Supercomputing Institute - University of Minnesota · 2014-01-16 · S evere acute respiratory syn-drome (SARS), ... CCP using only the genomic infor- ... Med. Chem. Lett.,16, 830-833,

Severe acute respiratory syn-drome (SARS), an emerginginfectious disease with severe

mortality, is a viral respiratory ill-ness caused by a human coronavirusknown as SARS-associated coron-avirus (SARS-CoV). The SARS-CoV genome encodes a chy-motrypsin-like cysteine proteinase(CCP) that processes polypeptidesrequired for viral replication andtranscription and represents an idealdrug target for treating SARS.

To identify new inhibitor leads ofCCP using only the genomic infor-mation, Mayo’s Computer-AidedMolecular Design Laboratory, ledby Yuan-Ping Pang, used terascalecomputers to predict a three-dimen-sional model of CCP in complexwith a substrate fragment. Thismodel was predicted by stochasticsampling of 200 molecular dynam-ics simulations (4.0 ns for each sim-ulation with a 1.0-fs time step and

Supercomputing Institute

Molecular Pharmacology and Experimental Therapeutics

Terascale Computers Help Identify Drug Candidate

to Treat SARS

Volume 22, Number 1

Also in This Issue

Statistics on Protein Ensembles . . .3Bioinformatics: Building

Bridges . . . . . . . . . . . . . . . . . . . .4In Memoriam: D. J. W. Grant . . .6Research Reports . . . . . . . . . . . . . .7

Spring 2006 Research Bulletin of the Supercomputing Institute

for Digital Simulation and Advanced Computation

continued on page 2

Figure 1. Overlay of the 23-µM inhibitor with a reported substrate fragment(ATVRLQp1Ap1’) bound in the active site of CCP (PDB codes: 1P76 and 2AJ5).

Institute of Technology

different initial velocities) per-formed on terascale computers (Pro-teins, 57, 747-757, 2004; Bioorg.Med. Chem. Lett., 16, 830-833,2006).

This laboratory subsequentlyscreened 361,413 small moleculesagainst the computer model andidentified 12 chemicals for antiviraltesting performed at Southern Re-search Institute in Birmingham, Al-abama. Of the 12 compounds test-ed in cell-based inhibition assays,one compound inhibited thehuman SARS-CoV Toronto-2 strainwith an EC50 of 23 µM (Figure 1).Four other compounds showed

13–17% inhibition at a drug con-centration of 32 µM. Interestingly,this laboratory found that screensusing two crystal structures of CCPin its bound and unbound statesfailed to identify the 23-µM in-hibitor. A screen using a newmodel, which is the same as theoriginal model but contracted by12% (Figure 2), also failed to iden-tify the 23-µM inhibitor, but itidentified two weak inhibitors thatare structurally very similar to the23-µM inhibitor (Bioorg. Med.Chem. Lett., 16, 830-833, 2006).

These results demonstrate thatidentifying active inhibitors of

SARS virus was sensitive to thestructural details of CCP, namely, aone-tenth reduction of an inter-atomic distance in CCP changedthe outcome of the screen. The re-sults suggest the need for terascalecomputers to fine-tune target struc-tures for successful identification ofdrug candidates. The results alsoshow that, given the SARS-CoVgenome only, one can identify asmall molecule that is able to pene-trate cells and rescue them fromviral infection, leapfrogging the ex-perimentally determined structuresof CCP. This advance will open afast track to antiviral agents.

Supercomputing Institute Research Bulletin Spring 20062

Molecular Pharmacology and Experimental Therapeutics

Figure 2. Overlay of CCP’s catalytic triad in the original model and the slightly contracted model that was generated by averagingwithout root mean square fit.

