Publications

Davidson, G.S., May, E., Faulon, J.-L., & Faulon, J.-L. (2004). Inferring genetic networks from microarray data [Conference]. https://www.osti.gov/biblio/957230

Hjalmarson, H.P., Schultz, P.A., & Schultz, P.A. (2004). Current understanding of the oxygen vacancy in SiO2 and its role in radiation effects in the MOS system [Conference]. https://www.osti.gov/biblio/957228

Eldred, M., Eldred, M., & Eldred, M. (2004). An RSQP for a single-level reliability optimization [Conference]. https://www.osti.gov/biblio/952821

Keiter, E., Hutchinson, S.A., Hoekstra, R.J., Russo, T.V., Rankin, E., Pawlowski, R., Wix, S.D., Fixel, D.A., & Fixel, D.A. (2004). Xyce Parallel Electronic Simulator : users' guide, version 2.0. https://doi.org/10.2172/919117

Keiter, E., Hutchinson, S.A., Hoekstra, R.J., Russo, T.V., Rankin, E., Pawlowski, R., Fixel, D.A., Wix, S.D., & Wix, S.D. (2004). Xyce Parallel Electronic Simulator : reference guide, version 2.0. https://doi.org/10.2172/919160

Salinger, A.G., Shadid, J.N., & Shadid, J.N. (2004). A bifurcation and stability analysis of isothermal impinging jets. Proposed for publication in the Journal of Fluid Mechanics.. https://www.osti.gov/biblio/952814

Plimpton, S.J., Schmidt, R., & Schmidt, R. (2004). Feature length-scale modeling of LPCVD & PECVD MEMS fabrication processes. Proposed for publication in the Journal of Microsystems Technologies.. https://www.osti.gov/biblio/952804

Shadid, J.N., Romero, L., & Romero, L. (2004). A new family of operator-splitting methods. Proposed for publication in Applied Numerical Mathematics.. https://www.osti.gov/biblio/953341

Knupp, P., Ober, C.C., & Ober, C.C. (2004). A manufactured solution for verifying CFD boundary conditions [Conference]. https://www.osti.gov/biblio/957272

Taylor, M.A. (2004). A new algorithm for computing multivariate Gauss-like quadrature points [Conference]. https://www.osti.gov/biblio/957270

Deeney, C., Jones, B.M., Mehlhorn, T., Robinson, A.C., Wunsch, S., & Wunsch, S. (2004). Three-dimensional ALEGRA-HEDP simulations of modulated wire arrays on MAGPIE [Conference]. https://www.osti.gov/biblio/957269

Keiter, E., Pawlowski, R., Hoekstra, R.J., Hutchinson, S.A., Russo, T.V., Coffey, T.S., Kolda, T.G., & Kolda, T.G. (2004). Continuation algorithms for MOSFET circuit simulation [Conference]. https://www.osti.gov/biblio/957265

Keiter, E., Pawlowski, R., Hutchinson, S.A., Hoekstra, R.J., Russo, T.V., Rankin, E., & Rankin, E. (2004). A comparison of nonlinear methods for coupled circuit-device simulation [Conference]. https://www.osti.gov/biblio/957264

Keiter, E., Hutchinson, S.A., Hoekstra, R.J., Russo, T.V., Rankin, E., & Rankin, E. (2004). The two-level Newton method and its application to electronic simulation [Conference]. https://www.osti.gov/biblio/957263

Hoekstra, R.J. (2004). ASC HPEMS Xyce circuit simulator : linear solver technology [Conference]. https://www.osti.gov/biblio/957267

Bartlett, R. (2004). Teuchos::RefCountPtr beginner's guide : an introduction to the Trilinos smart reference-counted pointer class for (almost) automatic dynamic memory management in C++. https://doi.org/10.2172/919177

Salerno, R.M., Barnett, N.B., Gaudioso, J.M., Estes, D., & Estes, D. (2004). Historical precedence and technical requirements of biological weapons use : a threat assessment. https://doi.org/10.2172/919162

Brightwell, R.B. (2004). A NIC-offload implementation of portals for quadrics QsNet [Conference]. https://www.osti.gov/biblio/888562

Brightwell, R.B., Phelps, S., Underwood, K.D., & Underwood, K.D. (2004). On characterizing the network resource usage of MPI applications. Proposed for publication in the Journal of Parallel and Distributed Computing.. https://www.osti.gov/biblio/950686

Laros, J.H. (2004). Future directions in cluster system software [Conference]. https://www.osti.gov/biblio/876260

