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<HTML>
<CENTER><A HREF = "main.html">Return to Steve Plimpton's home page</A>
</CENTER>
<HR>
<H3>Publications
</H3>
<P>Papers are listed chronologically in the next section. All have
viewable abstracts; some have downloadable PS, PDF, or HTML files.
See more complete info at <A HREF = "https://scholar.google.com/citations?user=Ny7N6KQAAAAJ&hl=en">Google
Scholar</A>.
If you're looking for papers on a specific topic, click on one of
these links:
</P>
<UL><LI><A HREF = "md.html">Molecular Dynamics</A> - parallel algorithms
<LI><A HREF = "mdsim.html">Molecular Dynamics</A> - simulation results
<LI><A HREF = "kmc.html">Kinetic Monte Carlo</A> - kinetic and Metropolis Monte Carlo modeling
<LI><A HREF = "dsmc.html">Direct Simulation Monte Carlo</A> - low-density reacting flows via particles
<LI><A HREF = "informatics.html">Informatics</A> - informatics algorithms and big-data processing
<LI><A HREF = "cell.html">Biological Cell Modeling</A> - particle-based reaction/diffusion modeling with <A HREF = "https://sjplimp.github.io/chemcell">ChemCell</A>
<LI><A HREF = "genehunter.html">GeneHunter</A> - genetic linkage analysis
<LI><A HREF = "chisels.html">ChISELS</A> - surface evolution model of semiconductor processing for micromachine devices (MEMS)
<LI><A HREF = "rad.html">Radiation Transport</A> - Boltzmann equation for thermal and X-ray radiation
<LI><A HREF = "qs.html">QuickSilver</A> - particle-in-cell (PIC) relativistic electromagnetics
<LI><A HREF = "pronto.html">PRONTO</A> - finite element transient dynamics (crash code) with contact detection
<LI><A HREF = "nimrod.html">NIMROD</A> - plasma simulation of tokamaks
<LI><A HREF = "quantum.html">Electronic Structure</A> - quantum mechanics of solids
<LI><A HREF = "dsmc.html">Direct Simulation Monte Carlo</A> - low-density reacting flows via particles
<LI><A HREF = "sar.html">Image Processing</A> - synthetic aperture radar (SAR) analysis
<LI><A HREF = "grain.html">Grain Growth</A> - Potts model on 2-d and 3-d lattices
<LI><A HREF = "ebeam.html">Electron Microscopy</A> - Monte Carlo trajectory simulation
<LI><A HREF = "algorithms.html">Parallel Algorithms</A> - HPCC RandomAccess benchmark, load-balancing, grid transfer, tinkertoy parallel programming, matrix-vector multiply and many-body algs
<LI><A HREF = "hpc.html">High Performance Computing (HPC)</A> - neuro-inspired computing, performance comparisons of parallel architectures
<LI><A HREF = "overview.html">Parallel Computing</A> - general overviews
</UL>
<HR>
<HR>
<H4>2023
</H4>
<P><B>Parallel simulation via SPPARKS of on-lattice kinetic and Metropolis
Monte Carlo models for materials processing</B>, J. A. Mitchell,
F. Abdeljawad, C. Battaile, C. Garcia-Cardona, E. A. Holm,
E. R. Homer, J. Madison, T. M. Rogers, A. P. Thompson, V. Tikare,
E. Webb, S. J. Plimpton, Modelling and Simulation in Materials Science
and Engineering, 31, 055001
(2023). (<A HREF = "abstracts/msmse23.html">abstract</A>) DOI:
<A HREF = "https://doi.org/10.1088/1361-651X/accc4b">https://doi.org/10.1088/1361-651X/accc4b</A>
</P>
<P><B>Entropic Mixing of Ring/Linear Polymer Blends</B>, G. S. Grest, T. Ge,
S. J. Plimpton, M. Rubinstein, T. C. O'Connor, ACS Polymers, 3,
209-216 (2023). (<A HREF = "abstracts/acs23.html">abstract</A>) DOI:
<A HREF = "https://doi.org/10.1021/acspolymersau.2c00050">https://doi.org/10.1021/acspolymersau.2c00050</A>
</P>
<HR>
<H4>2022
</H4>
<P><B>LAMMPS - A flexible simulation tool for particle-based materials
modeling at the atomic, meso, and continuum scales</B>, A. P. Thompson,
H. M. Aktulga, R. Berger, D. S. Bolintineanu, W. M. Brown,
P. S. Crozier, P. J. in 't Veld, A. Kohlmeyer, S. G. Moore, T. D.
Nguyen, R. Shan, M. J. Stevens, J. Tranchida, C. Trott,
S. J. Plimpton, Comp Phys Comm, 271, 108171 (2022).
(<A HREF = "abstracts/cpc22.html">abstract</A>) DOI:
<A HREF = "https://doi.org/10.1016/j.cpc.2021.108171">https://doi.org/10.1016/j.cpc.2021.108171</A>
