University of Minnesota Supercomputer Institute

Undergraduate Intern Summer Research Projects are Underway

The new summer undergraduate interns and their faculty advisors met on June 13 for a luncheon at the Supercomputer Institute. The event kicked off the 1995 Summer Undergraduate Internship Program in Scientific Computation and Graphics and provided an opportunity for the interns to meet one another and discuss their projects.

There were 216 applications for this summer's program and appointments were made for 31 applicants. Of those appointed, nine were from outside of the state of Minnesota, supported by the National Science Foundation, three were from Minnesota colleges other than the University of Minnesota, and 19 were from the University of Minnesota. The students from Minnesota are supported directly by the Minnesota Supercomputer Institute and also by the National Science Foundation.

Description and History of the Program

The Supercomputer Institute's Undergraduate Internship Program in Scientific Computing and Graphics was started in 1990. It provides special opportunities for undergraduate participation in the Supercomputer Institute's state-of-the-art research programs. Since its inception, there have been 46 different interns appointed during the academic year and 110 interns appointed during the summer sessions. During the academic year these appointments are part-time, and are available to University of Minnesota undergraduates while they take courses.

The program's objective is to promote and help support undergraduate involvement in ongoing and new supercomputing research and in software development efforts for scientific computing and graphics support. The Supercomputer Institute's goal is to attract talented undergraduates toscience and engineering careers, to encourage undergraduates to attend graduate school in science or engineering, and to enhance undergraduate education.

All student interns work closely under the direction of their project supervisor, who is a University of Minnesota faculty member. The interdisciplinary program involves several departments and colleges of the University of Minnesota. Institute-funded positions are open to undergraduates at the University of Minnesota for both academic year and summer appointments. National Science Foundation-funded positions are open to these students and to undergraduates at colleges and universities from outside of the University of Minnesota system for summer appointments on the University of Minnesota campus.

Project Updates

Following is a listing of the summer interns, their project supervisors, and brief descriptions of the research in progress halfway through the summer.

Michael R. Booth, a junior at the University of Minnesota majoring in Electrical Engineering is working on a project entitled "The Dynamics of Renal Circulation." Booth is working on this project with supervision from Dr. Carl S. Smith, Adjunct Professor of Surgery at Hennepin County Medical Center. They are investigating the renal arterial circulation system based on the geometry of the arterial tree.

Peter Braaten, a sophomore at the University of Minnesota majoring in Mathematics and Computer Science is interning on a project supervised by Professor Yousef Saad, of the Department Computer Science. The project is titled "Sparse Matrix Visualization Tools" and was begun last summer. Last summer's project entailed creating an interpreted programming language specifically designed for manipulating sparse matrices. Goals for this summer include increasing the speed when performing certain kinds of computations, devising an improved memory-management strategy, increasing portability, and making the code easier to maintain. Braaten has found that he has to take a new approach for implementing the interpreter. The interpreter can now evaluate most expressions, and Braaten is working on implementing various control structures.

Dola A. Bye, a senior from the University of Michigan majoring in Computer Science is working on a project with Professor David Levitt of the Department of Psychology, entitled "Development of Programs for Graphical Display and Mathematical Refinement of Protein Crystallographic Data." Bye's first task was to write a C program that interfaced with a FORTRAN program. The purpose was to convert a CCP4 (a commercial FORTRAN software package) output file into the internal representation that MAID (a C progam written by Professor Levitt) uses. She is now working on converting the graphics portions of MAID from IRIS GL to OPEN GL and X. OPEN GL calls will perform the drawing functions, while X calls will handle all of the windowing aspects.

Daniel S. Clark, a sophomore from Dartmouth College majoring in Physics, Steven J. Ford, a senior at the University of Minnesota majoring in Aerospace Engineering and Mechanics, and Matthew Litke, a junior at the University of Minnesota majoring in Aerospace Engineering and Mechanics are all interns on a project entitled "High-Performance Finite Element Computation and Visualization of Engineering Applications in Fluid Dynamics" The research is directed by Professor Tayfun E. Tezduyar, Department of Aerospace Engineering and Mechanics.

The past several weeks of Daniel Clark's internship have been devoted to the development of FORTRAN code for the finding of isosurfaces (surfaces of constant pressure, temperature, etc.) in tetrahedral finite element meshes. With the recent completion of the code, Clark has begun a new project involving the analysis of data simulating droplet formation in the passage of a gas stream over a liquid.

Steven Ford has been working on a particle trace program that reads mesh information and graphically displays selected boundaries. The program then generates a single particle at a random location within a specified starting area. This particle moves through the mesh tracing the fluid flow based on velocity data generated during the computational fluid dynamics solution.

Matthew Litke has been involved in a number of projects at the Army High Performance Computing Research Center. The main problem that he has been working on involves the simulation of a foreign gas entering a flow field around an M1 battle tank.

