junior, is a chemical engineering major working with Professors Donald Truhlar and Christopher Cramer, of the Department of Chemistry. Lang is using a self-consistent-field semiempirical solvation model to calculate the free energies of carbazoles and betacarbolines in aqueous solution and 1-octanol. The solvent 1-octanol is often used as a biomimic for cell membranes in rational drug design, and the partitioning behavior of organic molecules between the aqueous phase and a 1-octanol phase correlates well with the bioavailability of drug molecules. A long-term goal of this work is to design specific reaction parameters that allow computer modeling to predict the potential efficacy of potential drug molecules without the molecule ever having been made. Joseph Danzer, a junior from Harvey Mudd College in Claremont, California, is a chemistry major working with Professors Truhlar and Cramer. Danzer is using quantum mechanical molecular orbital theory to study the conformations of the sugar molecule, glucose. He is using a combination of high-level ab initio calculations for the gas-phase structures and the SM5 solvation model for the effect of the aqueous environment. He is studying both equilibrium structures and the saddle points connecting them, and the results will serve as benchmarks against which simpler models applicable to larger sugar molecules can be tested. Students who are interested in applying for next summer's internship program should check our website for upcoming application deadlines: http://www2.msi.umn.edu/Programs/uip/uip.html.

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