On many occasions, such aswhen accounting for struc-tural fluctuations or meas-

urement errors, a single rigid struc-ture may not be sufficient to repre-sent a protein. One approach tosolve this problem is to representthe possible conformations as a dis-crete set of observed conformations(called “ensemble”). ProfessorGuillermo Sapiro, Department ofElectrical and Computer Engineer-ing, and graduate student DiegoRother, following a different ap-proach, introduced a framework forestimating probability density func-tions in very high dimensions andthen applied it to representensembles of folded pro-teins obtained from molec-ular dynamics simulationsperformed by VijayPande’s group at StanfordUniversity (http://folding-.stanford.edu/). This repre-sentation is also advanta-geous for at least two addi-tional reasons: 1) it mayallow one to see aspectsthat were previously hid-den when the ensemblewas regarded as a set ofdiscrete conformations(e.g., the modes); and 2)provides a natural frame-work to perform certainoperations, e.g., compareensembles of the same pro-tein that were obtained bydifferent methods, or de-termine the probabilitythat a particular conforma-tion belongs to the ensem-ble.

The challenge faced bythis approach has been

known for years and was given thename of “curse of dimensionality.”It refers to the difficulty of estimat-ing probability densities in high di-mensions due to the fact that thesample size required increases expo-nentially with the number of di-mensions. The high dimensionalityof protein conformations, with hun-dreds to thousands degrees of free-dom, and the sample sizes often ofthe same order of magnitude pre-vent the application of standarddensity estimation techniques. Tosidestep the curse of dimensionality,these researchers’ approach exploitsthe dependency among the degrees

of freedom, using the available datain the “most efficient” way, accord-ing to a criterion derived from in-formation theory.

Using this approach, the Sapirogroup was able to detect discrepan-cies between the conformations sim-ulated by Pande’s group and the ex-perimental data obtained by McK-night et al. This might indicate thatthe ensemble of simulated structuresis not yet capturing the whole infor-mation about the native state andalso raises the question of howmuch confidence should be given toa single (experimental) structure.

Electrical Engineering

Spring 2006 Supercomputing Institute Research Bulletin 3

Figure 1. Graph of the log-density for selected factors. Black dots represent the molecular dynamics’ observa-tions used to compute the density; white circles represent the experimental structures; gray square is the “na-tive” (experimental average) structure; white ‘x’ and ‘*’ represent the least and most likely structures of themolecular dynamics’ ensemble respectively. Note that the native has some factors not located at the top ofthe density, thereby explaining why the overall probability of this single structure is low.

Statistics on Protein Ensembles

continued on page 4

The Fifth Annual Bioinfor-matics: Building BridgesSymposium was held at the

Digital Technology Center on April13 and 14, 2006. The symposiumincludes participants from academ-ics, industry, and non-profit institu-tions, with expertise in computerscience; physics; math; statistics;molecular, cellular and developmen-tal biology; biochemistry and bio-physics; animal science; ecology,evolution, and behavior; and thehealth sciences. The tutorials andpresentations were Webcast live viaUNITE.

The first day of the symposiumwas mostly dedicated to tutorials(see sidebar, this page). The finalevent of the day was a talk by Dr.Athanasios Lykidis of the Depart-ment of Energy Joint Genome Insti-tute (JGI). This talk, which was co-sponsored by the BioTechnology In-stitute and the Health InformaticsSeminar, was about microbialgenome analysis at the JGI.

Over 90 people preregistered forthe second day of the symposium.The events included six presenta-tions (sidebar, page 5) and eightposter sessions (sidebar, page 6).There were also three exhibits from

organizations at the University ofMinnesota, including the GraduateProgram in Bioinformatics, the Su-percomputing Institute, and theCenter for Computational Ge-nomics and Bioinformatics.

Cosponsors included the Divi-sion of Health Informatics, theGraduate Program in Bioinformat-

ics, the Graduate School, the Con-sortium for Bioinformatics andComputational Biology, the Super-computing Institute, the DigitalTechnology Center, the AcademicHealth Center, the College of Bio-logical Sciences, the Institute ofTechnology, the College of Agricul-tural, Food, and Natural Resource

Tutorials

Bioinformatics ProgrammingZheng Jin Tu, Supercomputing Institute

Biology for BioinformaticsBetsy Martinez-Vaz, Biochemistry, Molecular Biology and

