Processing nodes of the Cray XT and IBM Blue Gene Massively Parallel Processing (MPP) systems are composed of multiple execution units, sharing memory and network subsystems. Thes...
Sadaf R. Alam, Pratul K. Agarwal, Scott S. Hampton...
We have taken a NIST molecular dynamics simulation program (md3), which was configured as a single sequential process running on a CRAY C90 vector supercomputer, and parallelized ...
Large-scale simulations and computational modeling using molecular dynamics (MD) continues to make significant impacts in the field of biology. It is well known that simulations...
Sadaf R. Alam, Jeffrey S. Vetter, Pratul K. Agarwa...
Background: Recent approaches for predicting the three-dimensional (3D) structure of proteins such as de novo or fold recognition methods mostly rely on simplified energy potentia...
Current high-performance applications are typically implemented on large-scale general-purpose distributed or multiprocessing systems often based on commodity microprocessors. Fie...
Navid Azizi, Ian Kuon, Aaron Egier, Ahmad Darabiha...