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IPPS
2008
IEEE
15 years 11 months ago
Overcoming scaling challenges in biomolecular simulations across multiple platforms
NAMD† is a portable parallel application for biomolecular simulations. NAMD pioneered the use of hybrid spatial and force decomposition, a technique now used by most scalable pr...
Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. ...
ICSM
2007
IEEE
15 years 10 months ago
A Maintainable Software Architecture for Fast and Modular Bioinformatics Sequence Search
Bioinformaticists use the Basic Local Alignment Search Tool (BLAST) to characterize an unknown sequence by comparing it against a database of known sequences, thus detecting evolu...
Jeremy S. Archuleta, Eli Tilevich, Wu-chun Feng
IPPS
2007
IEEE
15 years 10 months ago
Optimizing the Fast Fourier Transform on a Multi-core Architecture
The rapid revolution in microprocessor chip architecture due to multicore technology is presenting unprecedented challenges to the application developers as well as system softwar...
Long Chen, Ziang Hu, Junmin Lin, Guang R. Gao
ISCA
2007
IEEE
196views Hardware» more  ISCA 2007»
15 years 10 months ago
Anton, a special-purpose machine for molecular dynamics simulation
The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle provide answers to some of the ...
David E. Shaw, Martin M. Deneroff, Ron O. Dror, Je...
CASES
2004
ACM
15 years 10 months ago
A hamming distance based VLIW/EPIC code compression technique
This paper presents and reports on a VLIW code compression technique based on vector Hamming distances [19]. It investigates the appropriate selection of dictionary vectors such t...
Montserrat Ros, Peter Sutton