The Supercomputing Insti-tute’s Undergraduate Intern-ship Program, now in its

16th year, gives undergraduates theopportunity to experience workingin a research environment. The in-terns get to participate in a chal-lenging and enriching educationalexperience that helps them decidewhether they want to pursue gradu-ate or professional education and re-search. The program encompassesdigital simulation and advancedcomputation and all aspects of high-performance computing and scien-tific modeling and simulation, aswell as graphics, visualization, infor-matics, and high-performance net-work communications. Interns givea presentation and write a reportabout their projects.

The Summer 2006 program in-cluded 23 interns who worked onprojects in a wide variety of fields.The interns were selected from 105applicants at colleges and universi-ties in the United States and PuertoRico. Seven of the interns workedon projects sponsored by the Super-computing Institute’s Research Ex-periences for Undergraduates (REU)grant from the National ScienceFoundation and seven were spon-sored by MSI internal funds. Twointerns worked on a project fundedby the Institute for the Theory ofAdvanced Materials in InformationTechnology, which is sponsored byNSF and the Institute for Compu-tational Engineering and Sciences atthe University of Texas in Austin,Texas (www.ices.utexas.edu/ccm/ita-mit/). Seven interns were hosted bythe Institute’s Virtual Laboratory forEarth and Planetary Materials(www.vlab.msi.umn.edu), which is

funded by NSF.Brian C. Atkinson, who attends

Creighton University in Omaha,Nebraska, worked with Professor J.Woods Halley, Department ofPhysics and Supercomputing Insti-tute Fellow. Mr. Atkinson, who is aphysics and mathematics majorwith a minor in problems of philos-ophy, worked on a project called“Simulations of Multiparticle Sys-tems.” This project involved paral-lelizing code for a simulation ofruthenium dioxide; Mr. Atkinsonresearched, tested, and timed re-placement functions for various ma-trix operations, changed existingcode so that it could be compiled totake advantage of the new functionsand run in parallel, and verified andtrouble-shot the new parallel code.

University of Minnesota studentAdam R. Burr, a biomedical engi-neering major with a minor inchemistry, worked with the researchgroup of Professor David D.Thomas, Department of Biochem-istry, Molecular Biology, and Bio-physics and Supercomputing Insti-tute Fellow. His project was called“Missing Structures and Hidden

Springs of Myosin.” Mr. Burr usedcomputational chemistry methodsto help interpret the results of elec-tron paramagnetic resonance experi-ments.

Deborah A. Chasman, who at-tends Carleton College in North-field, Minnesota as a computer sci-ence major, worked with ProfessorEfi Foufoula-Georgiou, Departmentof Civil Engineering and St. Antho-ny Falls Laboratory and Supercom-puting Institute Fellow. Ms. Chas-man’s project was entitled “Extrac-tion of Streams and Basins FromDigital Elevation Models.” She de-veloped a software package that willperform the same function as exist-ing tools used to extract river-basinproperties from digital elevationmodels, but is written in C, whichcan be parallelized to take advantageof multiple-processor machines.

Kelly A. Daniel attends TrumanState University in Kirksville, Mis-souri with a major in chemistry anda minor in biology and justice sys-tems. Ms. Daniel worked with thegroup of Professor Christopher J.

Supercomputing Institute Programs

Fall 2006 Supercomputing Institute Research Bulletin 7

Undergraduate Internship Program 2006

Front, left to right: Martin Lyness, Javier Roman Sanchez, Grace SchwabBack, left to right: Matthew Broten, Shuo Wang, Sarah Wieber, Holly Perryman,Andrew Leverentz

continued on page 10

Cramer, Department of Chemistryand Supercomputing Institute Fel-low, on a project called “CompetingReaction Pathways for a StaudingerIntermediate.” On this project, sheworked with existing simulationsthat were not corresponding withexperimental results, to try to fixthe simulations so that they didagree with experiment.

University of Wisconsin–Madi-son computer science major Joel T.Hestness worked with the researchgroup of Professor David J. Lilja,Department of Electrical and Com-puter Engineering and Supercom-puting Institute Fellow. For hisproject, “Module Redundancy andReliability: An Empirical Analysis ofan Analytical Model,” he workedwith an analytical model of thetradeoffs in using non-redundantcircuits as opposed to triple modu-lar redundancy (a method that em-ploys three copies of a circuit and amodule to vote for the majorityoutput of the three).

Andrew J. Leverentz, a mathe-matics major at Harvey Mudd Col-lege in Claremont, California,worked with Professor FernandoPorté-Agel, Department of CivilEngineering and St. Anthony FallsLaboratory and Supercomputing In-stitute Fellow. Mr. Leverentzworked on a project called “Visual-

izing the Atmospheric BoundaryLayer via Large Eddy Simulation.”This project centered on creating aWeb-based educational tool for dis-playing visualizations of large eddysimulation output.