</P>
<P><B>A parallel algorithm for the concurrent atomistic-continuum
methodology</B>, A. Diaz, B. Gu, Yang Li, S. J. Plimpton, D. L. McDowell,
Y. Chen, J Comp Phys, 463, 111140 (2022).
(<A HREF = "abstracts/jcp22.html">abstract</A>)
</P>
<HR>
<H4>2021
</H4>
<P><B>Rendezvous algorithms for large-scale modeling and simulation</B>,
S. J. Plimpton and C. Knight, J Parallel and Distributed Computing,
147, 184-195 (2021). (<A HREF = "abstracts/jpdc21.html">abstract</A>)
</P>
<P><B>Turbulence at the edge of continuum</B>, M. A. Gallis, J. R. Torczynski,
M. C. Krygier, N. P. Bitter, S. J. Plimpton, Phys Rev Fluids, 6,
013401 (2021). (<A HREF = "abstracts/prf21.html">abstract</A>)
</P>
<HR>
<H4>2020
</H4>
<P><B>Parallel algorithms for hyperdynamics and local hyperdynamics</B>,
S. J. Plimpton, D. Perez, A. F. Voter, J Chem Phys, 153, 054116
(2020). (<A HREF = "abstracts/jcp20.html">abstract</A>)
</P>
<P><B>Granular packings with sliding, rolling, and twisting friction</B>,
A. P. Santos, D. S. Bolintineanu, G. S. Grest, J. B. Lechman,
S. J. Plimpton, I. Srivastava, L. E. Silbert, Phys Rev E, 102, 032903
(2020). (<A HREF = "abstracts/pre20.html">abstract</A>)
</P>
<HR>
<H4>2019
</H4>
<P><B>Aspherical particle models for molecular dynamics simulation</B>,
T. D. Nguyen and S. J. Plimpton, Comp Phys Comm, 243, 12-24 (2019).
(<A HREF = "abstracts/cpc19.html">abstract</A>)
</P>
<P><B>Direct Simulation Monte Carlo on petaflop supercomputers and beyond</B>,
S. J. Plimpton, S. G. Moore, A. Borner, A. K. Stagg 1 , T. P. Koehler,
J. R. Torczynski, M. A. Gallis, Physics of Fluids, 31, 086101
(2019). (<A HREF = "abstracts/pof19.html">abstract</A>)
</P>
<HR>
<H4>2018
</H4>
<P><B>Effect of shape and friction on the packing and flow of granular
materials</B>, K. M. Salerno, D. S. Bolintineanu, G. S. Grest,
J. B. Lechman, S. J. Plimpton, I. Srivastava, L. E. Silbert, Phys Rev
E, 98, 050901 (2018).
(<A HREF = "abstracts/pre18.html">abstract</A>)
</P>
<P><B>Multiscale Co-Design Analysis of Energy, Latency, Area, and Accuracy
of a ReRAM Analog Neural Training Accelerator</B>, M. J. Marinella,
S. Agarwal, A. Hsia, I. Richter, R. Jacobs-Gedrim, J. Niroula,
S. J. Plimpton, E. Ipek, C. D. James, IEEE Journal on Emerging and
Selected Topics in Circuits and Systems, 8, 86-101 (2018).
(<A HREF = "abstracts/estcs18.html">abstract</A>)
</P>
<P><B>Highly scalable discrete-particle simulations with novel
coarse-graining: Accessing the microscale</B>, T. I. Mattox,
J. P. Larentzos, S. G. Moore, C. P. Stone, D. A. Ibanez,
A. P. Thompson, M. Lísal, J. K. Brennan, S. J. Plimpton, Molecular
Physics, 116, 2061–2069 (2018).
(<A HREF = "abstracts/mp18.html">abstract</A>)
</P>
<P><B>Gas-kinetic simulation of sustained turbulence in minimal Couette
flow</B>, M. A. Gallis, J. R. Torczynski, N. P. Bitter, T. P. Koehler,
S. J. Plimpton, and G. Papadakis, Phys Rev Fluids, 3, 071402(R)
(2018). (<A HREF = "abstracts/prf18.html">abstract</A>)
</P>
<P><B>Massively parallel symplectic algorithm for coupled magnetic spin
dynamics and molecular dynamics</B>, J. Tranchida, S. J. Plimpton,
P. Thibaudeau, A. P. Thompson, J Comp Phys, 372, 406-425 (2018).
(<A HREF = "abstracts/jcp18.html">abstract</A>)
</P>
<HR>
<H4>2017
</H4>
<P><B>Molecular-Level Simulations of Turbulence and Its Decay</B>,
M. A. Gallis, N. P. Bitter, T. P. Koehler, J. R. Torczynski,
S. J. Plimpton, G. Papadakis, Phys Rev Letters, 118, 064501 (2017).
(<A HREF = "abstracts/prl17.html">abstract</A>)
</P>
<P><B>Achieving Ideal Accuracies in Analog Neuromorphic Computing Using
Periodic Carry</B>, S. Agarwal, R. B. Jacobs-Gedrim, A. H. Hsia,
D. R. Hughart, E. J. Fuller, A. A. Talin, C. D. James, S. J. Plimpton,
and M. J. Marinella, 2017 IEEE Symposium on VLSI Technology, Kyoto,
Japan (2017). (<A HREF = "abstracts/vlsi17.html">abstract</A>)
</P>
<P><B>Li-Ion Synaptic Transistor for Low Power Analog Computing</B>,
E. J. Fuller, F. E. Gabaly, F. Léonard, S. Agarwal, S. J. Plimpton,
R. B. Jacobs-Gedrim, C. D. James, M. J. Marinella, A. A. Talin,
Advanced Materials, 29, 1604310 (2017). (<A HREF = "abstracts/am17.html">abstract</A>)
</P>
<P><B>A historical survey of algorithms and hardware architectures for
neural-inspired and neuromorphic computing applications</B>, C. D. James,
J. B. Aimone, N. E. Miner, C. M. Vineyard, F. H. Rothganger,
K. D. Carlson, S. A. Mulder, T. J. Draelos, A. Faust, M, J. Marinella,
J. H. Naegle, S. J. Plimpton, Biologically Inspired Cognitive
Architectures, 19, 49-64 (2017). (<A HREF = "abstracts/bica17.html">abstract</A>)
</P>
<HR>
<H4>2016
</H4>
<P><B>Increasing Molecular Dynamics Simulation Rates with an 8-Fold
Increase in Electrical Power Efficiency</B>, W. M. Brown, A. Semin,
M. Hebenstreit, S. Khvostov, K. Raman, S. J. Plimpton, SC16
Conference, SLC, Utah, Nov 2016. (<A HREF = "abstracts/sc16.html">abstract</A>)
