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ISSN Печать: 1543-1649
ISSN Онлайн: 1940-4352
Indexed in
Toward a Complex Automata Formalism for MultiScale Modeling
Краткое описание
Complex Automata were recently proposed as a paradigm to model multiscale complex systems. The concept is formalized and the scale separation map is further investigated in relation with its capability to specify the components of Complex Automata. Five classes of scale separation are identified, each potentially giving rise to a specific multiscale modeling paradigm. By introducing a generic submodel execution loop we identify multiscale coupling templates for each of the five regions. We show the relation between these templates and some multiscale models reported in the literature. Finally, a number of canonical examples are briefly discussed.
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Sloot P. M.A., Hoekstra A. G., Multi-scale modelling in computational biomedicine, Briefings in Bioinformatics, 11, 1, 2010. Crossref
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Walker D. C., Southgate J., The virtual cell--a candidate co-ordinator for 'middle-out' modelling of biological systems, Briefings in Bioinformatics, 10, 4, 2009. Crossref
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Evans D.J.W, Lawford P.V, Gunn J, Walker D, Hose D.R, Smallwood R.H, Chopard B, Krafczyk M, Bernsdorf J, Hoekstra A, The application of multiscale modelling to the process of development and prevention of stenosis in a stented coronary artery, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 366, 1879, 2008. Crossref
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Caiazzo Alfonso, Evans David, Falcone Jean-Luc, Hegewald Jan, Lorenz Eric, Stahl Bernd, Wang Dinan, Bernsdorf Jörg, Chopard Bastien, Gunn Julian, Hose Rod, Krafczyk Manfred, Lawford Pat, Smallwood Rod, Walker Dawn, Hoekstra Alfons, A Complex Automata approach for in-stent restenosis: Two-dimensional multiscale modelling and simulations, Journal of Computational Science, 2, 1, 2011. Crossref
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Dada Joseph O., Mendes Pedro, Multi-scale modelling and simulation in systems biology, Integrative Biology, 3, 2, 2011. Crossref
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Halliday I., Atherton M., Care C.M., Collins M.W., Evans D., Evans P.C., Hose D.R., Khir A.W., König C.S., Krams R., Lawford P.V., Lishchuk S.V., Pontrelli G., Ridger V., Spencer T.J., Ventikos Y., Walker D.C., Watton P.N., Multi-scale interaction of particulate flow and the artery wall, Medical Engineering & Physics, 33, 7, 2011. Crossref
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Lawford P.V., Ventikos Y., Khir A.W., Atherton M., Evans D., Hose D.R., Care C.M., Watton P.N., Halliday I., Walker D.C., Hollis A.P., Collins M.W., Modelling the interaction of haemodynamics and the artery wall: Current status and future prospects, Biomedicine & Pharmacotherapy, 62, 8, 2008. Crossref
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Bernsdorf Jörg, Wang Dinan, Berti Guntram, Two Complementary Approaches for Integrating a Lattice Boltzmann Flow Solver into Simulation Frameworks, Procedia Computer Science, 4, 2011. Crossref
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Caiazzo Alfonso, Falcone Jean-Luc, Chopard Bastien, Hoekstra Alfons G., Asymptotic analysis of Complex Automata models for reaction–diffusion systems, Applied Numerical Mathematics, 59, 8, 2009. Crossref
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Falcone Jean-Luc, Chopard Bastien, Hoekstra Alfons, MML: towards a Multiscale Modeling Language, Procedia Computer Science, 1, 1, 2010. Crossref
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Rycerz Katarzyna, Bubak Marian, Building and Running Collaborative Distributed Multiscale Applications, in Large-Scale Computing, 2012. Crossref
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Groen D., Borgdorff J., Bona-Casas C., Hetherington J., Nash R. W., Zasada S. J., Saverchenko I., Mamonski M., Kurowski K., Bernabeu M. O., Hoekstra A. G., Coveney P. V., Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations, Interface Focus, 3, 2, 2013. Crossref
