Publications

Z. Insepov, D. Wolf, and A. Hassanein, "Nanopumping Using Carbon Nanotubes," Nano Letters, vol. 6, no. 9, 2008, pp. 1893-1895. Also Preprint ANL/MCS-P1543-0908, September 2008. [pdf]
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R. J. Aiken, "The Grand Challenge of Managing the Petascale Facility," Argonne Report ANL/MCS-07/5, December 2006. [pdf]
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D. Karpeev, I. S. Aranson, L. S. Tsimring, and H. G. Kaper, "Interactions of Semiflexible Filaments and Molecular Motors," Phys. Rev. E, vol. 76, 2006, pp. 051905. Also Preprint ANL/MCS-P1381-1206, December 2006. [pdf]
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W. Gropp and R. Thakur, "Thread Safety in an MPI Implementation: Requirements and Analysis," Preprint ANL/MCS-P1382-1206, December 2006. [pdf]
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S. Pervez, G. Gopalakrishnan, R. M. Kirby, R. Thakur, and W. Gropp, "A Case Study in Using Formal Methods to Verify Programs That Use MPI One-Sided Communication," Preprint ANL/MCS-P1383-1206, December 2006. [pdf]
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D. Negrut, M. Anitescu, A. El-Azab, P. Zapol, "Quasicontinuum-like Reduction of DFT Calculations of Nanostructures," J. Nanosci. Nanotechnol., vol. 8, 2006, pp. 3729-3740. Also Preprint ANL/MCS-P1384-1206, December 2006. [pdf]
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R. Kettimuthu, W. Allcock, L. Liming, J. Navarro, and I. Foster, "GridCopy: Moving Data Fast on the Grid," Preprint ANL/MCS-P1387-1006, October 2006. [pdf]
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J. A. Insley, M. E. Papka, S. Dong, G. Karniadakis, and N. T. Karonis, "Runtime Visualization of the Human Arterial Tree," Preprint ANL/MCS-P1340-0406, October 2006. [pdf]
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S. Dong, J. Insley, N. T. Karonis, M.E.Papka, J.Binns, and G.Karniadakis, "Simulating and Visualizing the Human Arterial System on the TeraGrid," Future Generation Computing System, vol. 22, no. 8, 2006, pp. 1011-1017. Also Preprint ANL/MCS-P1344-0506, October 2006. [pdf]
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M. Anitescu, "Spectral Finite-Element Methods for Parametric Constrained Optimization Problems," Preprint ANL/MCS-P1379-1006, October 2006. [pdf]
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B. I. Gavrea, M. Anitescu, and F. A. Potra, "Convergence of a Class of Semi-implicit Time-stepping Schemes for Nonsmooth Rigid Multibody Dynamics," SIAM J. on Optimization, vol. 19, no. 2, 2006, pp. 969-1001. Also Preprint ANL/MCS-P1378-1006, October 2006. [pdf]
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P. Balaji, D. Buntinas, S. Balay, B. Smith, R. Thakur, and W. Gropp, "Nonuniformly Communicating Noncontiguous Data: A Case Study with PETSc and MPI," Preprint ANL/MCS-P1380-1006, October 2006. [pdf]
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J. Shin and P. D. Hovland, "Comparison of Two Activity Analyses for Automatic Differentiation: Context-Sensitive Flow-Insensitive vs. Context-Insensitive Flow-Sensitive," Preprint ANL/MCS-P1369-0906, September 2006. [pdf]
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M. D, "Sentra: A Database of Signal Transduction Proteins for Comparative Genome Analysis," Preprint ANL/MCS-P1371-0906, September 2006. [pdf]
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R. Fletcher, S. Leyffer, and P. Toint, "A Brief History of Filter Methods," SIAG/OPT Views-and-News, vol. 18, no. 1, 2006, pp. 2-12. Also Preprint ANL/MCS-P1372-0906, September 2006. [pdf]
