volume 19, number 1 supercomputing institute

Volume 19, Number 1

for Digital Simulation and Advanced Computation

Supercomputing Institute

Fall 2002 Research Bulletin of the Supercomputing Institute

Each year, the Supercomputing Institute hosts a groupof research scholars at the University of Minnesota. Inthe 2002–03 academic year, ten research scholars are

working closely with principal investigators of theSupercomputing Institute on projects partially funded by theU.S. Department of Energy, the National Aeronautics andSpace Administration, the National Institutes of Health, andthe National Science Foundation.

Serkan Erdin is working with Professor J. Woods Halley,Department of Physics and Supercomputing InstituteFellow. His project involves direct dynamics simulations ofthe water-oxide-metal interface, beginning with codes devel-oped by the Halley group for liquid water and the metal-metal oxide interface. The simulations will be used to studywater structure and possible hydrolysis at the water-oxideinterface as well as vacancy and interstitial transport in theoxide in order to understand the processes of passive filmformation and breakdown.

Dacian Daescu, Institute for Mathematics and ItsApplications, is developing computational tools and associ-ated software for assimilation of atmospheric measurementsinto chemical transport models (CTMs). CTMs aredesigned to describe physical and chemical processes in theatmosphere and their integrated impacts on atmosphericpollutant 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 InstituteFellow. Dr. Gadgil is extending an existing two-dimensional

Supercomputing Institute Programs

2002–2003 Research Scholars

continued on page 2

U of M Bioinformatics Summer Institute 2003 ..............4

2002 Undergraduate Internship Program ......................5

Modeling Transition Metal Chemistry ......................... 10

Computational Chemistry at the Interface....................13

First Annual Nanosimulation Workshop.......................18

Health Informatics Seminars......................................22

Research Reports.....................................................23

Also in This Issue

Top: Serkan ErdinBottom: Dacian Daescu

2 Supercomputing Institute Research Bulletin Fall 2002

model for limb development to incorporatenew molecular information about the mecha-nism of limb development and to develop athree-dimensional geometrically realistic com-putational model. This will enable a realisticsimulation of the limb development process,and thereby provide a computational tool thatcan be used to explore the effects of variousmutations and experimental interventions onthe growth of the limb and the pattern of

gene expression.William Herb of the St. Anthony Falls

Laboratory is working with Professor HeinzStefan (Department of Civil Engineering andSupercomputing Institute Associate Fellow) tostudy macrophyte growth in relation to light,temperature, and turbulent transport of dis-solved gases in lakes. Rooted macrophyte (vas-cular plant) beds in shallow lakes and the lit-toral zone of deeper lakes can have a signifi-cant impact on both lake ecology and waterquality. Dr. Herb is developing mechanisticrelationships between rooted macrophytes andthe distribution of light, temperature, and dis-solved gases within the water column in lakes,using a dual approach of experimental meas-urements and mathematical modeling.

Giuseppe Fadda is performing research onthe development of multiscale methods for thepassage of atomic to continuum scales, espe-cially for problems in materials science. He isworking on two specific projects. In the first,he is developing the theory of “EffectiveHamiltonians” to make it a more accurateresearch method. The second project involvesthe time scale problem in transforming mate-rials. Dr. Fadda is working with ProfessorMitchell Luskin (School of Mathematics andSupercomputing Institute Fellow) andProfessor Richard James (Department ofAerospace Engineering and Mechanics).

Emmanuel Lorin de la Grandmaison isworking with Professor Yousef Saad,Department of Computer Science andEngineering and Supercomputing InstituteFellow, to develop new algorithms for scalablemodeling in materials science. The goal of thisresearch is to introduce new methodologiesthat bypass computational limitations of cur-rent techniques for predicting properties ofmaterials. The excessive cost of the traditionaleigenvector-based approach, both in terms ofmemory requirements and computations,severely limits the capabilities of current elec-tronic structure codes. The project focusesspecifically on techniques that avoid eigen-

Top to Bottom:Chetan Gadgil,William Herb,Giuseppe Fadda,Emmanuel Lorin de laGrandmaison

3Fall 2002 Supercomputing Institute Research Bulletin

bases while at the same time offering the samefunctionality as eigenvector-based methods.

Yuri Nesmelov is working with Dr. DavidD. Thomas (Department of Biochemistry,Molecular Biology, and Biophysics andSupercomputing Institute Fellow) to investi-gate the computational design of microwavedevices for biophysical magnetic resonance.The goal of this research is to achieve a dra-matic improvement in the sensitivity of bio-physical electron paramagnetic resonance(EPR) spectroscopy. The approach is to designdielectric inserts to be used with standardcommercial cavity resonators.

Tina Poulsen is working with ProfessorJiali Gao, Department of Chemistry, andProfessor Donald G. Truhlar, Department ofChemistry and Supercomputing InstituteDirector. Her project investigates the opera-tion of short-chain and medium-chain acyl-coenzyme A dehydrogenase. This enzyme cat-alyzes the oxidation of straight-chain fattyacyl-coA thioesters to trans-2,3-enoyl-CoAderivatives with accompanying two-electronreduction of enzyme-bound flavin adeninedinucleotide. Dr. Poulsen is applying newmulti-dimensional dynamical methods incor-porating quantum mechanics to the calcula-tion of the reaction rate, the free energy ofactivation, and the kinetic isotope effects.

Joseph Resovsky, who is working withProfessor David Yuen (Department ofGeology and Geophysics and SupercomputingInstitute Fellow), is investigating the three-dimensional velocity and density structure ofthe earth seen by long-period seismic data.This project uses the neighborhood algorithmto directly explore model probabilities in themultidimensional space in which mantle den-sity and velocities are parameterized in radiallayers and expanded in spherical harmoniccoefficients.

Dongsu Ryu is working with ProfessorThomas W. Jones (Department of Astronomyand Supercomputing Institute Fellow) onproblems in computational astrophysics. The

primary goal of this research is to incorporateinto Dr. Ryu’s state-of-the-art cosmologicalcode the Jones group’s powerful tools for sim-ulating the transport of diffuse relativistic plas-mas self-consistently within nonrelativisticplasma flows. Dr. Ryu will also use the code as

Top to Bottom:Yuri Nesmelov, TinaPoulsen, JosephResovsky, Dongsu Ryu

continued on page 4

The University of MinnesotaBioinformatics Summer Institute(UMBSI) will hold its first program

in summer 2003. The Summer Institute pro-gram will consist of ten weeks of workshops,seminars, and research, and it is open to jun-ior and senior undergraduates in all fields ofscience and engineering. The applicationdeadline is February 28, 2003.

