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

Authors:
Leopold Grinberg;Joseph A. Insley;Vitali Morozov;Michael E. Papka;George Em Karniadakis;Dmitry Fedosov;Kalyan Kumaran
Affiliations:
Brown University, Providence, RI;Argonne National Laboratory, Argonne, IL;Argonne National Laboratory, Argonne, IL;Argonne National Laboratory, Argonne, Illinois;Brown University, Providence, RI;Institute of Complex Systems, FZ Juelich, Juelich, Germany;Argonne National Laboratory, Argonne, Illinois
Venue:
Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis
Year:
2011

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Abstract

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 domain 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).