Sala, M. (2004). Amesos 1.0 reference guide. https://doi.org/10.2172/919163

Sala, M., Heroux, M.A., Day, D.M., & Day, D.M. (2004). Trilinos 4.0 tutorial. https://doi.org/10.2172/919153

Sala, M., Hu, J.J., Tuminaro, R.S., & Tuminaro, R.S. (2004). ML 3.0 smoothed aggregation user's guide. https://doi.org/10.2172/919154

Shadid, J.N., van Bloemen Waanders, B.G., Bartlett, R., & Bartlett, R. (2004). Development of transport/inversion algorithms and capabilities for countermeasures to chem/bio/rad attacks in support of homeland security [Conference]. https://www.osti.gov/biblio/957214

Tuminaro, R.S., Shadid, J.N., & Shadid, J.N. (2004). The generalized global basis (GGB) method. Proposed for publication in IJNME.. https://www.osti.gov/biblio/876254

Wagner, G.J., Bochev, P., Christon, M.A., Collis, S.S., Lehoucq, R.B., Shadid, J.N., Slepoy, A., & Slepoy, A. (2004). A mathematical framework for multiscale science and engineering : the variational multiscale method and interscale transfer operators. https://doi.org/10.2172/975255

Sala, M., Hu, J.J., Tuminaro, R.S., & Tuminaro, R.S. (2004). ML 3.1 developer's guide. https://doi.org/10.2172/974885

Moore, R.C., Hasan, A., Larese, K., Headley, T., Zhao, H., Salas, F., & Salas, F. (2004). Containment of uranium in the proposed Egyptian geologic repository for radioactive waste using hydroxyapatite. https://doi.org/10.2172/918746

Shadid, J.N., Tuminaro, R.S., Devine, K., Hennigan, G., Lin, P.T., & Lin, P.T. (2004). Performance of fully-coupled domain decomposition preconditioners for finite element transport/reaction simulations. Proposed for publication in Journal of Computational Physics.. https://www.osti.gov/biblio/876377

Adams, M.F. (2004). Algebraic multigrid methods for constrained linear systems with applications to contact problems in solid mechanics. Numerical Linear Algebra with Applications, 11(2-3), pp. 141-153. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=10044257879&origin=inward

Debenedictis, E. (2004). Taking ASCI supercomputing to the end game. https://doi.org/10.2172/918778

Thompson, A.P. (2004). Molecular simulations of MEMS and membrane coatings (PECASE). https://doi.org/10.2172/918758

Roy, C.J., Nelson, C.C., Smith, T.M., Ober, C.C., & Ober, C.C. (2004). Verification of Euler/Navier-Stokes codes using the method of manufactured solutions. International Journal for Numerical Methods in Fluids, 44(6), pp. 599-620. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=1142306006&origin=inward

Devine, K., Boman, E.G., Devine, K., Heaphy, R.T., Hendrickson, B.A., Heroux, M.A., & Heroux, M.A. (2004). LDRD report : parallel repartitioning for optimal solver performance. https://doi.org/10.2172/918322

Hart, W.E. (2004). A filter-based evolutionary algorithm for constrained optimization. Proposed for publication in Evolutionary Computations.. https://www.osti.gov/biblio/971830

Oberkampf, W.L., Trucano, T.G., Hirsch, C., & Hirsch, C. (2004). Verification, validation, and predictive capability in computational engineering and physics [Conference]. Applied Mechanics Reviews. https://doi.org/10.2172/809603

Churchwell, C.J., Rintoul, M.D., Martin, S., Visco, D.P., Kotu, A., Larson, R., Sillerud, L.O., Brown, D.C., Faulon, J.-L., & Faulon, J.-L. (2004). The signature molecular descriptor: 3. Inverse-quantitative structure-activity relationship of ICAM-1 inhibitory peptides. Journal of Molecular Graphics and Modelling, 22(4), pp. 263-273. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=0842332242&origin=inward

Collins, M.J. (2004). Covering a set of points with a minimum number of turns [Conference]. International Journal of Computational Geometry and Applications. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=7444270315&origin=inward

Leung, V.J. (2004). Communication patterns and allocation strategies [Conference]. https://doi.org/10.2172/918398

Barton, D.C., Eidson, E.D., Schoenwald, D.A., Cox, R., Reinert, R.K., & Reinert, R.K. (2004). Simulating economic effects of disruptions in the telecommunications infrastructure. https://doi.org/10.2172/918354

