Title :
A new computational paradigm in multiscale simulations: Application to brain blood flow
Author :
Grinberg, Leopold ; Morozov, Vitali ; Fedosov, Dmitry ; Insley, Joseph A. ; Papka, Michael E. ; Kumaran, Kalyan ; Karniadakis, George Em
Author_Institution :
Div. of Appl. Math., Brown Univ., Providence, RI, USA
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 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).
Keywords :
Navier-Stokes equations; brain; data visualisation; haemodynamics; haemorheology; medical computing; molecular dynamics method; partial differential equations; DPD-LAMMPS; NεκTαr; Navier-Stokes solver; SIMDization; atomistic-based simulation codes; blood cell interaction; brain aneurysm; brain blood flow; computational paradigm; continuum-based simulation codes; dissipative particle dynamics; eventual aneurysm rupture; glycocalyx; macro-scale dynamics; multiscale biological system; multiscale physical system; multiscale simulations; multiscale visualization; partial differential equations; patient-specific cerebrovasculature; spectral element solver; stochastic molecular dynamics solver; thrombus formation; topology-aware communication; Aneurysm; Arteries; Blood; Computational modeling; Couplings; Mathematical model; Program processors; Cerebrovascular circulation; Continuum-atomistic simulations; Coupled solvers; Multi-scale modeling;
Conference_Titel :
High Performance Computing, Networking, Storage and Analysis (SC), 2011 International Conference for
Conference_Location :
Seatle, WA
Electronic_ISBN :
978-1-4503-0771-0