Michael C. Dennis, a sophomore at Northwestern University majoring in Chemical Engineering is working with Dr. Andrew Yeckel, of the Department of Chemical Engineering and Materials Science at the University of Minnesota, on a project entitled "Developing Visualization Software for Finite Element Models of Materials Processing Systems." A primary goal of the project is to visualize computer simulations of flow in a system to grow single-crystal potassium dihydrate phosphate (KDP) from solution. The ultimate goal of the project is to produce an animated movie of moving particles representing fluid flow around a KDP crystal. Dennis has been working on a program to convert simulation data from a parallel CM-5 format to one that the graphics application requires. The faculty supervisor is Professor Jeffrey J. Derby, Department of Chemical Engineering and Materials Science.

Dale J. Durham, a junior at the University of Minnesota majoring in Pharmacy is working on a project entitled "Biomolecular Structure and Dynamics: Force Field Development." Durham is using micellular modeling to build models of cholesterol and sodium taurocholate. The faculty supervisor is Professor David Ferguson of the Department of Medicinal Chemistry.

Nathan E. Endrud, a sophomore at the University of Minnesota majoring in Physics, is working on a project entitled "Numerical and Graphical Analysis of Simulation Data on Electrochemical Reactions" project with Professor J. Woods Halley from the School of Physics and Astronomy. Endrud has been working with Halley's research group on modeling transport in lithium polymer batteries. His primary task has been performing ab initio calculations using the electronic structure software package GAUSSIAN 92.

Andrew A. Engel, a senior at Hamline University majoring in Physics and Mathematics and Joseph B. Gaalaas, a junior at the University of Minnesota majoring in Physics, are both interns on a project entitled "Simulation of Diffusive Transport of Energetic Particles in Compressible Cosmic Fluids." The project is supervised by Professor Thomas W. Jones of the Department of Astronomy. Andrew Engel has been working to address the limitations inherent in a numerical simulation of an astrophysical jet. Gaalaas spent the first half of his summer internship putting the final touches on the two-dimensional magnetohydrodynamics project that he has been working on with Professor Jones and Dr. Adam Frank. This has included the creation of VHS and MPEG movies of the simulation and a World Wide Web home page to exhibit the latter.

Jeremy M. Goldblatt, a junior majoring in Electrical Engineering is working with Professor Phil I. Cohen of the Department of Electrical Engineering on a project entitled "Growth Simulations of Wide Bandgap Nitrides." Their research is aimed at improving crystal growth techniques used in the production of advanced electronic materials.

Blayne D. Green, a junior at the University of Minnesota majoring in Chemical Engineering, and David J. Hearn, a senior at Carleton College majoring in Biology, are working on a project with Professor George L. Wilcox of the Department of Pharmacology entitled "Use of a Large Neural Network to Predict Protein Structure From Sequence." Green has studied the UNIX operating system and C++ programming. He will spend the latter part of his internship using molecular modeling packages and the neural network to approximate three-dimensional structure from sequence information only.

David Hearn has investigated one method of relatively rapid protein structure determination using XPLOR. The research group will later examine the function and structure prediction with a neural network.

Jennifer M. Green, a sophomore at the University of Minnesota majoring in Computer Science is working with Professor Balkrishna (Radha)Radhakrishna, Department of Accounting, on a project entitled "Topics in Information and Financial Markets II-Empirical Investigation of Investor Behavior." The project aims to test theories of trading volume and study differences in trading behavior on the part of major market players, such as institutional investors and specialists, in response to new information that is not available to all market participants.

Brent T. Harrold, a junior from Gustavus Adolphus College majoring in Physics, and Tahirih C. Lackey, a sophomore from Jackson State University majoring in Physics and Chemistry, are working on a project entitled "Simulation of Chemically Reacting Flows" with Professor Graham Candler of the Department of Aerospace Engineering and Mechanics. Harrold is examining the chemical reaction N2->N + N that occurs in hypersonic flows. This reaction is being examined using a six-equation method and a fifty-equation method, to determine if the six-equation yields an accuracy sufficient enough for their purposes. Lackey is investigating the time-dependent interaction of a planar shock and a cylinder using a computational fluid dynamics method. She is using techniques that give the numerical solution realism that is otherwise difficult for computational scientists to achieve.

Gary L. Jones, a sophomore from Clark Atlanta University is working with Professor Olu Olatidoye, of the Army High Performance Computing Research Center, on a project entitled "Three-Dimensional Graphics Fluid-Structure Interaction Problems." The project associates fluid-structure interaction with parallel computing and graphics visualization.

David T. Kim, a sophomore from Rice University majoring in Chemical Engineering is working on a project entitled "Diffusion and Adsorption in Nano-scale Pores." The research involves the generation and visualization of isopotential surfaces in various zeolites and other molecular sieves. The faculty advisor is Professor Alon McCormick of the Department of Chemical Engineering and Materials Science.

Leslie N. Levine, a senior from the University of California at Davis majoring in Mathematics is working on a new project with Professor David Ferguson of the Department of Medicinal Chemistry. This research involves molecular dynamics simulations of the protein collagen. They are using the free energy method available in the GIBBS module of the AMBER package to do the calculations.

