Supercomputing Institute - msi.umn.edu. Kaushik Dayalis working with Department of Aerospace...

Recently, scientists have beenable to use an increasing di-versity of experimental tech-

niques to investigate diseases at themolecular level. These techniquesinclude various high-throughput ex-perimental methods to characterizechromosomal abnormalities, generegulation, gene expression, andprotein expression. To enable the re-search community to benefit fromthese technical advances, the MayoClinic and the University of Min-

nesota are engaged in collaborativeefforts to acquire experimentalequipment to be shared by bothgroups.

To support the activity of thecore facilities that operate thisequipment, Mayo and the Universi-ty have implemented or are current-ly implementing information-tech-nology (IT) infrastructures. Thesesystems will support core labs byproviding many operational featuressuch as sample tracking, financial

activities, and management ofequipment and human resources.

Supercomputing Institute

Supercomputing Infrastructure

The Research Organizer for Project Informa-

tion EXchange—TROPIX

Volume 23, Number 3

Also in This Issue

Call for Summer Intern Applica-tions . . . . . . . . . . . . . . . . . . .4

Research Scholars 2007–08 . . .5

AAAS Fellows Named . . . . . . .9

Research Reports . . . . . . . . . .10

Fall 2007 Research Bulletin of the Supercomputing Institute

for Digital Simulation and Advanced Computation

Institute of Technology

continued on page 2

Figure 1. Schematic of The Research Organizer for Project Information EXchange (TROPIX). Users will have a single seamlessinterface to core laboratories.


Supercomputing Institute Research Bulletin Fall 20072

But very little IT infrastructure ex-ists to support investigators in mak-ing use of these core labs: discover-ing services, annotating samples,submitting requests, tracking theprogress of their project, and facili-tating interaction between the inves-tigator and the biostatisticians orbioinformatics experts in charge ofthe analysis of the data produced.This missing support is even morecritically needed when consideringthat the cores and analytical re-sources are located at multiple sites.

To fulfill this need, the Super-computing Institute and the MayoClinic are collaborating on a projectcalled The Research Organizer forProject Information eXchange(TROPIX). TROPIX is a Web-based environment designed to sup-port researchers in submitting re-quests for core laboratory services

and in managing access to the re-sulting data. It will provide re-searchers with a single seamless in-terface to core laboratories for for-mulating a request, laying out theexperiment, providing sample anno-tation, accessing resulting data, andcommunicating this data to statisti-cians and informatics experts foranalysis. This process will be inde-pendent of the physical location ofthe core facility. A schematic of theTROPIX system is shown in Figure1.

As new instrumentation produceslarger volumes of data, it becomesmore difficult to transform the datainto knowledge without its beingplaced in a context that includes theexperimental design and sample in-formation. This data about data—called “metadata”—is crucial notonly for organizing and locating the

data, but also for its analysis.TROPIX will include tools to cap-ture metadata at core experimentalfacilities where data is first collected.The tools developed will allow re-searchers to easily access and processthe data collected at core lab facili-ties.

An important aspect of TROPIXis the successful integration of alltools into an environment where re-searchers can easily retrieve data andperform tasks that they do today onSupercomputing Institute and otherresources. The system being devel-oped will use a service-oriented ar-chitecture to provide data and ana-lytical resources to the researchers.TROPIX will allow researchers torecord appropriate information onthe origin of biospecimens to be an-alyzed; assemble experiment re-quests in accordance with experi-

Figure 2. Conceptual diagram of TROPIX architecture. The user interface modules are shown in the top section, and the federat-ed data and metadata sources are in the lower section.

mental specifications defined bycore facilities; track the progress ofexperiments; locate and access ex-perimental data produced; and facil-itate data analysis by linking experi-mental data to biostatistician andbioinformatics resources.

A graphical front end will allowcore labs to deposit data and alsoallow users to access, analyze, andshare data with other researchers.The grid infrastructure being devel-oped will also allow queries of dataor metadata that researchers havechosen to make public. TheTROPIX system is designed to be a“federated” system, meaning that itwill be implemented as distinct soft-ware components that communicatevia well-defined interfaces. This isnecessary to maintain security andaccess control while at the sametime presenting a unified figure tousers. Figure 2 illustrates theTROPIX infrastructure.

Services are being developed insuch a way that caGrid services canbe added to the new grid. caGrid isa core set of grid tools that is beingdeveloped as part of the caBig proj-ect funded by NCI (seehttps://cabig.nci.nih.gov/work-spaces/Architecture/caGrid for moreinformation). The caBig communityis developing many standard datatypes to communicate biological in-formation.

An important aspect of theTROPIX architecture is security.The security framework has fourcomponents, including de-identifi-cation, physical security, confiden-tiality, authentication, and authori-zation. De-identification involvesremoving all personal identifying in-formation from data relevant tohuman samples. Physical securityprovides for protection of the de-vices from unauthorized access.Confidentiality covers encryption of

the communication to ensure priva-cy and to prevent unauthorizedusers from sending unauthorized re-quests to the system. Authenticationverifies the credentials of the userand certifies that the person is whohe or she claims. The TROPIX sys-tem will use existing authenticationprotocols existing at the Universityand Mayo. The TROPIX authoriza-tion system will give users full con-trol over who can access their dataand metadata.

The TROPIX security systemwill employ the combination ofpublic/private key cryptography forencryption and certificates verifica-tion of signatures as defined by theX.509 standard. All communica-tions will be encrypted using stan-dard SSL connections. A schematicof the security architecture is shownin Figure 3.

