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Publications

Papers are listed chronologically in the next section. All have viewable abstracts; some have downloadable PS, PDF, or HTML files. If you're looking for papers on a specific topic, click on one of these links:



2012

Computational Aspects of Many-body Potentials, S. J. Plimpton and A. P. Thompson, MRS Bulletin, 37, 513-521 (2012). (abstract)

Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh, W. M. Brown, A. Kohlmeyer, S. J. Plimpton, A. N. Tharrington, Comp Phys Comm, 183, 449-459 (2012). (abstract)


2011

Evaporation of Lennard-Jones Fluids, S Cheng, J. B. Lechman, S. J. Plimpton, G. S. Grest, J Chem Phys, 134, 224704 (2011). (abstract)

Implementing Molecular Dynamics on Hybrid High Performance Computers - Short Range Forces, W. M. Brown, P. Wang, S. J. Plimpton, A. N. Tharrington, Comp Phys Comm, 182, 898-911, (2011). (abstract)

Parallel Simulation of 3D Sintering, C. G. Cardona, V. Tikare, S. J. Plimpton, Int J Computational Materials Science and Surface Engineering, 4, 37-54 (2011). (abstract)

MapReduce in MPI for Large-Scale Graph Algorithms, S. J. Plimpton and K. D. Devine, Parallel Computing, 37, 610-632 (2011). (abstract) (preprint)


2010

Mesoscale Hydrodynamics via Stochastic Rotation Dynamics: Comparison with Lennard-Jones Fluid, M. K. Petersen, J. B. Lechman, S. J. Plimpton, G. S. Grest, P. J. in't Veld, P. R. Schunk, J Chem Phys, 132, 174106 (2010). (abstract)

Software components for parallel multiscale simulation: an example with LAMMPS, B. Frantzdale, S. J. Plimpton, M. S. Shephard, Engineering with Computers, 26, 205-211 (2010). (abstract)

1D-to-3D transition of phonon heat conduction in polyethylene using molecular dynamics simulations, A. Henry, G. Chen, S. J. Plimpton, A. Thompson, Phys Rev B, 82, 144308 (2010). (abstract)

Equation-Free Accelerated Simulations of the Morphological Relaxation of Crystal Surfaces, G. J. Wagner, X. Zhou, S. J. Plimpton, Int J for Multiscale Computational Engineering, 8, 423-439 (2010). (abstract)


2009

Liquid crystal nanodroplets in solution, W. M. Brown, M. K. Petersen, S. J. Plimpton, and G. S. Grest, J Chem Phys, 130, 044901 (2009). (abstract)

General formulation of pressure and stress tensor for arbitrary many-body interaction potentials under periodic boundary conditions, A. P. Thompson, S. J. Plimpton, W. Mattson, J Chem Phys, 131, 154107 (2009). (abstract)

Crossing the Mesoscale No-Man's Land via Parallel Kinetic Monte Carlo, S. Plimpton, C. Battaile, M. Chandross, L. Holm, A. Thompson, V. Tikare, G. Wagner, E. Webb, X. Zhou, C. Garcia Cardona, A. Slepoy, Sandia report SAND2009-6226, October 2009. (abstract) (pdf)


2008

Substructured molecular dynamics using multibody dynamics algorithms, R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson, Intl J of Non-Linear Mechanics, 43, 1045-1055 (2008). (abstract)

Implementing peridynamics within a molecular dynamics code, M. L. Parks, R. B. Lehoucq, S. J. Plimpton, S. A. Silling, Comp Phys Comm, 179, 777-783 (2008). (abstract)

A Constant-Time Kinetic Monte Carlo Algorithm for Simulation of Large Biochemical Reaction Networks, A. Slepoy, A. P. Thompson, S. J. Plimpton, J Chem Phys, 128, 205101 (2008). (abstract)

Accurate and Efficient Methods for Modeling Colloidal Mixtures in an Explicit Solvent using Molecular Dynamics, P. J. in 't Veld, S. J. Plimpton, G. S. Grest, Comp Phys Comm, 179, 320-329 (2008). (abstract)


