Multiscale modeling: recent progress and open questions

Alowayyed S, Groen D, Coveney PV, Hoekstra A (2017) Multiscale computing in the exascale era. J Comput Sci 22:15–25. https://doi.org/10.1016/j.jocs.2017.07.004

Alowayyed S, Piontek T, Suter JL, Hoenen O, Groen D, Luk OO, Bosak B, Kopta P, Kurowski K, Perks O, Brabazon K, Jancauskas V, Coster D, Coveney PV, Hoekstra AG (2017) Patterns for high performance multiscale computing. Future Gener Comput Syst

Blegacem MB, Chopard B (2015) A hybrid HPC/cloud distributed infrastructure: coupling EC2 cloud resources with HPC clusters to run large tightly coupled multiscale applications. Future Gener Comput Syst. https://doi.org/10.1016/j.future.2014.08.003

Belgacem MB, Chopard B (2016) Muscle-hpc: a new high performance api to couple multiscale parallel applications. Future Gener Comput Syst 67:72–82. https://doi.org/10.1016/j.future.2016.08.009

Belgacem M Ben, Chopard B, Borgdorff J, Mamonski M, Rycerz K, Harezlak D (2013a) Distributed multiscale computations using the MAPPER framework. Procedia Comput Sci 18:1106–1115. https://doi.org/10.1016/j.procs.2013.05.276

Borgdorf J, Falcone JL, Lorenz E, Bona-Casas C, Chopard B, Hoekstra AG (2013b) Foundations of distributed multiscale computing: formalization, specification, analysis and execution. J Parallel Distrib Comput 73:465–483

Borgdorff J, Mamonski M, Bosak B, Groen D, Belgacem MB, Kurowski K, Hoekstra AG (2013c) Distributed multiscale computing with the multiscale modeling library and runtime environment. Procedia Comput Sci 18:1097–1105

Borgdorff J, Mamonski M, Bosak B, Groen D, Belgacem MB, Kurowski K, Hoekstra AG (2013) Multiscale computing with the multiscale modeling library and runtime environment. Procedia Comput Sci 18(0):1097–1105. https://doi.org/10.1016/j.procs.2013.05.275 . http://www.sciencedirect.com/science/article/pii/S1877050913004183

Borgdorff J, Belgacem MB, Bona-Casas C, Fazendeiro L, Groen D, Hoenen O, Mizeranschi A, Suter JL, Coster D, Coveney PV, Dubitzky W, Hoekstra AG, Strand P, Chopard B (2014) Performance of distributed multiscale simulations. Philos Trans A 372(2021):20130407

Caiazzo A, Falcone JL, Chopard B, Hoekstra AG (2009) Asymptotic analysis of complex automata models for reaction-diffusion systems. Appl Numer Math 59(8):2023–2034

Chopard B, Borgdorff J, Hoekstra AG (2014) A framework for multiscale modeling. Philos Trans A 372:20130,376

Dada JO, Mendes P (2011) Multi-scale modelling and simulation in systems biology. Integr Biol 3(2):86–96

Evans D, Lawford PV, Gunn J, Walker D, Hose DR, Smallwood R, Chopard B, Krafczyk M, Bernsdorf J, Hoekstra A (2008) The application of multi-scale modelling to the process of development and prevention of stenosis in a stented coronary artery. Philos Trans R Soc 366:3343–3360

Falcone JL, Chopard B, Hoekstra A (2010) MML: towards a multiscale modeling language. Procedia Comput Sci 1(11):819–826

Groen D, Borgdorff J, Bona-Casas C, Hetherington J, Nash RW, Zasada SJ, Saverchenko I, Mamonski M, Kurowski K, Bernabeu MO, Hoekstra AG, Coveney PV (2013) Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations. Interface Focus 3(2):20120087

Groen D, nad James Suter APB, Hetherington J, Zasada SJ, Coveney PV (2016) Fabsim: facilitating computational research through automation on large-scale and distributed e-infrastructures. Comput Phys Commun. https://doi.org/10.1016/j.cpc.2016.05.020

Hoekstra AG et al (2016) Towards the virtual artery: a multiscale model for vascular physiology at the pcb interface. Philos Trans R Soc A 374(0160):146. https://doi.org/10.1098/rsta.2016.0146

Hoekstra AG, Caiazzo A, Lorenz E, Falcone JL, Chopard B (2010) Modelling complex systems by cellular automata, chap. 3. Springer, Berlin

Hoekstra AG, Coveney P, Chopard B (2014) Position a paper on multiscale modeling and computing. Philos Trans A 372:20130377

Ingram G, Cameron I, Hangos K (2004) Classification and analysis of integrating frameworks in multiscale modelling. Chem Eng Sci 59:2171–2187

Künzli P, Tsunematsu K, Albuquerque P, Falcone JL, Chopard B, Bonadonna C (2016) Parallel simulation of particle transport in an advection field applied to tephra dispersal. Comput GeoSci 89:174–185

Lorenz E, Hoekstra A (2011) Heterogeneous multiscale simulations of suspension flow. Multiscale Model Simul 9:1301–1326

Malaspinas O, Turjman A, de Souza DR, Garcia-Cardena G, Raes M, Nguyen PTT, Zhang Y, Courbebaisse G, Lelubre C, Boudjelti KZ, Chopard B (2016) A spatio-temporal model for spontaneous thrombus formation in cerebral aneurysms. J Theor Biol 394:68–76

Merks RMH, Hoekstra AG, Kaandorp JA, Sloot PMA (2003) Models of coral growth: spontaneous branching, compactification and the laplacian growth assumption. J Theor Biol 224:153–166

Nikishovay A, Hoekstra A (2017) Semi-intrusive uncertainty quantification for multiscale models. SIAM J. Uncertain Quantif

Piontek T, Bosak B, Cinicki M, Grabowski P, Kopta P, Kulczewski M, Szejnfeld D, Kurowski K (2016) Development of science gateways using qcglessons learned from the deployment on large scale distributed and hpc infrastructures. J Grid Comput 14:559–573

Tahir H, Hoekstra A, Lorenz E, Lawford P, Hose D, Gunn J, Evans D (2011) Multiscale simulations of the dynamics of in-stent restenosis: impact of stent deployment and design. Interface Focus 1:365–367

Tahir H, Casas CB, Hoekstra A (2013) Modelling the effect of a functional endothelium on the development of in-stent restenosis. PLoS ONE 8(e66):138

Weinan E, Li X, Ren W, Vanden-Eijnden E (2007) Heterogeneous multiscale methods. A review. Commun Comput Phys 2:367–450

Yang A, Marquardt W (2009) An ontological conceptualizatin of multiscale models. Comput. Chem. Eng. 33:822–837