Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations

Interface Focus

Volumn 3, Issue 2, 2013, Pages

  Groen, D ^a   Borgdorff, J ^b   Bona Casas, C ^b   Hetherington, J ^a   Nash, R W ^a   Zasada, S J ^a   Saverchenko, I ^c   Mamonski, M ^d   Kurowski, K ^d   Bernabeu, M O ^a   Hoekstra, A G ^b   Coveney, P V ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

^c LEIBNIZ SUPERCOMPUTING CENTRE   (Germany)

^d POZNAN SUPERCOMPUTING AND NETWORKING CENTER   (Poland)

Author keywords

Blood flow; Cerebrovascular bloodflow; Distributed computing; High performance computing; In stent restenosis; Multiscale modelling

Indexed keywords

EID: 84875429520     PISSN: 20428898     EISSN: 20428901     Source Type: Journal    
DOI: 10.1098/rsfs.2012.0087     Document Type: Article

References (44)

1. Sloot PMA, Hoekstra AG. 2010 Multi-scale modelling in computational biomedicine. Brief. Bioinform. 11, 142-152. (doi:10.1093/bib/bbp038)
2. Kohl P, Noble D. 2009 Systems biology and the virtual physiological human. Mol. Syst. Biol. 5, 292. (doi:10.1038/msb.2009.51)
3. Tahir H, Hoekstra AG, Lorenz E, Lawford PV, Hose DR, Gunn J, Evans DJW. 2011 Multi-scale simulations of the dynamics of in-stent restenosis: impact of stent deployment and design. Interface Focus 1, 365-373. (doi:10.1098/rsfs.2010. 0024)
4. Migliavacca F, Dubini G. 2005 Computational modeling of vascular anastomoses. Biomech. Model. Mechanobiol. 3, 235-250. (doi:10.1007/s10237-005-0070-2)
5. Obiol-Pardo C, Gomis-Tena J, Sanz F, Saiz J, Pastor M. 2011 A multiscale simulation system for the prediction of drug-induced cardiotoxicity. J. Chem. Inform. Model. 51, 483-492. (doi:10.1021/ ci100423z)
6. Noble D. 2002 Modeling the heart-from genes to cells to the whole organ. Science 295, 1678-1682. (doi:10.1126/science.1069881)
7. Finkelstein A, Hetherington J, Li L, Margoninski O, Saffrey P, Seymour R, Warner A. 2004 Computational challenges of systems biology. Computer 37, 26-33. (doi:10.1109/MC.2004. 1297236)
8. Hetherington J et al. 2007 Addressing the challenges of multiscale model management in systems biology. Comp. Chem. Eng. 31, 962-979. (doi:10.1016/j.compchemeng.2006.10.004)
9. Southern J, Pitt-Francis J, Whiteley J, Stokeley D, Kobashi H, Nobes R, Kadooka Y, Gavaghan D. 2008 Multi-scale computational modelling in biology and physiology. Progr. Biophys. Mol. Biol. 96, 60-89. (doi:10.1016/j.pbiomolbio.2007.07.019)
10. Hegewald J, Krafczyk M, Tölke J, Hoekstra A, Chopard B. 2008 An agent-based coupling platform for complex automata. In Proc. 8th Int. Conf. on Computational Science, Part II, ICCS '08, Kraków, Poland, June 23-25, 2008, pp. 227-233. Berlin, Germany: Springer.
11. Borgdorff J et al. 2012 A distributed multiscale computation of a tightly coupled model using the multiscale modeling language. Proc. Comp. Sci. 9, 596-605. (doi:10.1016/j.procs.2012.04.064)
12. Grinberg L, Morozov V, Fedosov D, Insley JA, Papka ME, Kumaran K, Karniadakis GE. 2011 A new computational paradigm in multiscale simulations: application to brain blood flow. In 2011 Int. Conf. for High Performance Computing, Networking, Storage and Analysis (SC), Seattle, WA, November 12-18, 2011, pp. 1-12. Washington, DC: IEEE Computer Society.