Bioinformatics, which stands at the nexusof the biological and computational sciences,involves the systematic study of biological sys-tems and holds great promise for providingsolutions that improve the human condition.Research projects in the UMBSI include thephysical, structural, and func-tional properties of biologicalmacromolecules and their rela-tion to sequence, the definitionof data models and retrieval lan-guage extensions for integrateddatabases, the development offunctional genomics databases,genetic analysis including com-parative and evolutionaryapproaches, parallel algorithmdesign for data mining, the inte-gration of bioinformatics toolswith statistical mechanics, the useof expressed-sequence-tag analysisand DNA microarrays in micro-

bial biology and legume biology,plant/microbe symbioses, plant geneticsapplied to plant improvement, large-insertDNA libraries and high-throughput DNAsequencing, mathematical models of chemo-taxis and cell motion, the dynamics and ther-modynamics of biological processes, andbioethics.

The Institute will be coordinated by VipinKumar of the Computer Science andEngineering Department, Yiannis Kaznessis ofthe Department of Chemical Engineering andMaterials Science, and Arkady Khodursky ofthe Department of Molecular Biology andBiophysics. Twelve other faculty from the

Departments of Plant Biology,Laboratory Medicine andPathology, Physics, Medicine,Microbiology and VeterinaryPathobiology, Mathematics,Biostatistics, Agronomy and PlantGenetics, Bioinformatics,Computer Science andEngineering, and Chemistry willalso participate. Infrastructure andcomputing support will be pro-vided by the Digital TechnologyCenter and the SupercomputingInstitute.

For more information, seewww.bsi.umn.edu.


Collaborative Programs

University of Minnesota Bioinformatics Summer Institute 2003

Structure as magnifyingglass clarifying sequences:bioinformatics research iselucidating the relationshipbetween protein sequencesand structures, harnessingthe promise of genomics.

a tool to explore some of the most importantscenarios for generation of relativistic plasmaand to study the emissions and observableproperties of simulated clusters in order tocompare them to real observations of physicalclusters.

More information about the ResearchScholar program can be found on theInstitute’s Web site at:

www.msi.umn.edu/general/Programs/Descriptions/RS.html

The submission deadline for 2003–04scholarships is January 15, 2003.


This summer, 14 students participatedin the Undergraduate InternshipProgram at the Supercomputing

Institute. The interns were selected from 94applicants at colleges and universities aroundthe United States. They spent ten weeks work-ing closely with faculty members and theirgroups involved in research usingSupercomputing Institute resources.

The Undergraduate Internship Program,now in its twelfth year, gives undergraduatesthe opportunity to experience working in aresearch environment. The interns get to par-ticipate in a challenging and enriching educa-tional experience that helps them decidewhether they want to pursue graduate or pro-fessional education and research. The programencompasses digital simulation and advancedcomputation and all aspects of high-perform-ance computing and scientific modeling andsimulation, as well as graphics, visualization,informatics, and high-performance networkcommunications.

The interns also have the opportunity toparticipate in Institute-sponsored tutorials that

deal with various aspects of scientific comput-ing. At the end of the program, the internsgave presentations about their work to the restof the interns and to other researchers at theInstitute.

Benjamin Cosgrove, a BiomedicalEngineering major at the University ofMinnesota, worked in the research group ofAssistant Professor Victor Barocas of theDepartment of Biomedical Engineering. Ben’sproject was entitled, “Actin FilamentBranching: Three-Dimensional Modeling.”The project’s goal was to design a computersimulation to model the growth and branch-ing of an actin filament. Ben created a com-puter code that uses a Monte Carlo process tosimulate the forward and reverse chemicalreactions that contribute to the growth andbranching of an actin filament. As part of hispresentation, Ben showed an animation hehad developed of a branching filament.

Matthew Eggert worked with ProfessorSteven Girshick of the MechanicalEngineering Department. A Chemical

Supercomputing Institute Programs

2002 Undergraduate Internship Program

(Left to right) Matthew Eggert, Eric Johnson, Jennifer Klein, and Sosheel Saleem

continued on page 6


Engineering and Materials Science major fromthe University of Minnesota, Matt worked on“Hypersonic Plasma Particle Deposition.” Thegoal of this project was to model fluid flow ina reacting system through a currently existingexperimental nozzle and a proposed nozzlegeometry based upon two-dimensional model-ing. The new nozzle design is intended to mit-igate or eliminate problems associated withfluid recirculation.

Eric Johnson, a Biomedical Engineeringmajor at the University of Minnesota with aminor in Bioinformatics, worked in theresearch group of Associate Professor WilliamGleason, Department of Laboratory Medicineand Pathology. His project was “Developmentof System for Modeling Heparin/Heparan

Sulfate.” Eric has developed a model thatallows a researcher to create a custom simula-tion in just a few minutes. The model con-tains a library of individual residues fromwhich one can assemble a custom heparinchain. The researcher can also adjust otherparameters, and the necessary custom configu-ration and analysis scripts are created. Afterthe simulation is complete, it takes less than aminute to launch the analysis package thatsupplies the user with a full analysis.

University of Minnesota Computer Sciencemajor Christopher Kauffman worked withProfessor Yousef Saad’s research group. Hisproject was “SPMATH: An Interactive Tool forSparse Matrix Computations.” Chris spent hisinternship adding plotting functionality to theSPMATH software package. He researchedexisting plotting tools, found the one bestsuited to the needs of this project, and wrotecode in C++ to allow SPMATH to use thesedrawing functions. He also created documen-tation for future programmers.

Elmer Kim attends Harvey Mudd College.A Computer Science major with a minor inEconomics, Elmer worked with AssistantProfessor Yiannis Kaznessis of the ChemicalEngineering and Materials ScienceDepartment. Elmer’s project was entitled“Protein Structure Comparison Using VectorsBetween the Backbone Atoms.” Elmer usedPERL to write two programs. The first pro-gram places amino acid models in a line, andthe second program is used to compare twoprotein structures. Both these programs willbe used by the Kaznessis research group intheir work modeling protein structures.

Jennifer Klein, a Biochemistry major fromthe College of St. Benedict in St. Joseph,Minnesota, worked with Professor David D.Thomas of the Department of Biochemistry,Molecular Biology, and Biophysics. Jennifer’sproject was “Molecular Dynamics of Spin-Labeled Myosin.” Using several different pro-grams, Jennifer helped to construct a model ofmyosin, a form of protein. Not only will the

Top: Greg Williams (left) and Christopher KauffmanBottom: Margot LeClair during her final presentation.

model be useful for future simulations, thePERL scripts and techniques used to constructit are general enough to be used for modelingother proteins.

Margot LeClair, from Haverford Collegein Haverford, Pennsylvania, is a Chemistrymajor. She worked in the research group ofProfessor Steven Kass, Department ofChemistry, on “Structures, Energetics, andProperties of Organic Molecules.” Margot per-formed calculations to determine several prop-erties of certain biologically important zwit-terions, which are molecules with oppositelycharged centers. Her worked allowed her todetermine stable structures for several com-pounds; this indicates that these compoundscan be synthesized for future study.

