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Issue No.06 - Nov.-Dec. (2012 vol.14)
pp: 58-67
ABSTRACT
Several advances on the mathematical, computational, and visualization fronts have led to the first truly multiscale simulation and visualization of a realistic biological system.
INDEX TERMS
scientific computing, computer simulations, molecular dynamics, multiscale simulation
CITATION
Leopold Grinberg, Joseph A. Insley, Dmitry A. Fedosov, Vitali Morozov, Michael E. Papka, George Em Karniadakis, "Tightly Coupled Atomistic-Continuum Simulations of Brain Blood Flow on Petaflop Supercomputers", Computing in Science & Engineering, vol.14, no. 6, pp. 58-67, Nov.-Dec. 2012, doi:10.1109/MCSE.2012.127
REFERENCES
1. G.E. Karniadakis and S.J. Sherwin, Spectral/hp Element Methods for CFD, 2nd ed., Oxford Univ. Press, 2005.
2. G.E. Karniadakis, M. Israeli, and S. Orszag, “High-Order Splitting Methods for the Incompressible Navier-Stokes Equations.” J. Computational Physics, vol. 97, no. 1, 1991, pp. 414–443.
3. Y. Nakayama and R. Yamamoto, “Simulation Method to Resolve Hydrodynamic Interactions in Colloidal Dispersions,” Physical Rev. E, vol. 71, no. 3, 2005, article ID 036707.
4. X. Luo, M.R. Maxey, and G.E. Karniadakis, “Smoothed Profile Method for Particulate Flows: Error Analysis and Simulations,” J. Computational Physics, vol. 228, no. 5, pp. 1750–1769.
5. L. Grinberg and G. Karniadakis, “A New Domain Decomposition Method with Overlapping Patches for Ultrascale Simulations: Application to Biological Flows,” J. Computational Physics, vol. 229, no. 15, 2010, pp. 5541–5563.
6. H. Lei, B. Caswell, and G.E. Karniadakis, “Direct Construction of Mesoscopic Models from Microscopic Simulations,” Physical Rev. E, vol. 81, no. 2, 2010, article ID 026704.
7. P.J. Hoogerburgge and J.M.V.A. Koelman, “Simulating Microscopic Hydrodynamic Phenomena with Dissipative Particle Dynamics,” Europhysics Letters, vol. 19, no. 3, 1992, pp. 155–160.
8. P. Espanol and P. Warren, “Statistical-Mechanics of Dissipative Particle Dynamics,” Europhysics Letters, vol. 30, no. 4, 1995, pp. 191–196.
9. D.A. Fedosov and G.E. Karniadakis, “Triple-Decker: Interfacing Atomistic Mesoscopic-Continuum Flow Regimes,” J. Computational Physics, vol. 228, no. 4, 2009, pp. 1157–1171.
10. L. Grinberg, “Proper Orthogonal Decomposition of Atomistic Flow Simulations,” J. Computational Physics, vol. 231, no. 16, 2012, pp. 5542–5556.
11. W. Pan et al., “Hydrodynamic Interactions for Single Dissipative-Particle-Dynamics Particles and Their Clusters and Filaments, Physical Rev. E, vol. 78, no. 4, 2008, article ID 046706.
12. I.V. Pivkin, P.D. Richardson, and G.E. Karniadakis, “Blood Flow Velocity Effects and Role of Activation Delay Time on Growth and Form of Platelet Thrombi,” Proc. National Academy of Sciences USA, vol. 103, no. 46, 2006, pp. 17164–17169.
13. J.A. Insley, L. Grinberg, and M.E. Papka, “Visualizing Multiscale Simulation Data: Brain Blood Flow,” Proc. IEEE Symp. Large-Scale Data Analysis and Visualization, IEEE, 2011, pp. 3–7.
14. J.A. Insley, L. Grinberg, and M.E. Papka, “Visualization of Multiscale Simulation Data: Brain Blood Flow,” Proc. 2011 TeraGrid Conf., ACM, 2011, article no. 18.
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