Professor Ronald Siegel, Depart-ment of Pharmaceutics, hostedJayne L. Linstad, a mathematicsand physics major from MinnesotaState University, Moorehead. Ms.Linstad’s project was “A ProspectiveModel for Antiviral Therapy: Near-est Neighbor Cooperative BindingOnto Euclidian Solids.” For thisproject, Ms. Linstad wrote a MAT-LAB program to generate cooperativebinding isotherms for ligands bind-ing to the vertices or faces of Eu-clidean solids.

Casey L. Litchke, a biochem-istry and physiology major at theUniversity of Minnesota, workedwith Professor Kylie J. Walters, De-partment of Biochemistry, Molecu-lar Biology, and Biophysics. Hisproject was entitled “How to Deter-mine Protein Structure by NMRWith Specific Focus of Myosin VIISH3 Domain.” The goal of thisproject was to add to preliminarydata already collected about thestructure of myosin VII SH3 do-main and to further validate an ac-curate structure of this protein.

Josiah M. Manson, a computer

science major at Texas A&M Uni-versity in College Station, Texas,worked with the group of ProfessorThomas W. Jones, Department ofAstronomy and Supercomputing In-stitute Fellow. Mr. Manson’s projectwas entitled “Visualization and Sim-ulation of Radio Galaxy Jets.” Forthis project, he ran simulations ofradio galaxy jets to test the code andto investigate new areas of research.He also developed several tools tocopy data from the supercomputersand manipulate them on a desktopcomputer; the tools allow the groupto create larger simulations withdata that is more quickly available.

Holly A. Perryman worked withProfessor Heinz Stefan, Departmentof Civil Engineering and St. Antho-ny Falls Laboratory and Supercom-puting Institute Associate Fellow.Ms. Perryman attends Carroll Col-lege in Helena, Montana, where sheis a mathematics major with a com-puter science minor. Her projectwas entitled, “Analysis of Ground-water Input From Stream Tempera-ture Data.” The goal of the projectwas to use recorded stream watertemperatures in heat transport equa-tions developed at St. Anthony FallsLaboratory to find the ground waterflow rate into a stream reach.

Ryan J. Solinsky, who is major-ing in biomedical engineering witha minor in art at the University ofMinnesota, worked with AssociateProfessor Victor H. Barocas, De-partment of Biomedical Engineer-ing and Supercomputing InstituteAssociate Fellow. His project, thegoal of which was to improve visu-alization for the Barocas group, wasentitled “Improved Visualization forData Interpretation.” Mr. Solinskyhelped group members learn to usethe program ENSIGHT, developedvisualization data suitable for EN-

Supercomputing Institute Programs

Supercomputing Institute Research Bulletin Fall 20068

Left to right: Casey Litchke, Daniel Wilcox, Kelly Daniel, Michelle Orthmeyer,Adam Burr, Derek Straka

SIGHT that depicted the orientationdirection of collagen fibers in tissueequivalents, and used the programMAYA to create a three-dimensionalexperimental environment.

University of Minnesota studentDerek A. Straka, who is majoringin chemical engineering, chemistry,and biochemistry, worked with As-sociate Professor William B. Glea-son, Department of LaboratoryMedicine and Pathology and Super-computing Institute Fellow. Mr.Straka worked on a project called“Computational Studies of TyrosineKinase Inhibitors.” In this project,he used the results of AUTODOCK

simulations and ran molecular dy-namics simulations to better under-stand the interactions between asmall molecule and a protein.

Brigham Young Universityphysics and computer science majorDaniel E. Wilcox worked with Pro-fessor Douglas H. Ohlendorf, De-partment of Biochemistry, Molecu-lar Biology, and Biophysics and Su-percomputing Institute Fellow. Mr.Wilcox’s project was entitled “Auto-matically Refining the Structure ofIsomorphous Mutants of a Protein,Including Automatic Detection ofSolvents.” He translated a PERL

script that was previously developedto automatically refine proteinstructures for isomorphous mutantsof proteins into C++, extended itscapabilities for automatic detectionof solvents, and documented thenew code.

Since 2004, the internship pro-gram at the Supercomputing Insti-tute has included interns workingwith the Institute for the Theory ofAdvanced Materials in InformationTechnology (ITAMIT). The ITA-MIT interns were advised by Profes-sor Yousef Saad, Department ofComputer Science and Engineering

and Supercomputing Institute Fel-low. This year’s ITAMIT internswere Amy M. Coddington, aMacalester College (St. Paul, Min-nesota) student majoring in mathe-matics and music with a minor ingeology, and Nicholas J. Voshell, aUniversity of Minnesota mathemat-ics and physics major. Their projectwas entitled “Visualization and Cal-culation of Molecular ElectronicStructure.” Ms. Coddington andMr. Voshell worked with two pro-grams, Real Space Density Func-tional Theory, which calculates thewavefunction, charged density, andelectromagnetic potential in a mole-cule, and PARSEC Visual Toolbox,which takes the results from otherprograms and allows the user to vi-sualize various aspects of the mole-cule. They worked on improve-ments to these programs and ondocumentation for them.

