Theses and Publications

Ph.D. Theses

Author Year Title Document
Christophe Charpilloz 2015 Analysis of large biological data: metabolic network modularization and prediction of N-terminal acetylation open access
Mohamed Ben Belgacem 2015 Distributed and multiscale computing for scientific applications open access
Ranaivo Razakanirina 2014 Dynamics on complex networks: application to abstract micro-economical models open access
Daniel Lagrava 2012 Revisiting grid refinement algorithms for the lattice Boltzmann method open access
Kae Tsunematsu 2012 New numerical solutions for the description of volcanic particle dispersal open access
Andrea Parmigiani 2011 Lattice Boltzmann calculations of reactive multiphase flows in porous media open access
Olivier Marcou 2010 Modélisation et contrôle d'écoulements à surface libre par la méthode de Boltzmann sur réseau open access
Jean-Luc Falcone 2008 Understanding signal sequences with machine learning open access
Bernhard Sonderegger 2007 The anâtaxis phylogenetic reconstruction algorithm open access
Davide Alemani 2007 A lattice Boltzmann numerical approach for modelling reaction-diffusion processes in chemically and physically heterogeneous environments open access
Jonas Latt 2007 Hydrodynamic limit of lattice Boltzmann equations open access
Hung Phi Nguyen 2007 Numerical simulations of the Lattice Boltzmann method for determination of hydrodynamic properties of fractal aggregates open access
Stefan Marconi 2003 Mesoscopical Modelling of Complex Systems PDF
Alexandre Dupuis 2002 From a lattice Boltzmann model to a parallel and reusable implementation of a virtual river PDF
Alexandre Masselot 2000 A new numerical approach to snow transport and deposition by wind : a parallel lattice gas model open access

M.Sc. Theses

Author Year Title Document
Xavier Meyer 2011 Standard simplex study and implementation on GPUs (French) PDF
Daniel Lagrava 2006 Access to Satellite Image Metadata on the Grid PDF
Didier Baertschiger 2006 Multi-Processing Template Library (French) PDF

Publications

  • Extensive list of publications can be found : here

2016

  • Ben Belgacem Mohamed and Bastien Chopard (2016), Muscle-HPC: a new High Performance API to couple multiscale parallel applications. Future Generation Computer Systems, 2016, DOI.
  • Aziza Merzouki, Orestis Malaspinas and Bastien Chopard (2016), The mechanical properties of a cell-based numerical model of epithelium. Soft Matter journal, V(12), pp:4745-4754, DOI, HTTP.

2015

  • Ranaivo Razakanirina and Bastien Chopard, Risk analysis and controllability of credit market, in ESAIM: Proceedings and Surveys, vol. 49, pp. 91-101. 2015. DOI
  • Mohamed Ben Belgacem and Nabil Abdennadher: Towards a high level programming paradigm to deploy e-science applications with dynamic workflows on large scale distributed systems. In The 15th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2015). IEEE Computer Society, pp. 292-301. DOI.
  • Ben Belgacem Mohamed and Abdennadher Nabil (2015), “A high level framework to develop and run e-science applications on Cloud infrastructures”, IEEE HPCC 2015, New York, USA, August 24 – 26, 2015 DOI.

2014

  • Charpilloz, C., Veuthey, A., Chopard, B., Falcone, J. (2014). Motifs tree: A new method for predicting post-translational modifications. Bioinformatics, 30(14), 1974-1982. DOI HTTP
  • Mohamed Ben Belgacem, Bastien Chopard (2014): A hybrid HPC/cloud distributed infrastructure: Coupling EC2 cloud resources with HPC clusters to run large tightly coupled multiscale applications. Journal of Future Generation Computer Systems. DOIHTTP
  • Mohamed Ben Belgacem, Bastien Chopard, Jonas Lätt and Andrea Parmigiania (2014): A Framework for Building a Network of Irrigation Canals on a Distributed Computing Environment: a case study. Journal of Cellular Automata (JCA), Special Issue. Vol.0, pp. 1-16.
  • J. Borgdorff, M. Mamonski, B. Bosak, K. Kurowski, M. Ben Belgacem, B. Chopard, D. Groen, P.V. Coveney, A.G. Hoekstra, Distributed multiscale computing with MUSCLE 2, the Multiscale Coupling Library and Environment, Journal of Computational Science, Available online 18 April 2014, ISSN 1877-7503. DOI HTTP
  • J. Borgdor ff, M. Ben Belgacem, C. Bona-Casas, L. Fazendeiro, D. Groen, O. Hoenen, A. Mizeranschi, J. L. Suter, D. Coster, P. V. Coveney, W. Dubitzky, A. G. Hoekstra, P. Strand and B. Chopard, Performance of Distributed Multiscale Simulations. Journal of Royal Society - Philosophical Transactions A 372: 20130407, DOI.
  • Mohamed Ben Belgacem and Abdennadher Nabil (2014), “Skeleton paradigm for developing e-science applications on distributed platforms”, The 6th IEEE International Workshop on Multicore and Multithreaded Architectures and Algorithms (M2A2 2014), IEEE Computer Society, 2014.