13. Ciepiela E, Harȩzlak D, Kocot J, Bartyński T, Kasztelnik M, Nowakowski P, Gubala T, Malawski M, Bubak M. 2010 Exploratory programming in the virtual laboratory. In Proc. 2010 Int. Multiconf. on Computer Science and Information Technology (IMCSIT), Wisła, Poland, October 18-20, 2010, pp. 621-628. Washington, DC: IEEE Computer Society.
14. Groen D, Zasada SJ, Coveney PV. 2012 Survey of multiscale and multiphysics applications and communities. See http://arxiv.org/abs/1208.6444.
15. Hucka M et al. 2003 The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531. (doi:10.1093/ bioinformatics/btg015)
16. Lloyd CM, Halstead MDB, Nielsen PF. 2004 CellML: its future, present and past. Progr. Biophys. Mol. Biol. 85, 433-450. (doi:10.1016/j.pbiomolbio.2004. 01.004)
17. Hoekstra AG, Lorenz E, Falcone J-L, Chopard B. 2007 Toward a complex automata formalism for multiscale modeling. Int. J. Multiscale Comp. Eng. 5, 491-502. (doi:10.1615/IntJMultCompEng. v5.i6.60)
18. Hoekstra AG, Caiazzo A, Lorenz E, Falcone J-L, Chopard B. 2010 Complex automata: multi-scale modeling with coupled cellular automata (Understanding complex systems), pp. 29-57. Berlin, Germany: Springer.
19. Evans DJW et al. 2008 The application of multiscale modelling to the process of development and prevention of stenosis in a stented coronary artery. Phil. Trans. R. Soc. A 366, 3343-3360. (doi:10. 1098/rsta.2008.0081)
20. Caiazzo A et al. 2011 A complex automata approach for in-stent restenosis: two-dimensional multiscale modeling and simulations. J. Comp. Sci. 2, 9-17. (doi:10.1016/j.jocs.2010.09.002)
21. Borgdorff J, Falcone J-L, Lorenz E, Chopard B, Hoekstra AG. 2011 A principled approach to distributed multiscale computing, from formalization to execution. In Proc. IEEE 7th Int. Conf. on e-Science Workshops, Stockholm, Sweden, 5-8 December, 2011, pp. 97-104. Stockholm, Sweden: IEEE Computer Society Press.
22. Falcone J-L, Chopard B, Hoekstra A. 2010 Mml: towards a multiscale modeling language. Proc. Comp. Sci. 1, 819-826. (doi:10.1016/j.procs.2010. 04.089)
23. Zasada SJ, Mamonski M, Groen D, Borgdorff J, Saverchenko I, Piontek T, Kurowski K, Coveney PV. 2012 Distributed infrastructure for multiscale computing. In Proc. 2012 IEEE/ACM 16th Int. Symp on Distributed Simulation and Real Time Applications, DS-RT '12, Dublin, Ireland, October 25-27, 2012, pp. 65-74. Washington, DC: IEEE Computer Society.
24. Groen D, Rieder S, Grosso P, de Laat C, Portegies Zwart P. 2010 A light-weight communication library for distributed computing. Comp. Sci. Disc. 3. (doi:10.1088/1749-4699/3/1/015002)
25. Groen D, Portegies Zwart S, Ishiyama T, Makino J. 2011 High performance gravitational N-body simulations on a planet-wide distributed supercomputer. Comp. Sci. Disc. 4, 015001. (doi:10. 1088/1749-4699/4/1/015001)
26. Kurowski K, Piontek T, Kopta P, Mamonski M, Bosak B. 2010 Parallel large scale simulations in the PLgrid environment. Computational Methods Sci Technolo, Special Issue 2010, pp. 47-56.
27. Zasada SJ, Coveney PV. 2009 Virtualizing access to scientific applications with the application hosting environment. Comp. Phys. Commun. 180, 2513-2525. (doi:10.1016/j.cpc.2009.06.008)
28. Suter J, Groen D, Kabalan L, Coveney PV. 2012 Distributed multiscale simulations of clay-polymer nanocomposites. In Materials Research Society Spring Meeting, vol. 1470, San Francisco, CA, April 9-13, 2012 (MRS Online Proceedings Library). Cambridge, UK: Cambridge University Press.
