DNA STRUCTURE

Rob Coalson

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Scientific Significance:

The project is to calculate the coulombic interactions of a short DNA strand as a function of the B-Z coil (left to right handed helices) transition. The ability to utilize large numbers of processors has allowed us to determine that the calculated free energy of the DNA B->Z transition depends strongly on the dielectric constant profile across the solvent/DNA boundary. Previous calculations that we are aware of have not employed sufficiently fine lattices to determine the full dependency of the results on the dielectric constant profile. Such fine lattices are only possible on the T3D using 64 or 128 processors.

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Numerical Approach and Performance:

The computational task is to solve an equation, on a simple cubic lattice, which involves iterating on nearest neighbor elements. error estimates. For these large DNA calculations, performance has scaled linearly with the number of processors, up to and including 128 processors, and reaches approximately 18-19 MFLOPS/processor.

The T3D has dramatically outperformed the C90 for the DNA calculations. The amount of memory required for the fine lattice DNA calculations using 128 processors is simply not available on the C90, and the speed and throughput of the T3D both are significantly better than the C90. Total MFLOP measurements on the C90 reached, for optimum cases, 200-250 MFLOPS. Somewhat more complicated code achieved an overall performance of 2.4 GFLOPS on the T3D.

The scaling is indistinguishable from linear.

20 MFLOPS/PE
32 PE = 2.8 Equivalent C90 CPU's

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