The project began this summer


Fall 2007 Supercomputing Institute Research Bulletin 3

Figure 3. Schematic of TROPIX architecture’s secure communication.

continued on page 4

and is making rapid progress. Theteam has a grid in operation at theSupercomputing Institute for test-ing and development. They are de-veloping services that will handlethe data collected by the Genotyp-ing Shared Resource at the MayoClinic and the Microarray Core Fa-cility at the University by the end ofthe two-year project.

TROPIX is supported by directfunding from the Minnesota Part-nership for Biotechnology andMedical Genomics (www.minneso-tapartnership.info). The Partner-

ship, which includes Mayo, theUniversity, and the State of Min-nesota, is a collaborative venturethat seeks to position Minnesota asa world leader in biotechnology andmedical genomics applications thatwill result in important new medicaldiscoveries. The TROPIX project isintended to be a preliminary step tocreating a similar infrastructure thatwill be available for the entire Part-nership community. Most of the in-frastructure created will be readilytransferable to new cores.

Dr. H. Birali Runesha, Director

of Scientific Computing and Appli-cations at the Supercomputing In-stitute, and Dr. Jean-Pierre Kocher,Bioinformatics Core Director at theDepartment of Health Research,Mayo Clinic (Rochester, Minneso-ta), are the co-Principal Investiga-tors for this project. Other person-nel include Dr. Ben Lynch, Mr.Mark Nelson, and Mr. JohnChilton at the Supercomputing In-stitute, and Mr. David Mead andMs. Traci St. Martin at Mayo.


Supercomputing Institute Programs


Summer 2008Undergraduate Internship Program

The Supercomputing Institute is pleased to announce its Undergraduate Internship Program for Summer2008. Appointments are for full-time, 10-week internships, and will run from June 2 through August 8,2008. A student interested in becoming an intern must still be an undergraduate in August 2008 andmust be a citizen or permanent resident of the United States or its possessions. Interns will be paid astipend of $5,000 and are responsible for their own travel and housing costs.

All applications are evaluated competitively based on the qualifications of the applicant and the availabili-ty of a suitable project. Prospective applicants should review the research projects list and indicate projectsin which they are interested, although they may be offered other projects due to availability.

Complete application information, application forms, and project lists are available on the Supercomput-ing 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: [email protected]

All applications and letters of recommendation must be received byFebruary 29, 2008.



Each year, the SupercomputingInstitute provides grants forresearch scholarships for su-

percomputing research with Insti-tute Principal Investigators. The In-stitute has awarded 10 researchscholarships for 2007–2008. Pro-jects are also funded by outsideagencies; this year, outside fundingagencies include the Human Fron-tier Science Program, the NationalCenter for Earth-surface Dynamics,the National Institutes of Health,the National Science Foundation,the Russell Penrose Professor discre-tionary account, and the Office ofNaval Research.

Dr. Pierre Carrier is workingwith Professor Renata M. Wentz-covitch, Department of ChemicalEngineering and Materials Science,Supercomputing Institute Fellow,and Director of the Virtual Labora-tory for Earth and Planetary Materi-als (VLab). Dr. Carrier is workingon a project to evaluate the elasticproperties of materials known orspeculated to exist under severalalloy compositions in the earth’s

crust, mantle, or core. The methodthey are using has been shown to beextremely successful for cubic,tetragonal, and orthorhombic struc-tures. Dr. Carrier is working to gen-eralize the method to all crystalsymmetries and is implementing astable and general algorithm withinthe service-oriented grid/portal sys-tem through the VLab(www.vlab.msi.umn.edu).

Dr. Kaushik Dayal is workingwith Department of Aerospace En-gineering and Mechanics ProfessorRichard D. James and Assistant Pro-fessor Ryan S. Elliott. The objectiveof their research is to develop multi-scale methods for the prediction ofthe behavior of nanostructures thatchange shape when subjected to achange of temperature or mechani-cal and electromagnetic loads. Amain goal is the development andimplementation of new techniquesthat take advantage of the “Objec-tive Structure” framework to dra-matically reduce computation ex-pense for molecular dynamics andatomistic calculations. Dr. Dayal’s

current focus is to couple atomisticcalculations with emerging methodsin the field of numerical bifurca-tion.

Dr. L. Michel Espinoza-Fonse-ca is working with the group ofProfessor David D. Thomas, De-partment of Biochemistry, Molecu-lar Biology, and Biophysics and Su-percomputing Institute Fellow. Thegoal of their project is to use com-puter simulations to understand theordering or disordering effect ofphosphorylation muscle proteinsusing two systems as a model: theregulatory light chain of smoothmuscle myosin and phospholam-ban. Dr. Espinoza-Fonseca will alsobe addressing the energetics of theordering and disordering effect ofphosphorylation in order to create alink between conformational transi-tions and thermodynamics of phos-phorylation in muscle proteins.

Dr. Martin Kenward is workingwith the research group of AssistantProfessor Kevin D. Dorfman, De-partment of Chemical Engineeringand Materials Science. He is explor-

Research Scholars, 2007–2008

Above: Dr. Pierre Carrier, Dr. Kaushik Dayal

ing the biophysical mechanisms un-derlying DNAzyme catalysis.DNAzymes are short sequences ofsingle-stranded DNA that act as cat-alysts when folded in the presenceof a cofactor. The specific aim ofthe project is to correlate insightsgained from statistical physics with

available biochem-ical rate data inorder to determinethe structural fea-tures that give riseto stable, highlyactive DNAzymes.