</P>
<P><B>Direct simulation Monte Carlo investigation of the Rayleigh-Taylor
instability</B>, M. A. Gallis, T. P. Koehler, J. R. Torczynski, and
S. J. Plimpton, Phys Rev Fluids, 1, 043403 (2016).
(<A HREF = "abstracts/prf16.html">abstract</A>)
</P>
<P><B>Resistive Memory Device Requirements for a Neural Algorithm
Accelerator</B>, S. Agarwal, S. J. Plimpton, D. R. Hughart, A. H. Hsia,
I. Richter, J. A. Cox, C. D. James, M. J. Marinella, IEEE
International Joint Conf on Neural Networks (IJCNN 2016), Vancouver,
Canada, Jul 2016. (<A HREF = "abstracts/ijcnn16.html">abstract</A>)
</P>
<P><B>Oxygen Modulates the Effectiveness of Granuloma Mediated Host
Response to Mycobacterium tuberculosis: A Multiscale Computational
Biology Approach</B>, C. L. Sershen, S. J. Plimpton, E. E. May, Frontiers
in Cellular and Infection Microbiology, 6,
doi:10.3389/fcimb.2016.00006 (2016).
(<A HREF = "abstracts/frontiers16.html">abstract</A>)
</P>
<HR>
<H4>2015
</H4>
<P><B>Accelerating dissipative particle dynamics simulations for soft
matter systems</B>, T. Nguyen and S. J. Plimpton, Computational Materials
Science, 100, 173-180 (2015). (<A HREF = "abstracts/cms15.html">abstract</A>)
</P>
<P><B>Direct simulation Monte Carlo investigation of the Richtmyer-Meshkov
instability</B>, M. A. Gallis, T. P. Koehler, J. R. Torczynski, and
S. J. Plimpton, Physics of Fluids, 27, 084105 (2015).
(<A HREF = "abstracts/pof15.html">abstract</A>)
</P>
<P><B>Optimizing legacy molecular dynamics software with directive-based
offload</B>, W. M. Brown, J.-M. Y. Carrillo, N. Gavhane, F. M. Thakkar,
S. J. Plimpton, Comp Phys Comm, 195, 95-101 (2015).
(<A HREF = "abstracts/cpc15.html">abstract</A>)
</P>
<HR>
<H4>2014
</H4>
<P><B>Streaming data analytics via message passing with application to
graph algorithms</B>, S. J. Plimpton and T. Shead, J Parallel and
Distributed Computing, 74, 2687-2698 (2014).
(<A HREF = "abstracts/jpdc14.html">abstract</A>)
</P>
<P><B>Particle dynamics modeling methods for colloid suspensions</B>,
D. S. Bolintineanu, G. S. Grest, J. B. Lechman, F. Pierce,
S. J. Plimpton, and P. R. Schunk, Computational Particle Mechanics, 1,
321-356 (2014). (<A HREF = "abstracts/cpm14.html">abstract</A>)
</P>
<P><B>A Method for Modeling Oxygen Diffusion in an Agent-based Model with
Application to Host-Pathogen Infection</B>, C. L. Sershen,
S. J. Plimpton, E. E. May, EMBC'14 Conference (36th Annual Intl Conf
of the IEEE Engineering in Medicine and Biology Society), Chicago, IL,
Aug 2014. (<A HREF = "abstracts/embc14.html">abstract</A>)
</P>
<P><B>Direct Simulation Monte Carlo: The Quest for Speed</B>, M. A. Gallis,
J. R. Torczynski, S. J. Plimpton, D. J. Rader, T. Koehler, 29th Intl
Symposium on Rarefied Gas Dynamics in Xi'an, China, AIP Conf Proc,
1628, 27 (2014). (<A HREF = "abstracts/rgd14.html">abstract</A>)
</P>
<HR>
<H4>2013
</H4>
<P><B>Developing community codes for materials modeling</B>, S. J. Plimpton
and J. D. Gale, Current Opinion in Solid State and Materials Science
17, 271-276 (2013).
(<A HREF = "abstracts/cossms13.html">abstract</A>)
</P>
<P><B>Statistical ensemble analysis for simulating extrinsic noise-driven
response in NF-kappa B signaling networks</B>, J. Joo, S. J. Plimpton,
J. L. Faulon, BMC Systems Biology, 7, 45 (2013).
(<A HREF = "abstracts/bmc13.html">abstract</A>)
</P>
<P><B>Maintaining connected components for infinite graph streams</B>,
J. W. Berry, M. Oster, C. A. Phillips, S. J. Plimpton, T. M Shead,
BigMine-13, a KDD13 workshop - 2nd International Workshop on Big Data,
Streams and Heterogeneous Source Mining, Chicago, IL, Aug
2013. (<A HREF = "abstracts/bigmine13.html">abstract</A>)