Peter Mack is a Computer Science majorwith a minor in Mathematics at St. John’sUniversity in Collegeville, Minnesota. Heworked with Professor Thomas W. Jones inthe Department of Astronomy; his project wasentitled, “Visualizing Interacting GalaxyClusters With AMIRA.” Peter learned to useAMIRA and investigated its usefulness inmanipulating the Jones group’s large data sets,with an emphasis on locating mergers ofgalaxy clusters. This project showed thatAMIRA is a valuable tool for this group’sresearch, and Peter spent some time familiariz-ing the rest of the group with the program.

Computer Science major Sosheel Saleem ofthe University of Houston, Houston, Texas,worked in the research group of ProfessorLeonard Banaszak of the Department ofBiochemistry, Molecular Biology, andBiophysics. Sosheel worked on two projectsthis summer, “Protein Animation” and“Electrostatic Potential Mapping.” In the firstproject, he used the AMIRA program to visual-ize a molecule of the protein lipovitellin andto create digital images of it. He used theseimages to make a movie, which he showed tothe group during his presentation. In the sec-ond project, Sosheel created a program thatformatted an electrostatic potential grid fileinto an ASCII file so that it could be used byanother program for visualization.

Justin Sjulson, a Biomedical Engineeringmajor at the University of Minnesota, workedin the research group of Professor DavidGrant of the Department of Pharmaceutics.Justin’s research project was entitled “Effect ofSolvent Interaction Energy on CrystalGrowth.” Justin calculated the interactionenergy between crystal faces and three differ-ent solvents, water, methanol, and hexane.The goal was to see what the solvent effectswould be on the crystal’s growth, and, there-fore, the morphology. Justin also spent sometime calculating the morphology of the dpolymorph of phenylbutazone. These calcula-


(Left to right) Michael Tobin, Peter Mack, Margot LeClair, and Mychel Varner

continued on page 8


tions allow the prediction of crystal morphol-ogy in a vacuum.

Michael Tobin, from Macalester College inSt. Paul, Minnesota, worked with ProfessorDavid Lilja in the Electrical and ComputerEngineering Department. Michael is aComputer Science major with minors inMathematics, Japanese, and Music. His proj-ect was entitled “Boosting ProcessorPerformance Using Data Value Prediction.”Michael wrote a program that speeds up theprocess of data value prediction by having thedata prediction scheme implemented in a sep-arate application. Instead of running completeprograms to gather data prediction results,Michael’s program extracts information aboutwhich instructions were executed and whatthe computed values were and generates statis-tics about how successful the value predictionwas. The application is customizable, so that

the search parameters can be changed easily.Mychel Varner attends Truman State

University in Kirksville, Missouri. She is aChemistry major with a minor in Physics. Sheworked in the research group of ChristopherCramer, Department of Chemistry, on a proj-ect entitled “Modified Pseudopotentials forQuantum Mechanical/Molecular MechanicalCalculations on Metallocene Catalysts.” Inthis project, Mychel used density functionaltheory and hybrid quantum mechanical/mole-cular mechanical calculations to study thestructure of molecules and used the electronicstructure program GAUSSIAN to run calcula-tions.

Sterling Greg Williams is a CivilEngineering and English major at theUniversity of Minnesota. Greg worked withProfessor Heinz G. Stefan of the CivilEngineering Department and St. Anthony

(Left to right) Ben Cosgrove, AmyWong, Elmer Kim, and Justin Sjulson

Peter Mack and Jennifer Klein use theworkstations in the SupercomputingInstitute’s Scientific Development andVisualization Laboratory.


Falls Laboratory. His project was “ModelingIce Cover Characteristics of North AmericanLakes.” This project used multivariable regres-sion models, log-transform models, and acombination of the two (“hybrid models”) tomodel ice-in date, ice-out date, and ice thick-ness for 130 freshwater lakes in the UnitedStates and Canada. These parameters weremodeled as a function of mean air tempera-ture, latitude, average depth, elevation, andsurface area of each lake. The goal was todetermine which model most accurately pre-dicted measured results.

A Computer Science major with a minorin Japanese, Hiu (Amy) Wong attends theUniversity of North Carolina at Chapel Hill.Amy worked with Assistant Professor DongWang of the Department of Soil, Water, andClimate. Her project was “Using ComputerModeling to Predict Chemical Emission inSoil.” Amy worked with a program that trackssoil fumigants and chemical concentrations insoil. The project’s goal was to increase usabil-ity, especially for non-expert users. Amyadded several functions to the program,including a simpler installation file, optionsallowing the user to save files to differentlocations, and re-centering all the GUI com-ponents in each form in the program. Shealso looked at different ways to improve theprogram’s graphical depiction of chemicalconcentrations in soil.

Summer 2003Undergraduate Internship Program

The Supercomputing Institute is pleased to announce itsUndergraduate Internship Program for Summer 2003.Appointments are for full-time, ten-week internships, and will runfrom June 9 through August 14, 2003. A student interested inbecoming an intern must still be an undergraduate in August 2003and must be a citizen or permanent resident of the United States orits possessions.

All applications are evaluated competitively based on the qualifi-cations of the applicant and the availability of a suitable project.Prospective applicants should review the research projects list andindicate projects in which they are interested, although they may beoffered other projects due to availability.

Complete application information, application forms, and proj-ect lists are available on the Supercomputing Institute Web site at:

www.msi.umn.edu/general/Programs/uip/summer03.html

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: [email protected]

All applications and letters of recommendation must bereceived by February 28, 2003.


Chemistry is the science that concernsitself with the periodic table. Livingsystems, interestingly, turn out to be

composed of relatively few elements from thetable: the vast majority of biomass consistssimply of carbon, hydrogen, nitrogen, oxygen,sulfur, and phosphorus. As improved under-standing of living systems is an important goalfor a large number of chemists, substantialwork in the area of molecular modeling hasbeen focused on this handful of elements.

Happily enough, the biologically relevantelements are a pleasant set with which towork, at least from a quantum-mechanicalperspective. They are rather light in terms oftheir atomic mass, and this implies that theyhave relatively few electrons compared to theirheavier cousins. Since a key challenge ofmolecular quantum chemistry is determiningelectron probability density distributions,working with fewer electrons vastly simplifiesthe computational cost associated with a givenproblem.

A separate point of some importance is thateveryday organic and biological moleculestend to have what is known as a large frontier-orbital energy gap. The spatial probability dis-tribution of an electron defines the so-calledmolecular orbital (MO) in which it resides,and the principles of quantum mechanics dic-tate that such orbitals have precise energiesdictated by the kinetic energy of the electronand its interactions with all of the chargednuclei and the other electrons. The frontier-orbital energy gap, then, is the energy separa-tion between the highest-energy MO that isoccupied by an electron and the lowest-energyMO that is unoccupied. A large gap is typi-cally associated with all occupied MOs beingdoubly occupied (a molecule in which this sit-uation obtains is referred to as having a “sin-glet” electronic state).