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V. Nefedova, R. Jacob, I. Foster, Z. Liu, Y. Liu, E. Deelman, G. Mehta, M.-H. Su, and K. Vahi, "Automating Climate Science: Large Ensemble Simulations on the TeraGrid with the GriPhyN Virtual Data System," Preprint ANL/MCS-P1373-0906, September 2006. [pdf]
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B. Q. Deng, J. P. Allain, and L. L. Peng, "Effects of a Liquid Lithium Curtain as the Frist Wall in the Fuson Experimental Breeder (FEB-E) Reactor Plasma," Preprint ANL/MCS-P1375-0906, September 2006. [pdf]
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B. Q. Deng, J. P. Allain, Z. M. Luo, L. L. Peng, and J. C. Yan, "Near-Surface Bipartition Model for the Study of Material Response of Plasma-Facing Surfaces Exposed to Energetic Charged Particles," Preprint ANL/MCS-P1376-0906, September 2006. [pdf]
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J. P. Allain, M. D. Coventry, and D. N. Ruzic, "Kinematic and Thermodynamic Effects on Liquid Lithium Sputtering," Preprint ANL/MCS-P1377-0906, September 2006. [pdf]
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D. Buntinas, G. Mercier and W. Gropp, "Implementation and Shared-Memory Evaluation of MPICH2 over the Nemesis Communication Subsystem," Recent Advances in Parallel Virtual Machine and Message Passing Interface, Bonn, Germany, Springer, 2006, pp. 86-95. Also Preprint ANL/MCS-P1346-0506, September 2006. [pdf]
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G. von Laszewski, J. DiCarlo, B. Allcock, "A Portal for Visualizing Grid Usage," Preprint ANL/MCS-P1362-0806, August 2006. [pdf]
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B. Norris, S. Bhowmick, D. Kaushik, L. C. McInnes, "Middleware for Dynamic Adaptation of Component Applications," Preprint ANL/MCS-P1365-0806, August 2006. [pdf]
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J. N. Brooks, J. P. Allain, T. Rognlien, "Erosion/ Redecomposition Analysis of the ITER First Wall with Convective and Non-convective Plasma Transport," Physics of Plasmas, vol. 13, 2006, pp. 122502. Also Preprint ANL/MCS-P1366-0806, August 2006. [pdf]
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B. Lang, I. Foster, F. Siebenlist, R. Ananthakrishnan, T. Freeman, "Attribute Based Access Control for Grid Comptuing," Preprint ANL/MCS-P1367-0806, August 2006. [pdf]
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N. Desai, R. Bradshaw, J. Hagedorn, C. Lueninghoener, "Directing Change Using Bcfg2,," Preprint ANL/MCS-P1368-0906, August 2006. [pdf]
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R. E. Camley, G. Leaf, H. Kaper, M. Yan, and M. Grimsditch, "Phase Transitions and Reversal Mechanisms in Nanosized Magnetic Bars: The Influence of Bulk and Localized Spin Wave Modes," Preprint ANL/MCS-P1359-0706, July 2006. [pdf]
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M. Hereld, R. L. Stevens, W. van Drongelen, H. C. Lee, "Framework for Interactive Million-Neuron Simulation," Journal of Clinical Neurophysiology, vol. 24, no. 2, 2006, pp. 189-196. Also Preprint ANL/MCS-P1360-0706, July 2006. [pdf]
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W. van Drongelen, H. C. Lee, R. L. Stevens, M. Hereld, "Propagation of Seizurelike Activity in a Model of Neocortex," Preprint ANL/MCS-P1363-0706, July 2006. [pdf]
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Z. Insepov, A. Hassanein, and D. Swenson, "Computer Simulation of Surface Modification with Ion Beams," Preprint ANL/MCS-P1364-0706, July 2006. [pdf]
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M. Yan, G. Leaf, H. Kaper, V. Novosad, P. Vavassori, R. E. Camley, M. Grimsditch, "Dynamic Origin of Stripe Domains in Cobalt Bars," Preprint ANL/MCS-P1353-0606, June 2006. [pdf]
