Eleven undergraduate studentsparticipated in the Super-computing Institute’s 2004

Undergraduate Internship Program.The interns were selected from 125applicants at colleges and universi-ties in the United States and PuertoRico. They spent 10 weeks workingclosely with faculty members andtheir groups involved in research atthe Supercomputing Institute.

The Undergraduate InternshipProgram, now in its fourteenth year,gives undergraduates the opportuni-ty to experience working in a re-search environment. The internsparticipate in a challenging educa-tional experience that helps themdecide whether they want to pursuegraduate or professional educationand research. The program encom-passes digital simulation and ad-vanced computation and all aspectsof high-performance computing andscientific modeling and simulation,as well as graphics, visualization, in-formatics, and high-performancenetwork communications.

The interns also can participatein Institute-sponsored tutorials thatdeal with various aspects of scientif-ic computing. At the end of the

program, the interns gave presenta-tions about their work to the rest ofthe group and to faculty researchersat the Institute.

Nicha Chitphakdithai, a bio-medical engineering major at JohnsHopkins University in Baltimore,Maryland, worked with AssociateProfessor Victor A. Barocas, Depart-ment of Biomedical Engineeringand Supercomputing Institute Asso-ciate Fellow. Ms. Chitphakdithaiworked on two related projects,“ImageJ Plugin Development” and“Effects of Accommodation Mi-crofluctuations on Iris Contour.”The first project involved develop-ing an image-processing routine forImageJ software that calculated theposterior chamber volume from atwo-dimensional image of the eye.In the second project, Ms. Chit-phakdithai sought to determinehow microfluctuations of accommo-dation may contribute to pigmen-tary dispersion syndrome by using acomputer simulation to studychanges in iris contour during mi-crofluctuations.

A biology and computer sciencemajor at the University of Minneso-ta–Morris, Nicole Flohr worked

with Professor David D. Thomas,Department of Biochemistry, Mole-cular Biology, and Biophysics andSupercomputing Institute Fellow.Ms. Flohr’s project was entitled,“Molecular Dynamics of PentamericPhospholamban.” In this project,she used molecular modeling anddynamics simulations in coordina-tion with experimental data to de-termine the pentamer quaternaryconformation of the transmembraneprotein phospholamban.

Loren Greenman, a chemical en-gineering and chemistry major atthe University of Minnesota–TwinCities, worked with ProfessorChristopher J. Cramer, Departmentof Chemistry and SupercomputingInstitute Fellow. Mr. Greenman’sproject was entitled “MechanisticStudy of the Zinc Catalyzed Poly-merization of Lactones.” For thisproject, he studied the polymeriza-tion of small lactones catalyzed by azinc compound using ab initio anddensity functional theory methods.In his presentation, Mr. Greenmanshowed a proposed mechanism ofthe catalyzed polymerization ofbeta-propiolactone and compared itwith a non-catalyzed reaction.

Mark Hubenthal, who attends

Supercomputing Institute Programs

December 2004 Supercomputing Institute Research Bulletin 7

Summer 2004 Undergraduate Interns

Richard O’Konski, Jacob Kilian, Nicole Flohr, and Paul Shearer at the Welcome Re-ception

Nicha Chitphakdithai gives her presen-tation

Whitman College as a math andphysics major, worked with Profes-sor Fadil Santosa, Department ofMathematics. Mr. Hubenthal’s proj-ect was entitled, “Finite DifferenceModeling of Transient Waves.” Inthis project, he worked with finitedifference time domain (FDTD)methods, which are powerful toolsthat can be used with artificial ab-sorbing boundary conditions tosimulate the propagation of wavesin an infinite medium, and a morerecent approach, called the perfectlymatched layer (PML). Mr. Huben-thal presented various implementa-tions of FDTD with PML for scalarand vector wave equations using theYee scheme.

Jacob Kilian, a chemistry majorat the University of Minnesota–Twin Cities, worked with ProfessorJiali Gao, Department of Chemistryand Supercomputing Institute Fel-low on a project called, “An Analysisof Lewis Acid-Base InteractionsUsing Block-Localized Wavefunc-tions.” In this project, Mr. Kilianused the block-localized wavefunc-tion method to decompose the in-teraction energies of H-X— aminecomplexes into electrostatic, ex-change, polarization, and chargetransfer terms. He found that the

binding of hydrogen-bonded com-plexes is due to electrostatic interac-tions while ionic interactions aredominated by polarization andcharge-transfer terms.

