1. Challenge: Computing for the Life Sciences Gaining insight into protein science and protein folding mechanisms Simulating (thousands of) macromolecules Silicon cells … Interdisciplinary: Mathematics, Physics, Chemistry, Computer Science, Biology Method: molecular dynamics: integrating Newton’s law F=m.a for all atoms where F depends on all atoms! Initialization with the help of random numbers

2. Physical time for simulation10 –4 s Typical time-step size10 –15 s Number of MD time steps10 11 Atoms in a typical protein and water simulation32000 Approximate number of interactions in force calculation 10 9 Machine instructions per force calculation1000 Total number of machine instructions10 23 http://www.research.ibm.com/bluegene/ http://researchweb.watson.ibm.com/journal/sj/402/allen.html One year3 10 7 seconds Clock cycle 10 -9 s Three years * 10 6 processors = 3 * 3 10 7 * 10 6 * 10 9 = 10 23 machine instructions Protein folding The computational effort required to study protein folding is enormous. Using crude workload estimates for a petaflop/second capacity machine leads to an estimate of three years to simulate 100 microseconds.

3. Supercomputers (10 12 floating point operations / s) “Roadrunner” 1026 Teraflop/s (10 12 floating point operations / s) DOE Los Alamos Uses advanced versions of the processor in the Sony PlayStation 3 Vgl. Huygens (Sara 11.9.08) 60 Tflop peak (~rank 40) http://www.sara.nl/ news/recent/ opening_huygens/

4. Blue Gene L/P 478 Teraflops (10 12 floating point operations / s) fastest supercomputer till june 2008 not yet fast enough … Blue Gene L: max 478 Teraflops (10 12 floating point operations / s) fastest supercomputer till june 2008 not yet fast enough … up to 262,144 Blue Gene P up to 262,144 quad processor nodes, projected 3.56 Peta (=10 15 )flops 3.56 Peta (=10 15 ) flops wordt gebruikt voor de grootste radiotelescoop: http://www.lofar.nl

5. Dedicated chip Voor Moleculaire Dynamica MDGrape-3 281 Teraflops in 2007, 20 berekeningen parallel op chip http://mdgrape.gsc.riken.jp http://mdgrape.gsc.riken.jp slechts 0.3 Watt/gigaflop vergelijk 14 Watt/gigaflop Pentium 4