Seven interns were part of the re-search group of Professor David A.Yuen, Department of Geology andGeophysics and SupercomputingInstitute Fellow, working on proj-ects as part of the Institute’s VirtualLaboratory for Earth and PlanetaryMaterials (VLab).

Matthew J. Broten, a Universityof Minnesota computer sciencemajor, and Grace E. Schwab, a

computer science major with amathematics minor at MinnesotaState University, Mankato, workedtogether on a project called “PorkyPortlet, a Dynamic Visual Represen-tation of the Structure and Execu-tion Progress of Complex Work-flows.” Porky Portlet builds dia-grams representing the structure ofa workflow from either a standard-ized workflow document followinga set of specialized XML tags orVLab’s project-phase-task receiptdatabase system. Mr. Broten andMs. Schwab created a database read-er component enabling users to in-teract with this specialized databasesystem.

University of Minnesota studentMartin D. Lyness, who is majoringin computer science and computerengineering with a minor in busi-ness administration, worked on aproject called “Sphynx: Testing WebInterfaces to Improve Both the De-veloper’s and the End-User’s Experi-ence.” He designed a Web interfacetesting service to simplify the cre-ation of unit tests for Web applica-tions.

Adam R. Momsen is a Universi-ty of Minnesota computer sciencemajor with a minor in art. His proj-

Supercomputing Institute Programs

Fall 2006 Supercomputing Institute Research Bulletin 9

Left to right: Ryan Solinsky, Joel Hestness, Deborah Chasman, Adam Momsen,Jayne Linstad, Brian Atkinson, Josiah Manson, Amy Coddington, Nicholas Voshell

continued on page 12

ect was entitled “Simple and Intu-itive Visualization With the WebAutomation and Translation Toolkit(WATT) Client.” For this project,Mr. Momsen worked on a visualiza-tion Web service, WATT Client,which will employ the supercom-puters to quickly render extensivedatasets.

Javier Roman Sanchez, who at-tends the University of Puerto Ricoin Rio Piedras and is a major incomputer science in natural sciencewith a minor in math science innatural science, worked on a projectcalled “Comparison of Efficiency inFile Transfer Protocols.” He com-pared two methods for file transfer,Message Transmission OptimizationMechanism (MTOM) and DirectInternet Message Encapsulation(DIME), by benchmarking bothwith different sizes of JPEG files.His results showed that DIME wasfaster than MTOM by a factor offour; further tests are planned underdifferent conditions.

Shuo Wang is a University ofMinnesota English major with aminor in computer science. Hisproject, “Scientific Visualization andCollaboration,” allowed him towork with two computer simula-tions: a three-dimensional simula-tion of mantle convection withspherical harmonics and a tsunamisimulation code. He created visual-izations of the data from both simu-lations.

Saint Mary’s College (NotreDame, Indiana) student Sarah M.Wieber, who is majoring in mathe-matics and minoring in computerscience, worked on a project called“Scientific Applications for GoogleEarth.” It is possible to create ani-mated overlays, such as the tsunamisimulations Mr. Wang worked on,on Google Earth maps using Key-

hole Markup Language (KML), anXML format specific to GoogleEarth. Ms. Wieber created a user-friendly program in Java that allowsa user with no knowledge of KMLto create a KML file.

University of Minnesota chem-istry major Michelle A. Orthmeyerworked with the research group ofRegents Professor Donald G. Truh-lar, Department of Chemistry andSupercomputing Institute Fellow,on a project called “Structures andStability Order of Water HexamersWith Density Functional Theory.”This project is also part of theVLab. Ms. Orthmeyer studied seven

water hexamers using the GAUSSIAN

03 electronic structure computationpackage to run optimization and vi-brational frequency calculations; shealso performed density functiontheory calculations on these waterclusters.

Supercomputing Institute Programs

Supercomputing Institute Research Bulletin Fall 200610

Summer 2007Undergraduate Internship Program

The Supercomputing Institute is pleased to announce its Undergraduate In-ternship Program for Summer 2007. Appointments are for full-time, 10-weekinternships, and will run from June 4 through August 10, 2007. A student in-terested in becoming an intern must still be an undergraduate in August 2007and must be a citizen or permanent resident of the United States or its posses-sions. Interns will be paid a stipend of $4,800 and are responsible for their owntravel and housing costs.

All applications are evaluated competitively based on the qualifications of theapplicant and the availability of a suitable project. Prospective applicantsshould review the research projects list and indicate projects in which they areinterested, although they may be offered other projects due to availability.

Complete application information, application forms, and project lists areavailable on the Supercomputing Institute Web site at:

www.msi.umn.edu/general/Programs/uip/

Application forms and project lists are also available from:Undergraduate Internship CoordinatorUniversity of Minnesota Supercomputing Institute599 Walter117 Pleasant Street SEMinneapolis, MN 55455

Phone: (612) 626-7620Email: uip@msi.umn.edu

All applications and letters of recommendation must be received by February 28, 2007.