Dr. RyanOlson is workingwith Regents Pro-fessor Donald G.Truhlar, Depart-ment of Chemistryand Supercomput-ing Institute Fel-low. They are de-veloping new com-putational toolsfor photochem-istry and solventeffects on spectro-scopic observables.These tools willinclude computerprograms for di-rect diabatizationof correlated wavefunctions, meth-ods for calculatingsolvatochromicshifts, and algo-rithms for fittingthe coupled poten-tial energy surfacesneeded for multi-state dynamics cal-culations.

Dr. JoongcheolPaik is workingwith ProfessorFotis Sotiropoulos,Department of

Civil Engineering, Director of St.Anthony Falls Laboratory and Su-percomputing Institute Fellow, andAssociate Professor Fernando Porté-Agel, Department of Civil Engi-neering, St. Anthony Falls Laborato-ry and Supercomputing Institute

Fellow. Dr. Paik’s project is part oflarger effort ongoing at the St. An-thony Fall Laboratory that is aimedat developing a world-class experi-mental and computational researchprogram in the area of streamrestoration. The number of streamrestoration projects has risen dra-matically in the past several years,but strategies are based almost en-tirely on engineering intuition andad-hoc site-specific experimentation.This group’s goal is to develop thefirst high-resolution computationalframework for simulating turbulentflows in natural streams with real-life restoration structures at full-scale Reynolds numbers using co-herent structure-resolving turbu-lence models.

Dr. Abdallah Sayyed-Ahmad isworking with Assistant ProfessorYiannis Kaznessis, Department ofChemical Engineering and Materi-als Science and Supercomputing In-stitute Fellow. He has investigatedthe viability of utilizing relativebinding free energy calculations andmodel membrane mimics to predictthe antimicrobial activity and he-molytic toxicity of antimicrobialpeptides (AMPs) using the scorpi-on-derived AMP IsCT and two ofits analogs as test cases. The overallrankings of the relative bindingaffinity values of the two analogs tosodium dodecylsulphate and dode-cylphosphatidylcholine micelles arefound to be correlated with the ex-perimental antimicrobial activityand cytotoxicity measurements, re-spectively. The evident connectionof biophysical measurements of asimple model to biological functionand pharmacological profiles is sur-prising, but promising. Dr. Sayyed-Ahmad is investigating the generali-ty of these results by studying morepeptide structural classes with the



Above: Dr. L. Michel Espinoza-Fonseca, Dr. Martin KenwardDr. Ryan Olson



ultimate goal of engineering novelAMPs. Dr. Sayyed-Ahmad is alsoinvestigating the ability of continu-um approaches and implicit mem-brane models to predict the mostprobable orientation of the b-hair-pin antimicrobial peptide Protegrin-1 (PG-1) in DLPC lipid bilayers bycalculating the difference in thetransfer free energy from an aqueousenvironment to a membrane-waterenvironment. Results obtained froman implicit model can be utilized tosystematically provide starting con-figurations for full atomistic MDsimulation studies.

Dr. Carlos Silva-Lopez is work-ing with Professor Darrin M. York,Department of Chemistry and Su-percomputing Institute AssociateFellow. His project studies the phos-phoryl transfer in b-phosphogluco-mutase and the phosphoryl transes-terification in the hammerhead ri-bosome, based on the very recentlyreported crystallographic structuresof trapped intermediates for bothmacromolecules. This phosphorylchemistry is ubiquitous in biologyand has implications in the molecu-lar mechanisms of cell signaling,transcription, respiration, and other

functions. Dr.

LingchunSong is work-ing with Pro-fessor JialiGao, Depart-ment ofChemistry andSupercomput-ing InstituteFellow. He isinvolved withtwo projects inthe Gao labo-ratory. Thefirst uses abinitio valencebond theoryin combinedquantum me-chanical and molecular mechanicalpotentials in molecular dynamicssimulations to study chemical reac-tions in solutions, with an emphasison reduction and oxidation process-es and charge transfer systems in so-lution. The second project attemptsto extend previously developedmodeling methods to biological sys-tems, especially to modeling enzy-matic reactions.

Dr. Karen Tang is working withProfessor Judith Berman, Depart-ment of Genetics, Cell Biology, andDevelopment. Her project concernsglobal analysis of gene expressionand genome organization in theyeast Candida albicans, a humanpathogen. It extends on work begunby Professor Berman and her col-league Professor Naama Barkai,Weizmann Institute, Rehovot, Is-rael, which uses computational ap-

Above: , Dr. Abdallah Sayyed-Ahmad, Dr.Carlos Silva-Lopez

Above: Dr. Joongcheol Paik



Above: Dr. Lingchun Song, Dr. Karen Tang

proaches to reduce the inherentcomplexity in biological systemsfrom thousands of genes per organ-ism to the level of tens of expressionmodules composed of genes thatfunction together under specific ex-perimental conditions. These mod-ules often represent the major com-ponents of a biological system and,because there are few of them, they

can be used to understand, in broadstrokes, how organisms organizetheir components to execute tasks.Dr. Tang is working on several proj-ects intended to extend this methodso that it can be used by other re-searchers.

The Research Scholarship pro-gram is being discontinued after the2007–2008 academic year. Applica-

tions will no longer be accepted forthis program. The funds formerlyavailable will be used instead to es-tablish a program of seed grants inhigh-performance computing. Moreinformation will be available soonon our Web site.

