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GPU-Enabled Macromolecular Simulation: Challenges and Opportunities
Found in: Computing in Science & Engineering
By Michela Taufer,Narayan Ganesan,Sandeep Patel
Issue Date:January 2013
pp. 56-57
GPU-enabled simulation of fully atomistic macromolecular systems is rapidly gaining momentum, enabled by massive parallelism and the parallelizability of various components of the underlying algorithms and methodologies. Here, we consider key aspects requi...
FENZI: GPU-Enabled Molecular Dynamics Simulations of Large Membrane Regions Based on the CHARMM Force Field and PME
Found in: Parallel and Distributed Processing Workshops and PhD Forum, 2011 IEEE International Symposium on
By Narayan Ganesan,Michela Taufer,Brad Bauer,Sandeep Patel
Issue Date:May 2011
pp. 472-480
When studying membrane-bound protein receptors, it is necessary to move beyond the current state-of-the-art simulations that only consider small membrane patches and implicit solvent. Limits of traditional computer platforms negatively impact the model's l...
Sorting on architecturally diverse computer systems
Found in: Proceedings of the Third International Workshop on High-Performance Reconfigurable Computing Technology and Applications (HPRCTA '09)
By Narayan Ganesan, Roger D. Chamberlain
Issue Date:November 2009
pp. 39-46
Sorting is an important problem that forms an essential component of many high-performance applications. Here, we explore the design space of sorting algorithms in recon-figurable hardware, looking to maximize the benefit associated with high-bandwidth, mu...