Daniel Lebewitz, a mechanicalengineering major at the Universityof Colorado in Boulder, workedwith Professor Steven Girshick, De-partment of Mechanical Engineer-ing and Supercomputing InstituteAssociate Fellow. His project wasentitled “Parallel Modeling ofGrowth and Transport Models.” Forthis project, Mr. Lebewitz devel-oped a code to model growth ofparticles due to coagulation andtransport due to diffusion. Thismodel will be expanded to solve thecomplete aerosol general dynamicequation, which also accounts forparticle nucleation and surfacegrowth.

Eric Lindgren, a mathematicsmajor at Carleton College in North-field, Minnesota, worked with Pro-fessor James R. Chelikowsky, De-

partment of Chemical Engineeringand Materials Science and Super-computing Institute Fellow. Mr.Lindgren’s project, “The Next StepToward Smaller and Smaller: Quan-tum Dots,” is part of the researchbeing done by the Institute for theTheory of Advanced Materials inInformation Technology. Mr. Lind-gren explored the world of solid-state physics and worked with quan-tum dots. These are nanoscale semi-conductors with properties that dif-fer significantly from bulk materialsand offer exciting opportunities forsmaller and more versatile electron-ics.

Arnaldo Marrero, a chemistrymajor from the Universidad Metro-politana in San Juan, Puerto Rico,worked with Professor Steven R.Kass, Department of Chemistry andSupercomputing Institute AssociateFellow. In his project, “Computa-tional Study of Zwitterionic Pro-line,” Mr. Marrero explored zwitte-rionic amino acids using computa-tional methods, beginning with pro-line (Pro), one of the 20 essentialamino acids in biological systems.He performed conformationalsearches of Pro and its zwitterionicanalogs to determine the minimastructures that contribute the most

Supercomputing Institute Programs

Supercomputing Institute Research Bulletin December 20048

Left to right: Eric Lindgren, Paul Shear-er, Daniel Lebewitz, Mark Hubenthal,and Richard O’Konski

Left to right: Loren Greenman, NicoleFlohr, Nicha Chitphakdithai, BrendaSaxton, Jacob Kilian, and Arnaldo Mar-rero

to the properties of the molecule.Richard O’Konski, who attends

Kansas State University as a com-puter science major, worked withProfessor David J. Lilja, Depart-ment of Electrical and ComputerEngineering and SupercomputingInstitute Fellow. The Lilja group de-velops new methods to account forthe high transient error rates associ-ated with nanoscale devices used incomputer architectures. Mr. O’Kon-ski’s project, entitled “DirectedGraph Algorithms for MultipleFault Diagnosis in Verilog Systems,”dealt with the design of a C++ re-search aid application that buildscompleted directed graphs based onlarge verilog models. The applica-tion can be used to find all uniquepaths between potential error

sources in a system, possibly leasingto the classification of non-maskedand masked errors.

University of Minnesota–TwinCities neuroscience major BrendaSaxton worked with ProfessorMichael P. Murtaugh, Departmentof Veterinary and Biomedical Sci-ence. Her project was “Direct Physi-cal Characterization of PRRSV Viri-on Proteins.” Using mass spectrom-etry and a PRRSV protein sequencedatabase, Ms. Saxton directly identi-fied peptide fragments of PRRSVproteins in the virions. This infor-mation will help to identify likelyand unlikely targets for immuneprotection, to better understand theinfection process, and to guide thedevelopment of strategies for reduc-ing or preventing disease in infected

pigs.University of Minnesota physics

major Paul Shearer worked withthe group of Professor Thomas W.Jones, Department of Astronomyand Supercomputing Institute Fel-low. Mr. Shearer’s project, entitled“Synthetic Observation of RadioGalaxies,” involved conductingmagnetohydrodynamical simula-tions of the evolution of radiogalaxies and to make virtual, or“synthetic,” observations of the sim-ulated objects. This included per-forming data reduction on thesesynthetic observations to find outwhat the observations and data re-duction might reveal about the rela-tionship between observation of aradio galaxy and its actual physicalmakeup.

December 2004 Supercomputing Institute Research Bulletin 9

Summer 2005Undergraduate Internship Program

The Supercomputing Institute is pleased to announce its Undergraduate Internship Program for Summer 2005. Appoint-ments are for full-time, 10-week internships, and will run from June 6 through August 12, 2005. A student interested inbecoming an intern must still be an undergraduate in August 2005 and must be a citizen or permanent resident of theUnited States or its possessions. Interns will be paid a stipend of $4,800 and are responsible for their own travel and hous-ing costs.

All applications are evaluated competitively based on the qualifications of the applicant and the availability of a suitableproject. Prospective applicants should review the research projects list and indicate projects in which they are interested, al-though they may be offered other projects due to availability.

Complete application information, application forms, and project lists are available on the Supercomputing Institute Website 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, 2005.