Biophysics

Gene Ontology and Related SoftwareWayne Xu, Supercomputing Institute

Introduction to BLASTCarlos Sosa, IBM; Zheng Jin Tu, Supercomputing Institute

Literature Resources for BioinformaticsKevin Messner, University Libraries

The Integrated Microbial Genome SystemAthanasios Kykidis, Department of Energy Joint Genome In-

stitute

Introduction to Homology ModelingYuk Sham, Supercomputing Institute

Electrical Engineering

Events, Symposia, and Meetings


Bioinformatics: Building Bridges

The group’s results suggest that for agiven accuracy, the number of ob-servations in the ensemble does notneed to grow exponentially with thenumber of residues in the peptide,but only with the number of thoseactually affecting each other. Inother words, the “true” dimension

of the dataset is much smaller thanthe total number of torsion angles,being defined only by the interac-tions in small neighborhoods andnot across the whole protein.

The Sapiro group is currentlymodifying the algorithms to speedup the calculations and therefore be

able to deal with bigger problems(i.e. longer proteins). They also planto apply their methodology onother kinds of datasets (i.e. shapesand textures).

Sciences, Certusoft, IBM, SGI, andJames River Technical, Inc.

Poster and exhibit abstracts,speaker information, and other in-formation about this symposiumcan be found at:

http://www.binf.umn.edu/bisymp06/.



Presentations

Adversity, Diversity, and the Design for Dynamics and Evolution of Cellu-lar Networks

Adam Paul Arkin, University of California–Berkeley

Computational Studies of Enzyme Function and CatalysisJiali Gao, University of Minnesota

Bioinformatics for Genome Analysis and Data MiningEmmanuel Mongodin, Institute for Genome Research

Robustness of Spatial Patterning in DevelopmentHans Othmer, University of Minnesota

From Phenotype to Genotype and Back AgainLarry Wackett, University of Minnesota

Pharmacogenomics and Bioinformatics Richard M. Weinshilboum, Mayo Clinic College of Medicine

Right: Lingling Li, University of Minnesota, looks at one ofthe posters.

Below, left to right: Emmanuel Mongodin, Institute for Ge-nomic Research, and Lawrence Wackett, University of Min-nesota, talk during a break.

Left, left to right: Michael Steinbach, Universityof Minnesota; Vipin Kumar, University of Min-nesota; Richard Weinshilboum, Mayo ClinicCollege of Medicine; and Liewei Wang, MayoClinic College of Medicine, talk during thelunch break.



In Memoriam: David J. W. Grant

Professor David J. W. Grant, College of Pharmacy, passed away on December 9, 2005. ProfessorGrant had been a Principal Investigator of the Supercomputing Institute since 1996. He was alsoa long-time member of the Steering Committee for the Medicinal Chemistry–Supercomputing

Institute Visualization/Workstation Laboratory.

Professor Grant was an expert on the solid-state properties of drugs and was the founder and di-rector of the Drug Delivery Center in the College of Pharmacy. His research at the Supercomput-ing Institute concerned the molecular modeling of drug crystals. Some of the projects he workedon at the Supercomputing Institute included: prediction of crystal structures from powder pat-

terns; calculations of lattice energy of crystals from their unit cells; calculations of interaction en-ergy between various solutes and solvents; calculations of solvation energy of solutes by solvents;polymorph prediction of molecular crystals; interactions between molecules in crystals; ab initiogeometry optimization and energy calculations; and molecular dynamic calculations to under-

stand nucleation and crystal growth.

The staff and researchers of the Supercomputing Institute extend their deepest condolences toProfessor Grant’s family.

Predicting the Fate of Chemicals in the EnvironmentLynda Ellis, University of MinnesotaDave Roe, University of MinnesotaLawrence Wackett, University of Minnesota

Mining Structured and Unstructured Life SciencesData

Rohit Gupta, University of Minnesota

Whole Genome Transcriptome Analysis of Anophelesgambiae in Response to Bloodmeal and Malaria Infec-tion

Jun Li, University of MinnesotaJiannong Xu, University of MinnesotaMichelle Riehle, University of MinnesotaKenneth Vernick, University of Minnesota

Probabilistic Modeling of Multi-level Genetic Regula-tory Logic

Sharareh Noorbaloochi, University of MinnesotaJose F. Barbe, University of MinnesotaAhmed Tewfic, University of Minnesota