Transition metals, by contrast, are typicallyfound only in trace quantities in living sys-tems, although many of them are essential inthis regard (e.g., manganese, cobalt, iron, cop-per, and zinc). A critical feature of a transitionmetal is that, as an atom, it may formallycarry anywhere from one to ten electrons inatomic orbitals known as d orbitals. The ener-gies of d orbitals in a molecular environmentmay span only a fairly narrow range of energy.Thus, in the absence of having ten d electrons(which completely fills the d block), it is pos-sible for various occupations of the d orbitalsto generate different molecular electronicstates, some characterized by having electronsthat are not paired with electrons of oppositespin, and all of which may be relatively closein energy to one another. That situation opensup rich possibilities for chemistry, sinceunpaired electrons can more easily carry outuseful chemical transformations. It also, how-ever, poses special challenges for quantummechanical MO theory methodology, sincemany implementations of this theory thatfunction well in systems with large frontier-orbital energy gaps fail completely for thesmaller gaps one encounters in transitionmetals.

Researchers in the group of ProfessorChristopher J. Cramer of the ChemistryDepartment have been applying a quantummechanical model known as density func-tional theory (DFT) to better understand thestructures and reactivities of systems incorpo-rating transition metal atoms. At a fundamen-tal level, DFT works not with individual elec-trons and their orbitals, but instead with thetotal electron density; nevertheless, molecularorbitals are employed and often admit tointerpretation.

One example of their efforts has been thestudy of unusual inorganic metallocenes. A

Chemistry

Modeling Transition Metal Chemistry


metallocene is a molecule in which a transi-tion metal is sandwiched between two five-membered rings that have significant electrondensity above and below the planes defined bytheir constituent atoms. Thus, the orbitals ofthe rings can interact strongly with metal dorbitals (Figure 1)—the exact nature of theinteraction dictates the properties of the met-allocene. As a practical matter, metallocenesfind substantial use as catalysts in variouschemical transformations, most notably thepolymerization of small hydrocarbons to makecommodity materials like a form of poly-propylene characterized by a high degree oftransparency, which is an area of researchstudied in a previous period by Cramer andhis colleague Don Truhlar in collaborationwith Phillips Petroleum and in an internshipby Mychel Varner (see page 8).

Motivated by the experimental isolation ofthe highly unusual titanocene Ti(P5)2

2- (i.e.,all the apices in the metallocene rings arephosphorus atoms) in the laboratory ofProfessor John Ellis of the ChemistryDepartment, Cramer set out to explain whythis molecule was so remarkably stable com-

pared to an analogous metallocene using themuch more typical cyclopentadienide ring as aligand (i.e., all of the apices are carbon atomsthat also carry one hydrogen atom). The latterhas never been isolated and its nearest analogis a highly reactive molecule having twounpaired electrons. The key differencebetween the two arises because of the natureof the frontier molecular orbital, as illustratedin Figure 1. The degenerate pair of lower-energy orbitals is dominated by contributionsfrom the sandwiching rings, while the higher-energy orbital is dominated by a single dorbital on the metal. Because the phosphorus-ring orbitals are intrinsically lower in energycompared to the carbon-ring orbitals, this cre-ates a large energy gap that causes the fourhighest-energy electrons to spin-pair in theseorbitals, and a stable singlet state results. Inthe carbon-ring case, on the other hand, aphenomenon known as exchange permits anet energy gain after promoting two of theseelectrons into the pure metal orbital and leav-ing reactive unpaired electrons behind. Thisobservation offers key insights into how one

Figure 1. Frontier orbitals and the influence of the ring atoms on the frontier gap in different metallocenes. On the left, the gap issmall because the ring orbitals are comparatively high in energy, and the optimal electron occupation leaves one unpaired electron ineach of the formally lower energy orbitals. On the right, the comparatively lower energy of the ring orbitals for the phosphorus ringsleads to a large frontier orbital separation so that no unpaired electrons are generated. See also E. Urnezius, W. W. Brennessel, C. J.Cramer, J. E. Ellis, and P. v. R. Schleyer, Science, 295, p. 832 (2002).

continued on page 12

might go about tuning the energy gap toengineer a particular chemical reactivity intothe metallocene.

In a separate study, researchers ChrisKinsinger, Bethany Kormos, Ed Sherer, andJason Thompson in Cramer’s group addresseda controversial trinuclear palladium complexthat had been postulated to contain a centralpalladium atom in the +6 oxidation state,which means it has formally lost six electronsto its ligands. This state, Pd(VI), had neverbefore been observed even with ligandsknown to be very powerful as electron with-drawing agents, e.g., fluorine atoms, and theligands in this case were silicon groups(Figure 2), which have a lower tendency to


withdraw electrons. By using DFT and ana-lyzing the degree of bonding between the cen-tral palladium and its surrounding siliconatoms and between the individual siliconatoms themselves, the research team showedthat a more accurate description of the centralpalladium was to assign it an oxidation stateof +2. This state, Pd(II), is well-known andcommon. The molecule remains unique,however, insofar as the analysis implies thatsilicon-silicon single bonds can act as ligandsto the palladium atom, and tuning the degreeof this interaction again should prove to be apowerful tool in the design of palladium cata-lysts capable of carrying out specific chemicaltransformations.

Figure 2. Depending on how the electron density is distributed in space, one may consider the illustratedtrinuclear palladium complex to either have a central Pd(II) atom interacting with Si–Si bonds, or a centralPd(VI) atom interacting with six separate silyl groups. The MO in the center is the highest energy occupiedMO in the molecule, and clearly shows significant bonding interactions between pairs of Si atoms (the blue“sausages” to left and right of the center) in addition to a contribution from the central metal atom (thedumbbell at the precise center). Note that for maximum clarity the orbital picture is depicted after rotation ofthe molecular line structure 90 degrees clockwise in the plane of the paper and then 90 degrees counterclock-wise about the vertical axis in the plane of the paper. See also E. C. Sherer, C. R. Kissinger, B. L. Kormos,J. R. Thompson, and C. J. Cramer, Angewandte Chemie International Edition, 41, p. 1953 (2002).


On June 2–4, 2002, theSupercomputing Institute, theDepartment of Chemistry, and the

Minnesota Section of the American ChemicalSociety sponsored a Symposium onComputational Chemistry at the Interface aspart of the 34th Great Lakes RegionalMeeting of the American Chemical Society onthe University of Minnesota campus.

The symposium was kicked off by a ple-nary lecture by Mark Ratner of NorthwesternUniversity on interfacial phenomena associ-ated with molecular light-emitting diodes andother transport phenomena at molecular junc-tions.