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Borgdorff Joris, Falcone Jean-Luc, Lorenz Eric, Bona-Casas Carles, Chopard Bastien, Hoekstra Alfons G., Foundations of distributed multiscale computing: Formalization, specification, and analysis, Journal of Parallel and Distributed Computing, 73, 4, 2013. Crossref
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van der Sman R.G.M., Vergeldt F.J., Van As H., van Dalen G., Voda A., van Duynhoven J.P.M., Multiphysics pore-scale model for the rehydration of porous foods, Innovative Food Science & Emerging Technologies, 24, 2014. Crossref
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Borgdorff J., Ben Belgacem M., Bona-Casas C., Fazendeiro L., Groen D., Hoenen O., Mizeranschi A., Suter J. L., Coster D., Coveney P. V., Dubitzky W., Hoekstra A. G., Strand P., Chopard B., Performance of distributed multiscale simulations, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 372, 2021, 2014. Crossref
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van der Sman R G M, Broeze J, Multiscale analysis of structure development in expanded starch snacks, Journal of Physics: Condensed Matter, 26, 46, 2014. Crossref
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Borgdorff J., Mamonski M., Bosak B., Kurowski K., Ben Belgacem M., Chopard B., Groen D., Coveney P.V., Hoekstra A.G., Distributed multiscale computing with MUSCLE 2, the Multiscale Coupling Library and Environment, Journal of Computational Science, 5, 5, 2014. Crossref
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Hoekstra Alfons, Chopard Bastien, Coveney Peter, Multiscale modelling and simulation: a position paper, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 372, 2021, 2014. Crossref
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Borgdorff Joris, Lorenz Eric, Hoekstra Alfons G., Falcone Jean-Luc, Chopard Bastien, A Principled Approach to Distributed Multiscale Computing, from Formalization to Execution, 2011 IEEE Seventh International Conference on e-Science Workshops, 2011. Crossref
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Rycerz Katarzyna, Nowak Marcin, Pierzchala Pawel, Ciepiela Eryk, Harezlak Daniel, Bubak Marian, Comparison of Cloud and Local HPC Approach for MUSCLE-based Multiscale Simulations, 2011 IEEE Seventh International Conference on e-Science Workshops, 2011. Crossref
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Bernsdorf Jorg, Berti Guntram, Chopard Bastien, Hegewald Jan, Krafczyk Manfred, Wang Dinan, Lorenz Eric, Hoekstra Alfons, Towards Distributed Multiscale Simulation of Biological Processes, 2011 IEEE Seventh International Conference on e-Science Workshops, 2011. Crossref
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Hoekstra Alfons G., Alowayyed Saad, Lorenz Eric, Melnikova Natalia, Mountrakis Lampros, van Rooij Britt, Svitenkov Andrew, Závodszky Gábor, Zun Pavel, Towards the virtual artery: a multiscale model for vascular physiology at the physics–chemistry–biology interface, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 374, 2080, 2016. Crossref
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Liniov Alexey, Kustikova Valentina, Sysoyev Alexander, Zhiltsov Maxim, Polyakov Igor, Nasonov Denis, Butakov Nikolay, Architecture of Middleware to Provide the Multiscale Modelling Using Coupling Templates, in Supercomputing, 793, 2017. Crossref
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Nolan D., Lally C., Coupled Finite Element–Agent-Based Models for the Simulation of Vascular Growth and Remodeling, in Numerical Methods and Advanced Simulation in Biomechanics and Biological Processes, 2018. Crossref
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Chopard Bastien, Falcone Jean-Luc, Hoekstra Alfons G., Borgdorff Joris, A Framework for Multiscale and Multiscience Modeling and Numerical Simulations, in Unconventional Computation, 6714, 2011. Crossref
