$7.0/Mflops astrophysical N-body simulation with treecode on GRAPE-5
SC '99 Proceedings of the 1999 ACM/IEEE conference on Supercomputing
1.34 Tflops molecular dynamics simulation for NaCl with a special-purpose computer: MDM
Proceedings of the 2000 ACM/IEEE conference on Supercomputing
Avalon: an Alpha/Linux cluster achieves 10 Gflops for $15k
SC '98 Proceedings of the 1998 ACM/IEEE conference on Supercomputing
Scientific Simulations with Special Purpose Computers: The Grade Systems
Scientific Simulations with Special Purpose Computers: The Grade Systems
Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations
Proceedings of the 2003 ACM/IEEE conference on Supercomputing
Proceedings of the 2007 ACM/IEEE conference on Supercomputing
Proceedings of the 2007 ACM/IEEE conference on Supercomputing
Proceedings of the 2008 ACM/IEEE conference on Supercomputing
Millisecond-scale molecular dynamics simulations on Anton
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
Millisecond-scale molecular dynamics simulations on Anton
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
Progress towards petascale applications in biology: status in 2006
Euro-Par'06 Proceedings of the CoreGRID 2006, UNICORE Summit 2006, Petascale Computational Biology and Bioinformatics conference on Parallel processing
190 TFlops Astrophysical N-body Simulation on a Cluster of GPUs
Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
Exploiting 162-Nanosecond End-to-End Communication Latency on Anton
Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
ACM SIGARCH Computer Architecture News
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We have achieved a sustained performance of 55 TFLOPS for molecular dynamics simulations of the amyloid fibril formation of peptides from the yeast Sup35 in an aqueous solution. For performing the calculations, we used the MDGRAPE-3 system---a special-purpose computer system for molecular dynamics simulations. Its nominal peak performance was 415 TFLOPS for Coulomb force calculations; this is the highest-ever performance reported for classical molecular dynamics simulations. Amyloid fibril formation is known to be related to the occurrence of severe diseases such as Alzheimer's, Parkinson's, and Creutzfeldt-Jakob diseases. The Sup35 protein is a "yeast prion protein," which forms mini-crystals due to aggregation; it forms an effective platform for studying the formation process of amyloid fibrils. In these simulations, we first elucidate that the amyloid-forming peptides GNNQQNY aggregate at a higher frequency than non-amyloid-forming peptides SQNGNQQRG; further, the GNNQQNY peptides tend to form parallel two-stranded ß-sheets that would grow into a cross-ß amyloid nucleus. The results are consistent with those obtained experimentally. Furthermore, we could observe an early elongation of the amyloid nucleus. This result is expected to contribute toward a deeper understanding of the amyloid growth mechanism.