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A new computational paradigm in multiscale simulations: Application to brain blood flow

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7 Author(s)
Grinberg, L. ; Div. of Appl. Math., Brown Univ., Providence, RI, USA ; Morozov, V. ; Fedosov, D. ; Insley, J.A.
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Interfacing atomistic-based with continuum-based simulation codes is now required in many multiscale physical and biological systems. We present the computational advances that have enabled the first multiscale simulation on 190,740 processors by coupling a high-order (spectral element) Navier-Stokes solver with a stochastic (coarse-grained) Molecular Dynamics solver based on Dissipative Particle Dynamics (DPD). The key contributions are proper interface conditions for overlapped domains, topology-aware communication, SIMDization, multiscale visualization and a new do- main partitioning for atomistic solvers. We study blood flow in a patient-specific cerebrovasculature with a brain aneurysm, and analyze the interaction of blood cells with the arterial walls endowed with a glycocalyx causing thrombus formation and eventual aneurysm rupture. The macro-scale dynamics (about 3 billion unknowns) are resolved by NεκTαr - a spectral element solver; the micro-scale flow and cell dynamics within the aneurysm are resolved by an in-house version of DPD-LAMMPS (for an equivalent of about 100 billions molecules).

Published in:

High Performance Computing, Networking, Storage and Analysis (SC), 2011 International Conference for

Date of Conference:

12-18 Nov. 2011

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