Papers

 

2013:

S. Zimny, B. Chopard, E. Lorenz, O. Malaspinas, S. Roller, J. Bernsdorf, K. Jain: "A multiscale approach for the coupled simulation of blood flow and thrombus formation in intracranial aneurysms", Proceedings of the 10th International Workshop on Modeling and Computing Multiscale Systems, Barcelona, 2013

K. Rycerz, M. Bubak,  E. Ciepiela, D. Harezlak, T. Gubala, J. Meizner, M. Pawlik: "Composing, Execution and Sharing of Multiscale Applications", submitted to Future Generation Computer Systems

T. Gubala, K. Prymula, P. Nowakowski, M. Bubak: "Semantic Integration for Model-based Life Science Applications". In: SIMULTECH 2013 Proceedings of the 3rd International Conference on Simulation and Modeling Methodologies, Technologies and Applications, Reykjavik, Iceland 29 - 31 July, 2013, pp. 74-81 (accompanying poster).

W. Funika, M. Janczykowski, K. Jopek, M. Grzegorczyk: "An Ontology-based Approach to Performance Monitoring of MUSCLE-bound Multi-scale Applications", Procedia Computer Science, Volume 18, 2013, pp. 1126-1135, ISSN 1877-0509.

M.B. Belgacem, B. Chopard, J. Borgdorff, M. Mamonski, K. Rycerz, D. Harezlak: "Distributed Multiscale Computations Using the MAPPER Framework", Proceedings of the 2013 International Conference on Computational Science, Vol. 18, pp. 1106-1115.

N. Kennedy, P. Thompson, O. Schmidt, W. Dubitzky: "Bile Acid and Xenobiotic System", in Dubitzky, Werner, Wolkenhauer, Olaf, Cho, Kwang-Hyun, Yokota, Hiroki (Eds.), Encyclopaedia of Systems Biology, Springer.

N. Kennedy, A. Mizeranschi, P. Thompson, H. Zheng, W. Dubitzky: "Reverse engineering of gene regulation models from multi-condition experiments", in Proceedings of the 10th Annual IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, Singapore.

N Kennedy, A. Mizeranschi, P. Thompson, H. Zheng, W. Dubitzky: "An ensemble approach to infer significant gene-regulatory networks structures from sparse gene transcription time-series data", submitted to BMC Bioinformatics.

A. E. Mizeranschi, N. Kennedy, R. Scona, Q. Fazilleau, M. T. Swain, P. Thompson, and W. Dubitzky: "Multiscale Reverse-Engineering of Gene Regulation Networks with MAPPER", submitted to Journal of Computational Science.

A. E. Mizeranschi, N. Kennedy, P. Thompson, and W. Dubitzky: "Multiscale Modelling and 2-Stage Reverse-Engineering of Gene Regulatory Networks", submitted to BMC Bioinformatics.

A. E. Mizeranschi, N. Kennedy, P. Thompson, and W. Dubitzky: "Multiscale Rverse-Engineering of Large-Scale Gene Regulatory Networks", submitted to Future Generation Computer Systems.

K. Rycerz, E. Ciepiela, G. Dyk, D. Groen, T. Gubala, D. Harezlak, M. Pawlik, J. Suter, S. Zasada, P. Coveney, M. Bubak: "Support for Multiscale Simulations with Molecular Dynamics", Proceedings of the International Conference on Computational Science 2013, Procedia Computer Science 18, 1116--1125.

J. Borgdorff, M. Mamonski, B. Bosak, D. Groen, M. Ben Belgacem, K. Kurowski, A.G. Hoekstra: "Multiscale computing with the multiscale modeling library and runtime environment", Proceedings of the International Conference on Computational Science 2013, Procedia Computer Science 18, 1097--1105.

R.W. Nash, H.B. Carver, M.O. Bernabeu, J. Hetherington, D. Groen, T. Krüger, P.V. Coveney: "Choice of boundary condition for lattice-Boltzmann simulation of moderate Reynolds number flow in complex domains", submitted to Physics Review E.
 
D. Groen, S. Rieder, S. Portegies Zwart: "MPWide: a light-weight library for efficient message passing over wide area networks", submitted to the Journal of Open Research Software.

H.B. Carver, D. Groen, J. Hetherington, R.W. Nash, M.O. Bernabeu, P.V. Coveney: "Coalesced communication: a design pattern for complex parallel scientific software", submitted to Advances in Engineering Software.

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 the multiscale modeling library and runtime environment", submitted to the Journal of Computational Science.

D. Groen, J. Hetherington, H. B. Carver, R. W. Nash, M. O. Bernabeu, P. V. Coveney: "Analyzing and Modeling the Performance of the HemeLB Lattice-Boltzmann Simulation Environment", Journal of Computational Science (in press)

D. Groen, S. Zasada, P.V. Coveney. "Survey of Multiscale and Multiphysics Applications and Communities", accepted by IEEE Computing in Science and Engineering.

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. "Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations", Interface Focus 3: 20120087.

M. O. Bernabeu, R. W. Nash, D. Groen, H. B. Carver, J. Hetherington, T. Krueger and P. V. Coveney. "Impact of blood rheology on wall shear stress in a model of the middle cerebral artery", Interface Focus 3: 20120094.

