Particle-based methods for multiscale modeling of blood flow in the circulation and in devices: Challenges and future directions: Sixth international bio-fluid mechanics symposium and workshop March 28-30, 2008 Pasadena, California

Annals of Biomedical Engineering

Volumn 38, Issue 3, 2010, Pages 1225-1235

  Yamaguchi, Takami ^a   Ishikawa, Takuji ^a   Imai, Y ^a   Matsuki, N ^a   Xenos, Mikhail ^b   Deng, Yuefan ^c   Bluestein, Danny ^b  

^a TOHOKU UNIVERSITY   (Japan)

^b St Francis Hospital The Heart Center   (United States)

^c Stony Brook University   (United States)

Author keywords

Blood flow; Clotting; Devices; DPD; Multiscale modeling; Numerical methods; Particle dynamics; Platelets

Indexed keywords

BLOOD FLOW; CLOTTING; DPD; MULTI-SCALE MODELING; PARTICLE DYNAMICS;

BLOOD; BLOOD SUBSTITUTES; CONTACTS (FLUID MECHANICS); CONTINUUM MECHANICS; DYNAMICS; ELASTICITY; FLUID MECHANICS; HEMODYNAMICS; NUMBER THEORY; PLATELETS; PRESSURE EFFECTS; TRANSPORT PROPERTIES;

NUMERICAL METHODS;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; BLOOD FLOW VELOCITY; BLOOD VESSEL; COMPUTER SIMULATION; FORECASTING; HUMAN; PHYSIOLOGY;

ANIMALS; BLOOD FLOW VELOCITY; BLOOD VESSELS; COMPUTER SIMULATION; FORECASTING; HUMANS; MODELS, CARDIOVASCULAR;

EID: 77952011367     PISSN: 00906964     EISSN: 15739686     Source Type: Journal    
DOI: 10.1007/s10439-010-9904-x     Document Type: Conference Paper

References (72)