The first session was devoted to the inter-face of computational chemistry and chemicalbiology. Ron Elber of Cornell showed how tofilter high-frequency motions out of moleculardynamics simulations in order to provide con-trolled approximations to pathways forprocesses occurring on very long time scales(in atomic units), for example, protein fold-ing. Qiang Cui of the University of Wisconsinshowed how to calculate redox potentials ofenzyme cofactors by calculations in whichonly a small portion of the system needs to betreated by quantum mechanics. SharonHammes-Schiffer of Penn State used a real-time combined quantum mechanical/classicalmechanical dynamics free energy simulationwith a GROMOS empirical potential energysurface to elucidate a network of coupled pro-moting motions of the enzyme dihydrofolatereductase. John Straub of Boston Universitypresented a detailed analysis of the stablestructures of amyloid peptides and the factorsresponsible for their tendency to aggregate, asin Alzheimer’s disease. Maria Kurnikova ofMarquette University presented a dynamic lat-tice Monte Carlo Brownian dynamics modelof gramicidin as an extreme example of a nar-row channel in neurochemistry, and she eluci-dated the role of protein relaxation in lower-

Symposiums

Computational Chemistry at the Interface

continued on page 14

Top: Ron Elber, Cornell UniversityMiddle: Qiang Cui, University of WisconsinBottom: Sharon Hammes-Schiffer, Pennsylvania State University


ing the transport barrier. Jacopo Tomasi ofPisa, Italy surveyed the various approachesbeing used in continuum solvation calcula-tions including a new linear scaling algorithm.

The next session was devoted to the com-putational chemistry of nanostructured mate-rials. Jim Chelikowsky of the University ofMinnesota presented calculations on the opti-cal properties of quantum dots and nanocrys-talline silicon. Carl Melius of LawrenceLivermore National Laboratory presented adiscussion of the reaction-diffusion equationsinvolved in the design of nanoenergetic mate-rials along with quantum chemical calcula-tions to identify elementary reaction steps inoxidation. Edward Maginn of Notre Damepresented a lucid account of Knudsen sliplength as it controls fluid flows in nanopores.Randall Snurr of Northwestern Universitypresented molecular modeling studies of diffu-sion and reaction in two classes of nanoporousmaterials. Kendall Thomson of Purdueshowed how to refine structural correlationfunctions to match experimental distributionsand predict adsorption isotherms for water onactivated carbon. Paul Van Tassel of WayneState University used simulations to improveour understanding of how molecular templat-ing allows one to tailor the pore space geome-try of a disordered material by shifting the vander Waals loop in phase diagrams.

The final session of the symposium wasfocused on the interface of computational andenvironmental chemistry. Judith Perlinger ofMichigan Technological University, PaulTratnyek of the Oregon Graduate Institute ofScience and Technology, and PhillipGschwend of M.I.T. discussed various aspectsof linear free energy relationships and relatedcorrelation analysis as applied to kinetic datafor assessing and anticipating contaminantdegradation rates in aqueous systems; electrontransfer and enzyme catalysis were especiallyfeatured. Chris Cramer of the University ofMinnesota discussed a computational electro-chemistry approach developed with Eric V.Patterson of Truman State University andDon Truhlar of the University of Minnesotafor using self-consistent reaction field calcula-

Top: John Straub, Boston UniversityMiddle: Maria Kurnikova, Marquette UniversityBottom: Jacopo Tomasi, University of Pisa


tions to elucidate the reductive dechlorinationof hexachloroethane contaminants in groundwater. William Arnold of the University ofMinnesota discussed joint work with ChrisCramer and Paul Winget on similar problemsinvolving 1,1,2,2-tetrachloroethane. OlafWiest of Notre Dame discussed gas-phase andself-consistent reaction field calculations ofthe breakdown of the herbicide 2,4-dichlorophenoxyacetic acid in the environ-ment, and he elucidated the key radical stepsin the mechanism with special emphasis onhydroxyl radical attack.

The symposium was organized by ChrisCramer, Jiali Gao, Alon McCormick, andDon Truhlar.

In addition to the symposium, the meetingfeatured several other computational contribu-tions from Supercomputing Instituteresearchers. Ahren Jasper reported work withSam Stechmann and Don Truhlar on a trajec-tory surface hopping method with timeuncertainty for simulating the non-Born-Oppenheimer dynamics of photo-initiatedprocesses. The authors believe that this newalgorithm provides a physical solution to thepreviously troubling problem of frustratedhops. Shuhua Ma, Lakshmi Devi Kevasan,Ramkumar Rajamani, and Jiali Gao reportedmolecular dynamics simulations of the cat-alytic mechanisms of human cetheprin K andsqualene cyclase. Brent Gregerson, XabierLopez, Evelyn Mayaan, and Darrin York pre-sented a specific-reaction-parameterHamiltonian for phosphatic hydrolysis and amolecular dynamics study of a transition statemodel of the hammerhead ribosome. TinaPoulsen, Mireia Garcia-Viloca, Jiali Gao, andDon Truhlar presented combined quantummechanical molecular mechanical free energysimulations of the stepwise mechanism ofβ-oxidation by acyl-coenzyme A dehydroge-nase (see page 3). Lakshmi Devi Kevasan,Yirong Mo, and Jiali Gao presented an elec-tronic structure method to calculate pKa valueof imidazolium ion and acetic acid in aqueoussolution.

Finally, Mireia Garcia-Viloca, Jiali Gao,and Don Truhlar reported ensemble-averaged continued on page 16

Top: Carl Melius, Lawrence Livermore National Laboratory (left),and Jim Chelikowsky, University of Minnesota (right)Middle: Edward Maginn, Notre Dame UniversityBottom: (Left to right) Alon McCormick, University of Minnesota,Kendall Thomson, Purdue University, and Randall Snurr,Northwestern University


variational transition state theory calculationswith multidimensional tunneling, carried outwith a new CHARMMRATE module ofCHARMM, for primary and secondary kineticisotope effects for the reduction of 7,8-dihy-drofolate by hydride transfer from NADPHcatalyzed by dihydrofolate reductase. Theclosed conformation of the active site M20loop was found to be conserved through thesimulation. These calculations complementedthe work reported by Professor Hammes-Schiffer in that she used a molecular mechan-ics energy gap coordinate as the reaction coor-dinate whereas this study uses a difference inhydride bond distances, and, furthermore, thetwo groups used different protein force fieldsand substrate potential energy surfaces, yet theMinnesota calculations confirm the Penn Statefindings of distant regions of the enzymebeing coupled with the motion along the reac-tion coordinate. This convergence is veryencouraging for prospects of analyzing cooper-ative protein motions underlying enzymecatalysis, the effects of genomic variability, andthe effects of mutations on protein design. Infact, the symposium and contributed compu-tational chemistry papers as a whole left nodoubt as to the enormous promise of moderncomputational science, especially quantummechanics and simulations with atomic detail,for guiding the critical twenty-first centuryfields of nanomaterials, environmental chem-istry, neurochemistry, and chemical biology.The Supercomputing Institute is grateful to allthe participants for their contributions.