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Kovalenko Andriy, Gusarov Sergey, Multiscale methods framework: self-consistent coupling of molecular theory of solvation with quantum chemistry, molecular simulations, and dissipative particle dynamics, Physical Chemistry Chemical Physics, 20, 5, 2018. Crossref
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Alowayyed S., Piontek T., Suter J.L., Hoenen O., Groen D., Luk O., Bosak B., Kopta P., Kurowski K., Perks O., Brabazon K., Jancauskas V., Coster D., Coveney P.V., Hoekstra A.G., Patterns for High Performance Multiscale Computing, Future Generation Computer Systems, 91, 2019. Crossref
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Hoekstra Alfons G., Caiazzo Alfonso, Lorenz Eric, Falcone Jean-Luc, Chopard Bastien, Complex Automata: Multi-scale Modeling with Coupled Cellular Automata, in Simulating Complex Systems by Cellular Automata, 2010. Crossref
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Groen Derek, Knap Jaroslaw, Neumann Philipp, Suleimenova Diana, Veen Lourens, Leiter Kenneth, Mastering the scales: a survey on the benefits of multiscale computing software, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 377, 2142, 2019. Crossref
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Caiazzo Alfonso, Falcone Jean Luc, Chopard Bastien, Hoekstra Alfons G., Scale-Splitting Error in Complex Automata Models for Reaction-Diffusion Systems, in Computational Science – ICCS 2008, 5102, 2008. Crossref
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Chopard Bastien, Falcone Jean-Luc, Razakanirina Ranaivo, Hoekstra Alfons, Caiazzo Alfonso, On the Collision-Propagation and Gather-Update Formulations of a Cellular Automata Rule, in Cellular Automata, 5191, 2008. Crossref
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Ben Belgacem Mohamed, Chopard Bastien, Parmigiani Andrea, Coupling Method for Building a Network of Irrigation Canals on a Distributed Computing Environment, in Cellular Automata, 7495, 2012. Crossref
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Hoekstra Alfons G., Falcone Jean-Luc, Caiazzo Alfonso, Chopard Bastien, Multi-scale Modeling with Cellular Automata: The Complex Automata Approach, in Cellular Automata, 5191, 2008. Crossref
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Caiazzo Alfonso, Falcone Jean Luc, Chopard Bastien, Hoekstra Alfons G., Error Investigations in Complex Automata Models for Reaction-Diffusion Systems, in Cellular Automata, 5191, 2008. Crossref
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Tsunematsu Kae, Falcone Jean-Luc, Bonadonna Costanza, Chopard Bastien, Applying a Cellular Automata Method for the Study of Transport and Deposition of Volcanic Particles, in Cellular Automata, 5191, 2008. Crossref
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Chopard Bastien, Cellular Automata and Lattice Boltzmann Modeling of Physical Systems, in Handbook of Natural Computing, 2012. Crossref
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Borgdorff Joris, Mamonski Mariusz, Bosak Bartosz, Groen Derek, Belgacem Mohamed Ben, Kurowski Krzysztof, Hoekstra Alfons G., Multiscale Computing with the Multiscale Modeling Library and Runtime Environment, Procedia Computer Science, 18, 2013. Crossref
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Belgacem Mohamed Ben, Chopard Bastien, Borgdorff Joris, Mamoński Mariusz, Rycerz Katarzyna, Harezlak Daniel, Distributed Multiscale Computations Using the MAPPER Framework, Procedia Computer Science, 18, 2013. Crossref
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Yang Aidong, On the Common Conceptual and Computational Frameworks for Multiscale Modeling, Industrial & Engineering Chemistry Research, 52, 33, 2013. Crossref
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Caiazzo Alfonso, Evans David, Falcone Jean-Luc, Hegewald Jan, Lorenz Eric, Stahl Bernd, Wang Dinan, Bernsdorf Jörg, Chopard Bastien, Gunn Julian, Hose Rod, Krafczyk Manfred, Lawford Patricia, Smallwood Rod, Walker Dawn, Hoekstra Alfons G., Towards a Complex Automata Multiscale Model of In-Stent Restenosis, in Computational Science – ICCS 2009, 5544, 2009. Crossref