Bastien Chopard

University of Geneva, Genève, Geneva, Switzerland

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Publications (197)267.71 Total impact

  • Entropy 05/2015; 17(5):2606-2623. DOI:10.3390/e17052606 · 1.56 Impact Factor
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    ABSTRACT: We present performance results from ficsion, a general purpose parallel suspension solver, employing the Immersed-Boundary lattice-Boltzmann method (IB-LBM). ficsion is build on top of the open-source LBM framework Palabos, making use of its data structures and their inherent parallelism. We describe in brief the implementation and present weak and strong scaling results for simulations of dense red blood cell suspensions. Despite its complexity the simulations demonstrate a fairly good, close to linear scaling, both in the weak and strong scaling scenarios.
    Journal of Computational Science 04/2015; 9. DOI:10.1016/j.jocs.2015.04.006 · 1.57 Impact Factor
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    ABSTRACT: We discuss how maximum entropy methods may be applied to the reconstruction of Markov processes underlying empirical time series and compare this approach to usual frequency sampling. It is shown that, at least in low dimension, there exists a subset of the space of stochastic matrices for which the MaxEnt method is more efficient than sampling, in the sense that shorter historical samples have to be considered to reach the same accuracy. Considering short samples is of particular interest when modelling smoothly non-stationary processes, for then it provides, under some conditions, a powerful forecasting tool. The method is illustrated for a discretized empirical series of exchange rates.
    EPL (Europhysics Letters) 11/2014; 110(1). DOI:10.1209/0295-5075/110/10003 · 2.27 Impact Factor
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    ABSTRACT: We present the Multiscale Coupling Library and Environment: MUSCLE 2. This multiscale component-based execution environment has a simple to use Java, C++, C, Python and Fortran API, compatible with MPI, OpenMP and threading codes. We demonstrate its local and distributed computing capabilities and compare its performance to MUSCLE 1, file copy, MPI, MPWide, and GridFTP. The local throughput of MPI is about two times higher, so very tightly coupled code should use MPI as a single submodel of MUSCLE 2; the distributed performance of GridFTP is lower, especially for small messages. We test the performance of a canal system model with MUSCLE 2, where it introduces an overhead as small as 5% compared to MPI.
    Journal of Computational Science 09/2014; 5(5):719–731. DOI:10.1016/j.jocs.2014.04.004 · 1.57 Impact Factor
  • Alfons Hoekstra, Bastien Chopard, Peter Coveney
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    ABSTRACT: We argue that, despite the fact that the field of multiscale modelling and simulation has enjoyed significant success within the past decade, it still holds many open questions that are deemed important but so far have barely been explored. We believe that this is at least in part due to the fact that the field has been mainly developed within disciplinary silos. The principal topics that in our view would benefit from a targeted multidisciplinary research effort are related to reaching consensus as to what exactly one means by 'multiscale modelling', formulating a generic theory or calculus of multiscale modelling, applying such concepts to the urgent question of validation and verification of multiscale models, and the issue of numerical error propagation in multiscale models. Moreover, we believe that this would, in principle, also lay the foundation for more efficient, well-defined and usable multiscale computing environments. We believe that multidisciplinary research to fill in the gaps is timely, highly relevant, and with substantial potential impact on many scientific disciplines.
    Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences 08/2014; 372(2021). DOI:10.1098/rsta.2013.0377 · 2.86 Impact Factor
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    ABSTRACT: Multiscale simulations model phenomena across natural scales using monolithic or component-based code, running on local or distributed resources. In this work, we investigate the performance of distributed multiscale computing of component-based models, guided by six multiscale applications with different characteristics and from several disciplines. Three modes of distributed multiscale computing are identified: supplementing local dependencies with large-scale resources, load distribution over multiple resources, and load balancing of small- and large-scale resources. We find that the first mode has the apparent benefit of increasing simulation speed, and the second mode can increase simulation speed if local resources are limited. Depending on resource reservation and model coupling topology, the third mode may result in a reduction of resource consumption.
    Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences 08/2014; 372(2021). DOI:10.1098/rsta.2013.0407 · 2.86 Impact Factor
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    Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences 08/2014; 372(2021). DOI:10.1098/rsta.2013.0390 · 2.86 Impact Factor
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    ABSTRACT: We review a methodology to design, implement and execute multi-scale and multi-science numerical simulations. We identify important ingredients of multi-scale modelling and give a precise definition of them. Our framework assumes that a multi-scale model can be formulated in terms of a collection of coupled single-scale submodels. With concepts such as the scale separation map, the generic submodel execution loop (SEL) and the coupling templates, one can define a multi-scale modelling language which is a bridge between the application design and the computer implementation. Our approach has been successfully applied to an increasing number of applications from different fields of science and technology.
    Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences 08/2014; 372(2021). DOI:10.1098/rsta.2013.0378 · 2.86 Impact Factor
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    ABSTRACT: We discuss a characterization of complexity based on successive approximations of the probability density describing a system by means of maximum entropy methods, thereby quantifying the respective role played by different orders of interaction. This characterization is applied on simple cellular automata in order to put it in perspective with the usual notion of complexity for such systems based on Wolfram classes. The overlap is shown to be good, but not perfect. This suggests that complexity in the sense of Wolfram emerges as an intermediate regime of maximum entropy-based complexity, but also gives insights regarding the role of initial conditions in complexity-related issues.
  • Hitomi Anzai, Bastien Chopard, Makoto Ohta
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    ABSTRACT: Stent insertion for cerebral aneurysm has been studied using ideal and realistic aneurysms in recent years. Stent insertion aims at reducing the flow in an aneurysm. To minimize the average velocity in an aneurysm, we applied optimization to the strut position in a realistic aneurysm based on computational fluid dynamics. The result shows the effect on velocity reduction of strut placement in the inflow area.
    Journal of Flow Control, Measurement & Visualization 04/2014; 2(2):67-77. DOI:10.4236/jfcmv.2014.22009
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    ABSTRACT: Background: A modern technique for the treatment of cerebral aneurysms involves insertion of a flow diverter stent. Flow stagnation, produced by the fine mesh structure of the diverter, is thought to promote blood clotting in an aneurysm. However, apart from its effect on flow reduction, the insertion of the metal device poses the risk of occlusion of a parent artery. One strategy for avoiding the risk of arterial occlusion is the use of a device with a higher porosity. To aid the development of optimal stents in the view point of flow reduction maintaining a high porosity, we used lattice Boltzmann flow simulations and simulated annealing optimization to investigate the optimal placement of stent struts. Method: We constructed four idealized aneurysm geometries that resulted in four different inflow characteristics and employed a stent model with 36 unconnected struts corresponding to the porosity of 80%. Assuming intracranial flow, steady flow simulation with Reynolds number of 200 was applied for each aneurysm. Optimization of strut position was performed to minimize the average velocity in an aneurysm while maintaining the porosity. Results: As the results of optimization, we obtained non-uniformed structure as optimized stent for each aneurysm geometry. And all optimized stents were characterized by denser struts in the inflow area. Conclusion: The variety of inflow patterns that resulted from differing aneurysm geometries led to unique strut placements for each aneurysm type. Keywords: Cerebral aneurysm, Flow diverter, Design optimization, Computational fluid dynamics.
    Journal of Biomechanical Engineering 04/2014; 136(6). DOI:10.1115/1.4027411 · 1.75 Impact Factor
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    ABSTRACT: Post-translational modifications (PTMs) are important steps in the maturation of proteins. Several models exist to predict specific PTMs, from manually detected patterns to machine learning (ML) methods. On one hand the manual detection of patterns does not provide the most efficient classifiers and requires an important workload, on the other hand models built by ML are hard to interpret and do not increase biological knowledge. Therefore we developed a novel method based on patterns discovery and decision trees to predict PTMs. The proposed algorithm builds a decision tree, by coupling the C4.5 algorithm with genetic algorithms, producing high performance white box classifiers. Our method was tested on the initiator methionine cleavage (IMC) and N(α)-terminal acetylation (N-Ac), two of the most common PTMs. The resulting classifiers perform well when compared to existing models. On a set of eukaryotic proteins they display a cross-validated MCC of 0.83 (IMC) and 0.65 (N-Ac). When used to predict potential substrates of NatB and NatC our classifiers display better performance than the state of the art. Moreover we present an analysis of the model predicting IMC for H. sapiens proteins and demonstrate that we are able to extract experimentally known facts without prior knowledge. Those results validate the fact that our method produces white box models. Predictors for IMC and N-Ac and all datasets are freely available at: http://terminus.unige.ch/. jean-luc.falcone@unige.ch.
    Bioinformatics 03/2014; 30(14). DOI:10.1093/bioinformatics/btu165 · 4.62 Impact Factor
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    ABSTRACT: We introduce an event based framework of directional changes and overshoots to map continuous financial data into the so-called Intrinsic Network - a state based discretisation of intrinsically dissected time series. Defining a method for state contraction of Intrinsic Network, we show that it has a consistent hierarchical structure that allows for multi-scale analysis of financial data. We define an information theoretic measurement termed Liquidity that characterises the unlikeliness of price trajectories and argue that the new metric has the ability to detect and predict stress in financial markets. We show empirical examples within the Foreign Exchange market where the new measure not only quantifies liquidity but also acts as an early warning signal.
