Publications

Leininger, M. (2005). Open Source Software Project Review [Presentation]. https://www.osti.gov/biblio/1728473

Faulon, J.-L., Zhang, Z., Martino, A., Timlin, J.A., Haaland, D.M., Davidson, G.S., May, E., Slepoy, A., & Slepoy, A. (2005). Reverse engineering biological networks :applications in immune responses to bio-toxins. https://doi.org/10.2172/877733

Swiler, L.P. (2005). Validation of the thermal challenge problem using Bayesian Belief Networks. https://doi.org/10.2172/875636

Sasaki, D.Y., Koch, S.J., Thayer, G., Corwin, A.D., de Boer, M.P., Bunker, B.C., Bachand, G.D., Rivera, S.B., Gaudioso, J.M., Trent, A., Spoerke, E.D., & Spoerke, E.D. (2005). Assembly and actuation of nanomaterials using active biomolecules. https://doi.org/10.2172/875628

Frink, L.J., Frischknecht, A.L., Plimpton, S.J., Sasaki, D.Y., & Sasaki, D.Y. (2005). Modeling biomembranes. https://doi.org/10.2172/875627

Bader, B., Pawlowski, R., Kolda, T.G., & Kolda, T.G. (2005). Robust large-scale parallel nonlinear solvers for simulations. https://doi.org/10.2172/876345

Romero, L., Parks, M.L., & Parks, M.L. (2005). Taylor dispersion in high aspect ratio tubes of nearly rectangular cross section. Proposed for publication in the Journal of Fluid Mechanics.. https://www.osti.gov/biblio/886620

Gaudioso, J.M. (2005). Components of biosecurity I [Conference]. https://www.osti.gov/biblio/893557

Gaudioso, J.M. (2005). Components of biosecurity II [Conference]. https://www.osti.gov/biblio/893540

Gaudioso, J.M. (2005). Biosecurity in the United States - a case study [Conference]. https://www.osti.gov/biblio/893541

Howle, V.E. (2005). An Overview of Meros [Presentation]. https://www.osti.gov/biblio/1728504

Heffelfinger, G.S., Martino, A., Rintoul, M.D., & Rintoul, M.D. (2005). Genomics :GTL project quarterly report April 2005 [Presentation]. https://doi.org/10.2172/877716

Davidson, G.S., Boyack, K.W., & Boyack, K.W. (2005). Finding relevant documents in enormous clustered sets of scientific documents [Conference]. https://www.osti.gov/biblio/1465837

Gaudioso, J.M. (2005). The Biological Weapons Threat [Conference]. https://www.osti.gov/biblio/1465850

Rintoul, M.D. (2005). New Architectures and Algorithms Could Enable Higher Quality Automatic Translation Systems [Presentation]. https://www.osti.gov/biblio/1728523

Phipps, E.T. (2005). An Overview of Computational Science Research and Development at Sandia National Laboratories [Presentation]. https://www.osti.gov/biblio/1727358

Moreland, K. (2005). vtkPainter and Friends (2005-11-28) [Presentation]. https://www.osti.gov/biblio/1727359

Moreland, K. (2005). Using Ghost Cells in Parallel Filters [Presentation]. https://www.osti.gov/biblio/1727360

Barnette, D.W. (2005). Test and evaluation procedures for Sandia's Teraflops Operating System (TOS) on Janus. https://doi.org/10.2172/923085

O'Hern, T.J., Hammond, G.E., Orear, L., van Bloemen Waanders, B.G., & van Bloemen Waanders, B.G. (2005). Physical Modeling of Scaled Water Distribution System Networks. https://doi.org/10.2172/1143374

Swiler, L.P. (2005). Gaussian processes in response surface modeling [Conference]. https://www.osti.gov/biblio/878571

Vugrin, K.E.W., Swiler, L.P., Roberts, R.M., & Roberts, R.M. (2005). Confidence region estimation techniques for nonlinear regression :three case studies. https://doi.org/10.2172/877714

