Bastien Chopard

University of Geneva, Genève, Geneva, Switzerland

Are you Bastien Chopard?

Claim your profile

Publications (218)286.76 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Systems medicine is the application of systems biology concepts, methods, and tools to medical research and practice. It aims to integrate data and knowledge from different disciplines into biomedical models and simulations for the understanding, prevention, cure, and management of complex diseases. Complex diseases arise from the interactions among disease-influencing factors across multiple levels of biological organization from the environment to molecules. To tackle the enormous challenges posed by complex diseases, we need a modeling and simulation framework capable of capturing and integrating information originating from multiple spatiotemporal and organizational scales. Multiscale modeling and simulation in systems medicine is an emerging methodology and discipline that has already demonstrated its potential in becoming this framework. The aim of this chapter is to present some of the main concepts, requirements, and challenges of multiscale modeling and simulation in systems medicine.
    No preview · Article · Dec 2015 · Methods in molecular biology (Clifton, N.J.)
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The early stages of clot formation in blood vessels involve platelets adhesion-aggregation. Although these mechanisms have been extensively studied, gaps in their understanding still persist. We have performed detailed in-vitro experiments and developed a numerical model to better describe and understand this phenomenon. Unlike previous studies, we took into account both activated and non-activated platelets, as well as the 3D nature of the aggregation process. Our investigation reveals that blood albumin is a major parameter limiting platelet adhesion and aggregation. Our results also show that the well accepted Zydney-Colton shear-induced diffusivity is much too low to explain the observed deposition rate. Simulations are in very good agreement with observations and provide quantitative estimates of the adhesion and aggregation rates that are hard to measure experimentally.
    Full-text · Article · Nov 2015
  • Source
    Gregor Chliamovitch · Orestis Malaspinas · Bastien Chopard
    [Show abstract] [Hide abstract]
    ABSTRACT: In recent years, the maximum entropy principle has been applied to a wide range of different fields, often successfully. While these works are usually focussed on cross-disciplinary applications, the point of this letter is instead to reconsider a fundamental point of kinetic theory. Namely, we shall re-examine the Stosszahlansatz leading to the irreversible Boltzmann equation at the light of the MaxEnt principle. We assert that this way of thinking allows to move one step further than the factorization hypothesis and provides a coherent—though implicit—closure scheme for the two-particle distribution function. Such higher-order dependences are believed to open the way to a deeper understanding of fluctuating phenomena.
    Full-text · Article · Oct 2015 · Entropy
  • [Show abstract] [Hide abstract]
    ABSTRACT: Platelet spreading and retraction play a pivotal role in the platelet plugging and the thrombus formation. In routine laboratory, platelet function tests include exhaustive information about the role of the different receptors present at the platelet surface without information on the 3D structure of platelet aggregates. In this work, we develop, a method in Digital Holographic Microscopy (DHM) to characterize the platelet and aggregate 3D shapes using the quantitative phase contrast imaging. This novel method is suited to the study of platelets physiology in clinical practice as well as the development of new drugs.
    No preview · Article · Sep 2015 · Biomedical Optics Express
  • Source
    [Show description] [Hide description]
    DESCRIPTION: We propose a new numerical model to describe thrombus formation in cerebral aneurysms. This model combines CFD simulations with a set of bio-mechanical processes identified as being the most important to describe the phenomena at a large space and time scales. The hypotheses of the model are based on in vitro experiments and clinical observations. We document that we can reproduce very well the shape and volume of patient specific thrombus segmented in giant aneurysms.
    Full-text · Research · Jul 2015
  • Source

