RIKEN's MDGrape-3 is the first machine to break the petaflop barrier -- that's 1 quadrillion calculations (floating-point operations, to be specific) per second -- and it's three times faster than the currently ranked fastest computer in the world, IBM's BlueGene/L. But MDGrape-3 is so specialized that it can't run the software used to officially rank computing speed.
MDGrape-3 is designed for pharmaceutical research, specifically molecular dynamics simulation. In developing drugs, pharmaceutical companies have to analyze thousands on thousands of chemical compounds to find out how they'll affect the protein-bonding structures in the human body. Protein structures called enzymes are the building blocks that do all of the work within a cell, and the way these proteins bond with any drug compound introduced into the human body determines the body's response to that drug. MDGrape-3 produces simulations of these molecular interactions. What takes most computers hours or days to analyze takes MDGrape-3 a few seconds. This functionality is invaluable in drug research, and it could drastically cut the research time involved in the development of new cures. A subsidiary of pharmaceutical giant Merck has already booked time on the machine.
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