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ACM Trans Reconfigurable Technol Syst 2010 Nov;3(4)

Computer Architecture and Automated Design Laboratory; Department of Electrical and Computer Engineering; Boston University; Boston, MA 02215; Web: http://www.bu.edu/caadlab.

The acceleration of molecular dynamics (MD) simulations using high-performance reconfigurable computing (HPRC) has been much studied. Given the intense competition from multicore and GPUs, there is now a question whether MD on HPRC can be competitive. We concentrate here on the MD kernel computation: determining the short-range force between particle pairs. Read More

ACM Trans Reconfigurable Technol Syst 2008 Jun;1(2)

Dept. of Computer Science and Engineering, Washington University in St. Louis.

Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more running time or a cluster of machines to keep pace. Read More