</P>
<HR>
<H4>2012
</H4>
<P><B>Computational Aspects of Many-body Potentials</B>, S. J. Plimpton and
A. P. Thompson, MRS Bulletin, 37, 513-521 (2012).
(<A HREF = "abstracts/mrs12.html">abstract</A>)
</P>
<P><B>Implementing Molecular Dynamics on Hybrid High Performance Computers
- Particle-Particle Particle-Mesh</B>, W. M. Brown, A. Kohlmeyer,
S. J. Plimpton, A. N. Tharrington, Comp Phys Comm, 183, 449-459
(2012). (<A HREF = "abstracts/cpc12.html">abstract</A>)
</P>
<P><B>No-slip boundary conditions and forced flow in multiparticle
collision dynamics</B>, D. S. Bolintineanu, J. B. Lechman,
S. J. Plimpton, and G. S. Grest, Phys Rev E, 86, 066703 (2012).
(<A HREF = "abstracts/pre12.html">abstract</A>)
</P>
<HR>
<H4>2011
</H4>
<P><B>Evaporation of Lennard-Jones Fluids</B>, S Cheng, J. B. Lechman,
S. J. Plimpton, G. S. Grest, J Chem Phys, 134, 224704 (2011).
(<A HREF = "abstracts/jcp11.html">abstract</A>)
</P>
<P><B>Implementing Molecular Dynamics on Hybrid High Performance Computers
- Short Range Forces</B>, W. M. Brown, P. Wang, S. J. Plimpton,
A. N. Tharrington, Comp Phys Comm, 182, 898-911, (2011).
(<A HREF = "abstracts/cpc11.html">abstract</A>)
</P>
<P><B>Parallel Simulation of 3D Sintering</B>, C. G. Cardona, V. Tikare,
S. J. Plimpton, Int J Computational Materials Science and Surface
Engineering, 4, 37-54 (2011). (<A HREF = "abstracts/ijcmsse11.html">abstract</A>)
</P>
<P><B>MapReduce in MPI for Large-Scale Graph Algorithms</B>, S. J. Plimpton
and K. D. Devine, Parallel Computing, 37, 610-632
(2011). (<A HREF = "../abstracts/pc11.html">abstract</A>)
</P>
<HR>
<H4>2010
</H4>
<P><B>Mesoscale Hydrodynamics via Stochastic Rotation Dynamics: Comparison
with Lennard-Jones Fluid</B>, 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). (<A HREF = "abstracts/jcp10.html">abstract</A>)
</P>
<P><B>Software components for parallel multiscale simulation: an example
with LAMMPS</B>, B. Frantzdale, S. J. Plimpton, M. S. Shephard,
Engineering with Computers, 26, 205-211
(2010). (<A HREF = "abstracts/ec10.html">abstract</A>)
</P>
<P><B>1D-to-3D transition of phonon heat conduction in polyethylene using
molecular dynamics simulations</B>, A. Henry, G. Chen, S. J. Plimpton,
A. Thompson, Phys Rev B, 82, 144308 (2010).
(<A HREF = "abstracts/prb10.html">abstract</A>)
</P>
<P><B>Equation-Free Accelerated Simulations of the Morphological Relaxation
of Crystal Surfaces</B>, G. J. Wagner, X. Zhou, S. J. Plimpton, Int J for
Multiscale Computational Engineering, 8, 423-439 (2010).
(<A HREF = "abstracts/ijmce10.html">abstract</A>)
</P>
<HR>
<H4>2009
</H4>
<P><B>Liquid crystal nanodroplets in solution</B>, W. M. Brown,
M. K. Petersen, S. J. Plimpton, and G. S. Grest, J Chem Phys, 130,
044901 (2009). (<A HREF = "abstracts/jcp09.html">abstract</A>)
</P>
<P><B>General formulation of pressure and stress tensor for arbitrary
many-body interaction potentials under periodic boundary conditions</B>,
A. P. Thompson, S. J. Plimpton, W. Mattson, J Chem Phys, 131, 154107
(2009). (<A HREF = "abstracts/jcp09a.html">abstract</A>)
</P>
<P><B>Crossing the Mesoscale No-Man's Land via Parallel Kinetic Monte
Carlo</B>, 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. (<A HREF = "abstracts/sand09.html">abstract</A>) (<A HREF = "papers/sand09.pdf">pdf</A>)
