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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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
Cyberinfrastructure Days – Marshall University
April 7th, 2011
Rokadia et al. (2010)
Image by N. Chopra
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
Select a specific polymer chain
Remove all other polymer chains to study behavior of the selected chain
“Slice” through the system to study a specific phenomenon
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!