Arbenz, P., Hetmaniuk, U., Lehoucq, R.B., Tuminaro, R.S., & Tuminaro, R.S. (2005). A comparison of eigensolvers for large-scale 3D modal analysis using AMG-preconditioned iterative methods. International Journal for Numerical Methods in Engineering, 64(2), pp. 204-236. https://doi.org/10.1002/nme.1365

Hendrickson, B.A. (2005). Algorithms and architectures for high performance analysis of semantic graphs. https://doi.org/10.2172/974408

Dyck, M.L., Tangyunyong, P., Hill, T.A., Nakakura, C.Y., Headley, T., Rye, M.J., & Rye, M.J. (2005). Transmission electron microscopy and scanning capacitance microscopy analysis of dislocation-induced leakages in n-channel I/O transistors [Conference]. https://www.osti.gov/biblio/884701

Day, D.M., Bochev, P., Weiss, C.J., Robinson, A.C., & Robinson, A.C. (2005). Geophysical subsurface imaging and interface identification. https://doi.org/10.2172/875615

Silling, S.A. (2005). Peridynamic modeling of plain and reinforced concrete structures [Conference]. https://www.osti.gov/biblio/947772

Rupnow, K. (2005). Instruction behavior in Sandia scientific workloads [Conference]. https://www.osti.gov/biblio/968395

Rodrigues, A. (2005). Programming future architectures : dusty decks, memory walls, and the speed of light [Conference]. https://www.osti.gov/biblio/968394

Lynch, E. (2005). Simulating interconnection networks [Conference]. https://www.osti.gov/biblio/968393

Simonis, J. (2005). A Newton-Picard method [Conference]. https://www.osti.gov/biblio/969553

McFarland, J., Giunta, A.A., Swiler, L.P., & Swiler, L.P. (2005). Advanced uncertainty quantification methods for engineering applications [Conference]. https://www.osti.gov/biblio/969552

Romero, L., Whiting, J.J., Parks, M.L., & Parks, M.L. (2005). A reduced order model for the study of asymmetries in linear gas chromatography for homogeneous tubular columns. https://doi.org/10.2172/923173

Underwood, K.D., Rodrigues, A., & Rodrigues, A. (2005). The implications of spatial locality on scientific computing benchmark selection and analysis [Conference]. https://www.osti.gov/biblio/967825

Phipps, E.T., Salinger, A.G., Day, D.M., & Day, D.M. (2005). Bifurcation methods for large scale applications with examples from structural mechanics [Conference]. https://www.osti.gov/biblio/967824

Bochev, P. (2005). On least-squares variational principles for the discretization of optimization and control problems. Proposed for publication in Methods and Applications of Analysis.. https://doi.org/10.4310/MAA.2005.v12.n4.a3

Dyck, M.L., Tangyunyong, P., Hill, T.A., Nakakura, C.Y., Headley, T., Rye, M.J., & Rye, M.J. (2005). Transmission Electron Microscopy and Scanning Capacitance Microscopy Analysis of Dislocation-Induced Leakages in n-channel I/O Transistors. Proposed for publication in the Conference proceedings from the 31st International Symposium for Testing and Failure Analysis.. https://www.osti.gov/biblio/885112

Hendrickson, B.A., Underwood, K.D., & Underwood, K.D. (2005). How Relevant is Computer Architecture Research to Emerging Memory Intensive Applications? [Conference]. https://www.osti.gov/biblio/1122149

Doerfler, D.W. (2005). An Analysis of HyperTransport and Seastar Data Rates on Red Storm. https://doi.org/10.2172/1143302

Giunta, A.A., Swiler, L.P., Eldred, M., & Eldred, M. (2005). The promise and peril of uncertainty quantification using response surface approximations. Proposed for publication in Structure and Infrastructure Engineering.. https://www.osti.gov/biblio/884754

