Volume 19, Number 1

Fall 2002 Research Bulletin of the Supercomputing Institute

2002–2003 Research Scholars

Each year, the Supercomputing Institute hosts a group of research scholars at the University of Minnesota. In the 2002–03 academic year, ten research scholars are working closely with principal investigators of the Supercomputing Institute on projects partially funded by the U.S. Department of Energy, the National Aeronautics and Space Administration, the National Institutes of Health, and the National Science Foundation.

Serkan Erdin is working with Professor J. Woods Halley, Department of Physics and Supercomputing Institute Fellow. His project involves direct dynamics simulations of the water-oxide-metal interface, beginning with codes developed by the Halley group for liquid water and the metalmetal oxide interface. The simulations will be used to study water structure and possible hydrolysis at the water-oxide interface as well as vacancy and interstitial transport in the oxide in order to understand the processes of passive film formation and breakdown.

Dacian Daescu, Institute for Mathematics and Its Applications, is developing computational tools and associated software for assimilation of atmospheric measurements into chemical transport models (CTMs). CTMs are designed to describe physical and chemical processes in the atmosphere and their integrated impacts on atmospheric pollutant concentrations. Dr. Daescu is working with Professor Fadil Santosa, School of Mathematics.

Chetan Gadgil is working with Professor Hans Othmer, School of Mathematics and Supercomputing Institute Fellow. Dr. Gadgil is extending an existing two-dimensional model for limb development to incorporate new molecular information about the mechanism of limb development and to develop a three-dimensional geometrically realistic computational model. This will enable a realistic simulation of the limb development process, and thereby provide a computational tool that can be used to explore the effects of various mutations and experimental interventions on the growth of the limb and the pattern of gene expression.

William Herb of the St. Anthony Falls Laboratory is working with Professor Heinz Stefan (Department of Civil Engineering and Supercomputing Institute Associate Fellow) to study macrophyte growth in relation to light, temperature, and turbulent transport of dissolved gases in lakes. Rooted macrophyte (vascular plant) beds in shallow lakes and the littoral zone of deeper lakes can have a significant impact on both lake ecology and water quality. Dr. Herb is developing mechanistic relationships between rooted macrophytes and the distribution of light, temperature, and dissolved gases within the water column in lakes, using a dual approach of experimental measurements and mathematical modeling.

Giuseppe Fadda is performing research on the development of multiscale methods for the passage of atomic to continuum scales, especially for problems in materials science. He is working on two specific projects. In the first, he is developing the theory of “Effective Hamiltonians” to make it a more accurate research method. The second project involves the time scale problem in transforming materials. Dr. Fadda is working with Professor Mitchell Luskin (School of Mathematics and Supercomputing Institute Fellow) and Professor Richard James (Department of Aerospace Engineering and Mechanics).

Emmanuel Lorin de la Grandmaison is working with Professor Yousef Saad, Department of Computer Science and Engineering and Supercomputing Institute Fellow, to develop new algorithms for scalable modeling in materials science. The goal of this research is to introduce new methodologies that bypass computational limitations of current techniques for predicting properties of materials. The excessive cost of the traditional eigenvector-based approach, both in terms of memory requirements and computations, severely limits the capabilities of current electronic structure codes. The project focuses specifically on techniques that avoid eigen-bases while at the same time offering the same functionality as eigenvector-based methods.

Yuri Nesmelov is working with Dr. David D. Thomas (Department of Biochemistry, Molecular Biology, and Biophysics and Supercomputing Institute Fellow) to investigate the computational design of microwave devices for biophysical magnetic resonance. The goal of this research is to achieve a dramatic improvement in the sensitivity of biophysical electron paramagnetic resonance (EPR) spectroscopy. The approach is to design dielectric inserts to be used with standard commercial cavity resonators.

Tina Poulsen is working with Professor Jiali Gao, Department of Chemistry, and Professor Donald G. Truhlar, Department of Chemistry and Supercomputing Institute Director. Her project investigates the operation of short-chain and medium-chain acylcoenzyme A dehydrogenase. This enzyme catalyzes the oxidation of straight-chain fatty acyl-coA thioesters to trans-2,3-enoyl-CoA derivatives with accompanying two-electron reduction of enzyme-bound flavin adenine dinucleotide. Dr. Poulsen is applying new multi-dimensional dynamical methods incorporating quantum mechanics to the calculation of the reaction rate, the free energy of activation, and the kinetic isotope effects.

Joseph Resovsky, who is working with Professor David Yuen (Department of Geology and Geophysics and Supercomputing Institute Fellow), is investigating the threedimensional velocity and density structure of the earth seen by long-period seismic data. This project uses the neighborhood algorithm to directly explore model probabilities in the multidimensional space in which mantle density and velocities are parameterized in radial layers and expanded in spherical harmonic coefficients.

Dongsu Ryu is working with Professor Thomas W. Jones (Department of Astronomy and Supercomputing Institute Fellow) on problems in computational astrophysics. The primary goal of this research is to incorporate into Dr. Ryu’s state-of-the-art cosmological code the Jones group’s powerful tools for simulating the transport of diffuse relativistic plasmas self-consistently within nonrelativistic plasma flows. Dr. Ryu will also use the code as a tool to explore some of the most important scenarios for generation of relativistic plasma and to study the emissions and observable properties of simulated clusters in order to compare them to real observations of physical clusters.