29. Ben Belgacem M, Chopard B, Parmigiani A. 2012 Coupling method for building a network of irrigation canals on a distributed computing environment. In Cellular automata (eds G Sirakoulis, S Bandini). Lecture Notes in Computer Science, vol. 7495, pp. 309-318. Berlin, Germany: Springer.
30. WHO, World Heart Federation; World Stroke Organization (ed.) 2012 Global atlas on cardiovascular disease prevention and control. Policies, strategies and interventions. Geneva, Switzerland: World Health Organization.
31. Moustapha A et al. 2001 Percutaneous and surgical interventions for in-stent restenosis: long-term outcomes and effect of diabetes mellitus. J. Am. College Cardiol. 37, 1877-1882. (doi:/10.1016/ S0735-1097(01)01231-1)
32. Kastrati A, Hall D, Schömig A. 2000 Long-term outcome after coronary stenting. Curr. Control. Trials Cardiovasc. Med. 1, 48-54. (doi:10.1186/CVM-1-1-048)
33. Jukema JW, Verschuren JJW, Ahmed TAN, Quax PHA. 2011 Restenosis after PCI. Part 1: pathophysiology and risk factors. Nat. Rev. Cardiol. 9, 53-62. (doi:10.1038/nrcardio.2011.132)
34. Shi Y, Lawford P, Hose R. 2011 Review of zero-d and 1-d models of blood flow in the cardiovascular system. Biomed. Eng. Online 10, 33. (doi:10.1186/ 1475-925X-10-33)
35. van de Vosse FN, Stergiopulos N. 2011 Pulse wave propagation in the arterial tree. Annu. Rev. Fluid Mech. 43, 467-499. (doi:10.1146/annurev-fluid-122109-160730)
36. Sughimoto K, Liang F, Takahara Y, Yamazaki K, Senzaki H, Takagi S, Liu H. In press. Assessment of cardiovascular function by combining clinical data with a computational model of the cardiovascular system. J. Thorac. Cardiovasc. Surg.
37. Alastruey J, Moore SM, Parker KH, David T, Peiró J, Sherwin SJ. 2008 Reduced modelling of blood flow in the cerebral circulation: coupling 1-d, 0-d and cerebral auto-regulation models. Int. J. Numer. Methods Fluids 56, 1061-1067. (doi:10.1002/ fld.1606)
38. Mazzeo MD, Coveney PV. 2008 HemeLB: a high performance parallel lattice-Boltzmann code for large scale fluid flow in complex geometries. Comp. Phys. Commun. 178, 894-914. (doi:10.1016/j.cpc. 2008.02.013)
39. Carver HB, Nash RW, Bernabeu MO, Hetherington J, Groen D, Krüger T, Coveney PV. Submitted. Choice of boundary condition and collision operator for lattice-Boltzmann simulation of moderate Reynolds number flow in complex domains. Phys. Rev. E. (http://arxiv.org/abs/1211.0205)
40. Botti L, Piccinelli M, Ene-Iordache B, Remuzzi A, Antiga L. 2010 An adaptive mesh refinement solver for large-scale simulation of biological flows. Int. J. Numer. Methods Biomed. Engi. 26, 86-100. (doi:/10.1002/cnm.1257)
41. Groen D, Hetherington J, Carver HB, Nash RW, Bernabeu MO, Coveney PV. 2012 Analyzing and modeling the performance of the HemeLB lattice-Boltzmann simulation environment. See http://arxiv. org/abs/1209.3972.
42. Mulder G, Bogaerds ACB, Rongen P, van de Vosse FN. 2011 The influence of contrast agent injection on physiological flow in the circle of willis. Med. Eng. Phys. 33, 195-203. (doi:10.1016/j. medengphy.2010.09.021)
43. Carver HB, Groen D, Hetherington J, Nash RW, Bernabeu MO, Coveney PV. 2012 Coalesced communication: a design pattern for complex parallel scientific software. See http://arxiv.org/abs/ 1210.4400.
44. Bernabeu MO, Nash RW, Groen D, Carver HB, Hetherington J, Krüger T, Coveney PV. 2013 Impact of blood rheology on wall shear stress in a model of the middle cerebral artery. Interface Focus 3, (doi:10.1098/rsfs.2012.0094)