1. R Alan McCoy Y Deng 1997 Parallel embedded-atom method simulations with delayed electron density approximations Comp. Phys. Commun. 100 41 46 10.1016/S0010-4655(96)00136-1
2. R Alan McCoy Y Deng 1999 Parallel particle simulations of thin-film deposition Int. J. High Perform. Comput. Appl. 13 16 32 10.1177/ 109434209901300102
3. R Albert AL Barabasi N Carle A Dougherty 1998 Driven interfaces in disordered media: determination of universality classes from experimental data Phys. Rev. Lett. 81 2926 2929 10.1103/PhysRevLett.81.2926
4. P Bagchi 2007 Mesoscale simulation of blood flow in small vessels Biophys. J. 92 1858 1877 10.1529/biophysj.106.095042 17208982
5. P Bagchi PC Johnson AS Popel 2005 Computational fluid dynamic simulation of aggregation of deformable cells in a shear flow J. Biomech. Eng. 127 1070 1080 10.1115/1.2112907 16502649
6. HJC Berendsen D Vanderspoel R Vandrunen 1995 Gromacs-a message-passing parallel molecular-dynamics implementation Comput. Phys. Commun. 91 43 56 10.1016/0010-4655(95)00042-E
7. Bluestein, D., Y. Alemu, P. Rissland, K. Dumont, P. Verdonck, and Y. Deng (2007) Damage accumulation model, FSI, and multiscale simulations for studying the thrombogenic potential of prosthetic heart valves. In: Proc. ASME Summer Bioengineering Conference, Keystone, CO.
8. ES Boek PV Coveney HNW Lekkerkerker 1996 Computer simulation of rheological phenomena in dense colloidal suspensions with dissipative particle dynamics J. Phys. Condens. Matter. 8 9509 9512 10.1088/0953-8984/8/47/053
9. K Boryczko W Dzwinel DA Yuen 2003 Dynamical clustering of red blood cells in capillary vessels J. Mol. Model. (Online) 9 16 33
10. K Boryczko W Dzwinel DA Yuen 2004 Modeling fibrin aggregation in blood flow with discrete-particles Comput. Methods Programs Biomed. 75 181 194 10.1016/j.cmpb.2004.02.001 15265617
11. K Boryczko W Dzwinel DA Yuen 2005 Modeling heterogeneous mesoscopic fluids in irregular geometries using shared memory systems Mol. Sim. 31 45 56 10.1080/08927020412331299341
12. K Boryczko W Dzwinel DA Yuen 2002 Parallel implementation of the fluid particle model for simulating complex fluids in the mesoscale Concurrency Comp. Prac. Exp. 14 137 161 10.1002/cpe.619
13. JF Brady G Bossis 1988 Stokesian dynamics Annu. Rev. Fluid Mech. 20 111 157 10.1146/annurev.fl.20.010188.000551
14. YZ Chen X Chen YF Deng 2007 Simulating botulinum neurotoxin with constant pH molecular dynamics in Generalized Born implicit solvent Comp. Phys. Commun. 177 210 213 10.1016/j.cpc.2007.02.095
15. PA Cundall ODL Strack 1979 A discrete numerical model for granular assemblies Geotechnique 29 47 65 10.1680/geot.1979.29.1.47
16. ME Davis 2002 Ordered porous materials for emerging applications Nature 417 6891 813 821 10.1038/nature00785 12075343
17. Deng, Y., and R. A. McCoy. Computing sticking coefficients for Cu-Cu by localized molecular dynamics on parallel processors. In: Proceedings of High Performance Computing, edited by A. Tentner. San Diego, CA: The Society for Computer Simulation, 1996, pp. 18-24.
18. Deng, Y., R. A. McCoy, R. B. Marr, R. F. Peierls, and O. Yasar. Short-ranged interactions molecular dynamics for 400 million particles. In: High Performance Computing 1995, Proc. of the Society for Computer Simulation Multiconference (Phonix, AZ, Apr. 9-13, 1995), edited by A. Tentner. San Diego: The Society for Computer Simulation, 1995.
19. Y Deng RA McCoy R Peierls O Yasar 1995 Molecular dynamics on distributed-memory MIMD computers with load balancing Appl. Math. Lett. 8 37 41 10.1016/0893-9659(95)00027-N
20. Y Deng R Peierls C Rivera 2000 An adaptive load balancing method for parallel molecular dynamics simulations J. Comp. Phys. 161 250 263 10.1006/jcph.2000.6501
21. MM Dupin I Halliday CM Care L Alboul LL Munn 2007 Modeling the flow of dense suspensions of deformable particles in three dimensions Phys. Rev. E. Stat. Nonlin. Soft Matter. Phys. 75 6 Pt 2 066707 17677389
22. L Durlofsky JF Brady G Bossis 1987 Dynamic simulation of hydrodynamically interacting particles J. Fluid Mech. 180 21 49 10.1017/S002211208700171X
23. W Dwinzel DA Yuen K Boryczko 2002 Mesoscopic dynamics of colloids simulated with dissipative particle dynamics and fluid particle model J. Mol. Model. (Online) 8 33 43 10.1007/s00894-001-0068-3