Heroux, M.A., Sala, M., & Sala, M. (2004). Trilinos 3.1 tutorial. https://doi.org/10.2172/918276

Davidson, G.S., Haaland, D.M., Martin, S., & Martin, S. (2004). Application of multidisciplinary analysis to gene expression. https://doi.org/10.2172/918393

Pérez, V.M., Eldred, M., Renaud, J.E., & Renaud, J.E. (2004). Solving the infeasible trust-region problem using approximations [Conference]. Collection of Technical Papers - 10th AIAA/ISSMO Multidisciplinary Analysis and Optimization Conference. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=20344385993&origin=inward

Carr, R.D., Lancia, G.G., & Lancia, G.G. (2004). Compact optimization can outperform separation: A case study in structural proteomics. 4OR, 2(3), pp. 221-233. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=29044441607&origin=inward

Schaub, H., Smith, C.E., & Smith, C.E. (2003). Color Snakes for Dynamic Lighting Conditions on Mobile Manipulation Platforms [Conference]. IEEE International Conference on Intelligent Robots and Systems. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=0346148772&origin=inward

Auhl, R., Everaers, R., Grest, G.S., Kremer, K., Plimpton, S.J., & Plimpton, S.J. (2003). Equilibration of long chain polymer melts in computer simulations. Journal of Chemical Physics, 119(24), pp. 12718-12728. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=0842330642&origin=inward

Forsythe, J.C., Speed, A., Lippitt, C.E., Schaller, M.J., Xavier, P.G., Thomas, E.V., Schoenwald, D.A., & Schoenwald, D.A. (2003). Final report for the endowment of simulator agents with human-like episodic memory LDRD. https://doi.org/10.2172/918401

Heroux, M.A. (2003). Epetra developers coding guidelines. https://doi.org/10.2172/918292

Cooper, J.A., Johnston, A.M., & Johnston, A.M. (2003). Unique Signal mathematical analysis task group FY03 status report. https://doi.org/10.2172/918228

Plimpton, S.J., Slepoy, A., & Slepoy, A. (2003). ChemCell : a particle-based model of protein chemistry and diffusion in microbial cells. https://doi.org/10.2172/918231

Robinson, A.C., Farnsworth, G., & Farnsworth, G. (2003). Improved kinematic options in ALEGRA. https://doi.org/10.2172/918209

Rao, R.R., Noble, D.R., Schunk, P.R., Wilkes, E.D., Baer, T.A., Notz, P.K., & Notz, P.K. (2003). Large deformation solid-fluid interaction via a level set approach. https://doi.org/10.2172/918218

Davidson, G.S., Sinclair, M.B., Thomas, E.V., Werner-Washburne, M., Martin, S., Boyack, K.W., Wylie, B.N., Haaland, D.M., Timlin, J.A., Keenan, M.R., & Keenan, M.R. (2003). High throughput instruments, methods, and informatics for systems biology. https://doi.org/10.2172/918232

Haill, T.A., Garasi, C.J., Robinson, A.C., & Robinson, A.C. (2003). ALEGRA-MHD : Version 4.0. https://doi.org/10.2172/918373

Torgerson, M.D., Beaver, C., Collins, M.J., Draelos, T.J., Gallup, D.R., Neumann, W., & Neumann, W. (2003). Hybrid cryptography key management. https://doi.org/10.2172/918318

Rintoul, M.D., Sears, M.P., Plimpton, S.J., & Plimpton, S.J. (2003). Parallel tempering Monte Carlo in LAMMPS. https://doi.org/10.2172/918289

Schaller, M.J., Pryor, R., & Pryor, R. (2003). Developing close combat behaviors for simulated soldiers using genetic programming techniques. https://doi.org/10.2172/918361

Tomkins, J.L., Camp, W.J., & Camp, W.J. (2003). Architectural requirements for the Red Storm computing system. https://doi.org/10.2172/918236

Debenedictis, E. (2003). The Sandia petaflops planner. https://doi.org/10.2172/918306

Leung, V.J., Phillips, C.A., & Phillips, C.A. (2003). Algorithmic support for commodity-based parallel computing systems. https://doi.org/10.2172/918344

Swiler, L.P., Campbell, J.E., Lowder, K.S., Doser, A., & Doser, A. (2003). Algorithm development for Prognostics and Health Management (PHM). https://doi.org/10.2172/918353