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J. Bresnahan, R. Kettimuthu, I. Foster, "XIOPerf: A Tool for Evaluating Network Protocols," Preprint ANL/MCS-P1354-0606, June 2006. [pdf]
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Y. Zhao, M. Wilde, and I. Foster, "Applying the Virtual Data Provenance Model," Preprint ANL/MCS-P1355-0606, June 2006. [pdf]
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M. Yan, G. Leaf, H. Kaper, V. Novosad, P. Vavassori, R. E. Camley, and M. Grimsditch, "Formation of Stripe Domains in Cobalt Bars via Magnetic Soft Mode Instability," Preprint ANL/MCS-P1356-0606, June 2006. [pdf]
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J. M. Schopf, L. Pearlman, N. Miller, C. Kesselman, I. Foster, M. D, "Monitoring the Grid with the Globus Toolkit MDS4," Preprint ANL/MCS-P1357-0606, June 2006. [pdf]
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S. Byna, X.-H. Sun, R. Thakur, and W. Gropp,, "Automatic Memory Optimizations for Improving MPI Derived Datatype Performance," Preprint ANL/MCS-P1358-0606, June 2006. [pdf]
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P. Beckman, K. Iskra, K. Yoshii, and S. Coghlan, "The Influence of Operating Systems on the Performance of Collective Operations at Extreme Scale," Preprint ANL/MCS-P1345-0506, May 2006. [pdf]
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W. Gropp and R. Thakur,, "Issues in Developing a Thread-Safe MPI Implementation," Preprint ANL/MCS-P1347-0506, May 2006. [pdf]
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R. Latham, R. Ross, and R. Thakur, "Can MPI Be Used for Persistent Parallel Services?," Preprint ANL/MCS-P1348-0506, May 2006. [pdf]
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W. van Drongelen, H. Koch, F. P. Elsen, H. C. Lee, A. Mrejeru, E. Doren, C. J. Marcuccilli, M. Hereld, R. L. Stevens, and J.-M. Ramirez, "The Role of Persistent Sodium current in Bursting Activity of Mouse Neocortical Networks in Vitro," Preprint ANL/MCS-P1349-0506, May 2006. [pdf]
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S. Pervez, G. Gopalakrishnan, R. M. Kirby, R. Thakur, W. Gropp, "Formal Verification of Programs That Use MPI One-Sided Communication," Preprint ANL/MCS-P1350-0506, May 2006. [pdf]
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T. Lee and P. F. Fischer, "A Lattice Boltzmann Equation Method without Parasitic Currents and Its Application in Droplet Coalescence," Preprint ANL/MCS-P1351-0506, May 2006. [pdf]
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M. Nieto, J. P. Allain, V. Titov, M. R. Hendricks, A. Hassanein, D. Rokusek, C. Chrobak, C. Tarrio, Y. Barad, S. Grantham, T. Lucatorto, and B. Rice, "Effect of Xenon Bombardment on Ruthenium-Coated Grazing Incidence Collector Mirror Lifetime for EUV Lithography," Preprint ANL/MCS-P1338-0406, April 2006. [pdf]
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S. Langella, S. Oster, S. Hastings, F. Siebenlist, T. Kurc, and J. Saltz, "Dorian: Grid Service Infrastructure for Identity Management and Federation," Preprint ANL/MCS-P1339-0406, April 2006. [pdf]
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J. A. Insley, M. E. Papka, S. Dong, G. Karniadakis, and N. T. Karonis, "Runtime Visualization of the Human Arterial Tree," Preprint ANL/MCS-P1340-0406, April 2006. [pdf]
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I. Constandache, D. Olmedilla, F. Siebenlist, W. Nejdl, "Policy-driven Negotiation for Authorization in the Grid," Preprint ANL/MCS-P1341-0406, April 2006. [pdf]
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W. D. Gropp and A. Lumsdaine, "Parallel Tools and Environments: A Survey," Preprint ANL/MCS-P1342-0406, April 2006. [pdf]