Supercomputing Institute People


Supercomputing Institute PIs Named AAAS Fellows

Four Principal Investigators (PIs) of the Supercomputing Institute have been named Fellows ofthe American Association for the Advancement of Science (AAAS). They are:

Professor Judith Berman, Department of Genetics, Cell Biology, and Devel-opment. The Berman research group uses the Basic Sciences Computing Lab-oratory (BSCL) and the Computational Genetics Laboratory to aid in theirinvestigations into the human pathogenic fungus Candida albicans.

Professor David J. Lilja, Head, Department of Electrical and Computer En-gineering and Supercomputing Institute Fellow. Professor Lilja and his re-search group use MSI supercomputers in their work in designing high-per-formance and parallel processor systems.

Professor John D. Lipscomb, Department of Biochemistry, Molecular Biolo-gy, and Biophysics. The Lipscomb group uses the BSCL in their research intooxygenase enzymes, which are compounds that utilize molecular oxygen to ox-idize a wide range of biological and manmade compounds with the incorpora-tion of one or both atoms of oxygen into the products.

Regents Professor Lanny D. Schmidt, Department of Chemical Engineeringand Materials Science and Supercomputing Institute Associate Fellow. Profes-sor Schmidt and his group use reaction kinetics and complex fluid dynamicsto create models on the supercomputers that describe oxidation processes re-lated to their research into catalysts for the partial oxidation of fuels.

More-detailed descriptions of the work these PIs do using Institute resources can be found inour Annual Research Report, which is online at: www.msi.umn.edu/ general/Reports/annual.html

AAAS Fellows are selected based on their contributions to science and technology. The AAASannounced this year’s Fellows in the October 26, 2007 issue of the journal Science and on theirWeb site (www.sciencemag.org/).


Aerospace Engineering

and Mechanics

2007/146, September 2007Self-Intersection in an AnisotropicSolid in the Absence of Singularity—Part I: Analytical ResultsA. R. Aguiar and R. Fosdick

2007/147, September 2007Self-Intersection in an AnisotropicSolid in the Absence of Singularity—Part II: Computational ResultsA. R. Aguiar, R. Fosdick, and J. A. G. Sanchez

2007/174, October 2007A Numerical Method for DNS/LES ofTurbulent Reacting FlowsJ. Doom, Y. Hou, and K. Mahesh

Agronomy and Plant

Genetics

2007/234, November 2007 and CB 2007-75

A Walk on the Wild Side: MiningWild Wheat and Barley Collectionsfor Rust Resistance GenesB. J. Steffenson, P. Olivera, J. K.Roy, Y. Jin, K. P. Smith, and G. J.Muehlbauer

Biochemistry, Molecular

Biology, and Biophysics

2007/157, September 2007 and CB 2007-55

Mechanisms of Occupational Asthma:Not All Allergens Are EqualJ. F. Regal, A. L. Greene, and R. R.Regal

2007/164, October 2007 and CB 2007-59

Arylamine N-Acetyltransferases: Char-acterization of the Substrate Specifici-ties and Molecular Interactions of En-vironmental Arylamines With HumanNAT1 and NAT2L. Liu, A. Von Vett, N. Zhang, K. J.Walters, C. R. Wagner, and P. E.Hanna

2007/172, October 2007 and CB 2007-60

Finding Intermediates in the O2 Acti-vation Pathways of Non-Heme IronOxygenasesE. G. Kovaleva, M. B. Neibergall,S. Chakrabarty, and J. D. Lipscomb

2007/189, October 2007 and CB 2007-65

Molecular Dynamics Simulations Re-veal a Disorder-to-Order Transitionon Phosphorylation of Smooth MuscleMyosinL. M. Espinoza-Fonseca, D. Kast,and D. D. Thomas

2007/195, November 2007 and CB 2007-67

PRR5, a Novel Component of mTORComplex 2, Regulates Platelet-derivedGrowth Factor Receptor β Expressionand SignalingS.-Y. Woo, D.-H. Kim, C.-B. Jun,Y.-M. Kim, E. Vander Haar, S. Lee,J. W. Hegg, S. Bandhakavi, T. J.Griffin, and D.-H. Kim,

2007/196, November 2007 and CB 2007-68

iTRAQ Reagent-Based QuantitativeProteomic Analysis on a Linear IonTrap Mass SpectrometerT. J. Griffin, H. Xie, S. Bandhakavi,J. Popko, A. Mohan, J. V. Carlis,and L. Higgins

2007/210, November 2007 and CB 2007-70

Extensive Mutagenesis ExperimentsCorroborate a Structural Model forthe DNA Deaminase Domain ofAPOBEC3GK.-M. Chen, N. Martemyanova,Y. Lu, K. Shindo, H. Matsuo, andR. S. Harris

Biomedical Engineering

2007/156, September 2007 and CB 2007-54

Microtubule Assembly Dynamics atthe NanoscaleH. T. Schek III, M. K. Gardner,J. Cheng, D. Odde, and A. J. Hunt

2007/190, October 2007Simulation of Flow Around a Thin,Flexible Obstruction by Means of aDeforming Grid Overlapping a FixedGridK. Liu, H. Radhakrishnan, andV. H. Barocas

2007/191, October 2007 and CB 2007-66

Deterministic Material-Based Averag-ing Theory Model of Collagen GelMicromechanicsP. L. Chandran and V. H. Barocas