2007

Sensitivity Analysis of a Computational Model of the IKK-NF-kB-A20 Signal Transduction Network, J. Joo, S. J. Plimpton, S. Martin, L. Swiler, J. L. Faulon, Annals of the New York Acadamey of Sciences, Volume on Reverse Engineering Biological Networks, 1115, 221-239 (2007). (abstract)


2006

Computing the mobility of grain boundaries, K. G. F. Janssens, D. Olmsted, E.A. Holm, S. M. Foiles, S. J. Plimpton, and P. M. Derlet, Nature Materials, 5, 124-127 (2006). (abstract)

A Simple Synchronous Distributed-Memory Algorithm for the HPCC RandomAccess Benchmark, S. J. Plimpton, R. Brightwell, C. Vaughan, K. Underwood, M. Davis, Proc of Cluster 2006 - IEEE International Conf on Cluster Computing, Sept 2006. (abstract) (pdf)


2005

Microbial cell modeling via reacting diffusing particles, S. J. Plimpton and A. Slepoy, Journal of Physics: Conference Series 16, 305-309 (2005). (abstract) (pdf)

Parallel Sn Sweeps on Unstructured Grids: Algorithms for Prioritization, Grid Partitioning, and Cycle-Detection, S. J. Plimpton, B. Hendrickson, S. Burns, W. Mclendon III, L. Rauchwerger, Nuclear Science and Engineering, 150, 267-283 (2005). (abstract) (postscript) (ps.gz)

Finding Strongly Connected Components in Distributed Graphs, W. McLendon, B. Hendrickson, S. J. Plimpton, L. Rauchwerger, J Parallel and Distributed Computing, 65, 901-910 (2005). (abstract) (pdf) (pdf.gz)

Effect of Deformation Path Sequence on the Behavior of Nanoscale Copper Bicrystal Interfaces, D. E. Spearot, K. I. Jacob, D. L. McDowell, S. J. Plimpton, J Engr Materials and Technology, 127, 374-382 (2005). (abstract)

Feature Length-Scale Modeling of LPCVD and PECVD MEMS Fabrication Processes, L. C. Musson, P. Ho, S. J. Plimpton, R. C. Schmidt, Journal of Microsystems Technologies, 12, 137-142 (2005). (abstract) (pdf)


2004

Discrete element simulations of stress distributions in silos: Crossover from two to three dimensions, J. W. Landry, G. S. Grest, S. J. Plimpton, Powder Technology, 139, 233-239 (2004). (abstract)

Effect of end-tethered polymers on surface adhesion of glassy polymers, S. W. Sides, G. S. Grest, M. J. Stevens, S. J. Plimpton, Journal of Polymer Science, Part B (Polymer Physics), 42, 199-208 (2004). (abstract)

Nonlinear Magnetohydrodynamics Simulation Using High-order Finite Elements, C. R. Sovinec, A. H. Glasser, T. A. Gianakon, D. C. Barnes, R. A. Nebel, S. E. Kruger, D. D. Schnack, S. J. Plimpton, A. Tarditi, and M. S. Chu, J Comp Phys, 195, 355-386 (2004). (abstract)

A Parallel Rendezvous Algorithm for Interpolation Between Multiple Grids, S. J. Plimpton, B. Hendrickson, J. Stewart, J Parallel and Distributed Computing, 64, 266-276 (2004). (abstract) (pdf) (pdf.gz)


2003

Confined granular packings: Structure, stress, and forces, G. S. Grest, J. W. Landry, S. J. Plimpton, L. E. Silbert, Phys Rev E, 67, 041303 (2003). (abstract)

Equilibration of long chain polymer melts in computer simulations, R. Auhl, R. Everaers, G. S. Grest, K. Kremer, S. J. Plimpton, J Chem Phys, 119, 12718-12728 (2003). (abstract)

