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IPPS
2007
IEEE
15 years 6 months ago
On the Path to Enable Multi-scale Biomolecular Simulations on PetaFLOPS Supercomputer with Multi-core Processors
1 Biological processes occurring inside cell involve multiple scales of time and length; many popular theoretical and computational multi-scale techniques utilize biomolecular simu...
Sadaf R. Alam, Pratul K. Agarwal
ASAP
2007
IEEE
157views Hardware» more  ASAP 2007»
15 years 3 months ago
Automatic Generation and Optimisation of Reconfigurable Financial Monte-Carlo Simulations
Monte-Carlo simulations are used in many applications, such as option pricing and portfolio evaluation. Due to their high computational load and intrinsic parallelism, they are id...
David B. Thomas, Jacob A. Bower, Wayne Luk
BMCBI
2007
103views more  BMCBI 2007»
14 years 12 months ago
Dynamic simulation of regulatory networks using SQUAD
Background: The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncove...
Alessandro Di Cara, Abhishek Garg, Giovanni De Mic...
BMCBI
2008
211views more  BMCBI 2008»
14 years 12 months ago
CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment
Background: Searching for similarities in protein and DNA databases has become a routine procedure in Molecular Biology. The Smith-Waterman algorithm has been available for more t...
Svetlin Manavski, Giorgio Valle
FPGA
2004
ACM
174views FPGA» more  FPGA 2004»
15 years 5 months ago
A compiled accelerator for biological cell signaling simulations
The simulation of large systems of biochemical reactions is a key part of research into molecular signaling and information processing in biological cells. However, it can be impr...
John F. Keane, Christopher Bradley, Carl Ebeling