Classification of Secreted Proteins Using a Single Do-main

Carlos Sosa, IBM and Supercomputing InstituteEric Klee, Mayo ClinicStephen Ekker, University of MinnesotaLynda Ellis, University of Minnesota

Data Mining for the Detection of Transcription Mod-ules

Michael Steinbach, University of Minnesota

Computational Simulations Uncover the GatingMechanism of Nicotinic Acetylcholine Receptor

Hai-long Wang, Mayo Clinic

Normalization of Microarrays in Transcription Inhi-bition Experiments

Yan Zheng, University of MinnesotaCava Reilly, University of Minnesota

Poster Presentations

Research Reports


Agronomy and

Plant Genetics

2005/251, December 2005 and CB 2005-72

Quantitative Trait Loci for Multi-ple Disease Resistance in Wild Bar-leyS. J. Yun, L. Gyenis, P. M.Hayes, I. Matus, K. P. Smith,B. J. Steffenson, and G. J.Muehlbauer

Astronomy

2006/21, March 2006Numerical Studies of DiffusiveShock Acceleration at SphericalShocksH. Kang and T. W. Jones

Biochemistry, Molecular

Biology, and Biophysics

2005/238, December 2005 and CB 2005-67

Structure of the Streptococcal CellWall C5a PeptidaseC. K. Brown, Z.-Y. Gu, Y. V.Matsuka, S. S. Purushothaman,L. A. Winter, P. P. Cleary, S. B.Olmsted, D. H. Ohlendorf, andC. A. Earhart

2005/239, December 2005 and CB 2005-68

Structure of Peptide SexPheromone Receptor PrgX andPrgX/pheromone Complexes andRegulation of Conjugation in En-terococcus faecalisK. Shi, C. K. Brown, Z.-Y. Gu,B. K. Kozlowicz, G. M. Dunny,D. H. Ohlendorf, and C. A.Earhart

2005/240, December 2005 and CB 2005-69

Structure of Catechol 1,2-dioxyge-nase From Pseudomonas arvillaC. A. Earhart, M. W. Vetting,R. Gosu, I. Michaud-Soret,L. Que Jr., and D. H. Ohlen-dorf

2005/250, December 2005 and CB 2005-71

Directed Evolution of Bacillussubtilis Lipase A by Use of Enan-tiomeric Phosphonate Inhibitors:Crystal Structures and Phage Dis-play SelectionM. J. Dröge, Y. L. Boersma,G. van Pouderoyen, T. E.Vrenken, C. J. Rüggeberg, M. T.Reetz, B. W. Dijkstra, and W. J.Quax

2006/26, March 2006 and CB 2006-3

Manganese-Substituted CarbonicAnhydrase as a New PeroxidaseK. Okrasa and R. J. Kazlauskas

2006/35, April 2006 and CB 2006-6

Expression, Purification, Crystal-lization and Preliminary X-rayDiffraction of a Novel Nitro-somonas Europaea Cytochrome,Cytochrome P460B. O. Elmore, A. R. Pearson,C. M. Wilmot, and A. B. Hoop-er

Biomedical Engineering

2006/39, April 2006A Cortical Potential ImagingStudy From Simultaneous Extra-and Intra-cranial ElectricalRecordings by Means of the FiniteElement MethodY. Zhang, L. Ding, W. van Dron-gelen, K. Hecos, D. Frim, andB. He

2006/40, April 2006 and CB 2006-9

Estimation of Number of Indepen-dent Brain Electric Sources Fromthe Scalp EEGsX. Bai and B. He

Center for Drug Design

2005/232, December 2005 and CB 2005-63

Rationally Designed NucleosideAntibiotics That InhibitSiderophore Biosynthesis of My-cobacterium tuberculosisR. V. Somu, H. Boshoff,C. Qiao, E. M. Bennett, C. E.Barry III, and C. C. Aldrich

Chemical Engineering

and Materials Science

2005/222, December 2005On the Effects of Furnace Gradi-ents on Interface Shape During theGrowth of Cadmium Zinc Tel-luride in EDG FurnacesL. Lun, A. Yeckel, M. Reed,C. Szeles, P. Daoutidis, and J. J.Derby

