A New Computational Paradigm in Multiscale Simulations: Application to Brain Blood Flow

Grinberg, L., Insley, J.A., Morozov, V., Papka, M.E., Karniadakis, G.E., Fedosov, D., Kumaran, K.

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).

Publication Date: 
October, 2011
Name of Publication Source: 
SC '11 Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis
Page Numbers: 
Conference Location: 
Seattle, Washington