2013

  • Borgdorff, Joris and Falcone, Jean-Luc and Lorenz, Eric and Bona-Casas, Carles and Chopard, Bastien and Hoekstra, Alfons G., Foundations of distributed multiscale computing: Formalization, specification, and analysis, Journal of parallel and distributed computing, (2013), Volume 73, Number 4, Pages 465-483, DOI
  • Bastien Chopard, Pham van Thang and Laurent Lefevre, An asymmetric Lattice Boltzmann model for the 1D shallow water equation, Computers and Fluids, 88, (2013), pp. 225-231 DOI
  • Mohamed Ben Belgacem, Bastien Chopard, Joris Borgdorff, Mariusz Mamoński, Katarzyna Rycerz, Daniel HarezlakDistributed Multiscale Computations Using the MAPPER Framework, International Conference on Computational Science, (2013), Volume 18, Pages 1106–1115, DOI
  • Joris Borgdorff, Mariusz Mamonski, Bartosz Bosak, Derek Groen, Mohamed Ben Belgacem, Krzysztof Kurowski, Alfons G Hoekstra, Multiscale Computing with the Multiscale Modeling Library and Runtime Environment, Procedia Computer Science, (2013), Volume 18, Number 0, Pages 1097-1105, DOI
  • Olivier Marcou, Bastien Chopard, Samira El Yacoubi, Boussad Hamroun, Laurent Lefèvre and Eduardo Mendes, A Lattice Boltzmann model to study sedimentation phenomena in irrigation canals CiCP, vol 13(3), pp 880–899, (2013)
  • Joris Borgdorf, Jean-Luc Falcone, Eric Lorenz, Carles Bona-Casas, Bastien Chopard, Alfons G. Hoekstra, Foundations of Distributed Multiscale Computing: Formalization, Specification, Analysis and Execution J. of parallel and distributed computing, vol. 73 (2013), pp. 465-483, DOI
  • Andrea Parmigiani, Jonas Latt, Mohamed Ben Belgacem and Bastien Chopard, A Lattice Boltzmann simulation of the Rhone river, Int. J. Mod. Phys. C, 24(11):1340008, (2013)
  • Jonas Latt, Dimitrios Kontaxakis, Laurent Chatagny, Felix Muggli and Bastien Chopard Hybrid lattice Boltzmann method for the simulation of static mixers, Int. J. Mod. Phys. C, 24(11): 1340009, (2013)
  • G. Ionescu and B. Chopard. An agent-based model for the bibliometric h-index.. Eur. Phys. J. B 86:426, (2013) DOI
  • Ranaivo Razakanirina and Bastien Chopard, Dynamics of Artificial Markets on Irregular Topologies, in Proceedings of the European Conference on Complex Systems 2012, Brussel, 2013, pp. 1019–1031, DOI