2005/231, December 2005Decreasing Lateral Segregation inCadmium Zinc Telluride Via Am-poule Tilting During VerticalBridgman GrowthL. Lun, A. Yeckel, P. Daoutidis,and J. J. Derby

2005/241, December 2005Size-Dependent Spintronic Proper-ties of Dilute Magnetic Semicon-ductor NanocrystalsX. Huang, A. Makmal, J. R.Chelikowsky, and L. Kronik

2005/242, December 2005Ab Initio Absorption Spectra of GeNanocrystalsG. Nesher, L. Kronik, and J. R.Chelikowsky

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

Research Reports


2005/243, December 2005Surface Passivation Method forSemiconductor NanostructuresX. Huang, E. Lindgren, and J. R.Chelikowsky

2005/244, December 2005Ab Initio Calculations of the Pho-toelectron Spectra of TransitionMetal ClustersS. Li, M. M. G. Alemany, andJ. R. Chelikowsky

2005/245, December 2005Real-Space Pseudopotential Calcu-lations of the Ground-State andExcited-State Properties of theWater MoleculeM. Lopez del Puerto, M. L.Tiago, I. Vasiliev, and J. R. Che-likowsky

2005/246, December 2005First-Principles GW-BSE Excita-tions in Organic MoleculesM. L. Tiago and J. R. Che-likowsky

2005/252, April 2006Surfactant Effects on Buoyancy-Driven Viscous Interactions of De-formable DropsM. A. Rother, A. Z. Zinchenko,and R. H. Davis

2006/15, March 2006Numerical Methods for ElectronicStructure Calculations of MaterialsY. Saad, J. R. Chelikowsky, andS. M. Shontz

2006/22, March 2006Mass Transfer Limitations at Crys-tallizing Interfaces in an AtomicForce Microscopy Fluid Cell: A Fi-nite Element AnalysisD. Gasperino, A. Yeckel, B. K.Olmsted, M. D. Ward, and J. J.Derby

2006/30, April 2006Self-Consistent-Field CalculationsUsing Chebyshev-Filtered SubspaceIterationY. Zhou, Y. Saad, M. L. Tiago,and J. R. Chelikowsky

2006/37, April 2006 and CB 2006-7

The Fractional Contributions ofElementary Modes to the Metabo-lism of Escherichia coli and TheirEstimation From Reaction En-tropiesA. P. Wlaschin, C. T. Trinh,R. Carlson, and F. Srienc

Chemistry

2005/224, December 2005Decoherence in Combined Quan-tum Mechanical and Classical Me-chanical Methods for Dynamics asIllustrated for Non-Born-Oppen-heimer TrajectoriesD. G. Truhlar

2005/247, December 2005Variational Transition State Theo-ryB. C. Garrett and D. G. Truhlar

2005/248, December 2005 and CB 2005-71

Quantum Chemical Characteriza-tion of the Structures, Thermo-chemical Properties, and Singlet-Triplet Splittings of Didehydro-quinolinium and Didehydroiso-quinolinium IonsJ. J. Nash, H. I. Kenttämaa, andC. J. Cramer

2005/249, December 2005How Useful Are Vibrational Fre-quencies of Isotopomeric O2 Frag-ments for Assessing Local Symme-try? Some Simple Systems and theVexing Case of a Galactose Oxi-dase ModelC. R. Kinsinger, B. F. Gherman,L. Gagliardi, and C. J. Cramer

2005/253, April 2006Quantum Chemical and MasterEquation Studies of the MethylVinyl Carbonyl Oxides Formed inIsoprene OzonolysisK. A. Kuwata, L. C. Valin, andA. D. Converse

2006/9, February 2006Pseudo-Two-Dimensional Struc-tures (HXYH)3n2H6n (XY =GaN, SiC, GeC, SiSi, or GeGe; n= 1-3): Density Functional Char-acterization of Structures and En-ergeticsB. L. Kormos, C. J. Cramer, andW. L. Gladfelter

2006/10, February 2006Large Gas-Solid Structural Differ-ences in Complexes of Haloacetoni-triles With Boron TrifluorideJ. A. Phillips, J. A. Halfen, J. P.Wrass, C. C. Knutson, and C. J.Cramer