2007/227, November 2007 and CB 2007-71

Multiscale, Structure-Based Modelingfor the Elastic Mechanical Behavior ofArterial WallsT. Stylianopoulos and V. H. Barocas

2007/228, November 2007 and CB 2007-72

Volume-Averaging Theory for theStudy of the Mechanics of CollagenNetworksT. Stylianopoulos and V. H. Barocas

2007/229, November 2007 and CB 2007-73

Three-Dimensional Simulation ofAnisotropic Cell-Driven Collagen GelCompactionT. K. Ohsumi, J. E. Flaherty, M. C.Evans, and V. H. Barocas

Center for Drug Design

2007/143, September 2007 and CB 2007-49

A Mechanism-Based Aryl Carrier Pro-tein/Thiolation Domain AffinityProbeC. Qiao, D. J. Wilson, E. M. Ben-nett, and C. C. Aldrich

2007/148, September 2007 and CB 2007-50

Rationally Designed Dual Inhibitorsof HIV Reverse Transcriptase and Inte-graseZ. Wang, E. Bennett, D. J. Wilson,C. Salomon, and R. Vince

Names of Supercomputing Institute principal investigators appear in bold type.

Research Reports

2007/150, September 2007 and CB 2007-52

Synthesis of 4-phenoxybenzamide Ade-nine Dinucleotide as NAD AnalogueWith Inhibitory Activity againstEnoyl-ACP Reductase (InhA) of My-cobacterium TuberculosisL. Bonnac, G.-Y. Gao, L. Chen,K. Felczak, E. Bennett, H. Xu,T. Kim, N. Liu, H. Oh, P. J. Tonge,and K. W. Pankiewicz

Chemical Engineering

and Materials Science

2007/155, September 2007First Principles Investigation of thePostspinel Transition in Mg2SiO4Y. G. Yu, R. M. Wentzcovitch,T. Tsuchiya, K. Umemoto, and D. J.Weidner,

2007/230, November 2007Tailoring Self-Assembled MetallicPhotonic Crystals for Modified Ther-mal EmissionS. E. Han, A. Stein, and D. J. Nor-ris

Chemistry

2007/132, August 2007Evaluation of Various DFT Protocolsfor Computing 1H and 13C Chemi-cal Shifts to Distinguish Stereoisomers:Diastereomeric 2-, 3-, and 4-Methyl-cyclohexanols as a Test SetK. W. Wiitala, Z. F. Al-Rashid,V. Dvornikovs, T. R. Hoye, andC. J. Cramer

2007/133, August 2007Mononuclear Cu-O2 Complexes:Geometries, Spectroscopic Properties,Electronic Structures, and ReactivityC. J. Cramer, and W. B. Tolman

2007/134, August 2007Aromatic Hydroxylation Reactivity ofa Mononuclear Cu(II)-AlkylperoxoComplexA. Kunishita, J. Teraoka, J. D. Scan-lon, T. Matsumoto, M. Suzuki, C. J.Cramer, and S. Itoh

2007/135, August 2007Heterobimetallic Dioxygen Activation:Synthesis and Reactivity of Mixed Cu-Pd and Cu-Pt Bis(µ-oxo) ComplexesJ. T. York, A. Llobet, C. J. Cramer,and W. B. Tolman

2007/136, August 2007Self-Sorting Chiral Subcomponent Re-arrangement During CrystallizationM. Hutin, C. J. Cramer, L. Gagliar-di, A. R. M. Shahi, G. Bernardinelli,R. Cerny, and J. R. Nitschke

2007/137, August 2007Benzylic Cations With Triplet GroundStates: Computational Studies of ArylCarbenium Ions, Silylenium Ions, Ni-trenium Ions, and Oxenium Ions Sub-stituted With Meta π DonorsA. H. Winter, D. E. Falvey, C. J.Cramer, and B. F. Gherman

2007/138, August 2007Three Polymorphs of 4-4’-diiodoben-zalazine, and 4-chloro-4’-iodobenza-lazineC. R. Ojala, W. H. Ojala, D. Brit-ton, and C. J. Cramer

2007/176, October 2007A Charge-Dependent Model forMany-Body Polarization, Exchangeand Dispersion Interactions in HybridQM/MM CalculationsT. J. Giese, and D. M. York

2007/177, October 2007Extension of Adaptive Tree Code andFast Multipole Methods to High An-gular Momentum Particle ChargeDensitiesT. J. Giese and D. M. York

2007/178, October 2007Contracted Auxiliary Gaussian BasisIntegral and Derivative EvaluationT. J. Giese, and D. M. York

2007/198, November 2007Mixed-Valence States Formation inConformationally Flexible Metal-free5,10,15,20-tetraferrocenylporphyrinand 5,10-bisferrocenyl-15,20-bisphenylporphyrinV. N. Nemykin, C. D. Barrett,R. G. Hadt, R. I. Subbotin, A. Y.Maximov, E. V. Polshin, and A. Y.Koposov

2007/199, November 2007Mercury-Free Preparation, Character-ization, and Molecular Structure ofTricyanovinylferrocene Using an Un-usual Reaction Between Ferrocene andTetracyanoethyleneV. N. Nemykin, A. Y. Maximov, andA. Y. Koposov

2007/200, November 2007Influence of Molecular Geometry, Ex-change-Correlation Functional, andSolvent Effects in the Modeling of Ver-tical Excitation Energies in Phthalo-cyanines Using TDDFT and PCM-TDDFT Methods: Can ModernComputational Chemistry MethodsExplain Experimental Controversies?V. N. Nemykin, R. G. Hadt, R. V.Belosludov, H. Mizuseki, andY. Kawazoe