</P>
<HR>
<H4>2008
</H4>
<P><B>Substructured molecular dynamics using multibody dynamics
algorithms</B>, R. M. Mukherjee, P. S. Crozier, S. J. Plimpton,
K. S. Anderson, Intl J of Non-Linear Mechanics, 43, 1045-1055 (2008).
(<A HREF = "abstracts/ijnlm08.html">abstract</A>)
</P>
<P><B>Implementing peridynamics within a molecular dynamics code</B>,
M. L. Parks, R. B. Lehoucq, S. J. Plimpton, S. A. Silling, Comp Phys
Comm, 179, 777-783 (2008). (<A HREF = "abstracts/cpc08a.html">abstract</A>)
</P>
<P><B>A Constant-Time Kinetic Monte Carlo Algorithm for Simulation of Large
Biochemical Reaction Networks</B>, A. Slepoy, A. P. Thompson,
S. J. Plimpton, J Chem Phys, 128, 205101
(2008). (<A HREF = "abstracts/jcp08.html">abstract</A>)
</P>
<P><B>Accurate and Efficient Methods for Modeling Colloidal Mixtures in an
Explicit Solvent using Molecular Dynamics</B>, P. J. in 't Veld,
S. J. Plimpton, G. S. Grest, Comp Phys Comm, 179, 320-329
(2008). (<A HREF = "abstracts/cpc08.html">abstract</A>)
</P>
<HR>
<H4>2007
</H4>
<P><B>Sensitivity Analysis of a Computational Model of the IKK-NF-kB-A20
Signal Transduction Network</B>, 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). (<A HREF = "abstracts/annals07.html">abstract</A>)
</P>
<HR>
<H4>2006
</H4>
<P><B>Computing the mobility of grain boundaries</B>, 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). (<A HREF = "abstracts/nature06.html">abstract</A>)
</P>
<P><B>A Simple Synchronous Distributed-Memory Algorithm for the HPCC
RandomAccess Benchmark</B>, S. J. Plimpton, R. Brightwell, C. Vaughan,
K. Underwood, M. Davis, Proc of Cluster 2006 - IEEE International Conf
on Cluster Computing, Sept 2006. (<A HREF = "abstracts/cluster06.html">abstract</A>)
</P>
<HR>
<H4>2005
</H4>
<P><B>Microbial cell modeling via reacting diffusing particles</B>,
S. J. Plimpton and A. Slepoy, Journal of Physics: Conference Series
16, 305-309 (2005). (<A HREF = "abstracts/jp05.html">abstract</A>)
</P>
<P><B>Parallel Sn Sweeps on Unstructured Grids: Algorithms for
Prioritization, Grid Partitioning, and Cycle-Detection</B>,
S. J. Plimpton, B. Hendrickson, S. Burns, W. Mclendon III, L.
Rauchwerger, Nuclear Science and Engineering, 150, 267-283 (2005).
(<A HREF = "abstracts/nse05.html">abstract</A>)
</P>
<P><B>Finding Strongly Connected Components in Distributed Graphs</B>,
W. McLendon, B. Hendrickson, S. J. Plimpton, L. Rauchwerger, J
Parallel and Distributed Computing, 65, 901-910 (2005).
(<A HREF = "abstracts/jpdc05.html">abstract</A>)
</P>
<P><B>Effect of Deformation Path Sequence on the Behavior of Nanoscale
Copper Bicrystal Interfaces</B>, D. E. Spearot, K. I. Jacob,
D. L. McDowell, S. J. Plimpton, J Engr Materials and Technology, 127,
374-382 (2005). (<A HREF = "abstracts/jemt05.html">abstract</A>)
</P>
<P><B>Feature Length-Scale Modeling of LPCVD and PECVD MEMS Fabrication
Processes</B>, L. C. Musson, P. Ho, S. J. Plimpton, R. C. Schmidt,
Journal of Microsystems Technologies, 12, 137-142
(2005). (<A HREF = "abstracts/jmt05.html">abstract</A>)
</P>
<HR>
<H4>2004
</H4>
<P><B>Discrete element simulations of stress distributions in silos:
Crossover from two to three dimensions</B>, J. W. Landry, G. S. Grest,
S. J. Plimpton, Powder Technology, 139, 233-239
(2004). (<A HREF = "abstracts/pt04.html">abstract</A>)
</P>
<P><B>Effect of end-tethered polymers on surface adhesion of glassy
polymers</B>, S. W. Sides, G. S. Grest, M. J. Stevens, S. J. Plimpton,
Journal of Polymer Science, Part B (Polymer Physics), 42, 199-208
(2004). (<A HREF = "abstracts/jps04.html">abstract</A>)
</P>
<P><B>Nonlinear Magnetohydrodynamics Simulation Using High-order Finite
Elements</B>, 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). (<A HREF = "abstracts/jcp04.html">abstract</A>)
</P>
<P><B>A Parallel Rendezvous Algorithm for Interpolation Between Multiple
Grids</B>, S. J. Plimpton, B. Hendrickson, J. Stewart, J Parallel and
Distributed Computing, 64, 266-276 (2004). (<A HREF = "abstracts/jpdc03a.html">abstract</A>)
</P>
<HR>
<H4>2003
</H4>
<P><B>Confined granular packings: Structure, stress, and forces</B>,
G. S. Grest, J. W. Landry, S. J. Plimpton, L. E. Silbert, Phys Rev E,
67, 041303 (2003). (<A HREF = "abstracts/pre03.html">abstract</A>)
</P>
<P><B>Equilibration of long chain polymer melts in computer simulations</B>,
R. Auhl, R. Everaers, G. S. Grest, K. Kremer, S. J. Plimpton, J Chem
Phys, 119, 12718-12728 (2003). (<A HREF = "abstracts/jcp03.html">abstract</A>)
</P>
<P><B>Parallel Genehunter: Implementation of a Linkage Analysis Package for
Distributed-Memory Architectures</B>, 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). (<A HREF = "abstracts/jpdc03.html">abstract</A>)
