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10 Years at GSC (Genomic Sciences Center)

Successful development of the fastest LSI in the world



The High Performance Biocomputing Research Team, the Bioinformatics Group has succeeded to develop the MDGRAPE-3 chip, the fastest LSI in the world with the performance of 230 gigaflops.
  The research team is now developing the dedicated computer `MDGRAPE-3’, which will be the fastest computer in the world.
The MDGRAPE-3 chip, which we have developed, is the core component of the system. The MDGRAPE-3 is a dedicated computer for molecular dynamics simulations, in which the orbits of atoms in matter are precisely simulated by Newton’s law using computers. Specialization to the specific application makes us possible to achieve high performance compared with general-purpose computers.
The success in the development of the LSI enables us to break a petaflops (ability to perform a quadrillion operations per second) barrier in 2006.
  The MDGRAPE-3 will enable precise estimations of the affinities of drug candidates to proteins, which is quite important to accelerate novel drug design. It will also clarify atomic mechanism of protein functions, thus we can investigate atomic origin of diseases often caused by mutation in proteins by a computer. The MDGRAPE-3 will become a powerful tool for such nano-scale studies in molecular biology and nanotechnology.
  This achievement has been presented in Hot Chips 16 international symposium (Stanford University, Palo Alto, California, USA, August 22-24, 2004).