2007/201, November 2007Preparation, Characterization, Molec-ular and Electronic Structures,TDDFT, and TDDFT/PCM Study ofthe Solvatochromism in Cyanovinyl-ferrocenesV. N. Nemykin, E. A. Makarova,J. O. Grosland, R. G. Hadt, andA. Y. Koposov

2007/212, November 2007Dumbbells and Onions in TernaryNucleationR. B. Nellas, B. Chen, and J. I.Siepmann

2007/213, November 2007Retention Mechanism in Reversed-Phase Liquid Chromatography: AMolecular PerspectiveJ. L. Rafferty, L. Zhang, J. I. Siep-mann, and M. R. Schure

2007/214, November 2007Prediction of the Bubble Point Pres-sure for the Binary Mixture ofEthanol and 1,1,1,2,3,3,3-heptafluo-ropropane From Gibbs EnsembleMonte Carlo Simulations using theTraPPE Force FieldN. Rai, J. L. Rafferty, A. Maiti, andJ. I. Siepmann

Research Reports


Research Reports


2007/215, November 2007Prediction of Viscosities and Vapor-Liquid Equilibria for Five PolyhydricAlcohols by Molecular SimulationM. S. Kelkar, J. L. Rafferty, E. J.Maginn, and J. I. Siepmann

2007/216, November 2007Transferable Potentials for PhaseEquilibria. 9. Explicit Hydrogen De-scription of Benzene and Five-Mem-bered and Six-Membered HeterocyclicAromatic CompoundsN. Rai and J. I. Siepmann

2007/217, November 2007Spatial Correlation of Dipole Fluctua-tions in Liquid WaterM. J. McGrath, J. I. Siepmann, I.-F.W. Kuo, and C. J. Mundy

2007/224, November 2007Monte Carlo Simulations of an Isolat-ed n-Octadecane Chain Solvated inWater-Acetonitrile MixturesL. Sun, J. I. Siepmann, and M. R.Schure

2007/225, November 2007Study of Bite Angle Effects in Hydro-formylationP. D. Achord, P. Kiprof, andB. Barker

Civil Engineering

2007/193, November 2007Detached Eddy Simulation of FlowAround Two Wall-Mounted Cubes inTandemJ. Paik, F. Sotiropoulos, andF. Porté-Agel

2007/194, November 2007Dynamic Models for the Subgrid ScaleMixing of Reactants in AtmosphericTurbulent Reacting FlowsJ.-F. Vinuesa and F. Porté-Agel

2007/203, November 2007Subfilter-Scale Fluxes Over a SurfaceRoughness Transition. Part I: Mea-sured Fluxes and Energy Transfer RatesM. A. Carper and F. Porté-Agel

2007/204, November 2007Subfilter-Scale Fluxes Over a SurfaceRoughness Transition. Part II: A Pri-ori Study of Large-Eddy SimulationModelsM. A. Carper and F. Porté-Agel

2007/218, November 2007Large-Eddy Simulation of the StableAtmospheric Boundary Layer usingDynamic Models With Different Aver-aging SchemesR. Stoll and F. Porté-Agel

2007/219, November 2007From Imaging to Material Identifica-tion: A Generalized Concept of Topo-logical SensitivityB. Guzina and I. Chikichev

2007/220, November 2007A Linear Sampling Approach to In-verse Elastic Scattering in Piecewise-Homogeneous DomainsB. Guzina and A. I. Madyarov

2007/221, November 2007A Linear Sampling Method for the In-verse Transmission Problem in Near-Field ElastodynamicsK. Baganas, B. Guzina, A. Char-alambopoulos, and G. D. Manolis

2007/222, November 2007Elastic Scatterer Reconstruction via theAdjoint Sampling MethodS. N. Fata, and B. Guzina

2007/223, November 2007Subgrid-Scale Transport of ReactingScalars in Large-Eddy Simulations ofAtmospheric Boundary LayersJ.-F. Vinuesa, F. Porté-Agel, S. Basu,and R. Stoll

2007/231, November 2007Transient Heat Conduction in aPorous MediumE. Gordeliy, S. L. Crouch, and S. G.Mogilevskaya

2007/232, November 2007Transient Heat Conduction in aMedium with Two Circular Cavities:Semi-Analytical SolutionE. Gordeliy, S. L. Crouch, and S. G.Mogilevskaya

Computer Science

and Engineering

07/139, September 2007A Comparison of Preconditioners forComplex-Valued MatricesD. Osei-Kuffuor and Y. Saad

2007/140, September 2007On Complex Preconditioning for theSolution of the Kohn-Sham Equationfor Molecular TransportD. Osei-Kuffuor, L. Kong, Y. Saad,and J. R. Chelikowsky

2007/154, September 2007COBRA: An Adaptive Runtime Bina-ry Optimization Framework for Mul-tithreaded ApplicationsJ. Kim, W.-C. Hsu, and P.-C. Yew

2007/202, November 2007 and CB 2007-69

Identifying Clinical and GeneticMarkers of Human Disease by Classi-fying Features on GraphsT. Hwang, H. Sicotte, D. Wigle,J.-P. Kocher, V. Kumar, andR. Kuang

2007/211, November 2007Implementations of Asynchronous Self-Organizing Maps on OpenMP andMPI Parallel ComputersJ. Hu, L. Zhang, and J. Cheng