Top: Paul Van Tassell, Wayne State UniversityMiddle: Judith Perlinger, Michigan Technological University Bottom: Paul Tratnyek, Oregon Graduate Institute of Scienceand Technology


Above left: Phillip Gschwend, M.I.T.

Above right: William Arnold, University ofMinnesota

Conference participants during a break.Left to right: Chris Cramer, University of Minnesota;Judith Perlinger, Michigan Technological University;Olaf Wiest, Notre Dame University; Don Truhlar,University of Minnesota; (back to camera) JacopoTomasi, University of Pisa

University of Minnesota students prior to the first presentation.Left to right, front row: Edward Sherer, Benjamin Ellingson, Vanessa Audette, Benjamin Lynch,Amanda WensmannLeft to right, back row: Amy Anshutz, Nathan Shultz

The First Annual NanosimulationWorkshop was held at the Universityof Minnesota’s Twin Cities campus on

August 26, 2002. The workshop was jointlysponsored by the Supercomputing Instituteand the Center for NanoEnergetics Research(CNER). CNER is a research center created inthe spring of 2001 at four university sitesthrough the United States Department ofDefense–University Research Initiative forNanoTechnology (DURINT). The Universityof Minnesota is the lead institution; the othersare the University of Delaware, OklahomaState University, and South Dakota School ofMines and Technology.

The talks included presentations by CNERresearchers and complementary research by adistinguished group of invited speakers. Theworkshop was organized by Don Truhlar.


Symposiums

First Annual Nanosimulation WorkshopNanosimulation Workshop Speakers

Sotiris E. Pratsinis, ETH ZurichAggregate Titania Nanoparticles byCoagulation and Surface Growth

Donald L. Thompson, Oklahoma StateUniversityReactions on Al2O3 Particles

Priya Vashishta, Louisiana State UniversityMultimillion Atom Simulation of NanoSystems on Parallel Computers–Nanopixel,Nanoindentation, and Oxidation ofAluminum Nanoparticles

Carl F. Melius, Lawrence LivermoreNational LaboratoryA Multi-Scale Computational Framework forTreating Complex Chemical Kinetics

Sean Garrick, University of MinnesotaModeling and Simulation of NanoparticleFormation and Growth in Turbulent ReactingFlows

Bruce C. Garrett, Pacific NorthwestNational LaboratoryThermodynamics and Kinetics of AqueousNanoparticles Important in HomogeneousGas-to-Liquid Nucleation

Lance R. Collins, Cornell UniversityEffect of Turbulence on the Nucleation andGrowth of Aerosol Particles

James T. Muckerman, Brookhaven NationalLaboratoryElectronic Particles of Ti8C12

Michael Zachariah, University ofMinnesotaModeling Nanoparticles

Sotiris E. Pratsinis (left), ETH Zurich, and Michael Zachariah,University of Minnesota, at the check-in table.


Jan A. Puszynski (left), South Dakota School of Mines andTechnology, and Carl F. Melius, Lawrence Livermore NationalLaboratory, enjoy a break.

James T. Muckerman (left), Brookhaven National Laboratory, talkswith Robert W. Shaw, U.S. Army Research Office.

Sotiris E. Pratsinis, ETH Zurich, gives his presentation. (Left to right) Donald L. Thompson, Oklahoma State University,David M. Mann, U.S. Army Research Office, and Thomas B. Brill,University of Delaware, discuss Professor Thompson’s talk.

Lance R. Collins (left), Cornell University, and R. Bertrum Diemer,DuPont Engineering Technology, talk during a break.

Alon V. McCormick, University of Minnesota, introduces aspeaker.


Sean Garrick, University of Minnesota, during his talk. Michael R. Berman, Air Force Office of Scientific Research, andRuth M. Doherty, Office of the Undersecretary of Defense forScience and Technology, during a break.

(Left to right) Thomas B. Brill, University of Delaware, BarrieE. Homan, U.S. Army Research Laboratory, and Jan A.Puszynski, South Dakota School of Mines and Technology,enjoy lunch.

David R. Whitcomb and Lilia P. Burleva, both of the EastmanKodak Company, at lunch.

Priya Vashishta, Louisiana State University, during his presenta-tion.

(Left to right) Donald L. Thompson, Oklahoma StateUniversity, Alba Lalitha Ramaswamy, University of Maryland,and Bruce C. Garrett, Pacific Northwest Laboratories, discusstheir research.


Przemyslaw F. Staszewski (left), Grazyna Maria Staszewska, andNathan E. Schultz, all DURINT participants at the Universityof Minnesota, discuss one of the presentations.

(Left to right) Steve P. Rojas, Office of the Undersecretary ofDefense (Acquisition, Technology, and Logistics), Cary F.Chabalowski, U.S. Army Research Laboratory, Joseph A.Lannan, Army Armament Research Development andEngineering Center, and Michael J. McQuaid, U.S. ArmyResearch Laboratory

(Left to right) Chad G. Rumchick, Air Force ResearchLaboratory, Dennis Wilson, Nanotechnologies, Inc., William H.Wilson, Air Force Research Laboratory, Ruth M. Doherty,Office of the Undersecretary of Defense for Science andTechnology, and Steve P. Rojas, Office of the Undersecretary ofDefense (Acquisition, Technology, and Logistics)

Alison Kubota, Lawrence Livermore National Laboratory, talksto Chandrashekhar G. Sowane, University of Minnesota.

(Left to right) Alon V. McCormick, University of Minnesota,and Michael J. McQuaid and Barrie E. Homan, U.S. ArmyResearch Laboratory


The Supercomputing Institute, alongwith the Digital TechnologyCenter, is co-sponsoring a series of

seminars for the Graduate Program inHealth Informatics at the University ofMinnesota. Speakers from the University ofMinnesota, other research institutions, gov-ernment, and industry give presentationson a variety of topics from the health infor-matics field. Some individual seminars arealso co-sponsored by the BioTechnologyInstitute or the Mathematics Colloquium.

The graduate program in Health

Informatics trains students in the applica-tion of computer and information sciencesto the quantitative aspects and decisionneeds of the health and life sciences. HealthInformatics encompasses not only mathe-matics, statistics, and computing, but alsoincludes other engineering, management,and information sciences applied to prob-lems arising in biology, medicine, and thedelivery of health care. The symposiumseries is organized by Professor Lynda Ellisof the Department of Laboratory Medicineand Pathology.

Collaborative Programs

Health Informatics Seminars

Eloise Gelner and Bill Brand, both of theImmunization Registry of the MinnesotaDepartment of Health, gave a talk entitled“Minnesota Immunization InformationConnection” on September 26.

