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High performance implementation of hydrodynamic interactions and applications with the sub-cellular element method

Andrei Frunza
Computational Science and Engineering Laboratory, ETH Zurich
ETH Zurich, Computational Science and Engineering Laboratory, 2012

@article{frunza2012high,

   title={High performance implementation of hydrodynamic interactions and applications with the sub-cellular element method},

   author={Frunza, A. and Tauriello, G. and Koumoutsakos, P.},

   year={2012}

}

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An O(N^2) algorithm for computing hydrodynamic interaction (HI) in Brownian dynamics (BD) simulation has been implemented. A CPU and a GPU versions have been build, with the GPU one being tuned for performance, up to 40% of the maximum peak performance being obtained. The implementation was validated through simulations of diffusion polymers and comparisons of the yielded parameters with theoretical values. The hydrodynamic interactions were added to cell stretching experiments, in which the cells are modelled with the sub-cellular element method and a delayed failure behaviour was observed.
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