</P>
<P><B>A Load-Balancing Algorithm for a Parallel Electromagnetic
Particle-in-Cell Code</B>, S. J. Plimpton, D. B. Seidel, M. F. Pasik,
R. S. Coats, G. R. Montry, Comp Phys Comm, 152, 227-241 (2003).
(<A HREF = "abstracts/cpc03.html">abstract</A>)
</P>
<HR>
<H4>2002
</H4>
<P><B>Boundary effects and self-organization in dense granular flows</B>,
L. E. Silbert, G. S. Grest, S. J. Plimpton, D. Levine, Physics of
Fluids, 14, 2637-2646 (2002). (<A HREF = "abstracts/pf02.html">abstract</A>)
</P>
<P><B>Torsion/simple shear of single crystal copper</B>, 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). (<A HREF = "abstracts/jemt02.html">abstract</A>)
</P>
<P><B>Development and Performance of a PVM Based Parallel Geometric Modeler
for MEMS</B>, C. Jorgensen, D. Melander, R. Schmidt, S. J. Plimpton, in
Proc of Modeling and Simulation of Microsystems (MSM), Puerto Rico,
April 2002, 218-221. (<A HREF = "abstracts/msm02.html">abstract</A>)
</P>
<P><B>Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to
Hierarchical Modeling</B>, G. S. Heffelfinger, ..., S. J. Plimpton, ...,
OMICS - A Journal of Integrative Biology, 6, 305-330
(2002). (<A HREF = "abstracts/omics02.html">abstract</A>)
</P>
<HR>
<H4>2001
</H4>
<P><B>Length scale and time scale effects on the plastic flow of FCC
metals</B>, M. F. Horstemeyer, M. I. Baskes, S. J. Plimpton, Acta
Materialia, 49, 4363-4374 (2001). (<A HREF = "abstracts/am01.html">abstract</A>)
</P>
<P><B>Computational nanoscale plasticity simulations using embedded atom
potentials</B>, M. F. Horstemeyer, M. I. Baskes, S. J. Plimpton,
Theoretical and Applied Fracture Mechanics, 37, 49-98
(2001). (<A HREF = "abstracts/tafm01.html">abstract</A>)
</P>
<P><B>Granular flow down an inclined plane: Bagnold scaling and rheology</B>,
L. E. Silbert, D. Ertas, G. S. Grest, T. C. Halsey, D. Levine,
S. J. Plimpton, Phys Rev E, 64, 051302
(2001). (<A HREF = "abstracts/pre01a.html">abstract</A>)
</P>
<P><B>Identifying Strongly Connected Components in Parallel</B>, W. McLendon
III, B. Hendrickson, S. J. Plimpton, L. Rauchwerger, in Proc of SIAM
Parallel Processing for Scientific Computing Conf, March
2001. (<A HREF = "abstracts/siam01a.html">abstract</A>)
</P>
<P><B>Scalability and Performance of Two Large Linux Clusters</B>,
R. Brightwell and S. J. Plimpton, J of Parallel and Distributed
Computing, 61, 1546-1569 (2001). (<A HREF = "abstracts/jpdc01.html">abstract</A>)
</P>
<P><B>Tinkertoy Parallel Programming: Complicated Applications from Simple
Tools</B>, B. Hendrickson and S. J. Plimpton, in Proc of SIAM Parallel
Processing for Scientific Computing Conf, March
2001. (<A HREF = "abstracts/siam01b.html">abstract</A>)
</P>
<HR>
<H4>2000
</H4>
<P><B>Parallel Algorithms for Radiation Transport on Unstructured Grids</B>,
S. J. Plimpton, B. A. Hendrickson, S. P. Burns, W. McLendon III, Proc
of SuperComputing 2000 (SC2000), Dallas, TX, November
2000. (<A HREF = "abstracts/sc00.html">abstract</A>)
</P>
<P><B>Parallel Strategies for Crash and Impact Simulations</B>, K. Brown,
S. Attaway, S. J. Plimpton, B. Hendrickson, Computer Methods in
Applied Mechanics and Engineering, 184, 375-390
(2000). (<A HREF = "abstracts/cmame00.html">abstract</A>)
</P>
<HR>
<H4>1999
</H4>
<P><B>Spatial correlations of mobility and immobility in a glass-forming
Lennard-Jones liquid</B>, C. Donati, S. C. Glotzer, P. H. Poole,
W. Kob, S. J. Plimpton, Phys Rev E, 60, 3107-3119
(1999). (<A HREF = "abstracts/pre99.html">abstract</A>)
</P>
<P><B>The diffusion of simple penetrants in tangent site polymer melts</B>,
D. R. Rottach, P. A. Tillman, J. D. McCoy, S. J. Plimpton,
J. G. Curro, J Chem Phys, 111, 9822-9831
(1999). (<A HREF = "abstracts/jcp99.html">abstract</A>)
</P>
<P><B>The NIMROD Code: A New Approach to Numerical Plasma Physics</B>,
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). (<A HREF = "abstracts/plasma99.html">abstract</A>)
</P>
<P><B>Massively Parallel Computing: A Sandia Perspective</B>, 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). (<A HREF = "abstracts/parco99.html">abstract</A>)
</P>
<HR>
<H4>1998
</H4>
<P><B>Stringlike cooperative motion in a supercooled liquid</B>, C. Donati,
J. F. Douglas, W. Kob, S. J. Plimpton, P. H. Poole, S. C. Glotzer,
Phys Rev Lett, 80, 2338-2341 (1998). (<A HREF = "abstracts/prl98.html">abstract</A>)
</P>
<P><B>The effect of added salt on polyelectrolyte structure</B>, M. J. Stevens
and S. J. Plimpton, Eur Phys J B, 2, 341-345
(1998). (<A HREF = "abstracts/ep98.html">abstract</A>)
</P>
<P><B>Dislocation nucleation and defect structure during surface