    SSRN Electronic Journal 02/2014; DOI:10.2139/ssrn.2393428
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    ABSTRACT: Fragments associated with explosive volcanic eruptions range from microns to meters in diameter, with the largest ones following ballistic trajectories from the eruptive vent. Recent field observations suggest that bombs ejected during Strombolian eruptions may collide while airborne. We developed a Discrete Event Simulator to study numerically the impact of such collisions on hazard assessment. We show that the area where bombs can land might be significantly increased when collisions occur. As a consequence, if collisions are dominant, the deposition distance cannot be used to estimate important eruption parameters, such as exit speed.
    Computers & Geosciences 02/2014; 63:62–69. DOI:10.1016/j.cageo.2013.10.016 · 2.05 Impact Factor
  • Journal of cellular automata 01/2014; 9(Special Issue: Cellular Automata Applications for Research and Industry):225-240. · 0.24 Impact Factor
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    ABSTRACT: Mammals exhibit a remarkable variety of phenotypes and comparative studies using novel model species are needed to uncover the evolutionary developmental mechanisms generating this diversity. Here, we undertake a developmental biology and numerical modeling approach to investigate the development of skin appendages in the spiny mouse, Acomys dimidiatus. We demonstrate that Acomys spines, possibly involved in display and protection, are enlarged awl hairs with a concave morphology. The Acomys spines originate from enlarged placodes that are characterized by a rapid downwards growth which results in voluminous follicles. The dermal condensation (dermal papilla) at the core of the follicle is very large and exhibits a curved geometry. Given its off-centered position, the dermal papilla generates two waves of anisotropic proliferation, first of the posterior matrix, then of the anterior inner root sheath (IRS). Higher in the follicle, the posterior and anterior cortex cross-section areas substantially decrease due to cortex cell elongation and accumulation of keratin intermediate filaments. Milder keratinization in the medulla gives rise to a foamy material that eventually collapses under the combined compression of the anterior IRS and elongation of the cortex cells. Simulations, using linear elasticity theory and the finite-element method, indicate that these processes are sufficient to replicate the time evolution of the Acomys spine layers and the final shape of the emerging spine shaft. Our analyses reveal how hair follicle morphogenesis has been altered during the evolution of the Acomys lineage, resulting in a shift from ancestral awl follicles to enlarged asymmetrical spines. This study contributes to a better understanding of the evolutionary developmental mechanisms that generated the great diversity of skin appendage phenotypes observed in mammals.
    EvoDevo 01/2014; 5:33. DOI:10.1186/2041-9139-5-33 · 3.10 Impact Factor
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    Mohamed Ben Belgacem, Bastien Chopard
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    ABSTRACT: In this paper, we report on the experimental results of running a large, tightly coupled, distributed multiscale computation over a hybrid High Performance Computing (HPC) infrastructures. We connected EC2 based cloud clusters located in USA to university clusters located in Switzerland. We ran a concurrent multiscale MPI based application on this infrastructure and measured the overhead induced by extending our HPC clusters with EC2 resources. Our results indicate that accommodating some parts of the multiscale computation on cloud resources can lead to low performance without a proper adjustment of CPUs power and workload. However, by enforcing a load-balancing strategy one can benefit from the extra Cloud resources.
    Future Generation Computer Systems 01/2014; DOI:10.1016/j.future.2014.08.003 · 2.64 Impact Factor
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    ABSTRACT: We present a global overview of the methodology developed within the MAPPER European project to design, implement and run a multiscale simulation on a distributed supercomputing infrastructure. Our goal is to highlight the main steps required when developing an application within this framework. More specifically, we illustrate the proposed approach in the case of hydrology applications. A performance model describing the execution time of the application as a function of its spatial resolution and the hardware performance is proposed. It shows that Distributed Multiscal Computation is beneficial for large scale problems.
    Procedia Computer Science 12/2013; 18:1106 - 1115. DOI:10.1016/j.procs.2013.05.276
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    ABSTRACT: This paper considers a multiscale description of thrombus formation and its simplified numerical implementation in the case of cerebral aneurysms. In particular, we extend previously introduced generic 2D models towards 3D patient specific aneurysm geometries. The multiscale amplification method contributes to considerably reducing simulation time. This allows us to achieve a mesh resolution high enough to resolve details of the stent geometry which is triggering flow conditions to induce clotting. Simulation results presented in this paper are qualitatively in a good agreement with clinical observations.
    Procedia Computer Science 12/2013; 18:1006. DOI:10.1016/j.procs.2013.05.266