Bishop, J.E., Voth, T.E., Brown, K.H., & Brown, K.H. (2005). Semi-infinite target penetration by ogive-nose penetrators : ALEGRA/SHISM code predictions for ideal and non-ideal impacts [Conference]. https://www.osti.gov/biblio/948219

Oldfield, R., Riesen, R., Ward, H.L., Lawry, W.F., & Lawry, W.F. (2005). A lightweight approach to file system development [Conference]. https://www.osti.gov/biblio/969119

Rogers, D., Garasi, C.J., & Garasi, C.J. (2005). Prism : a multi-view visualization toll [i.e. tool] for multi-physics simulations [Conference]. https://www.osti.gov/biblio/969108

Abbott, R.G. (2005). Automated spatio-temporal knowledge elicitation for a computer-based training system [Conference]. https://www.osti.gov/biblio/969105

Preece, D.S., Berg, V.S., Risenmay, M., & Risenmay, M. (2005). Bullet impact on steel and Kevlar/steel armor-experimental data and hydrocode modeling with Eulerian and Lagranian methods [Conference]. https://www.osti.gov/biblio/968368

Sala, M., Spotz, W.F., Heroux, M.A., & Heroux, M.A. (2005). An overview of PyTrilinos. Proposed for publication in ACM Transactions on Mathematical Software.. https://www.osti.gov/biblio/971804

Sala, M. (2005). On the Design of Interfaces to Serial and Parallel Direct Solver Libraries. https://doi.org/10.2172/1143357

Draper, B.L., Shaneyfelt, M.R., Young, R.W., Headley, T., Dondero, R., & Dondero, R. (2005). Arsenic ion implant energy effects on CMOS gate oxide hardness. Proposed for publication in the IEEE Transactions on Nuclear Science.. https://www.osti.gov/biblio/970707

Ridzal, D. (2005). Use of iterative linear solvers in a Lagrange-Newton SQP algorithm for large-scale nonlinear optimization [Conference]. https://www.osti.gov/biblio/969833

Boman, E.G., Devine, K., Heaphy, R.T., Hendrickson, B.A., & Hendrickson, B.A. (2005). Parallel hypergraph partitioning for scientific computing [Conference]. https://www.osti.gov/biblio/968387

Gaudioso, J.M. (2005). Introduction to the security of pathogens in laboratory environments [Conference]. https://www.osti.gov/biblio/968385

Gaudioso, J.M. (2005). Bioterrorism and biosecurity in the United States [Conference]. https://www.osti.gov/biblio/968383

Edwards, H.C. (2005). SIERRA framework for massively parallel scientific & engineering applications [Conference]. https://www.osti.gov/biblio/968419

Hendrickson, B.A. (2005). Latent semantic analysis, bipartite graphs, and Laplacian embeddings [Conference]. https://www.osti.gov/biblio/968175

Hemmert, K.S., Rodrigues, A., Underwood, K.D., & Underwood, K.D. (2005). Accelerating list management for MPI [Conference]. https://www.osti.gov/biblio/967795

Brannon, R., Strack, O.E., & Strack, O.E. (2005). Incorporating micro-heterogeneity in field-scale fragmentation analyses to (partially) address mesh-dependency [Conference]. https://www.osti.gov/biblio/900429

Scovazzi, G., Bochev, P., & Bochev, P. (2005). A multiscale discontinuous galerkin method with the computational structure of a continuous galerkin method [Conference]. https://www.osti.gov/biblio/967818

Scovazzi, G. (2005). Stabilized Lagrangian hydrodynamics : a new multiscale method for shock hydrodynamics [Conference]. https://www.osti.gov/biblio/967805

May, E., Johnston, A.M., & Johnston, A.M. (2005). Bits and bases, parallel paradigms for communication. Proposed for publication in IEEE Engineering in Medicine and Biology Magazine.. https://www.osti.gov/biblio/971825

Knupp, P. (2005). A target-matrix paradigm for mesh optimization [Conference]. https://www.osti.gov/biblio/967786

Debenedictis, E. (2005). Maintaining scalability of information processing systems [Conference]. https://www.osti.gov/biblio/968412