24. W Dzwinel K Boryczko DA Yuen 2003 A discrete-particle model of blood dynamics in capillary vessels J. Colloid Interface Sci. 258 163 173 10.1016/S0021-9797(02)00075-9 12600784
25. P Espanol 1998 Fluid particle model Phys. Rev. E 57 2930 2948 10.1103/PhysRevE.57.2930
26. B Fang G Martyna YF Deng 2007 A fine grained parallel smooth particle mesh Ewald algorithm for biophysical simulation studies: Application to the 6-D torus QCDOC supercomputer Comp. Phys. Commun. 177 362 377 10.1016/j.cpc.2007.01. 011
27. N Filipovic M Kojic A Tsuda 2008 Modelling thrombosis using dissipative particle dynamics method Philos. Transact. A Math. Phys. Eng. Sci. 366 18 3265 3279 10.1098/rsta.2008.0097 18593663
28. N Filipovic D Ravnic M Kojic SJ Mentzer S Haber A Tsuda 2008 Interactions of blood cell constituents: Experimental investigation and computational modeling by discrete particle dynamics algorithm Microvasc. Res. 75 279 284 10.1016/j.mvr.2007.09.007 18068201
29. RD Groot PB Warren 1997 Dissipative particle dynamics: bridging the gap between atomistic and mesoscopic simulation J. Chem. Phys. 107 4423 4435 10.1063/1.474784
30. NG Hadjiconstantinou AT Patera 1997 Heterogeneous atomistic-continuum representations for dense fluid systems Int. J. Mod. Phys. C 8 967 976 10.1142/S0129183197000837
31. TY Hou XH Wu 1997 A multiscale finite element method for elliptic problems in composite materials and porous media J. Comput. Phys. 134 169 189 10.1006/jcph.1997.5682
32. T Ishikawa JT Locsei TJ Pedley 2008 Development of coherent structures in concentrated suspensions of swinning model micro-organisms J. Fluid Mech. 615 401 431 10.1017/S0022112008003807
33. T Ishikawa TJ Pedley 2008 Coherent structures in monolayers of swimming particles Phys. Rev. Lett. 100 088103 10.1103/PhysRevLett.100.088103 18352669
34. KGF Janssens D Olmsted EA Holm SM Foiles SJ Plimpton PM Derlet 2006 Computing the mobility of grain boundaries Nat. Mater. 5 124 127 10.1038/nmat1559 16400330
35. L Kale R Skeel M Bhandarkar R Brunner A Gursoy N Krawetz J Phillips A Shinozaki K Varadarajan K Schulten 1999 NAMD2: greater scalability for parallel molecular dynamics J. Comput. Phys. 151 283 312 10.1006/jcph.1999.6201
36. H Kamada K Tsubota S Wada T Yamaguchi 2006 Computer simulation of formation and collapse of primary thrombus due to platelet aggregation using particle method Trans. JSME B 72 1109 1115 (in Japanese)
37. Keaveny, E. E., I. V. Pivkin, M. Maxey, and G. E. Karniadakis. A comparative study between dissipative particle dynamics and molecular dynamics for simple- and complex-geometry flows. J. Chem. Phys. 123:104107, 2005.
38. PE Kechagia IN Tsimpanogiannis YC Yortsos PC Lichtner 2002 On the upscaling of reaction-transport processes in porous media with fast or finite kinetics Chem. Eng. Sci. 57 2565 2577 10.1016/S0009-2509(02)00124-0
39. Y Komeiji M Haraguchi U Nagashima 2001 Parallel molecular dynamics simulation of a protein Parallel Comput. 27 977 987 10.1016/S0167-8191(01)00079- 5
40. H Kondo Y Imai T Ishikawa K Tsubota T Yamaguchi 2009 Hemodynamic analysis of microcirculation in malaria infection Ann. Biomed. Eng. 37 702 709 10.1007/s10439-009-9641-1 19160054
41. J Koplik JR Banavar 1995 Continuum deductions from molecular hydrodynamics Ann. Rev. Fluid Mech. 27 257 292 10.1146/annurev.fl.27.010195. 001353
42. J Koplik JR Banavar 1995 Corner flow in the sliding plate problem Phys. Fluids 7 3118 3125 10.1063/1.868619
43. S Koshizuka Y Oka 1996 A particle method for incompressible viscous flow with fluid fragmentations Nucl. Sci. Eng. 123 421 434
44. S Kumar C Huang G Zheng E Bohm A Bhatele JC Phillips H Yu LV Kale 2008 Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system IBM J. Res. Dev. 52 177 188
45. AJC Ladd R Verberg 2001 Lattice-Boltzmann simulations of particle-fluid suspensions J. Statist. Phys. 104 1191 1251 10.1023/A:1010414013942
46. H Miyazaki T Yamaguchi 2003 Formation and destruction of primary thrombi under the influence of blood flow and von Willebrand factor analyzed by a discrete element method Biorheology 40 265 272 12454415
47. JJ Monaghan 1992 Smoothed particle hydrodynamics Ann. Rev. Astron. Astrophys. 30 543 574 10.1146/annurev.aa.30.090192.002551
48. D Mori K Yano K Tsubota T Ishikawa S Wada T Yamaguchi 2008 Computational study on effect of red blood cells on primary thrombus formation Thromb. Res. 123 114 121 10.1016/j.thromres.2008.03.006 18448151