Parallel Genehunter: Implementation of a Linkage Analysis Package for Distributed-Memory Architectures, G. C. Conant, S. J. Plimpton, W. Old, A. Wagner, P. R. Fain, T. R. Pacheco, and G. Heffelfinger, Journal of Parallel and Distributed Computing, 63, 674-682 (2003). (abstract) (pdf) (pdf.gz)

A Load-Balancing Algorithm for a Parallel Electromagnetic Particle-in-Cell Code, S. J. Plimpton, D. B. Seidel, M. F. Pasik, R. S. Coats, G. R. Montry, Comp Phys Comm, 152, 227-241 (2003). (abstract) (pdf) (pdf.gz)


2002

Boundary effects and self-organization in dense granular flows, L. E. Silbert, G. S. Grest, S. J. Plimpton, D. Levine, Physics of Fluids, 14, 2637-2646 (2002). (abstract)

Torsion/simple shear of single crystal copper, M. F. Horstemeyer, T. J. Lim, W. Y. Lu,, D. A. Mosher, M. I. Baskes, V. C. Prantil, S. J. Plimpton, J of Engineering Materials and Technology (Transactions of the ASME), 124, 322-328 (2002). (abstract)

Development and Performance of a PVM Based Parallel Geometric Modeler for MEMS, C. Jorgensen, D. Melander, R. Schmidt, S. J. Plimpton, in Proc of Modeling and Simulation of Microsystems (MSM), Puerto Rico, April 2002, 218-221. (abstract) (pdf)

Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling, G. S. Heffelfinger, ..., S. J. Plimpton, ..., OMICS - A Journal of Integrative Biology, 6, 305-330 (2002). (abstract)


2001

Length scale and time scale effects on the plastic flow of FCC metals, M. F. Horstemeyer, M. I. Baskes, S. J. Plimpton, Acta Materialia, 49, 4363-4374 (2001). (abstract)

Computational nanoscale plasticity simulations using embedded atom potentials, M. F. Horstemeyer, M. I. Baskes, S. J. Plimpton, Theoretical and Applied Fracture Mechanics, 37, 49-98 (2001). (abstract)

Granular flow down an inclined plane: Bagnold scaling and rheology, L. E. Silbert, D. Ertas, G. S. Grest, T. C. Halsey, D. Levine, S. J. Plimpton, Phys Rev E, 64, 051302 (2001). (abstract)

Identifying Strongly Connected Components in Parallel, W. McLendon III, B. Hendrickson, S. J. Plimpton, L. Rauchwerger, in Proc of SIAM Parallel Processing for Scientific Computing Conf, March 2001. (abstract) (postscript) (ps.gz)

Scalability and Performance of Two Large Linux Clusters, R. Brightwell and S. J. Plimpton, J of Parallel and Distributed Computing, 61, 1546-1569 (2001). (abstract) (postscript) (ps.gz)

Tinkertoy Parallel Programming: Complicated Applications from Simple Tools, B. Hendrickson and S. J. Plimpton, in Proc of SIAM Parallel Processing for Scientific Computing Conf, March 2001. (abstract) (postscript) (ps.gz)


2000

Parallel Algorithms for Radiation Transport on Unstructured Grids, S. J. Plimpton, B. A. Hendrickson, S. P. Burns, W. McLendon III, Proc of SuperComputing 2000 (SC2000), Dallas, TX, November 2000. (abstract) (postscript) (ps.gz)

Parallel Strategies for Crash and Impact Simulations, K. Brown, S. Attaway, S. J. Plimpton, B. Hendrickson, Computer Methods in Applied Mechanics and Engineering, 184, 375-390 (2000). (abstract)


1999

Spatial correlations of mobility and immobility in a glass-forming Lennard-Jones liquid, C. Donati, S. C. Glotzer, P. H. Poole, W. Kob, S. J. Plimpton, Phys Rev E, 60, 3107-3119 (1999). (abstract)

The diffusion of simple penetrants in tangent site polymer melts, D. R. Rottach, P. A. Tillman, J. D. McCoy, S. J. Plimpton, J. G. Curro, J Chem Phys, 111, 9822-9831 (1999). (abstract)

