Molecular Dynamics Simulations and the Importance of Advanced Cyberinfrastructure Resources. Douglas E. Spearot Assistant Professor of Mechanical Engineering Faculty Campus Champion for Cyberinfrastructure University of Arkansas Fayetteville, AR 72701
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Advanced Cyberinfrastructure Resources
Douglas E. Spearot
Assistant Professor of Mechanical Engineering
Faculty Campus Champion for Cyberinfrastructure
University of Arkansas
Fayetteville, AR 72701
Cyberinfrastructure Days – Marshall University
April 7th, 2011
Rokadia et al. (2010)
www.nano-lab.comWhy Molecular Dynamics?
Example: Defects in Carbon Nanotubes
Zhang et al. (2005; 2007)
Second-order ordinary differential equation which can be numerically integrated to find new atomic positions!
Example: Polymers / Biomolecules
Example: Small cube of FCC Cu
“Star of Arkansas”
Current world record: 320 billion atoms with EAM potential
(T. Germann et al., using 131,072 cores on IBM BlueGene/L at LLNL)
Atomistic model of a nanocrystalline metal
Large Simulation Model
Small Simulation Model
The “inverse” Hall-Petch relationship can be captured via atomistic simulations
Rajgarhia, Spearot, et al. (2010) Journal of Materials Research, 25, 411.
Need visualization tools to sort, view and analyze a large amount of temporal and spatial data!
Paul Navratil, TACC
For atomistic/molecular simulations, geometric primitives are “spheres” meant to represent each atom in the system
Remove all other polymer chains to study behavior of the selected chain
Polymer/nanoparticle interface; impact of nanoparticle on chain dynamics
For atomistic/molecular simulations, cyberinfrastructure must include HPC hardware, atomistic software, visualization software, and support personnel!