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JCC
2006
103views more  JCC 2006»
13 years 7 months ago
Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics
: The major bottleneck of today's atomistic molecular dynamics (MD) simulations is that because of the enormous computational effort involved, only processes at nanoseconds to...
Oliver F. Lange, Lars V. Schäfer, Helmut Grub...
ARC
2010
Springer
183views Hardware» more  ARC 2010»
13 years 8 months ago
Integrated Design Environment for Reconfigurable HPC
Using FPGAs to accelerate High Performance Computing (HPC) applications is attractive, but has a huge associated cost: the time spent, not for developing efficient FPGA code but fo...
Lilian Janin, Shoujie Li, Doug Edwards
IPPS
2008
IEEE
14 years 2 months ago
Parallel mining of closed quasi-cliques
Graph structure can model the relationships among a set of objects. Mining quasi-clique patterns from large dense graph data makes sense with respect to both statistic and applica...
Yuzhou Zhang, Jianyong Wang, Zhiping Zeng, Lizhu Z...
BMCBI
2004
123views more  BMCBI 2004»
13 years 7 months ago
Interaction profile-based protein classification of death domain
Background: The increasing number of protein sequences and 3D structure obtained from genomic initiatives is leading many of us to focus on proteomics, and to dedicate our experim...
Drew Lett, Michael Hsing, Frederic Pio
ISCA
2007
IEEE
196views Hardware» more  ISCA 2007»
14 years 2 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...