Joris Borgdorff, Jean-Luc Falcone, Eric Lorenz, Carles Bona-Casas, Bastien Chopard, Alfons G. Hoekstra. "Foundations of distributed multiscale computing: Formalization, specification, and analysis", Journal of Parallel and Distributed Computing 73 (2013) pp. 465-483

2012:

Mohamed Ben Belgacem, Bastien Chopard and Andrea Parmigiani. "Coupling Method for Building a Network of Irrigation Canals on a Distributed Computing Environment", Proceedings of the 10th International Conference on Cellular Automata for Research and Industry, ACRI 2012, Santorini Island, Greece, September 24-27, 2012. Springer LNCS 7495.

Andrea Parmigiani, Jonas Latt, Mohamed Ben Belgacem and Bastien Chopard. "A Lattice Boltzmann simulation of the Rhone river", submitted to the International Journal of Modern Physics C.

K. Rycerz, E. Ciepiela, D. Harezlak, T. Gubała, G. Dyk, J. Meizner, M. Bubak, J. Borgdorff, and A. G. Hoekstra. An Environment for Programming and Execution of Multiscale Applications. ACM Transactions on Modeling and Computer Simulation (in review)

K. Rycerz, D. Harężlak, G. Dyk, E. Ciepiela, T. Gubała, J. Meizner, and M. Bubak. Programming and Execution of Multiscale Applications. submitted to Cracow Grid Workshop 2012, 22-24 October 2012, Kraków, Poland

B. Bodziechowski, E. Ciepiela, M. Bubak. Assessment of Software Quality with Static Source Code Analysis: GridSpace2 Case Study. submitted to Cracow Grid Workshop 2012, 22-24 October 2012, Kraków, Poland

J. Borgdorff, C. Bona-Casas, M. Mamonski, K. Kurowski, T. Piontek, B. Bosak, K. Rycerz, et al. (2012). A Distributed Multiscale Computation of a Tightly Coupled Model Using the Multiscale Modeling Language. Procedia Computer Science, 9, 596–605. Presented at ICCS 2012. doi:10.1016/j.procs.2012.04.064

S. Zasada, M. Mamonski, D. Groen, J. Borgdorff, I. Saverchenko, T. Piontek, et al.: "Distributed Infrastructure for Multiscale Computing", Proceedings of the 2012 IEEE/ACM 16th International Symposium on Distributed Simulation and Real Time Applications, pp. 65--74.

D. Groen, J. Borgdorff, S. Zasada, C. Bona-Casas, J. Hetherington, R. Nash, A. Hoekstra, P. Coveney, A Distributed Infrastructure for Multiscale Biomedical Simulations, Virtual Physiological Human Conference 2012.

J. Suter, D. Groen, L. Kabalan and P. Coveney: Distributed Multiscale Simulations of Clay-Polymer Nanocomposites, Materials Research Symposium, San Francisco, United States of America, April 2012.

2011:

N. Kennedy, P. Thompson, H. Zheng and W. Dubitzky: "Multi-Scale modelling of the Bile Acid and Xenobiotic System", in Proceedings of the 2011 International Conference on Bioinformatics & Computational Biology, USA, 2011.

J. Borgdorff, J. Falcone, E. Lorenz, B. Chopard, and A. Hoekstra: A principled approach to Distributed Multiscale Computing, from formalization to execution, In Proceedings of The Seventh IEEE International Conference on e-Science Workshops, Stockholm, Sweden, 5-8 December 2011.  IEEE Computer Society, Washington, DC, USA, 97 - 104, 2011. doi:10.1109/eScienceW.2011.9

D. Groen, J. Suter, P. Coveney: Modelling Distributed Multiscale Simulation Performance: An Application to Nanocomposites, In Proceedings of The Seventh IEEE International Conference on e-Science Workshops, Stockholm, Sweden, 5-8 December 2011.  IEEE Computer Society, Washington, DC, USA, 105 - 111, 2011. doi:10.1109/eScienceW.2011.37

D. Groen, S. Zasada, P. Coveney: Taxonomy of Multiscale Computing Communities, In Proceedings of The Seventh IEEE International Conference on e-Science Workshops, Stockholm, Sweden, 5-8 December 2011.  IEEE Computer Society, Washington, DC, USA, 120 - 127, 2011. doi:10.1109/eScience.2011.11

K. Rycerz and M. Bubak: Building and Running Collaborative Distributed Multiscale Applications. In: W. Dubitzky, K. Kurowsky, B. Schott (Eds) Large-Scale Computing Techniques for Complex System Simulations, Chapter 6, pp. 111-130. J. Wiley and Sons, 2011 http://www.wiley-vch.de/publish/en/books/ISBN978-0-470-59244-1

K. Rycerz, M. Nowak, P. Pierzchala, M. Bubak, E. Ciepiela and D. Harezlak: Comparision of Cloud and Local HPC approach for MUSCLE-based Multiscale Simulations. In Proceedings of The Seventh IEEE International Conference on e-Science Workshops, Stockholm, Sweden, 5-8 December 2011. IEEE Computer Society, Washington, DC, USA, 81-88, 2011. doi:10.1109/eScienceW.2011.21

K. Rycerz, M. Bubak: Component Approach to Distributed Multiscale Simulations. In: Proc. SIMULTECH 2011, 1st International Conference on Simulation, Modeling Technologies and Applications, July 29-31, 2011, Noordwijkerhout, The Netherlands, pp. 122 - 127 (2011)

S. Zasada, D. Groen, P. coveney: Developing an infrastructure to support multiscale modelling and simulation. Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery, Article No. 30, July 17-21, 2011.

K. Rycerz, E. Ciepiela, J. Kocot, M. Nowak, P. Pierzchała, M. Bubak: Towards an Environment for Multiscale Applications, abstract at KUKDM in Zakopane, Poland, 2011