indentation</B>, C. L. Kelchner, S. J. Plimpton, J. C. Hamilton, Phys Rev
B, 58, 11085-11088 (1998). (<A HREF = "abstracts/prb98.html">abstract</A>)
</P>
<P><B>The structure and thermodynamics of energetically and structurally
asymmetric polymer blends</B>, P. A. Tillman, D. R. Rottach, J. D. McCoy,
S. J. Plimpton, J. G. Curro, J Chem Phys, 109, 806-814
(1998). (<A HREF = "abstracts/jcp98.html">abstract</A>)
</P>
<P><B>Molecular-Dynamics Simulations of Low-Energy (25-200 eV) Argon Ion
Interactions with Silicon Surfaces: Sputter Yields and Product
Formation Pathways</B>, N. A. Kubota, D. J. Economou, S. J. Plimpton, J
of Appl Phys, 83, 4055-4063 (1998). (<A HREF = "abstracts/jap98.html">abstract</A>)
</P>
<P><B>Parallel Transient Dynamics Simulations: Algorithms for Contact
Detection and Smoothed Particle Hydrodynamics</B>, S. J. Plimpton,
S. Attaway, B. Hendrickson, J. Swegle, C. Vaughan, D. Gardner, J
Parallel and Distributed Computing, 50, 104- 122
(1998). (<A HREF = "abstracts/jpdc98.html">abstract</A>)
</P>
<P><B>A Parallel Contact Detection Algorithm for Transient Solid Dynamics
Simulations Using PRONTO3D</B>, 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). (<A HREF = "abstracts/compmech98.html">abstract</A>)
</P>
<P><B>Plane-wave Psuedopotential Electronic Structure Calculations on
Parallel Supercomputers</B>, 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). (<A HREF = "abstracts/fong98.html">abstract</A>)
</P>
<HR>
<H4>1997
</H4>
<P><B>Particle-Mesh Ewald and rRESPA for Parallel Molecular Dynamics
Simulations</B>, S. J. Plimpton, R. Pollock, M. Stevens, in Proc of the
Eighth SIAM Conference on Parallel Processing for Scientific
Computing, Minneapolis, MN, March 1997. (<A HREF = "abstracts/siam97.html">abstract</A>)
</P>
<P><B>Dynamical heterogeneities in a supercooled Lennard-Jones liquid</B>,
W. Kob, C. Donati, S. J. Plimpton, P. H. Poole, S. C. Glotzer, Phys
Rev Lett, 79, 2827- 2830 (1997). (<A HREF = "abstracts/prl97.html">abstract</A>)
</P>
<P><B>The effect of attractions on the structure and thermodynamics of
model polymer blends</B>, P. A. Tillman, D. R. Rottach, J. D. McCoy,
S. J. Plimpton, J. G. Curro, J Chem Phys, 107, 4024-4032
(1997). (<A HREF = "abstracts/jcp97.html">abstract</A>)
</P>
<P><B>Transient Solid Dynamics Simulations on the Sandia/Intel Teraflop
Computer</B>, 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. (<A HREF = "abstracts/sc97.html">abstract</A>)
</P>
<P><B>Potts-model Grain Growth Simulations: Parallel Algorithms and
Applications</B>, S. A. Wright, S. J. Plimpton, T. P. Swiler, R. M. Fye,
M. F. Young, E. A. Holm, SAND Report 97-1925, August
1997. (<A HREF = "abstracts/sand97.html">abstract</A>)
</P>
<HR>
<H4>1996
</H4>
<P><B>A New Parallel Method for Molecular-Dynamics Simulation of
Macromolecular Systems</B>, S. J. Plimpton and B. A. Hendrickson, J Comp
Chem, 17, 326-337 (1996). (<A HREF = "abstracts/jcc96.html">abstract</A>)
</P>
<P><B>Transient Dynamics Simulations: Parallel Algorithms for Contact
Detection and Smoothed Particle Hydrodynamics</B>, S. J. Plimpton,
S. Attaway, B. Hendrickson, J. Swegle, C. Vaughan, D. Gardner, in
Proc of SuperComputing '96, Pittsburgh, PA, November
1996. (<A HREF = "abstracts/sc96.html">abstract</A>)
</P>
<HR>
<H4>1995
</H4>
<P><B>Fast Parallel Algorithms for Short-Range Molecular Dynamics</B>,
S. J. Plimpton, J Comp Phys, 117, 1-19
(1995). (<A HREF = "abstracts/jcompphys95.html">abstract</A>)
</P>
<P><B>Parallel Molecular Dynamics Algorithms for Simulation of Molecular
Systems</B>, 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). (<A HREF = "abstracts/acs95.html">abstract</A>)
</P>
<P><B>Computational Limits of Classical Molecular-Dynamics Simulations</B>,
S. J. Plimpton, Computational Materials Science, 4, 361-364
(1995). (<A HREF = "abstracts/cms95.html">abstract</A>)
</P>
<P><B>Molecular dynamics simulation of athermal polymer blends: Comparison
with integral-equation theory</B>, C. S. Stevenson, J. G. Curro,
J. D. McCoy, S. J. Plimpton, J Chem Phys, 103, 1208-1215
(1995). (<A HREF = "abstracts/jcp95a.html">abstract</A>)
</P>
<P><B>Molecular dynamics simulation of athermal polymer blends: Finite
system size considerations</B>, C. S. Stevenson, J. D. McCoy,
S. J. Plimpton, J. G. Curro, J Chem Phys, 103, 1200-1207
(1995). (<A HREF = "abstracts/jcp95b.html">abstract</A>)
</P>
<P><B>Modeling a nematic liquid crystal</B>, S. S. Patnaik, S. J. Plimpton,
R. Pachter, W. W. Adams, Liquid Crystals, 19, 213-220
(1995). (<A HREF = "abstracts/lc95.html">abstract</A>)
</P>