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J. Binns, J. DiCarlo, J. A. Insley, T. Leggett, C. Lueninghoener, J.-P. Navarro, and M. E. Papka, "Enabling Community Access to TeraGrid Visualization Resources, Concurrency and Computation: Practice and Experience," Concurr. Comput.-Pract. Exp., vol. 19, no. 6, 2006, pp. 783 - 794. Also Preprint ANL/MCS-P1334-0306, March 2006. [pdf]
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E. M. Glass, M. D, "Pathos and PathoGene Databases - Support for Biodefense and Emerging Infectious Disease Research," Preprint ANL/MCS-P1329-0306, March 2006. [pdf]
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D. Sulakhe, M. D, "GNARE - A Grid-Based Server for the Analysis of User Submitted Genomes," Preprint ANL/MCS-P1330-0306, March 2006. [pdf]
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T. Freeman, K. Keahey, B. Sotomayor, X. Zhang, I. Foster, and D. Scheftner, "Virtual Clusters for Grid Communities," Preprint ANL/MCS-P1331-0306, March 2006. [pdf]
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P. Beckman, K. Iskra, K. Yoshii, and S. Coghlan, "Operating System Issues for Petascale Systems," ACM SIGOPS Operating Systems Review, vol. 40, no. 2, ACM, 2006, pp. 29-33. Also Preprint ANL/MCS-P1332-0306, March 2006. [pdf]
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M. Yan, G. Leaf, H. Kaper, V. Novosad, P. Vavassori, R. E. Camley, and M. Grimsditch, "Stripe Domains, Dynamic Modes, and Magnetic Phase Transitions," Preprint ANL/MCS-P1333-0306, March 2006. [pdf]
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J. Binns, J. DiCarlo, J. A. Insley, T. Leggett, C. Lueninghoener, J.-P. Navarro, and M. E. Papka, "Enabling Community Access to TeraGrid Visualization Resources," Preprint ANL/MCS-P1334-0306, March 2006.
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T. Lee and P. Fischer, "Eliminating Parasitic Currents in the Lattice Boltzmann Equation Method for Nonideal Gases," Preprint ANL/MCS-P1335-0306, March 2006. [pdf]
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P. F. Fischer, F. Loth, S. E. Lee, S.-W. Lee, D. S. Smith, H. S. Bassiouny, "Simulation of High Reynolds Number Vascular Flows," Preprint ANL/MCS-P1337-0306, March 2006. [pdf]
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R. Judson, S. Lefvert, E. Olson, T. D. Uram, "Virtual Venue Management Users Manual: Access Grid Toolkit Documentation, Version 2.3," Technical Memorandum ANL/MCS-TM-287, February 2006. [pdf]
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M. Hereld, M. E. Papka, J. Binns, and R. L. Stevens, "CupHolder: A Multi-Person Interactive High-Resolution Workstation," Preprint ANL/MCS-P1322-0206, February 2006. [pdf]
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V. Sizyuk, A. Hassanein, V. Morozov, and T. Sizyuk, "Heights Integrated Model as Instrument for Simulation of Hydrodynamic, Radiation Transport, and Heat Conduction Phenomena of Laser-Produced Plasma in EUV Applications," Argonne Report ANL-MCS-CPH-06/56, February 2006. [pdf]
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S. Leyffer, "Complementarity Constraints as Nonlinear Equations: Theory and Numerical Experience," Preprint ANL/MCS-P1320-0206, February 2006. [pdf]
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J. P. Allain, M. Nieto, A. Hassanein, V. Titov, P. Plotkin, M. Hendricks, E. Hinson, C. Chrobak, M. H. L. van der Velden, B. Rice,, "Effect of Charged-Particle Bombardment on Collector Mirror Reflectivity in EUV Lithography Devices," 2006, . Also Preprint ANL/MCS-P1323-0206, February 2006. [pdf]
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B. Lang, I. Foster, F. Siebenlist, R. Ananthakrishnan, T. Freeman, "A Multipolicy Authorization Framework for Grid Security," 2006, . Also Preprint ANL/MCS-P1324-0206, February 2006. [pdf]