2006/11, February 2006 and CB 2006-1

Models for Dioxygen Activation bythe CuB Site of Dopamine β-Monooxygenase and Peptidylglycineα-Hydroxylating MonooxygenaseB. F. Gherman, D. E. Heppner,W. B. Tolman, and C. J. Cramer

2006/12, February 2006Theoretical Models on the Cu2O2Torture Track: Mechanistic Impli-cations for Oxytyrosinase andSmall-Molecule AnaloguesC. J. Cramer, M. Wloch,P. Piecuch, C. Puzzarini, andL. Gagliardi

2006/13, February 2006Adding Explicit Solvent Moleculesto Continuum Solvent Calcula-tions for the Calculation of Aque-ous Acid Dissociation ConstantsC. P. Kelly, C. J. Cramer, andD. G. Truhlar

2006/23, March 2006High-Spin and Low-Spin Iron(II)Complexes With Facially-Coordi-nated Borohydride LigandsM. P. Mehn, S. D. Brown, T. K.Paine, W. W. Brennessel, C. J.Cramer, J. C. Peters, andL. Que, Jr.


Research Reports


2006/24, March 2006Density Functional Characteriza-tion of Methane Metathesis withCp*2MR (M = Sc, Y, Lu; R = Me,tBuCH2). Structural and KineticConsequences of Alkyl Steric BulkN. L. Woodrum and C. J.Cramer

2006/42, April 2006, andCB 2006-11

QCRNA1.0: A Database ofQuantum Calculations for RNACatalyisT. J. Giese, B. A. Gregersen,Y. Liu, E. Mayaan, A. Moser,K. Range, O. Nieto Faza,C. Silva Lopez, A. Rodriguez deLera, G. Schaftenaar, X. Lopez,T.-S. Lee, G. Karypis, andD. M. York

2006/43, April 2006, andCB 2006-12

CHARMM Force Field Parametersfor Simulation of Reactive Inter-mediates in Native and Thio-sub-stituted RibozymesE. Mayaan, A. Moser, A. D.Mackerell, Jr., and D. M. York

2006/44, April 2006, andCB 2006-13

Nucleophilic Attack on PhosphateDiesters: A Density FunctionalStudy of In-Line Reactivity in Di-anionic, Monoanionic, and Neu-tral SystemsX. Lopez, A. Dejaerere,F. Leclerc, D. M. York, andM. Karplus

2006/45, April 2006, and CB 2006-14

Transesterification Thio Effects ofPhosphate Diesters: Free EnergyBarriers, Kinetic and EquilibriumIsotope Effects From Density-Func-tional TheoryY. Liu, B. A. Gregersen,A. Hengge, and D. M. York

Computer Science

and Engineering

2005/227, December 2005Efficient Execution of ParallelElectronic Structure Calculationson SMP ClustersN. Ustemirov and M. Sosonkina

2005/228, December 2005Parallel Solvers for Flexible Ap-proximation Schemes in Multipar-ticle SimulationM. Sosonkina and I. Tsukerman

2005/229, December 2005Concurrent Execution of ElectronicStructure Calculations in SMPEnvironmentsN. Ustemirov, M. Sosonkina,M. S. Gordon, and M. Schmidt

2005/230, December 2005Component-Based Iterative Meth-ods for Sparse Linear SystemsJ. Jones, M. Sosonkina, andY. Saad

2006/15, March 2006Numerical Methods for ElectronicStructure Calculations of MaterialsY. Saad, J. R. Chelikowsky, andS. M. Shontz

2006/16, March 2006Orthogonal Neighborhood Preserv-ing Projections: A Projection-BasedDimensionality Reduction Tech-niqueE. Kokiopoulou and Y. Saad

2006/17, March 2006A Greedy Strategy for Coarse-GridSelectionS. MacLachlan and Y. Saad

2006/18, March 2006On Correction Equations and Do-main Decomposition for Comput-ing Invariant SubspacesB. Philippe and Y. Saad

2006/19, March 2006Schur Complement Preconditionersfor Distributed General SparseLinear SystemsY. Saad