Dennis J. O’Kane’s talk on October 4 was enti-tled “Medical Genomics: Realizing the Promisesof the Human Genome Project.” Dr. O’Kane isfrom the Mayo Clinic and the Mayo MedicalSchool.


Names of University of Minnesota principal investigators appear in bold type.

Research R

eportsAerospace Engineering

and Mechanics

2002/127, August 2002Finite Element Method Simulation of TurbulentWavy Core-Annular Flows Using a k-wTurbulence Model MethodT. Ko, H. G. Choi, R. Bai, and D. D. Joseph

2002/128, August 2002Multiple Equilibrium Positions and Lift ofSingle Particle in Newtonian and Oldroyd-BFluidsT. Ko, N. A. Patankar, and D. D. Joseph

2002/129, August 2002Power Law Correlations for the Lift Force on aParticle in Plane Poiseuille FlowJ. Wang and D. D. Joseph

Astronomy

2002/101, August 2002Numerical Studies of Cosmic Ray Injection andAccelerationH. Kang, T. W. Jones, and U. D. J. Gieseler

2002/115, August 2002Simulations of Nonthermal Electron Transportin Multidimensional Flows: SyntheticObservations of Radio GalaxiesI. L. Tregillis, T. W. Jones, D. Ryu, and C.Park

2002/116, August 2002Simulations of Nonthermal Electron Transportin Multidimensional Flows: Application toRadio GalaxiesT. W. Jones, I. L. Tregillis, and D. Ryu

2002/117, August 2002On the Possible Reason for Nondetection of TeVProtons in Supernova RemnantsM. A. Malkov, P. H. Diamond, and T. W.Jones

Biomedical Engineering

2002/131, August 2002Lipid–Protein Interactions in LipovitellinJ. R. Thompson and L. J. Banaszak

Chemical Engineering and Materials Science

2002/109, August 2002Surface Oxidation Effects on the OpticalProperties of Silicon NanocrystalsI. Vasiliev, J. R. Chelikowsky, and R. M.Martin

2002/110, August 2002First-Principles Density-Functional Calculationsfor Optical Spectra of Clusters and NanocrystalsI. Vasiliev, S. Ögüt, and J. R. Chelikowsky

2002/111, August 2002Local Structure of Liquid GeTe via NeutronScattering and Ab Initio SimulationsJ. Y. Raty, V. V. Godlevsky, J. P. Gaspard, C.Bichara, M. Bionducci, R. Bellissent, R.Céolin, J. R. Chelikowsky, and Ph. Ghosez

2002/112, August 2002Electronic Structure and Spin Polarization ofMnxGa1 - xNL. Kronik, M. Jain, and J. R. Chelikowsky

2002/113, August 2002Hybridization and Bond-Orbital Componentsin Site-Specific X-Ray Photoelectron Spectra ofRutile TiO2J. C. Woicik, E. J. Nelson, L. Kronik, M.Jain, J. R. Chelikowsky, D. Heskett, L. E.Berman, and G. S. Herman

Chemistry

2002/96, July 2002Obtaining the Right Orbitals is the First Step toCalculating Accurate Binding Energies for Cu+

IonB. J. Lynch and D. G. Truhlar

2002/99, August 2002Molecular Simulation of ConcurrentGas–Liquid Interfacial Adsorption andPartitioning in Gas–LiquidChromatographyC. D. Wick, J. I. Siepmann, and M. R.Schure

2002/120, August 2002Direct Diabatization of Electronic States by theFourfold Way. II. Dynamical Correlation andRearrangement ProcessesH. Nakamura and D. G. Truhlar

2002/121, August 2002Vapor–Liquid Phase Equilibria for Linear andBranched Alkane Monolayers Physisorbed onAu(111)J. J. Potoff and J. I. Siepmann

2002/130, August 2002Vapor–Liquid Phase Equilibria of TriacontaneIsomers: Deviations From the Principle ofCorresponding StatesN. D. Zhuravlev, M. G. Martin, and J. I.Siepmann

2002/138, September 2002Quantum Mechanics Studies of the IntrinsicConformation of TrehaloseA. D. French, G. P. Johnson, A.-M. Kelterer,M. K. Dowd, and C. J. Cramer

2002/139, September 2002Internal Loop–Helix Coupling in the Dynamicsof the RNA Duplex (GC*C*AGU-UCGCUGGC)2E. C. Sherer and C. J. Cramer

2002/140, September 2002Parametrization of a Universal Solvation Modelfor Molecules Containing SiliconP. Winget, J. D. Thompson, C. J. Cramer,and D. G. Truhlar

2002/141, September 2002Efficient Aminoacylation of the tRNAAla

Acceptor Stem: Dependence on the 2:71 BasePairP. J Beuning, M. C. Nagan, C. J. Cramer, K.Musier-Forsyth, J.-L. Gelpí, and D. Bashford

2002/142, September 2002Electronic Structure and Bonding inHexacoordinate Silyl–Palladium ComplexesE. C. Sherer, C. R. Kinsinger, B. L. Kormos,J. D. Thompson, and C. J. Cramer

2002/143, September 2002Reductive Dechlorination of 1,1,2,2-TetrachloroethaneW. A. Arnold, P. Winget, and C. J. Cramer

2002/144, September 2002Adiabatic Connection Method for X– +RXNucleophilic Substitution Reactions (X = F, Cl)B. L. Kormos and C. J. Cramer

2002/145, September 2002Discrimination of C1:G72 MicrohelixAla byAlaRS is Based on Specific Atomic GroupsRather Than Conformational Effects: An NMRand MD AnalysisD. A. Kallick, M. C. Nagan, P. J. Beuning, S.Kerimo, M. R. Tessmer, C. J. Cramer, and K.Musier-Forsyth

2002/164, October 2002Vapor-Liquid Interfacial Properties of MutuallySaturated Water/1-Butanol SolutionsB. Chen, J. I. Siepmann, and M. L. Klein

2002/165, October 2002Fluid Properties Simulation Challenge:Predictions by the Great Lakes RegressorsC. D. Wick, J. M. Stubbs, N. D. Zhuravlev,J. I. Siepmann, T. Morrow, E. J. Maginn, J.J. Potoff, S. Wierzchowski, and D. A. Kofke

Civil Engineering

2002/107, August 2002Phosphorus Dynamics in Jessie Lake: Mass FluxAcross the Sediment-Water InterfaceH. Wang, M. Hondzo, and B. Stauffer

2002/118, August 2002Moore’s Law and Numerical ModelingV. R. Voller and F. Porté-Agel

2002/119, August 2002Scale Dependence and Subgrid-Scale Modelingin LESF. Porté-Agel, J. R. Stoll, M. Carper, N.Bjelogrlic, and A. Fagerness

2002/122, August 2002Simulation of Failure Around a CircularOpening in RockA. Fakhimi, F. Carvalho, T. Ishida, and J. F.Labuz

