A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics
- Authors:
- Publication Date:
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1550232
- Grant/Contract Number:
- HDTRA1-14-1-0074; FG02-13ER16415; SC0014607
- Resource Type:
- Publisher's Accepted Manuscript
- Journal Name:
- Computer Physics Communications
- Additional Journal Information:
- Journal Name: Computer Physics Communications Journal Volume: 219 Journal Issue: C; Journal ID: ISSN 0010-4655
- Publisher:
- Elsevier
- Country of Publication:
- Netherlands
- Language:
- English
Citation Formats
Byun, Hye Suk, El-Naggar, Mohamed Y., Kalia, Rajiv K., Nakano, Aiichiro, and Vashishta, Priya. A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics. Netherlands: N. p., 2017.
Web. doi:10.1016/j.cpc.2017.05.028.
Byun, Hye Suk, El-Naggar, Mohamed Y., Kalia, Rajiv K., Nakano, Aiichiro, & Vashishta, Priya. A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics. Netherlands. doi:https://doi.org/10.1016/j.cpc.2017.05.028
Byun, Hye Suk, El-Naggar, Mohamed Y., Kalia, Rajiv K., Nakano, Aiichiro, and Vashishta, Priya. Sun .
"A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics". Netherlands. doi:https://doi.org/10.1016/j.cpc.2017.05.028.
@article{osti_1550232,
title = {A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics},
author = {Byun, Hye Suk and El-Naggar, Mohamed Y. and Kalia, Rajiv K. and Nakano, Aiichiro and Vashishta, Priya},
abstractNote = {},
doi = {10.1016/j.cpc.2017.05.028},
journal = {Computer Physics Communications},
number = C,
volume = 219,
place = {Netherlands},
year = {2017},
month = {10}
}
Free Publicly Available Full Text
Publisher's Version of Record
DOI: https://doi.org/10.1016/j.cpc.2017.05.028
DOI: https://doi.org/10.1016/j.cpc.2017.05.028
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 1 work
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Rigorous synchronous relaxation algorithm for parallel kinetic Monte Carlo simulations of thin film growth
journal, March 2005
- Shim, Yunsic; Amar, Jacques G.
- Physical Review B, Vol. 71, Issue 11
Long-range electron transport in Geobacter sulfurreducens biofilms is redox gradient-driven
journal, September 2012
- Snider, R. M.; Strycharz-Glaven, S. M.; Tsoi, S. D.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 38
Quantum Molecular Dynamics in the Post-Petaflops Era
journal, November 2015
- Romero, Nichols A.; Nakano, Aiichiro; Riley, Katherine M.
- Computer, Vol. 48, Issue 11
A new algorithm for Monte Carlo simulation of Ising spin systems
journal, January 1975
- Bortz, A. B.; Kalos, M. H.; Lebowitz, J. L.
- Journal of Computational Physics, Vol. 17, Issue 1
Exascale computing and big data
journal, June 2015
- Reed, Daniel A.; Dongarra, Jack
- Communications of the ACM, Vol. 58, Issue 7
Thermally activated long range electron transport in living biofilms
journal, January 2015
- Yates, Matthew D.; Golden, Joel P.; Roy, Jared
- Physical Chemistry Chemical Physics, Vol. 17, Issue 48
Billion-atom synchronous parallel kinetic Monte Carlo simulations of critical 3D Ising systems
journal, February 2011
- Martínez, E.; Monasterio, P. R.; Marian, J.
- Journal of Computational Physics, Vol. 230, Issue 4
Rapid electron exchange between surface-exposed bacterial cytochromes and Fe(III) minerals
journal, March 2013
- White, G. F.; Shi, Z.; Shi, L.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 16
Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
journal, December 1990
- Elber, R.; Karplus, M.
- Journal of the American Chemical Society, Vol. 112, Issue 25
Dielectric Genome of van der Waals Heterostructures
journal, June 2015
- Andersen, Kirsten; Latini, Simone; Thygesen, Kristian S.
