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» Large Scale Simulation of Parallel Molecular Dynamics
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GI
2009
Springer
15 years 10 months ago
Massively-Parallel Simulation of Biochemical Systems
: Understanding biological evolution prompts for a detailed understanding of the realized phenotype. Biochemical and gene regulatory dynamics are a cornerstone for the physiology o...
Jens Ackermann, Paul Baecher, Thorsten Franzel, Mi...
GRID
2004
Springer
15 years 11 months ago
High Performance Threaded Data Streaming for Large Scale Simulations
We have developed a threaded parallel data streaming approach using Logistical Networking (LN) to transfer multi-terabyte simulation data from computers at NERSC to our local anal...
Viraj Bhat, Scott Klasky, Scott Atchley, Micah Bec...
ANSS
2007
IEEE
15 years 10 months ago
MDL, A Domain-Specific Language for Molecular Dynamics
Molecular Dynamics (MD) involves solving Newton's equations of motion for a molecular system and propagating the system by time-dependent updates of atomic positions and velo...
Trevor M. Cickovski, Chris Sweet, Jesús A. ...
IPPS
2010
IEEE
15 years 3 months ago
Improving numerical reproducibility and stability in large-scale numerical simulations on GPUs
The advent of general purpose graphics processing units (GPGPU's) brings about a whole new platform for running numerically intensive applications at high speeds. Their multi-...
Michela Taufer, Omar Padron, Philip Saponaro, Sand...
APVIS
2011
14 years 5 months ago
Loose capacity-constrained representatives for the qualitative visual analysis in molecular dynamics
Molecular dynamics is a widely used simulation technique to investigate material properties and structural changes under external forces. The availability of more powerful cluster...
Steffen Frey, Thomas Schlömer, Sebastian Grot...