The NIMROD Code: A New Approach to Numerical Plasma Physics, A. H. Glasser, C. R. Sovinec, R. A. Nebel, T. A. Gianakon, S. J. Plimpton, M. S. Chu, D. D. Schnack, and the NIMROD Team, Plasma Physics and Controlled Fusion, 41, A747- A755 (1999). (abstract) (html)

Massively Parallel Computing: A Sandia Perspective, D. E. Womble, S. S. Dosanjh, B. A. Hendrickson, M. A. Heroux, S. J. Plimpton, J. L. Tomkins, D. S. Greenberg, Parallel Computing, 25, 1853-1876 (1999). (abstract) (ps) (ps.gz)


1998

Stringlike cooperative motion in a supercooled liquid, C. Donati, J. F. Douglas, W. Kob, S. J. Plimpton, P. H. Poole, S. C. Glotzer, Phys Rev Lett, 80, 2338-2341 (1998). (abstract)

The effect of added salt on polyelectrolyte structure, M. J. Stevens and S. J. Plimpton, Eur Phys J B, 2, 341-345 (1998). (abstract)

Dislocation nucleation and defect structure during surface indentation, C. L. Kelchner, S. J. Plimpton, J. C. Hamilton, Phys Rev B, 58, 11085-11088 (1998). (abstract)

The structure and thermodynamics of energetically and structurally asymmetric polymer blends, P. A. Tillman, D. R. Rottach, J. D. McCoy, S. J. Plimpton, J. G. Curro, J Chem Phys, 109, 806-814 (1998). (abstract)

Molecular-Dynamics Simulations of Low-Energy (25-200 eV) Argon Ion Interactions with Silicon Surfaces: Sputter Yields and Product Formation Pathways, N. A. Kubota, D. J. Economou, S. J. Plimpton, J of Appl Phys, 83, 4055-4063 (1998). (abstract)

Parallel Transient Dynamics Simulations: Algorithms for Contact Detection and Smoothed Particle Hydrodynamics, S. J. Plimpton, S. Attaway, B. Hendrickson, J. Swegle, C. Vaughan, D. Gardner, J Parallel and Distributed Computing, 50, 104- 122 (1998). (abstract) (postscript) (ps.gz)

A Parallel Contact Detection Algorithm for Transient Solid Dynamics Simulations Using PRONTO3D, S. W. Attaway, B. A. Hendrickson, S. J. Plimpton, D. R. Gardner, C. T. Vaughan, K. H. Brown, M. W. Heinstein, Computational Mechanics, 22, 143-159 (1998). (abstract)

Plane-wave Psuedopotential Electronic Structure Calculations on Parallel Supercomputers, J. S. Nelson and S. J. Plimpton, chapter in Topics in Computational Materials Science, edited by C. Y. Fong, published by World Scientific, 61-95 (1998). (abstract)


1997

Particle-Mesh Ewald and rRESPA for Parallel Molecular Dynamics Simulations, S. J. Plimpton, R. Pollock, M. Stevens, in Proc of the Eighth SIAM Conference on Parallel Processing for Scientific Computing, Minneapolis, MN, March 1997. (abstract) (postscript) (ps.gz)

Dynamical heterogeneities in a supercooled Lennard-Jones liquid, W. Kob, C. Donati, S. J. Plimpton, P. H. Poole, S. C. Glotzer, Phys Rev Lett, 79, 2827- 2830 (1997). (abstract)

The effect of attractions on the structure and thermodynamics of model polymer blends, P. A. Tillman, D. R. Rottach, J. D. McCoy, S. J. Plimpton, J. G. Curro, J Chem Phys, 107, 4024-4032 (1997). (abstract)

Transient Solid Dynamics Simulations on the Sandia/Intel Teraflop Computer, S. Attaway, T. Barragy, K. Brown, D. Gardner, B. Hendrickson, S. J. Plimpton, C. Vaughan, Gordon Bell finalist paper, in Proc of SuperComputing '97, San Jose, CA, November 1997. (abstract) (html)