49. D Mori K Yano K Tsubota T Ishikawa S Wada T Yamaguchi 2008 Simulation of platelet adhesion and aggregation regulated by fibrogen and von Willebrand factor Thromb. Heamost. 99 108 111
50. JD Moulton JE Dendy JM Hyman 1998 The black box multigrid numerical homogenization algorithm J. Comput. Phys. 142 80 108 10.1006/jcph.1998.5911
51. A Nakano ME Bachlechner TJ Campbell RK Kalla A Omeltchenko K Tsuruta P Vashishta S Ogata I Ebbsjo A Madhukar 1998 Atomistic simulation of nanostructured materials IEEE Comput. Sci. Eng. 5 68 78 10.1109/99.735897
52. MT Nelson W Humphrey A Gursoy A Dalke LV Kale RD Skeel K Schulten 1996 NAMD: a parallel, object oriented molecular dynamics program Int. J. Supercomput. Appl. 10 251 268 10.1177/109434209601000401
53. KJ Oh Y Deng 2007 An efficient parallel implementation of the smooth particle mesh Ewald method for molecular dynamics simulations Comp. Phys. Commun. 177 426 431 10.1016/j.cpc.2007.05.005
54. JC Phillips R Braun W Wang J Gumbart E Tajkhorshid E Villa C Chipot RD Skeel L Kale K Schulten 2005 Scalable molecular dynamics with NAMD J. Comput. Chem. 26 1781 1802 10.1002/jcc.20289 16222654
55. IV Pivkin GE Karniadakis 2006 Coarse-graining limits in open and wall-bounded dissipative particle dynamics systems J. Comput. Chem. 124 184101
56. IV Pivkin GE Karniadakis 2005 A new method to impose no-slip boundary conditions in dissipative particle dynamics J. Comput. Phys. 207 114 128 10.1016/j.jcp.2005.01.006
57. IV Pivkin PD Richardson G Karniadakis 2006 Blood flow velocity effects and role of activation delay time on growth and form of platelet thrombi Proc. Natl. Acad. Sci. USA. 103 17164 17169 10.1073/pnas.0608546103 17085579
58. SJ Plimpton B Hendrickson SP Burns W McLendon L Rauchwerger 2005 Parallel S-n sweeps on unstructured grids: Algorithms for prioritization, grid partitioning, and cycle detection Nucl. Sci. Eng. 150 267 283
59. C Pozrikidis 2005 Numerical simulation of cell motion in tube flow Ann. Biomed. Eng. 33 165 178 10.1007/s10439-005-8975-6 15771270
60. C Pozrikidis 2003 Numerical simulation of the flow-induced deformation of red blood cells Ann. Biomed. Eng. 31 1194 1205 10.1114/1.1617985 14649493
61. TZ Qian XP Wang 2005 Driven cavity flow: From molecular dynamics to continuum hydrodynamics Multiscale Model. Sim. 3 749 763 10.1137/040604868
62. M Revenga I Zuniga P Espanol 1999 Boundary conditions in dissipative particle dynamics Comp. Phys. Commun. 122 309 311 10.1016/S0010-4655(99)00341-0
63. C Sagui TA Darden 1999 Molecular dynamics simulations of biomolecules: long-range electrostatic effects Ann. Rev. Biophys. Biomol. Struct. 28 155 179 10.1146/annurev.biophys.28.1.155
64. KY Sanbonmatsu CS Tung 2007 High performance computing in biology: multimillion atom simulations of nanoscale systems J. Struct. Biol. 157 470 480 10.1016/j.jsb.2006.10.023 17187988
65. GW Schmid-Schonbein KR Diller 2005 Transport processes in biomedical systems: a roadmap for future research directions Ann. Biomed. Eng. 33 1136 1141 10.1007/s10439-005-5633-y 16133922
66. M Serrano P Espanol 2001 Thermodynamically consistent mesoscopic fluid particle model Phys. Rev. E Stat. Nonlin. Soft Matter. Phys. 64 2 046115 11690098
67. K Tsubota S Wada H Kamada Y Kitagawa R Lima T Yamaguchi 2006 A particle method for blood flow simulations-application to flowing red blood cells and platelets J. Earth Simulator 5 2 7
68. K Tsubota S Wada T Yamaguchi 2006 Particle method for computer simulation of red blood cell motion in blood flow Comput. Meth. Programs Biomed. 83 139 146 10.1016/j.cmpb.2006.06.005
69. K Tsubota S Wada T Yamaguchi 2006 Simulation study on effects of deformabilities of red blood cells on blood flow using particle method Trans. JSME B 72 1483 1489 (in Japanese)
70. K Tsubota S Wada T Yamaguchi 2006 Simulation study on effects of hematocrit on blood flow properties using particle method J. Biomech. Sci. Eng. 1 159 170 10.1299/jbse.1.159
71. K Yano D Mori K Tsubota S Wada T Yamaguchi 2007 Analysis of destruction process of the primary thrombus under the influence of the blood flow J. Biomech. Sci. Eng. 2 34 44 10.1299/jbse.2.34
72. F Zhu E Tajkhorshid K Schulten 2002 Pressure-induced water transport in membrane channels studied by molecular dynamics Biophys. J. 83 154 160 10.1016/S0006-3495(02)75157-6 12080108