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D. Sulakhe, A. Rodriguez, M. Wilde, I. Foster, N. Maltsev,, "Using Multiple Grid Resources for Bioinformatics Applications in GADU," 2006, . Also Preprint ANL/MCS-P1325-0206,, February 2006. [pdf]
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L. C. McInnes, J. Ray, R. Armstrong, T. L. Dahlgren, A. Malony, B. Norris, S. Shende, J. P. Kenny, and J. Steensland, "Computational Quality of Service for Scientific CCA Applications: Composition, Substitution, and Reconfiguration," 2006, . Also Preprint ANL/MCS-P1326-0206, February 2006. [pdf]
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P. Fischer, F. Loth, S.-W. Lee, D. Smith, H. Tufo, and H. Bassiouny, "Parallel Simulation of High Reynolds Number Vascular Flows," 2006, . Also Preprint ANL/MCS-P1327-0206, February 2006. [pdf]
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B. Lang, I. Foster, F. Siebenlist, R. Ananthakrishnan, T. Freeman, "A Multipolicy Authorization Framework for Grid Security," Proc. Fifth IEEE Symp. on Network Computing and Application, IEEE Computer Society, 2006, pp. 269-272. Also Preprint ANL/MCS-P1328-0206, February 2006. [pdf]
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P. Hovland, B. Norris, J. Utke, M. M. Strout, "Term Graphs for Imperative Programming Languages," 2006, . Also Preprint ANL/MCS-P1311-0106, January 2006. [pdf]
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B. Kreaseck, L. Ramos, S. Easterday, M. Strout, P. Hovland, "Hybrid Static/Dynamic Activity Analysis," 2006, . Also Preprint ANL/MCS-P1312-0106, January 2006. [pdf]
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M. M. Strout and P. Hovland, "Linearity Analysis for Automatic Differentiation," 2006, . Also Preprint ANL/MCS-P1313-0106, January 2006. [pdf]
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S. Bhowmick and P. Hovland, "A Polynomial Time Algorithm for the Detection of Axial Symmetry in Directed Acyclic Graphs," 2006, . Also Preprint ANL/MCS-P1314-0106, January 2006. [pdf]
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J. M. Schopf, I. Raicu, L. Pearlman, N. Miller, C. Kesselman, I. Foster, M. D'Arcy, "Monitoring and Discovery in a Web Services Framework: Functionality and Performance of Globus Toolkit MDS4," 2006, . Also Preprint ANL/MCS-P1315-0106, January 2006. [pdf]
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K. Keahey, I. Foster, T. Freeman, A. Rana, B. Sotomayor, F. Würthwein, "Division of Labor: Tools for Growth and Scalability of Grids," 2006, . Also Preprint ANL/MCS-P1316-0106, January 2006. [pdf]
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K. Keahey, J. Chase, I. Foster, "Virtual Playgrounds: Managing Virtual Resources in the Grid," 2006, . Also Preprint ANL/MCS-P1317-0106, January 2006. [pdf]
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I. Foster, K. Keahey, C. Kesselman, E. Laure, M. Livny. S. Martin, M. Rynge, and G. Singh, "Embedding Community-Specific Resource Managers in General-Purpose Grid Infrastructure," 2006, . Also Preprint ANL/MCS-P1318-0106,, January 2006. [pdf]
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I. R. Judson, E. Olson, S. D. Price, T. D. Uram, "Web Services Toolkit Interoperability," 2006, . Also Preprint ANL/MCS-P1319-0106, January 2006. [pdf]
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Darius Buntinas, Guillaume Mercier and William Gropp, "Design and Evaluation of Nemesis, a Scalable Low-Latency Message-Passing Communication Subsystem," Proceedings of the 6th IEEE International Symposium on Cluster Computing and the Grid, Singapore, Singapore, IEEE Computer Society, 2009, , . [pdf]
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