Potts-model Grain Growth Simulations: Parallel Algorithms and Applications, S. A. Wright, S. J. Plimpton, T. P. Swiler, R. M. Fye, M. F. Young, E. A. Holm, SAND Report 97-1925, August 1997. (abstract)


1996

A New Parallel Method for Molecular-Dynamics Simulation of Macromolecular Systems, S. J. Plimpton and B. A. Hendrickson, J Comp Chem, 17, 326-337 (1996). (abstract) (postscript) (ps.gz)

Transient Dynamics Simulations: Parallel Algorithms for Contact Detection and Smoothed Particle Hydrodynamics, S. J. Plimpton, S. Attaway, B. Hendrickson, J. Swegle, C. Vaughan, D. Gardner, in Proc of SuperComputing '96, Pittsburgh, PA, November 1996. (abstract) (html)


1995

Fast Parallel Algorithms for Short-Range Molecular Dynamics, S. J. Plimpton, J Comp Phys, 117, 1-19 (1995). (abstract) (pdf) (tar file of figures if they don't display correctly in the PDF file)

Parallel Molecular Dynamics Algorithms for Simulation of Molecular Systems, S. J. Plimpton and B. A. Hendrickson, chapter in Parallel Computing in Computational Chemistry, edited by T. G. Mattson, published by the American Chemical Society, Symposium Series 592, 114-132 (1995). (abstract) (postscript) (ps.gz)

Computational Limits of Classical Molecular-Dynamics Simulations, S. J. Plimpton, Computational Materials Science, 4, 361-364 (1995). (abstract) (postscript) (ps.gz)

Molecular dynamics simulation of athermal polymer blends: Comparison with integral-equation theory, C. S. Stevenson, J. G. Curro, J. D. McCoy, S. J. Plimpton, J Chem Phys, 103, 1208-1215 (1995). (abstract)

Molecular dynamics simulation of athermal polymer blends: Finite system size considerations, C. S. Stevenson, J. D. McCoy, S. J. Plimpton, J. G. Curro, J Chem Phys, 103, 1200-1207 (1995). (abstract)

Modeling a nematic liquid crystal, S. S. Patnaik, S. J. Plimpton, R. Pachter, W. W. Adams, Liquid Crystals, 19, 213-220 (1995). (abstract)

Molecular-statics and molecular-dynamics study of diffusion along 001 tilt grain boundaries in Ag, C. L. Liu and S. J. Plimpton, Phys Rev B, 51, 4523-4528 (1995). (abstract)

Molecular-dynamics simulations of grain-boundary diffusion in Al using embedded-atom method potentials, C. L. Liu and S. J. Plimpton, J Materials Research, 10, 1589-1592 (1995). (abstract)

Parallel Algorithms for Dynamically Partitioning Unstructured Grids, P. Diniz, S. J. Plimpton, B. Hendrickson, R. Leland, in Proc of 7th SIAM Conference on Parallel Processing for Scientific Computing, San Francisco, CA, February 1995, p 615. (abstract) (postscript) (ps.gz)

Parallel Many-Body Simulations Without All-to-All Communication, B. A. Hendrickson and S. J. Plimpton, J Parallel and Distributed Computing, 27, 15-25 (1995). (abstract) (postscript) (ps.gz)

An Efficient Parallel Algorithm for Matrix-Vector Multiplication, B. A. Hendrickson, R. W. Leland, S. J. Plimpton, Int J of High Speed Computing, 7, 73-88 (1995). (abstract) (postscript) (ps.gz)

Basis-Set Convergence of Highly Defected Sites in Amorphous-Carbon, J. S. Nelson, E. B. Stechel, A. F. Wright, S. J. Plimpton, P. A. Schultz, M. P. Sears, Phys Rev B, 52, 9354-59 (1995). (abstract)