<P><B>Molecular-statics and molecular-dynamics study of diffusion along
001 tilt grain boundaries in Ag</B>, C. L. Liu and S. J. Plimpton, Phys
Rev B, 51, 4523-4528 (1995). (<A HREF = "abstracts/prb95a.html">abstract</A>)
</P>
<P><B>Molecular-dynamics simulations of grain-boundary diffusion in Al
using embedded-atom method potentials</B>, C. L. Liu and S. J. Plimpton,
J Materials Research, 10, 1589-1592
(1995). (<A HREF = "abstracts/jmr95.html">abstract</A>)
</P>
<P><B>Parallel Algorithms for Dynamically Partitioning Unstructured Grids</B>,
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. (<A HREF = "abstracts/siam95.html">abstract</A>)
</P>
<P><B>Parallel Many-Body Simulations Without All-to-All Communication</B>,
B. A. Hendrickson and S. J. Plimpton, J Parallel and Distributed
Computing, 27, 15-25 (1995). (<A HREF = "abstracts/jpdc95.html">abstract</A>)
</P>
<P><B>An Efficient Parallel Algorithm for Matrix-Vector Multiplication</B>,
B. A. Hendrickson, R. W. Leland, S. J. Plimpton, Int J of High Speed
Computing, 7, 73-88 (1995). (<A HREF = "abstracts/ijhsc95.html">abstract</A>)
</P>
<P><B>Basis-Set Convergence of Highly Defected Sites in Amorphous-Carbon</B>,
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). (<A HREF = "abstracts/prb95b.html">abstract</A>)
</P>
<HR>
<H4>1994
</H4>
<P><B>Massively-Parallel Methods for Engineering and Science Problems</B>,
W. J. Camp, S. J. Plimpton, B. A. Hendrickson, R. W. Leland,
Communications of the ACM, 37, 31-41 (1994). (<A HREF = "abstracts/cacm94.html">abstract</A>)
</P>
<P><B>Parallel Particle Simulations of Low-Density Fluid Flows</B>,
S. J. Plimpton and T. J. Bartel, in Proc of High Performance
Computing 1994, San Diego, CA, April 1994, p 31. (<A HREF = "abstracts/hpc94.html">abstract</A>)
</P>
<HR>
<H4>1993
</H4>
<P><B>Parallel Molecular Dynamics With the Embedded Atom Method</B>,
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. (<A HREF = "abstracts/mrs92.html">abstract</A>)
</P>
<P><B>Plane-wave Electronic- Structure Calculations on a Parallel
Supercomputer</B>, J. S. Nelson, S. J. Plimpton, M. P. Sears, Phys Rev
B, 47, 1765-1774 (1993). (<A HREF = "abstracts/prb93.html">abstract</A>)
</P>
<P><B>A Massively-Parallel Digital Processor for Spotlight
Synthetic-Aperture Radar</B>, G. A. Mastin, S. J. Plimpton, D. Ghiglia,
Int J of Supercomputer Applications, 7, 97-112
(1993). (<A HREF = "abstracts/ijsa93.html">abstract</A>)
</P>
<P><B>Parallel Simulation of Electron-Solid Interactions: A Rapid Aid for
Electron- Microscope Data Interpretation</B>, J. R. Michael,
S. J. Plimpton, A. D. Romig Jr., Ultramicroscopy, 51, 160-167
(1993). (<A HREF = "abstracts/ultra93.html">abstract</A>)
</P>
<HR>
<H4>1992
</H4>
<P><B>Is SIMD Enough for Scientific and Engineering Applications on
Massively Parallel Computers ?</B>, 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. (<A HREF = "abstracts/compcon92.html">abstract</A>)
</P>
<P><B>Direct Monte Carlo Simulation of Ionized Rarefied Flows on Large MIMD
Parallel Supercomputers</B>, 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. (<A HREF = "abstracts/rgd92.html">abstract</A>)
</P>
<P><B>Monte Carlo Particle Simulation of Low-Density Fluid Flow on MIMD
Supercomputers</B>, 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). (<A HREF = "abstracts/shpcc92.html">abstract</A>)
</P>
<P><B>Parallel Simulation of Electron-Solid Interactions for
Electron-Microscopy Modeling</B>, S. J. Plimpton, J. R. Michael,
A. D. Romig, Jr., J of SuperComputing, 6, 139-151
(1992). (<A HREF = "abstracts/jsc92.html">abstract</A>)
</P>
<HR>
<H4>1991
</H4>
<P><B>Load Balancing and Performance of a Gridless Particle Simulation on
MIMD, SIMD, and Vector Supercomputers</B>, 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. (<A HREF = "abstracts/siam91.html">abstract</A>)
</P>
<P><B>Synthetic Aperture Radar Image Processing on Parallel
Supercomputers</B>, S. J. Plimpton, G. A. Mastin, D. Ghiglia, in Proc of
Supercomputing '91, Albuquerque, NM, November 1991, p
446. (<A HREF = "abstracts/sc91.html">abstract</A>)
</P>
<HR>
<H4>1990
</H4>
<P><B>Molecular Dynamics Simulations of Grain-Boundary Diffusion for
Varying Tilt Angle Geometries</B>, 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. (<A HREF = "abstracts/mrs90.html">abstract</A>)
</P>
<P><B>Effect of Interatomic Potential on Simulated Grain-Boundary and Bulk
Diffusion: A Molecular-Dynamics Study</B>, S. J. Plimpton and E. D. Wolf,
Phys Rev B, 41, 2712-2721 (1990). (<A HREF = "abstracts/prb90.html">abstract</A>)
</P>
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