Jones, B.M., Deeney, C., McKenney, J., Garasi, C.J., Mehlhorn, T., Robinson, A.C., Coverdale, C.A., & Coverdale, C.A. (2005). Seeded perturbations in wire array Z-Pinches [Conference]. https://www.osti.gov/biblio/968938

Jones, B.M., Deeney, C., Garasi, C.J., Mehlhorn, T., Robinson, A.C., Coverdale, C.A., & Coverdale, C.A. (2005). Seeded perturbations in wire array z-pinches [Conference]. https://www.osti.gov/biblio/969101

Hooper, R., Hopkins, M.M., Pawlowski, R., & Pawlowski, R. (2005). Assessing cost and performance in transitioning from loose to strong coupling [Conference]. https://www.osti.gov/biblio/969554

Gaudioso, J.M. (2005). Introduction to biosecurity [Conference]. https://www.osti.gov/biblio/969862

Gaudioso, J.M. (2005). Generic select agent biosecurity plan template [Conference]. https://www.osti.gov/biblio/969861

Gaudioso, J.M. (2005). Components of a biosecurity program [Conference]. https://www.osti.gov/biblio/969860

Gaudioso, J.M. (2005). Compliance with the select agent regulations [Conference]. https://www.osti.gov/biblio/969859

Gaudioso, J.M. (2005). Biosecurity risk assessment [Conference]. https://www.osti.gov/biblio/969858

Plimpton, S.J., Crozier, P., Vaughan, C.T., & Vaughan, C.T. (2005). Red Storm performance of molecular dynamics modeling [Conference]. https://www.osti.gov/biblio/970265

Heinstein, M., Scovazzi, G., Robinson, A.C., & Robinson, A.C. (2005). Lagrangian modeling at Sandia National Laboratories: current status and future directions [Conference]. https://www.osti.gov/biblio/969837

Heinstein, M., Scovazzi, G., Robinson, A.C., & Robinson, A.C. (2005). Lagrangian modeling at Sandia National Laboratories : current status and future directions [Conference]. https://www.osti.gov/biblio/969832

Bishop, J.E., Hensinger, D.M., Voth, T.E., Wong, M.K., Robinson, A.C., & Robinson, A.C. (2005). Coupled Mesh Lagrangian/ALE modeling: opportunities and challenges [Conference]. https://www.osti.gov/biblio/970210

Bishop, J.E., Hensinger, D.M., Voth, T.E., Wong, M.K., Robinson, A.C., & Robinson, A.C. (2005). Coupled Mesh Lagrangian/ALE modeling: opportunities and challenges [Conference]. https://www.osti.gov/biblio/970209

Bochev, P. (2005). Application of uncertainty propagation and sensitivity analysis in validation [Conference]. https://www.osti.gov/biblio/969880

Bochev, P. (2005). Applications of algebraic topology to compatible spatial discretizations [Conference]. https://www.osti.gov/biblio/969879

Gaudioso, J.M., Salerno, R.M., & Salerno, R.M. (2005). Laboratory biosafety components [Conference]. https://www.osti.gov/biblio/969854

Gaudioso, J.M., Salerno, R.M., & Salerno, R.M. (2005). Laboratory biosafety principles [Conference]. https://www.osti.gov/biblio/969851

Brightwell, R.B., Riesen, R., Underwood, K.D., & Underwood, K.D. (2005). Analyzing the impact of overlap, offload, and independent progress for MPI. Proposed for publication in the International Journal of High Performance Computing Applications.. https://www.osti.gov/biblio/971821

Hopkins, M.M., Pawlowski, R., Hooper, R., & Hooper, R. (2005). Enabling newton-based coupling within a multi-physics environment using NOX - an object-oriented nonlinear solver library [Conference]. https://www.osti.gov/biblio/969845

Doerfler, D.W., Vaughan, C.T., & Vaughan, C.T. (2005). Characterizing compiler performance for the AMD Opteron processor on a parallel platform [Conference]. https://www.osti.gov/biblio/970241