1994

Massively-Parallel Methods for Engineering and Science Problems, W. J. Camp, S. J. Plimpton, B. A. Hendrickson, R. W. Leland, Communications of the ACM, 37, 31-41 (1994). (abstract) (postscript) (ps.gz)

Parallel Particle Simulations of Low-Density Fluid Flows, S. J. Plimpton and T. J. Bartel, in Proc of High Performance Computing 1994, San Diego, CA, April 1994, p 31. (abstract) (postscript) (ps.gz)


1993

Parallel Molecular Dynamics With the Embedded Atom Method, S. J. Plimpton and B. A. Hendrickson, in Materials Theory and Modelling, edited by J. Broughton, P. Bristowe, and J. Newsam, MRS Proceedings 291, Pittsburgh, PA, 1993, p 37. (abstract) (postscript) (ps.gz)

Plane-wave Electronic- Structure Calculations on a Parallel Supercomputer, J. S. Nelson, S. J. Plimpton, M. P. Sears, Phys Rev B, 47, 1765-1774 (1993). (abstract)

A Massively-Parallel Digital Processor for Spotlight Synthetic-Aperture Radar, G. A. Mastin, S. J. Plimpton, D. Ghiglia, Int J of Supercomputer Applications, 7, 97-112 (1993). (abstract) (postscript) (ps.gz)

Parallel Simulation of Electron-Solid Interactions: A Rapid Aid for Electron- Microscope Data Interpretation, J. R. Michael, S. J. Plimpton, A. D. Romig Jr., Ultramicroscopy, 51, 160-167 (1993). (abstract)


1992

Is SIMD Enough for Scientific and Engineering Applications on Massively Parallel Computers ?, S. J. Plimpton, S. S. Dosanjh, R. B. Krall, in Proc of 37th IEEE International Computer Conference, COMPCON '92, San Francisco, CA, February 1992. p 95-102. (abstract) (postscript) (ps.gz)

Direct Monte Carlo Simulation of Ionized Rarefied Flows on Large MIMD Parallel Supercomputers, T. J. Bartel, S. J. Plimpton, C. R. Justiz, in Proc of 18th International Symposium on Rarefied Gas Dynamics, Vancouver, Canada, July 1992, published by AIAA, A94-30156, p 155-165. (abstract)

Monte Carlo Particle Simulation of Low-Density Fluid Flow on MIMD Supercomputers, S. J. Plimpton and T. J. Bartel, in Proc of Scalable High Performance Computing Conference, Williamsburg, VA, April 1992, p 212, and in Computing Systems in Engineering, 3, 333-336 (1992). (abstract) (postscript) (ps.gz)

Parallel Simulation of Electron-Solid Interactions for Electron-Microscopy Modeling, S. J. Plimpton, J. R. Michael, A. D. Romig, Jr., J of SuperComputing, 6, 139-151 (1992). (abstract) (postscript) (ps.gz)


1991

Load Balancing and Performance of a Gridless Particle Simulation on MIMD, SIMD, and Vector Supercomputers, S. J. Plimpton, I. Shokair, J. Wagner, in Proc of 5th SIAM Conference on Parallel Processing for Scientific Computing, Houston, TX, March 1991, p 507-512. (abstract) (postscript) (ps.gz)

Synthetic Aperture Radar Image Processing on Parallel Supercomputers, S. J. Plimpton, G. A. Mastin, D. Ghiglia, in Proc of Supercomputing '91, Albuquerque, NM, November 1991, p 446. (abstract) (postscript) (ps.gz)


1990

Molecular Dynamics Simulations of Grain-Boundary Diffusion for Varying Tilt Angle Geometries, S. J. Plimpton, in Atomic Scale Calulations of Structure in Materials, edited by M. S. Daw and M. A. Schluter, MRS Proceedings 193, Pittsburgh, PA, 1990, p 333-336. (abstract)

Effect of Interatomic Potential on Simulated Grain-Boundary and Bulk Diffusion: A Molecular-Dynamics Study, S. J. Plimpton and E. D. Wolf, Phys Rev B, 41, 2712-2721 (1990). (abstract)