2006/20, March 2006Face Recognition Using OPRA -facesE. Kokiopoulou and Y. Saad

2006/27, March 2006Acyclic Subgraph based DescriptorSpaces for Chemical CompoundRetrieval and ClassificationN. Wale and G. Karypis

2006/28, April 2006 and CB 2006-4

Effective Optimization Algorithmsfor Fragment-Assembly Based Pro-tein Structure PredictionK. W. DeRonne and G. Karypis

2006/29, April 2006 and CB 2006-5

Genomic View of Systemic Au-toimmunity in MRLlpr MiceJ. Liu, G. Karypis, K. L. Hip-pen, A. L. Vegoe, P. Ruiz, G. S.Gilkeson, and T. W. Behrens

2006/30, April 2006Self-Consistent-Field CalculationsUsing Chebyshev-Filtered SubspaceIterationY. Zhou, Y. Saad, M. L. Tiago,and J. R. Chelikowsky

2006/31, April 2006Instability of Creeping Flow Past aDeformable Wall: The Role ofDepth-Dependent ModulusV. Gkanis and S. Kumar

2006/32, April 2006A Chebyshev-Davidson Algorithmfor Large Symmetric EigenproblemsY. Zhou and Y. Saad

2006/42, April 2006, andCB 2006-11

QCRNA1.0: A Database ofQuantum Calculations for RNACatalyisT. J. Giese, B. A. Gregersen,Y. Liu, E. Mayaan, A. Moser,K. Range, O. Nieto Faza,C. Silva Lopez, A. Rodriguez deLera, G. Schaftenaar, X. Lopez,T.-S. Lee, G. Karypis, andD. M. York

Research Reports


Diagnostic and

Biological Sciences

2005/236, December 2005 and CB 2005-65

Streptococci Dominate the DiverseFlora Within Buccal CellsJ. D. Rudney, R. Chen, andG. Zhang

Electrical and

Computer Engineering

2006/3, January 2006Analyzing the Processor Bottlenecksin SPEC CPU 2000J. J. Yi, A. Joshi, R. Sendag,L. Eeckhout, and D. J. Lilja

2006/4, January 2006Comparing Simulation Techniquesfor Microarchitecture-Aware Floor-PlanningV. Nookala, Y. Chen, D. J. Lilja,and S. S. Sapatnekar

2006/6, January 2006Evaluating the Efficacy of Statisti-cal Simulation for Design SpaceExploration A. Joshi, J. J. Yi, R. H. Bell Jr.,L. Eeckhout, L. John, and D. J.Lilja

Experimental and

Clinical Pharmacology

2006/38, April 2006 and CB 2006-8

Heteroactivator Effects on the Cou-pling and Spin State Equilibriumof CYP2C9C. W. Locuson, P. M. Gannett,and T. S. Tracy

Geology and Geophysics

2006/1, January 2006 and VLab 2006-1

Sensitivity Study of the ThermalState in the Lower Mantle by 3-DConvection With Post-PerovskitePhase TransitionM. Kameyama and D. A. Yuen

2006/2, January 2006Unsolved Problems in the Lower-most MantleK. Hirose, S. Karato, V. F.Cormier, J. P. Brodholt, andD. A. Yuen

2006/7, February 2006A Multiscale Cellular AutomataModel for Simulating ComplexTransportation SystemsP. Topa, W. Dzwinel, and D. A.Yuen

2006/8, February 2006Upper-Mantle Versus Lower-Man-tle Plumes: Are They The Same?C. Matyska and D. A. Yuen

2006/14, February 2006 and VLab 2006-2

Dynamics of Superplumes in theLower MantleD. A. Yuen, M. Monnereau,U. Hansen, M. Kameyama, andC. Matyska

2006/33, April 2006Tsunami and Earthquake Visual-ization Inspired by Light Interfer-enceX. Yuan, M. X. Nguyen, Y. Liu,D. A. Yuen, B. Chen, and Y. Shi

Mathematics

2006/36, April 2006The G-Convergence of a Sharp In-terface Thin Film Model WithNon-Convex Elastic EnergyP. Belík and M. Luskin