May, E., Johnston, A.M., Hart, W.E., Watson, J., Pryor, R., Rintoul, M.D., & Rintoul, M.D. (2003). Detection and reconstruction of error control codes for engineered and biological regulatory systems. https://doi.org/10.2172/918239

Oldfield, R. (2003). Improving data access for computational grid applications. Proposed for publication in Cluster Computing: The Journal of Networks, Software and Applications.. https://www.osti.gov/biblio/891280

Rohrer, B.R. (2003). Avoiding spurious submovement decompositions: A globally optimal algorithm. Biological Cybernetics, 89(3), pp. 190-199. https://doi.org/10.1007/s00422-003-0428-4

Debenedictis, E. (2003). A network architecture for Petaflops supercomputers. https://doi.org/10.2172/918315

Christon, M.A., Ketcheson, D.I., Robinson, A.C., & Robinson, A.C. (2003). An assessment of semi-discrete central schemes for hyperbolic conservation laws. https://doi.org/10.2172/918357

Robinson, A.C., Garasi, C.J., & Garasi, C.J. (2003). Three-dimensional z-pinch wire array modeling with ALEGRA-HEDP. Proposed for publication in the Computer Physics Communications., 164(1-3), pp. 1-8. https://www.osti.gov/biblio/1005420

Laros, J.H., Ward, H.L., & Ward, H.L. (2003). Implementing scalable disk-less clusters using the Network File System (NFS) [Conference]. https://www.osti.gov/biblio/1005419

Bessette, G.C., Vaughan, C.T., Bell, R.L., Attaway, S.W., & Attaway, S.W. (2003). Modeling air blast on thin-shell structures with Zapotec [Conference]. https://www.osti.gov/biblio/1005394

Hendrickson, B.A., Hart, W.E., Phillips, C.A., & Phillips, C.A. (2003). Supercomputing and discrete algorithms : a symbiotic relationship [Conference]. https://www.osti.gov/biblio/1005427

Bochev, P., Gunzburger, M., Shadid, J.N., & Shadid, J.N. (2003). Stability of Streamline Upwind Petrov-Galerkin (SUPG) finite elements for transient advection-diffusion problems. Proposed for publication in Journal of Computer Methods in Application and Mechanical Engineering., 193(23-26), pp. 1-27. https://www.osti.gov/biblio/1005399

Romero, V., Gunzburger, M., & Gunzburger, M. (2003). Initial evaluation of Centroidal Voronoi Tessellation method for statistical sampling and function integration [Conference]. https://www.osti.gov/biblio/1005414

Drumheller, D.S., Kuszmaul, S.S., & Kuszmaul, S.S. (2003). Acoustic telemetry. https://doi.org/10.2172/918379

Trucano, T.G., Pilch, M., Oberkampf, W.L., & Oberkampf, W.L. (2003). On the role of code comparisons in verification and validation. https://doi.org/10.2172/918244

Debenedictis, E., Christopher, T.W., & Christopher, T.W. (2003). Radiation transport algorithms on trans-petaflops supercomputers of different architectures. https://doi.org/10.2172/913222

Heroux, M.A., Kolda, T.G., Long, K., Hoekstra, R.J., Pawlowski, R., Phipps, E.T., Salinger, A.G., Williams, A.B., Hu, J.J., Lehoucq, R.B., Thornquist, H., Tuminaro, R.S., Willenbring, J.M., Bartlett, R., Howle, V.E., & Howle, V.E. (2003). An overview of Trilinos. https://doi.org/10.2172/918383

Heroux, M.A., Willenbring, J.M., & Willenbring, J.M. (2003). Trilinos users guide. https://doi.org/10.2172/918334

Tangyunyong, P., Headley, T., Rye, M.J., Hill, T.A., Nakakura, C.Y., Soden, J., Colr, E.I., Flores, R.S., Shaneyfelt, M.R., Dockerty, R.C., & Dockerty, R.C. (2003). Novel application of transmission electron microscopy and scanning capacitance microscopy for defect root cause identification and yield enhancement [Conference]. https://www.osti.gov/biblio/1004355

Bunker, B.C., Boal, A., Headley, T., Tissot, R.G., & Tissot, R.G. (2003). Microtubule-templated biomimetic mineralization of lepidocrocite. Proposed for publication in Advanced Functional Materials., 14(1), pp. 1-19. https://www.osti.gov/biblio/1004362

Larese, K., Moore, R.C., Hasan, A., Headley, T., Zhao, H., Salas, F., & Salas, F. (2003). Containment of uranium in the proposed Egyptian geologic repository for radioactive waste using hydroxyapatite [Conference]. https://www.osti.gov/biblio/1004367