Ecology, Evolution,

and Behavior

2007/158, October 2007 and CB 2007-56

Systems Biology of the Clock in Neu-rospora CrassaW. Dong, X. Tang, Y. Yu, R. Nilsen,J. Griffith, J. Arnold, and H.-B.Schuttler


Electrical and

Computer Engineering

2007/152, September 2007SCRAP: A Statistical Approach forCreating a Database Query WorkloadBased on Performance BottlenecksJ. Skarie, B. K. Debnath, D. J. Lilja,and M. F. Mokbel

2007/153, September 2007Analysis of Statistical Sampling inMicroarchitecture Simulation: Metric,Methodology and Program Character-izationS. V. Kodakara, J. Kim, D. J. Lilja,W.-C. Hsu, and P.-C. Yew

2007/182, October 2007Exchange Coupled Composite MediaR. Victora and X. Shen

2007/183, October 2007Effect of Pole Tip Geometry on Rem-nant FieldX. Shen and R. Victora

2007/184, October 2007Effect of Pinholes in Magnetic TunnelJunctionsX. I. Chen and R. Victora

2007/185, October 2007Feasibility of Recording 1 Tb/in2

Areal DensityX. Shen, S. Hernandez, and R. Vic-tora

2007/207, November 2007Spontaneous Exchange BiasJ. Saha and R. Victora

2007/208, November 2007Comparison Between MicromagneticSimulation and Experiment for theCo/γ-FeMn Exchange-Biased SystemJ. Saha, J. S. Parker, B. T. Bolon,A. Abin-Fuentes, C. Leighton, andR. H. Victora

Geology and Geophysics

2007/141, September 2007Visualization of Earthquake ClustersOver Multi-Dimensional SpaceD. A. Yuen, W. Dzwinel, Y. Ben-Zion, and B. Kadlec

2007/163, October 2007Probabilistic Forecast of TsunamiHazards along Chinese CoastY. Liu, Y. Shi, E. Sevre, D. A. Yuen,and H. Xing

2007/173, October 2007WATT: A Compiler for AutomatedVisualization Service GenerationE. F. Bollig, F. M. Lyness, G. Er-lebacher, and D. A. Yuen

2007/192, November 2007Two New Approaches in Solving theNonlinear Shallow Water Equationsfor Tsunami WavesC. Zhang, M. G. Knepley, D. A.Yuen, and Y. Shi

2007/197, November 2007The Impact of Electronic ThermalConductivity on Mantle Convectionof Super-Earth PlanetsA. P. van den Berg, D. A. Yuen

2007/209, November 2007A Framework of Massively ParallelSimulation of Regional EarthquakeActivitiesH. Zhang, Z. Wu, D. Wang,D. Zhang, S. Chen, Z. Yan,H. Wang, K. I. Kim, D. Yuen, andY. Shi

2007/235, November 2007Adaptive Wavelets for Analyzing Dis-persive Seismic WavesA. Kritski, A. P. Vincent, D. A.Yuen, and T. Carlsen

Health Science Research

(Mayo)

2007/202, November 2007 and CB 2007-69

Identifying Clinical and GeneticMarkers of Human Disease by Classi-fying Features on GraphsT. Hwang, H. Sicotte, D. Wigle,J.-P. Kocher, V. Kumar, andR. Kuang

Mathematics

2007/168, October 2007Goal-Oriented Atomistic-ContinuumAdaptivity for the QuasicontinuumApproximationM. Arndt and M. B. Luskin

2007/169, October 2007Error Estimation and Atomistic-Con-tinuum Adaptivity for the Quasicon-tinuum Approximation of a Frenkel-Kontorova ModelM. Arndt and M. B. Luskin

2007/170, October 2007Analysis of a Force-Based Quasicon-tinuum ApproximationM. Dobson and M. B. Luskin

2007/179, October 2007 and CB2007-62

Taxis Equations for Amoeboid CellsR. Erban and H. G. Othmer

2007/180, October 2007 and CB 2007-63

Robustness of Embryonic Spatial Pat-terning in Drosophila MelanogasterD. Umulis, M. B. O’Connor andH. G. Othmer

2007/181, October 2007 and CB 2007-64

A Hybrid Model for Tumor SpheroidGrowth in Vitro I: Theoretical Devel-opment and Early ResultsY. Kim, M. A. Stolarska, and H. G.Othmer

Mechanical Engineering

2007/144, September 2007Modeling of the Arc ReattachmentProcess in Plasma TorchesJ. P. Trelles, E. Pfender, and J. V.Heberlein

2007/145, September 2007Non-Equilibrium Modeling of ArcPlasma TorchesJ. P. Trelles, J. V. Heberlein, andE. Pfender

2007/161, October 2007Discharge of Thermal Storage Tanksvia Immersed Baffled Heat Exchang-ers: Numerical Model of Flow andTemperature FieldsY. Su and J. Davidson

2007/162, October 2007Multi-Zone Porous Medium Model ofThermal/Fluid Processes During Dis-charge of an Inclined RectangularStorage Vessel via an Immersed HeatExchangerY. Su and J. Davidson

Research Reports


Research Reports


2007/166, October 2007Numerical Simulation of a BPHThermal Therapy—A Case Study In-volving TUMTJ. P. Abraham, E. M. Sparrow, andS. Ramadhyani

2007/167, October 2007Fluid Flow in a System with SeparateLaminar and Turbulent ZonesE. M. Sparrow, J. C. K. Tong, andJ. P. Abraham