Mechanical Engineering

2006/5, January 2006Simulation Results of Arc Behaviorin Different Plasma Spray TorchesJ. P. Trelles and J. V. R. Heber-lein

Medicine

2005/225, December 2005 and CB 2006-61

In Vivo Assessment of the RelativeContributions of Deletion, Anergy,and Editing to B Cell Self-Toler-anceK. L. Hippen, B. R. Schram,L. E. Tze, K. A. Pape, M. K.Jenkins, and T. W. Behrens

2005/226, December 2005 and CB 2006-62

Peripheral Blood Gene ExpressionProfiling in Rheumatoid ArthritisF. M. Batliwalla, E. C. Baechler,X. Xiao, W. Li, S. Balasubraman-ian, H. Khalili, A. Damle, W. A.Ortmann, A. Perrone, A. B. Kan-tor, P S. Gulko, M. Kern,R. Furie, T. W. Behrens, andP. K. Gregersen

2006/29, April 2006 and CB 2006-5

Genomic View of Systemic Au-toimmunity in MRLlpr MiceJ. Liu, G. Karypis, K. L. Hip-pen, A. L. Vegoe, P. Ruiz, G. S.Gilkeson, and T. W. Behrens

Microbiology

2005/225, December 2005 and CB 2006-61

In Vivo Assessment of the RelativeContributions of Deletion, Anergy,and Editing to B Cell Self-Toler-anceK. L. Hippen, B. R. Schram,L. E. Tze, K. A. Pape, M. K.Jenkins, and T. W. Behrens


Instructions for obtaining copies of UMSI Research Reports can be found on our Web site:

www.msi.umn.edu/cgi-bin/reports/searchv2.html

Research Reports


2005/238, December 2005 and CB 2005-67

Structure of the Streptococcal CellWall C5a PeptidaseC. K. Brown, Z.-Y. Gu, Y. V.Matsuka, S. S. Purushothaman,L. A. Winter, P. P. Cleary, S. B.Olmsted, D. H. Ohlendorf, andC. A. Earhart

2005/239, December 2005 and CB 2005-68

Structure of Peptide SexPheromone Receptor PrgX andPrgX/pheromone Complexes andRegulation of Conjugation in En-terococcus faecalisK. Shi, C. K. Brown, Z.-Y. Gu,B. K. Kozlowicz, G. M. Dunny,D. H. Ohlendorf, and C. A.Earhart

Neuroscience and

Neurology

2005/235, December 2005 and CB 2005-64

Modeling the Signaling EndosomeHypothesis: Why a Drive to theNucleus is Better Than a (Ran-dom) WalkC. L. Howe

Physics

2005/223, December 2005Finite Density QCD With aCanonical ApproachP. de Forcrand and S. Kratochvi-la

2005/233, December 2005Practical Applicability of theJarzynski Relation in StatisticalMechanics: A Pedagogical ExampleR. C. Lua and A. Y. Grosberg

2005/234, December 2005Limits of Analogy Between Self-Avoidance and Topology-DrivenSwelling of Polymer LoopsN. T. Moore and A. Y. Grosberg

2005/237, December 2005 and CB 2005-66

First Passage Times and Asymme-try of DNA TranslocationR. C. Lua and A. Y. Grosberg

2006/34, April 2006First Order Phase Transitions inFerromagnet/Superconductor Lay-ered StructuresP. H. Barsic, O. T. Valls, andK. Halterman

Plant Pathology

2005/251, December 2005 and CB 2005-72

Quantitative Trait Loci for Multi-ple Disease Resistance in Wild Bar-leyS. J. Yun, L. Gyenis, P. M.Hayes, I. Matus, K. P. Smith,B. J. Steffenson, and G. J.Muehlbauer

2006/25, March 2006 and CB 2006-2

Insights Into Symbiotic NitrogenFixation in Medicago truncatulaM. Tesfaye, D. A. Samac, andC. P. Vance

2006/41, April 2006, and CB 2006-10

Towards Efficient Isolation of RGene Orthologs From MultipleGenotypes: Optimization of LongRange-PCRM. J. Sanchez and J. M.Bradeen

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