Roger P. Levy, a junior at the University of Arizona majoring in Mathematics, is working with Professor Robert Tranquillo of the Department of Chemical Engineering and Materials Science on a project entitled "Visualization of Dynamical Features of the Navier-Stokes Equations." Levy's work is based on the assumption that chemotaxis is important in directing fibroblast migration, orientation, and traction during wound contraction. Levy has modeled chemoattractant diffusion in an assay proposed to determine cell behavior in a chemotattractant gradient, and is presently working on models of a cylindrical collagen gel "wound assay" with plans to introduce chemoattractant diffusion and effects on fibroblasts into the compaction model.

Benjamin T. Liu, a junior at the University of Minnesota majoring in Chemical Engineering and Materials Science is working on a project entitled "Graphic Interpretation and Parameter Estimation of Spatial Growth Distribution Within Plant Somatic Embryos." He is analyzing the formation of multicellular aggregates, or spheroids, in biological systems. The faculty advisor is Professor Wei-Shou Hu of the Department of Chemical Engineering and Materials Science.

Xiao-yu Luo, a senior majoring in Electrical Engineering is working with Professor Douglas H. Ohlendorf of the Department of Biochemistry in the Medical School on a project entitled "Computational Modelling of Superantigens." Luo has been constructing novel protein models consisting of the domain A of the native Toxic Shock Syndrome Toxin I.

Patrick K. Notz, a senior at the University of Minnesota majoring in Chemical Engineering, is working on a project whose aim is to take theoretical, fluid flow models, both exact and numerical, and draw detailed portraits of various flow configurations using the computer graphics facilities available at the Supercomputer Institute. The project is entitled "Plotting Flow Portraits by Supercomputer," and is supervised by Professor L.E. Scriven of the Department of Chemical Engineering and Materials Science

Shanieka Y. Pennamon, a junior majoring in Civil Engineering at the Georgia Institute of Technology is working on a project entitled "ComputationalApproaches to Pharmaceutical Problems." The faculty advisor is Professor William B. Gleason, Department of Laboratory Medicine and Pathology. This project involves comparison of experimentally determined X-ray powder patterns with those calculated from results of single crystal X-ray studies. Such calculations allow one to determine whether a single crystal structure is representative of a bulk pharmaceutical.

Jason R. Phillips, a senior at the University of Minnesota majoring in Mathematics and Computer Science is working with Professor Jack L. Lewis of Department of Orthopaedic Surgery on a project entitled "Computer Graphics Animation of Human Joint Motion." Phillips has been working on a computer-based dynamic knee model which is approaching its final form.

Hendi Susanto, a junior at the University of Minnesota majoring in Chemical Engineering is working on a project entitled "Performance of Least Sensitivity Principle for Design of Boundary Conditions on Open Flow Boundaries." This research effort involves the undertaking of a graded set of case studies which examine steady, two-dimensional nonlinear flow prototypes. This research project is directed by Professor L.E. Scriven, Department of Chemical Engineering and Materials Science.

Zoran Svetlicic, a sophomore at the University of Minnesota majoring in Computer Science is working on a project entitled "Incorporation of Quantum Effects in the Simulation of Proton Transfer Reactions in the Condensed Phase" The faculty advisor is Professor Donald G. Truhlar of the Department of Chemistry. This project involves a simulation of proton transfer in a three-body reaction in a solvent bath. During the first part of the summer, these researchers added quantum mechanical effects to the simulation. This involved significant changes to the potential energy surface in order to replicate the conditions from reference works. They are now running simulation runs incorporating the solvent bath effects.

Vincent Voelz, a sophomore at the University of Minnesota majoring in Mathematics and Physics is working with Professor David D. Thomas of the Department of Biochemistry, Medical School on a project entitled "Supercomputer Simulations of Muscle Molecular Biophysics." Voelz has been working on a computer program that calculates the rotational diffusion of molecules through arbitrary restricted cones of motion. The program considers the orientation of a phosphorescent probe dipole on the molecule, and is able to produce the time-course anisotropy decay curves that would be measured in experiment. Voelz has been modifying and debugging existing routines to insure that program output matches theoretical predictions for known scenarios.

Dawn Werner, a sophomore at the University of Minnesota majoring in Computer Science, is working on a project entitled "Parallel Algorithms for the Generalized Stokes Problem" which concerns the development of parallel preconditioned iterative schemes for solving the symmetric indefinite linear systems that arise from constrained optimization problems. An important goal of the project is to develop a collection of iterative solvers that are suitable for different parallel architectures. The project supervisor is Professor Ahmed Sameh, Department of Computer Science.

Paul Anderson is a senior at the University of Minnesota majoring in Computer Science. Anderson provides user and system administrative support at the Medicinal Chemistry/Supercomputer Institute Visualization-Workstation Laboratory. In addition to maintaining the workstations, Anderson assists other users of the facility with various applications and molecular modeling software and works to develop software products for use at the laboratory. This work is being supervised by Supercomputer Institute Technical Support Coordinator, Robert Milius.