    Full-text · Dataset · Jul 2015
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Particular intra-aneurysmal blood flow conditions, created naturally by the growth of an aneurysm or induced artificially by implantation of a flow diverter stent (FDS), can potentiate intra-aneurysmal thrombosis. The aim of this study was to identify hemodynamic indicators, relevant to this process, which could be used as a prediction of the success of a preventive endovascular treatment. A cross sectional study on 21 patients was carried out to investigate the possible association between intra-aneurysmal spontaneous thrombus volume and the dome to neck aspect ratio (AR) of the aneurysm. The mechanistic link between these two parameters was further investigated through a Fourier analysis of the intra-aneurysmal shear rate (SR) obtained by computational fluid dynamics (CFD). This analysis was first applied to 10 additional patients (4 with and 6 without spontaneous thrombosis) and later to 3 patients whose intracranial aneurysms only thrombosed after FDS implantation. The cross sectional study revealed an association between intra-aneurysmal spontaneous thrombus volume and the AR of the aneurysm (R(2)=0.67, p<0.001). Fourier analysis revealed that in cases where thrombosis occurred, the SR harmonics 0, 1, and 2 were always less than 25/s, 10/s, and 5/s, respectively, and always greater than these values where spontaneous thrombosis was not observed. Our study suggests the existence of an SR threshold below which thrombosis will occur. Therefore, by analyzing the SR on patient specific data with CFD techniques, it may be potentially possible to predict whether or the intra-aneurysmal flow conditions, after FDS implantation, will become prothrombotic. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.
    Full-text · Article · Jul 2015 · Journal of Neurointerventional Surgery
  • Source
    Daniel Lagrava · Orestis Malaspinas · Jonas Latt · Bastien Chopard
    [Show abstract] [Hide abstract]
    ABSTRACT: In all kinds of engineering problems, and in particular in methods for computational fluid dynamics based on regular grids, local grid refinement is of crucial importance. To save on computational expense, many applications require to resolve a wide range of scales present in a numerical simulation by locally adding more mesh points. In general, the need for a higher (or a lower) resolution is not known a priori, and it is therefore difficult to locate areas for which local grid refinement is required. In this paper, we propose a novel algorithm for the lattice Boltzmann method, based on physical concepts, to automatically construct a pattern of local refinement. We apply the idea to the two-dimensional lid-driven cavity and show that the automatically refined grid can lead to results of equal quality with less grid points, thus sparing computational resources and time. The proposed automatic grid refinement strategy has been implemented in the parallel open-source library Palabos.
    Full-text · Article · Jul 2015
  • Gregor Chliamovitch · Alexandre Dupuis · Bastien Chopard
    [Show abstract] [Hide abstract]
    ABSTRACT: We develop ideas proposed by Van der Straeten to extend maximum entropy principles to Markov chains. We focus in particular on the convergence of such estimates in order to explain how our approach makes possible the estimation of transition probabilities when only short samples are available, which opens the way to applications to non-stationary processes. The current work complements an earlier communication by providing numerical details, as well as a full derivation of the multi-constraint two-state and three-state maximum entropy transition matrices.
    No preview · Article · Jun 2015 · Entropy
  • [Show abstract] [Hide abstract]
    ABSTRACT: In this paper, we model discrete time series as discrete Markov processes of arbitrary order and derive the approximate distribution of the Kullback-Leibler divergence between a known transition probability matrix and its sample estimate. We introduce two new information-theoretic measurements: information memory loss and information codependence structure. The former measures the memory content within a Markov process and determines its optimal order. The latter assesses the codependence among Markov processes. Both measurements are evaluated on toy examples and applied on high frequency foreign exchange data, focusing on 2008 financial crisis and 2010/2011 Euro crisis.
    No preview · Article · May 2015 · Entropy
  • Source
    [Show abstract] [Hide abstract]
    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.
    Full-text · Article · Apr 2015 · Journal of Computational Science
  • Source
    R. M. Razakanirina · B. Chopard

    Preview · Article · Feb 2015
  • Source
    [Show abstract] [Hide abstract]
    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.
    Full-text · Article · Nov 2014 · EPL (Europhysics Letters)
  • Source
    [Show abstract] [Hide abstract]
    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.
    Full-text · Article · Sep 2014 · Journal of Computational Science
  • Source
    [Show abstract] [Hide abstract]
    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.
    Full-text · Article · Sep 2014 · EvoDevo
  • Alfons Hoekstra · Bastien Chopard · Peter Coveney
    [Show abstract] [Hide abstract]
    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.
    No preview · Article · Aug 2014 · Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences
  • Source
    [Show abstract] [Hide abstract]
    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.
    Full-text · Article · Aug 2014 · Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences
  • Source
    B Chopard · Joris Borgdorff · A G Hoekstra
    [Show abstract] [Hide abstract]
    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.
    Full-text · Article · Aug 2014 · Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences
  • Source

    Full-text · Article · Aug 2014 · Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences
  • Source
    Gregor Chliamovitch · Bastien Chopard · Lino Velasquez
    [Show abstract] [Hide abstract]
    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.
    Preview · Article · Aug 2014

Publication Stats

4k Citations
286.76 Total Impact Points

Institutions

  • 1970-2015
    • University of Geneva
      • • Department of Computer Science
      • • Department of Theoretical Physics
      Genève, Geneva, Switzerland
  • 2011
    • Claude Bernard University Lyon 1
      Villeurbanne, Rhône-Alpes, France
  • 2000-2004
    • University of Lausanne
      Lausanne, Vaud, Switzerland
  • 1991
    • Massachusetts Institute of Technology
      Cambridge, Massachusetts, United States