2002/123, August 2002Numerical Simulation of Unsteady CavitatingFlowsC. C. S. Song and Q. Qin

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Supercomputing Institute Research Bulletin Fall 2002

2002/124, August 2002Current Status of CFD for Cavitating FlowsC. C. S. Song

2002/132, August 2002The Effects of Light Competition on theSeasonal Growth of Single and Multiple SpeciesMacrophyte Beds in LakesW. R. Herb and H. G. Stefan

2002/136, August 2002Model for In Situ PerchloroetheneDechlorination via Membrane-DeliveredHydrogenL. W. Clapp, M. J. Semmens, P. J. Novak,and R. M. Hozalski

2002/137, August 2002Modeling of Lake Ice Characteristics in NorthAmericaG. Williams and H. G. Stefan

Computer Science and Engineering

2002/105, August 2002Adapting Algebraic Recursive Multilevel Solvers(ARMS) for Solving CFD ProblemsY. Saad, A. Soulaimani, and R. Touihri

2002/106, August 2002Using the Parallel Algebraic Recursive MultilevelSolver in Modern Physical ApplicationsX. Cai, Y. Saad, and M. Sosonkina

Electrical and Computer Engineering

2002/134, August 2002Kalman Filtering for Power Estimation inMobile CommunicationsT. Jiang, N. D. Sidiropoulos, G. B.Giannakis

2002/135, August 2002Improving Processor Performance by Simplifyingand Bypassing Trivial ComputationsJ. J. Yi and D. J. Lilja

2002/146, September 2002Effects of Processor Parameter Selection onSimulation ResultsJ. J. Yi and D. J. Lilja

2002/147, September 2002The Spatial Characteristics of Load InstructionsJ. J. Yi, R. Sendag, and D. J. Lilja

2002/148, September 2002The Spatial Characteristics of Load Instructionsin the SPEC 2000 BenchmarksJ. J. Yi, R. Sendag, and D. J. Lilja

2002/151, September 2002A Statistically Rigorous Approach for ImprovingSimulation MethodologyJ. J. Yi, D. J. Lilja, and D. M. Hawkins

2002/152, September 2002Effects of Grain Boundaries on MagneticProperties of Recording MediaR. H. Victora, S. D. Willoughby, J. M.MacLaren, and J. Xue

2002/160, October 2002A Statistically Rigorous Method for Workloadand Input Set CharacterizationJ. J. Yi, D. M. Hawkins, and D. J. Lilja

2002/163, October 2002Using Incorrect Speculation to Prefetch Data ina Concurrent Multithreaded ProcessorY. Chen, R. Sendag, and D. J. Lilja

Geology and Geophysics

2002/100, August 2002The Physical Properties of Marine Sediments asInferred from Wavelet Correlation AnalysisA. Kritski, D. A. Yuen, and A. P. Vincent

2002/103, August 2002Dynamical Clustering of Red Blood Cells inCapillary VesselsK. Boryczko, W. Dzwinel, and D. A. Yuen

2002/104, August 2002Substitution Mechanism of Al2O3 in MgSiO3Perovskite Under High Pressure Conditions asDeduced From First Principles CalculationsT. Yamamoto, D. A. Yuen, and T. Ebisuzaki

2002/114, August 2002Clustering Revealed in High-ResolutionSimulations and Visualization of Multi-Resolution Features in Fluid-Particle ModelsK. Boryczko, W. Dzwinel, and D. A. Yuen

2002/125, August 2002Performances for Spectral Large-Scale ParallelImplementation of 2-D Poisson Equation Witha Periodic LatticeX. Thibert-Plante, D. A. Yuen, and A. P.Vincent


Research R

eports

2002/126, August 2002Four Dynamical Regimes for a Starting PlumeModelC. A. Hier Majumder, D. A. Yuen, and A. P.Vincent

2002/153, September 2002Continuous Wavelet-Like Filter for a SphericalSurface and Its Application to LocalizedAdmittance Function on MarsM. Kido, D. A. Yuen, and A. P. Vincent

2002/154, September 2002A Simplified Mantle Convection Model forThermal Conductivity StratificationT. K. B. Yanagawa, M. Nakada, and D. A.Yuen

2002/155, September 2002Web-Based Interrogation of Large-ScaleGeophysical Data Sets From Handheld DeviceZ. A. Garbow, G. Erlebacher, D. A. Yuen, J.M. Boggs, and F. W. Dubuffet

2002/156, September 2002Role of Wavelets in the Physical and StatisticalModeling of Complex Geological ProcessesD. A. Yuen, G. Erlebacher, O. V. Vasilyev, D.E. Goldstein, and M. Fuentes

2002/157, September 2002A Wavelet Toolkit for Visualization and Analysisof Large Data Sets In Earthquake ResearchG. Erlebacher and D. A. Yuen

2002/158, September 2002Multi-Resolution Tectonic Features Over theEarth Inferred From the Wavelet TransformedGeoidL. Vecsey, C. A. Hier Majumder, and D. A.Yuen

2002/161, October 2002Multi-Resolution Clustering Analysis and 3-DVisualization of Multitudinous SyntheticEarthquakesW. Dzwinel, D. A. Yuen,Y. Kenoko, K.Boryczko, and Y. Ben-Zion

Mathematics

2002/150, September 2002On Correlations of CM-Type Maass WaveformsUnder the Horocyclic FlowD. A. Hejhal and H. Christianson

2002/159, October 2002Conservative Multigrid Methods for Cahn-Hilliard FluidsJ. Kim, K. Kang, and J. Lowengrub

Mechanical Engineering

2002/149, September 2002Direct Numerical Simulation of NanoparticleCoagulation in a Temporal Mixing LayerS. Modem, S. C. Garrick, M. R. Zachariah,and K. E. J. Lehtinen

2002/162, October 2002Numerical Modeling of Silicon Oxide ParticleFormation and Transport in a One-Dimensional Low-Pressure Chemical VaporDeposition ChamberS.-M. Suh, M. R. Zachariah, and S. L.Girshick

Neuroscience

2002/108, August 2002Computing Transient Gating Charge Movementof Voltage-Dependent Ion ChannelsA. Varghese and L. M. Boland

Physics

2002/97, July 2002Anomalously Light States in Super-Yang-MillsChern-Simons TheoryJ. R. Hiller, S. S. Pinsky, and U. Trittmann

2002/98, July 2002Nonperturbative Solution of SupersymmetricGauge TheoriesJ. R. Hiller

2002/102, August 2002Vortices in Layered Superconductors withColumnar Pins: A Density Functional StudyC. Dasgupta and O. T. Valls

2002/133, August 2002Properties of the Bound States of Super-Yang–Mills-Chern–Simons TheoryJ. R. Hiller, S. S. Pinsky, and U. Trittmann


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