Boyack, K.W., Backer, A., & Backer, A. (2003). The memory of science : recent effects of growth and aging. Proposed for publication in Nature.. https://www.osti.gov/biblio/1004356

Mansure, A., Drumheller, D.S., & Drumheller, D.S. (2003). Advanced drilling concepts [Conference]. https://www.osti.gov/biblio/1005043

Raymond, D., Drumheller, D.S., Kuszmaul, S.S., & Kuszmaul, S.S. (2003). Self-induced bit vibrations (2.2.3c) [Conference]. https://www.osti.gov/biblio/1005066

Hart, W.E., Carr, R.D., & Carr, R.D. (2003). A comparison of computational methods for the maximum contact map overlap of protein pairs. Proposed for publication in INFORMS J on Computing.. https://www.osti.gov/biblio/1005034

Hart, W.E., Delaurentis, J.M., & Delaurentis, J.M. (2003). Convergence of a discretized self-adaptive evolutionary algorithm on multi-dimensional problems. Proposed for publication in IEEE Transactions on Evolutionary Computation.. https://www.osti.gov/biblio/1005077

Boman, E.G., Parekh, O., & Parekh, O. (2003). Combinatorial and algorithmic aspects of the null spaces of symmetric H-matrices [Conference]. https://www.osti.gov/biblio/993896

Bochev, P., Gunzburger, M., & Gunzburger, M. (2003). On least-squares methods for the Kelvin principle. Proposed for publication in SIAM Journal of Numerical Analysis.. https://www.osti.gov/biblio/993894

Preece, D.S., Saul, W.V., & Saul, W.V. (2003). Blastwall effects on down range explosively-induced overpressure [Conference]. https://www.osti.gov/biblio/1002119

Wenner, C.A., Spencer, F.W., & Spencer, F.W. (2003). The impact of instructions on aircraft visual inspection performance : a first look at the overall results [Conference]. https://www.osti.gov/biblio/1002035

Underwood, K.D., Brightwell, R.B., & Brightwell, R.B. (2003). Implications of a PIM architectural model for MPI [Conference]. https://www.osti.gov/biblio/1002079

Hjalmarson, H.P., Shaneyfelt, M.R., Schwank, J.R., Edwards, A.H., Hembree, C., Mattsson, T., & Mattsson, T. (2003). Mechanisms for radiation dose-rate sensitivity of bipolar transistors [Conference]. https://www.osti.gov/biblio/1002031

Wills, A.E. (2003). Equation of state for a high-density glass [Conference]. https://www.osti.gov/biblio/1002045

Rohrer, B.R. (2003). Submovement overlap as a measure of movement smoothness [Conference]. https://www.osti.gov/biblio/1002127

Rohrer, B.R. (2003). Submovements grow larger, fewer, and more blended during stroke recovery. Proposed for publication in Journal of Neuroscience., 8(4), pp. 1-46. https://www.osti.gov/biblio/1003984

Crossno, P.J., Rogers, D., Brannon, R., Coblentz, D.D., & Coblentz, D.D. (2003). Tensor visualization using Mohr diagrams. Proposed for publication in Coordinated & Multiple Views in Exploratory Visualization, Special Issue of Information Visualization Journal, Vol 2 No. 4, Palgrave/Macmillan.. https://www.osti.gov/biblio/1002074

Debenedictis, E., Christopher, T.W., & Christopher, T.W. (2003). Projection of the Cost-Effectiveness of PIMs for Particle Transport Codes. https://doi.org/10.2172/820890

Carr, R.D. (2003). A practical application of compact optimization. Proposed for publication in the Journal of 40R.. https://www.osti.gov/biblio/926784

Brannon, N., Lippitt, C.E., & Lippitt, C.E. (2003). Generative visualization system for subject matter experts [Conference]. https://www.osti.gov/biblio/926816

Doerry, A.W., Dickey, F.M., Romero, L., & Romero, L. (2003). Windowing functions for SAR data with spectral gaps [Conference]. https://www.osti.gov/biblio/926790

Hjalmarson, H.P., Edwards, A.H., Schultz, P.A., Hjalmarson, H.P., & Hjalmarson, H.P. (2003). Spontaneous ionization of hydrogen atoms at the Si-SiO2 interface. Proposed for publication in Physical Review B., 69(12). https://www.osti.gov/biblio/990012