2012

  • D. Lagrava, O. Malaspinas, J. Latt, B. Chopard, Advances in multi-domain lattice Boltzmann grid refinement, Journal of Computational Physics, Volume 231, Issue 14, (2012), 4808-4822, DOI, Preprint
  • Anna-Sapfo Malaspinas, Orestis Malaspinas, Steven N. Evans, and Montgomery Slatkin, Estimating Allele Age and Selection Coefficient from Time-Serial Data, Genetics, (2012), 192:599-607, 2012, DOI, Preprint
  • Mohamed Ben Belgacem, Bastien Chopard, Andrea Parmigiani, Coupling Method for Building a Network of Irrigation Canals on a Distributed Computing Environment, Cellular Automata, Lecture Notes in Computer Science, (2012), Volume 7495, Pages 309-318, DOI, link to PDF
  • Hitomi Anzai, Makoto Ohta, Jean-Luc Falcone, Bastien Chopard, Optimization of flow diverters for cerebral aneurysms J. of Computational Science, vol. 3 pp 1–7, (2012)
  • Ranaivo Razakanirina and Bastien Chopard Labour and Goods Market Dynamics Using an Abstract Microeconomical Model, Acta Physica Polinica B, Proceedings Supplement vol. 5 (2012) page 0131, DOI

2011

  • Xavier Meyer, Paul Albuquerque and Bastien Chopard, A multi-GPU implementation and performance model for the standard simplex method, submitted to the 17th International European Conference on Parallel and Distributed Computing (Euro-Par 2011), Preprint
  • O. Malaspinas, B. Chopard, J. Latt, General regularized boundary condition for multi-speed lattice Boltzmann models, Computers & Fluids, Volume 49, Issue 1, 2011, DOI, Preprint.
  • Tsunematsu, Kae and Chopard, Bastien and Falcone, Jean-Luc and Bonadonna, Costanza, Comparison of Two Advection-Diffusion Methods for Tephra Transport in Volcanic Eruptions, Communications in computational physics, (2011), Volume 9, Number 5, Pages 1323-1334, DOI
  • Alfonso Caiazzo, David Evans, Jean-Luc Falcone, Jan Hegewald, Eric Lorenz, Bernd Stahl, Dinan Wang, Joerg Bernsdorf, Bastien Chopard, Julian Gunn, Rod Hose, Manfred Krafczyk, Pat Lawford, Rod Smallwood, Dawn Walker, Alfons Hoekstra, A Complex Automata approach for In-stent Restenosis: two-dimensional multiscale modeling and simulations, J. of Comp. Sciences, (2011). DOI
  • C Huber, J. Dufek and B. Chopard, A simple algorithm to enfore Dirichlet boundary conditions in complex geometries. Int. J. M. Phys. C, vol 22(10), 1093–1105, (2011) DOI.
  • A. Parmigiani, C. Huber, O. Bachmann and B. Chopard. Pore-scale mass and reactant transport in multiphase porous media flows, Journal of Fluid Mechanics, volume 686, pp. 40-76, (2011).

2010

  • Ranaivo Mahaleo Razakanirina and Bastien Chopard, Using Cellular Automata on a Graph to Model the Exchanges of Cash and Goods, ACRI, (2010), S. Bandini et al. (Eds.): ACRI 2010, LNCS (6350), pp. 163–172, Springer-Verlag Berlin Heidelberg 2010, DOI, Preprint
  • Degruyter, W.; Burgisser, A.; Bachmann, O. & Malaspinas, O. Synchrotron X-ray microtomography and lattice Boltzmann simulations of gas flow through volcanic pumices, GEOSPHERE, (2010), 6, 470-481, DOI
  • Mohamed Ben Belgacem, Nabil Abdennadher and Marko Niinimaki, Virtual EZ Grid: A Volunteer Computing Infrastructure for Scientific Medical Applications, Advances in Grid and Pervasive Computing, Springer Berlin Heidelberg, (2010), Volume 6104, Pages 385-394, DOI
  • Christian Huber, Bastien Chopard and Michael Manga, A lattice Boltzmann model for coupled diffusion mixed diffusion, J. Comp. Phys. vol. 229, pp 7956-7976, (2010).
  • B. Stahl, B. Chopard and J. Latt, On the way to compute the wall-shear stress in LB models with first order boundary condition. Computer & Fluids, 39 pp. 1625-1633, (2010).
  • Pham van Thang, Bastien Chopard, Laurent Lefèvre, Diemer Anda Ondo, Eduardo Mendes, Study of the 1D lattice Boltzmann shallow water equation and its coupling to build a canal network, Journal of Computational Physics 229 (2010) 7373–7400, DOI