Doerfler, D.W., Vaughan, C.T., & Vaughan, C.T. (2005). Characterizing compiler performance for the AMD Opteron processor on a parallel platform [Conference]. https://www.osti.gov/biblio/970239

Plimpton, S.J. (2005). Effect of deformation path sequence on the behavior of nanoscale copper bicrystal interfaces. Proposed for publication in the Journal of Engineering Materials and Technology.. https://doi.org/10.1115/1.1867983

Plimpton, S.J. (2005). Nonlinear magnetohydrodynamics simulation using high-order finite elements. Proposed for publication in the Journal of Computational Physics.. https://www.osti.gov/biblio/970734

Boman, E.G., Manne, N., & Manne, N. (2005). A Scalable Parallel Graph Coloring Algorithm for Distributed Memory Computers [Conference]. https://www.osti.gov/biblio/1118713

Carr, R.D. (2005). A 1/2-integral relaxation for the A-matching problem. Journal of the Operation Research Letters. https://www.osti.gov/biblio/1145147

Thompson, A.P. (2005). A Scalable Parallel Molecular Dynamics Code for Reactive Force Fields [Conference]. https://www.osti.gov/biblio/1119769

Boman, E.G. (2005). Limits on the quality of combinatorial support bounds. Proposed for publication in Linear Algebra and Its Applications.. https://www.osti.gov/biblio/972152

Sala, M., Shadid, J.N., Tuminaro, R.S., & Tuminaro, R.S. (2005). An improved convergence bound for aggregation-based domain decomposition preconditioners. Proposed for publication in the SIAM Journal on Matrix Analysis and Applications.. https://www.osti.gov/biblio/972459

Hutchinson, S.A., Keiter, E., Hoekstra, R.J., Russo, T.V., Rankin, E., Pawlowski, R., Fixel, D.A., Schiek, R.L., Bogdan, C.W., & Bogdan, C.W. (2005). Xyce Parallel Electronic Simulator - Users' Guide Version 2.1. https://doi.org/10.2172/1143300

Schultz, P.A. (2005). Quantum DFT and multiscale simulations [Conference]. https://www.osti.gov/biblio/969120

Rempe, S.B., Schultz, P.A., Chandross, M., & Chandross, M. (2005). Density functional theory study of transition metal porphine adsorption on gold surface and electric field induced conformation changes. Proposed for publication in the Journal of the American Chemical Society.. https://www.osti.gov/biblio/970708

Sprigg, J.A., Ehlen, M., & Ehlen, M. (2005). Dynamic nash equilibrium in an overlapping-generations model:a methodological exercise in economic simulation. Proposed for publication as a report.. https://www.osti.gov/biblio/903150

Stubblefield, W.A., Huff, T.B., & Huff, T.B. (2005). A situated perspective on technical knowledge management [Conference]. https://www.osti.gov/biblio/970300

Debenedictis, E. (2005). Reversible logic for supercomputing [Conference]. https://www.osti.gov/biblio/970284

Draganescu, A. (2005). Dynamic data-driven inversion for terascale simulations real-time identification of airborne contaminants [Conference]. https://www.osti.gov/biblio/969866

Devine, K. (2005). How to program on 50,000 processors [Conference]. https://www.osti.gov/biblio/970202

Devine, K. (2005). A model for resource-aware load balancing on heterogeneous clusters. Proposed for publication in the IEEE Transactions on Parallel and Distributed Systems.. https://www.osti.gov/biblio/970704

Boman, E.G., Devine, K., Heaphy, R.T., & Heaphy, R.T. (2005). Parallel hypergraph partitioning for scientific computing [Conference]. https://www.osti.gov/biblio/970199

Castro, J.P., Hough, P.D., Gray, G.A., Eldred, M., & Eldred, M. (2005). Multifidelity modeling approaches in simulation simulation--based optimization based optimization [Conference]. https://www.osti.gov/biblio/1145132