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Unraveling Protein Folding: Supercomputing in Life Sciences

This interdisciplinary approach integrates mathematics, physics, chemistry, computer science, and biology to simulate macromolecules for protein folding insights. Molecular dynamics using Newton's laws requires immense computational resources. Supercomputers like Blue Gene and MDGrape play a crucial role in accelerating these simulations, reducing the time required from years to microseconds. Advanced technologies such as dedicated chips have revolutionized the efficiency of these computations, showcasing the innovative progress in computing for life sciences.

mckenzie-harmon
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Unraveling Protein Folding: Supercomputing in Life Sciences

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  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. 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. Physical time for simulation 10–4 s Typical time-step size 10–15 s Number of MD time steps 1011 Atoms in a typical protein and water simulation 32000 Approximate number of interactions in force calculation 109 Machine instructions per force calculation 1000 Total number of machine instructions 1023 Protein folding http://www.research.ibm.com/bluegene/ http://researchweb.watson.ibm.com/journal/sj/402/allen.html One year 3 107 seconds Clock cycle 10-9 s Three years * 106 processors = 3 * 3 107 * 106 * 109 = 1023 machine instructions

  3. Supercomputers “Roadrunner”1026 Teraflop/s (1012 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 Blue Gene L: max 478 Teraflops (1012 floating point operations / s) fastest supercomputer till june 2008not yet fast enough … Blue Gene Pup to 262,144 quad processor nodes, projected 3.56 Peta (=1015)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 chiphttp://mdgrape.gsc.riken.jp • slechts 0.3 Watt/gigaflopvergelijk 14 Watt/gigaflop Pentium 4

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