- Nano Letters, Vol. 15, Issue 7
Synchronous parallel kinetic Monte Carlo for continuum diffusion-reaction systems
journal, April 2008
- Martínez, E.; Marian, J.; Kalos, M. H.
- Journal of Computational Physics, Vol. 227, Issue 8
Kinetic Monte Carlo Simulations and Molecular Conductance Measurements of the Bacterial Decaheme Cytochrome MtrF
journal, September 2014
- Byun, Hye Suk; Pirbadian, Sahand; Nakano, Aiichiro
- ChemElectroChem, Vol. 1, Issue 11
Shewanella oneidensis MR-1 nanowires are outer membrane and periplasmic extensions of the extracellular electron transport components
journal, August 2014
- Pirbadian, S.; Barchinger, S. E.; Leung, K. M.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 35
\mathcal{O}(N) methods in electronic structure calculations
journal, February 2012
- Bowler, D. R.; Miyazaki, T.
- Reports on Progress in Physics, Vol. 75, Issue 3
Reaction-rate theory: fifty years after Kramers
journal, April 1990
- Hänggi, Peter; Talkner, Peter; Borkovec, Michal
- Reviews of Modern Physics, Vol. 62, Issue 2
The ‘porin-cytochrome’ model for microbe-to-mineral electron transfer: Microbe-to-mineral electron transfer
journal, May 2012
- Richardson, David J.; Butt, Julea N.; Fredrickson, Jim K.
- Molecular Microbiology, Vol. 85, Issue 2
A combined electrochemical and optical trapping platform for measuring single cell respiration rates at electrode interfaces
journal, June 2015
- Gross, Benjamin J.; El-Naggar, Mohamed Y.
- Review of Scientific Instruments, Vol. 86, Issue 6
Theoretical foundations of dynamical Monte Carlo simulations
journal, July 1991
- Fichthorn, Kristen A.; Weinberg, W. H.
- The Journal of Chemical Physics, Vol. 95, Issue 2
Electrical transport along bacterial nanowires from Shewanella oneidensis MR-1
journal, October 2010
- El-Naggar, M. Y.; Wanger, G.; Leung, K. M.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 42
Current Status of Transition-State Theory
journal, January 1996
- Truhlar, Donald G.; Garrett, Bruce C.; Klippenstein, Stephen J.
- The Journal of Physical Chemistry, Vol. 100, Issue 31
Nanoscopic mechanisms of singlet fission in amorphous molecular solid
journal, April 2013
- Mou, Weiwei; Hattori, Shinnosuke; Rajak, Pankaj
- Applied Physics Letters, Vol. 102, Issue 17
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
journal, December 1976
- Gillespie, Daniel T.
- Journal of Computational Physics, Vol. 22, Issue 4
Exponential multiplicity of inherent structures
journal, January 1999
- Stillinger, Frank H.
- Physical Review E, Vol. 59, Issue 1
A fast algorithm for particle simulations
journal, December 1987
- Greengard, L.; Rokhlin, V.
- Journal of Computational Physics, Vol. 73, Issue 2
Parallel replica method for dynamics of infrequent events
journal, June 1998
- Voter, Arthur F.
- Physical Review B, Vol. 57, Issue 22
A space–time-ensemble parallel nudged elastic band algorithm for molecular kinetics simulation
journal, February 2008
- Nakano, Aiichiro
- Computer Physics Communications, Vol. 178, Issue 4
A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations
journal, May 2014
- Shimojo, Fuyuki; Hattori, Shinnosuke; Kalia, Rajiv K.
- The Journal of Chemical Physics, Vol. 140, Issue 18
Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
journal, December 2013
- Kohlhoff, Kai J.; Shukla, Diwakar; Lawrenz, Morgan
- Nature Chemistry, Vol. 6, Issue 1