2007/205, November 2007Microscopic Theory for Nanoparticle-Surface Collisions in Crystalline Sili-conP. Valentini and T. Dumitrica

2007/206, November 2007Effect of Small Shape Changes on theOptical Response of Highly SymmetricSilicon Quantum DotsS. G. Hao, D.-B. Zhang, andT. Dumitrica

Medicinal Chemistry

2007/175, October 2007 and CB2007-61

“o-Naphthalenedicarboxaldehyde De-rivative of 7’-Aminonaltrindole as aSelective δ-Opioid Receptor AffinityLabelS. P. Haris, Y. Zhang, B. Le Bour-donnec, C. R. McCurdy, and P. S.Portoghese

Medicine

2007/233, November 2007 and CB 2007-74

eIF4E-Induced Progression of PrimaryHMECs Along the Cancer Pathway isAssociated With Targeted Translation-al Deregulation of Oncogenic Driversand InhibitorsO. Larsson, S. Li, O. A. Issaenko,S. Avdulov, M. Peterson, K. Smith,P. B. Bitterman, and V. A. Pol-unovsky

Operations and

Management Science

2007/187, October 2007Screening Designs for Model Discrimi-nationV. Agboto, W. Li, and C. Nacht-sheim

Physical Medicine

and Rehabilitation

2007/159, September 2007 and CB 2007-57

Modelling the Measurement of Tho-racic Tissue Impedance Layers withLocal Electrode ArraysR. P. Patterson and F. Yang

2007/160, September 2007 and CB 2007-58

The Contribution of the Lungs toThoracic Impedance Measurements: ASimulation Study Based on a HighResolution Finite Difference ModelF. Yang and R. P. Patterson

Physics

2007/165, October 2007Odd Triplet Pairing in Clean Super-conductor/Ferromagnet Heterostruc-turesK. Halterman, P. H. Barsic, andO. T. Valls

2007/171, October 2007Discovery of Very Large AmplitudeWhistler-Mode Waves in Earth’s Radi-ation BeltsC. A. Cattell, J. R. Wygant,K. Goetz, K. Kersten, P. J. Kellogg,T. von Rosenvinge, S. D. Bale,I. Roth, M. Temerin, M. K. Hud-son, R. A. Mewaldt, M. Wieden-beck, M. Maksimovic, R. Ergun,M. Acuna, and C. T. Russell

2007/188, October 2007On the Phase Diagram of QCD atFinite Isospin DensityP. de Forcrand, M. A. Stephanov,and U. Wenger

2007/226, November 2007Phase Diagram of Randomly PinnedVortex Matter in Layered Supercon-ductors: Dependence on the Details ofthe Point PinningC. Dasgupta and O. T. Valls

Plant Biology

2007/151, September 2007 and CB 2007-53

Allele-Specific Expression Patterns Re-veal Biases and Embryo-Specific Par-ent-of-Origin Effects in Hybrid MaizeN. Springer and R. M. Stupar

Plant Pathology

2007/234, November 2007 and CB 2007-75

A Walk on the Wild Side: MiningWild Wheat and Barley Collectionsfor Rust Resistance GenesB. J. Steffenson, P. Olivera, J. K.Roy, Y. Jin, K. P. Smith, and G. J.Muehlbauer


UMSI Research Reports can be accessed on our Web site: www.msi.umn.edu/cgi-bin/reports/searchv2.html

Past editions of the Research Bulletin are available in PDF on our Web site:

www.msi.umn.edu/general/Bulletin/

The 2007 Annual Research Report of the Supercomputing Institute is now available. You can download a PDFfrom our Web site:

www.msi.umn.edu/general/Reports/annual.html

or request a copy by sending email to: [email protected]

or mail to:University of Minnesota

Supercomputing Institute599 Walter

117 Pleasant Street SEMinneapolis, Minnesota 55455

Research Reports


Please help us keep our

mailing list up to date

Check one:

❏ Add name to mailing list

❏ Make corrections/changes as shown

❏ Remove name from mailing list

Name__________________________Institution ______________________Address __________________________________________________________________________________________________________________

Phone _________________________Email__________________________

This information can be mailed to the

Su p e rcomputing Institute, 599 Wa l t e r,

117 Pleasant St reet SE, Minneapolis, MN 55455,

f a xed to (612) 624-8861, or emailed to re q u e s t s @ m s i . u m n . e d u

For more information on the University of Minnesota Su-percomputing Institute, please contact us at the addressgiven below. You may also consult the Supercomputing In-stitute’s Internet pages:

www.msi.umn.edu

This information is available in alternative formats uponrequest by individuals with disabilities. Please send email to [email protected] or call 612-625-1818.

Editor/photographer: Tracey A. Bartlett

The University of Minnesota is committed to the policy that allpersons shall have equal access to its programs, facilities, andemployment without regard to race, color, creed, religion, na-tional origin, sex, age, marital status, disability, public assistancestatus, veteran status, or sexual orientation.

© 2007 Un i versity of Mi n n e s o t a

Contains a minimum of 10% postconsumer waste

Supercomputing Institute 599 Walter117 Pleasant Street SEMinneapolis, MN 55455

Change Service Requested

Supercomputing Institute - msi.umn.edu. Kaushik Dayalis working with Department of Aerospace...

Documents

Transcript of Supercomputing Institute - msi.umn.edu. Kaushik Dayalis working with Department of Aerospace...