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Project-Team Bang Biophysique, Analyse Numérique · PDF file1. Team BANG (Biophysique, Analyse Numérique et Géophysique) is a continuation of the former project M3N. Head of project-team

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Text of Project-Team Bang Biophysique, Analyse Numérique · PDF file1. Team BANG (Biophysique,...

  • c t i v i t y

    te p o r

    2007

    THEME NUM

    INSTITUT NATIONAL DE RECHERCHE EN INFORMATIQUE ET EN AUTOMATIQUE

    Project-Team Bang

    Biophysique, Analyse Numrique etGophysique

    Paris - Rocquencourt

    http://www.inria.fr/recherche/equipes/listes/theme_NUM.en.htmlhttp://www.inria.frhttp://www.inria.fr/recherche/equipes/bang.en.htmlhttp://www.inria.fr/inria/organigramme/fiche_ur-rocq.en.html

  • Table of contents

    1. Team . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12. Overall Objectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

    2.1. Introduction 12.2. Highlights of the year 2

    3. Scientific Foundations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23.1. Introduction 23.2. Mathematical Modeling 23.3. Multiscale analysis 23.4. Numerical Algorithms 2

    4. Application Domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .34.1. Panorama 34.2. Tissue growth and cell movment 34.3. Free surface flows 34.4. Semiconductors 3

    5. Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35.1. Introduction 35.2. OPTMTR 35.3. EMC2 35.4. HET_2D 35.5. CellSys 4

    6. New Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46.1. Tissue growth and cell movment 4

    6.1.1. Dynamics of age-and-cyclin structured cell populations; applications to cell cycle mod-elling: 4

    6.1.2. Pharmacokinetic-pharmacodynamic (PK-PD) modelling for anticancer therapy 56.1.3. Inverse problem in structured populations 56.1.4. Single-cell-based models of tumor growth and tissue regeneration 56.1.5. Chemotaxis and cell movement 6

    6.2. Free surface geophysical flows 86.2.1. Multilayer Saint-Venant system 96.2.2. Derivation of a non-hydrostatic shallow water model 96.2.3. Overland flows 9

    7. Other Grants and Activities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107.1. Actions at region level 107.2. European actions 11

    7.2.1. RTN network HYKE 117.2.2. RTN network M3CS-TuTh 117.2.3. NoE Biosim 117.2.4. Strep Tempo 11

    7.3. International actions 118. Dissemination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

    8.1. Scientific community 128.2. Teaching 128.3. Participation to congresses, workshops,... 12

    9. Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13

  • 1. TeamBANG (Biophysique, Analyse Numrique et Gophysique) is a continuation of the former project M3N.

    Head of project-teamBenoit Perthame [ Universit Paris 6 & ENS, HdR ]

    Vice-head of project teamAmerico Marrocco [ DR ]

    Administrative assistantMaryse Desnous [ TR, partial time ]

    Staff member InriaMarie-Odile Bristeau [ DR, partial time 4/5 ]Jean Clairambault [ CR ]Marie Doumic-Jauffret [ CR,Dtache ENPC ]Dirk Drasdo [ DR ]

    Research scientists (partner)Franois Bouchut [ DR, ENS-DMA ]Hatem Zaag [ CR1, ENS-DMA ]

    Ph. D. studentsVincent Calvez [ Elve ENS ]Tomas Morales [ Seville University ]Neijla Nouaili [ Tunis University, until september ]Annabelle Ballesta [ since june ]Nick Jagiella [ since september ]Thomas Lepoutre [ since september ]Stefan Hhme [ Leipzig University ]Axel Krinner [ Leipzig University ]

    Student internThomas Lepoutre [ ENS Lyon, march-june ]Luna Dimitrio [ march-june ]

    2. Overall Objectives

    2.1. IntroductionBANG (Biophysique, Analyse Numrique et Gophysique) is a continuation of the former project M3N. Itaims at developing models and numerical methods for two kinds of problems involving Partial DifferentialEquations. Firstly problems from life sciences (cell movement, tissue growth, cancer modeling, pharmacol-ogy,...) are considered. Secondly models for complex fluid flows are studied (flows with a free surface, flowsof holes and electrons in semiconductors).

    The common scientific features behind these applications come from models involving coupled systems ofPDEs (as Keller-Segel or Saint-Venant systems) that are solved (simulated) on computers involving newalgorithms.

  • 2 Activity Report INRIA 2007

    2.2. Highlights of the year Bang is preparing a CEA-EDF-INRIA school on cancer modeling. B. Perthame has been hired as a senior member of IUF.

    3. Scientific Foundations

    3.1. IntroductionPartial Differential Equations are mathematical tools that allow to represent efficiently the evolution ofcomplex physical phenomena. They represent averages of large systems of particles or cells.

    Since the XIXth century this formalism has shown its efficiency and ability to explain both qualitative andquantitative behaviors. The knowledge that has been gathered on such physical models, on algorithms forsolving them on computers, on industrial implementation, opens the hope for success when dealing with lifesciences also. This is one of the main goals of BANG. At small spatial scales the partial differential equationmodels are complemented by agent-based models which permit to capture phenomena on the spatial scale ofthe individual matter components.

    3.2. Mathematical ModelingWhat are the relevant physical or biological variables, what are the possible dominant effects ruling theirdynamics, how to analyse the information coming out from a mathematical model and interpret them in thereal situations under consideration ? These are the questions leading to select a mathematical model, generallyalso to couple several of them in order to render all physical or biomedical features which are selected byspecialist partners (engineers, physicists, medical doctors). These are usually based on Navier-Stokes systemfor fluids (as in free surface fluid flows), on parabolic-hyperbolic equations (Saint-Venant system for shallowwater, flows of electrons/holes in semiconductors, Keller-Segel model of chemotaxis).

    3.3. Multiscale analysisThe complete physical or biomedical description is usually complex and requires very small scales. Efficiencyof computer resolution leads to simplifications using averages of quantities. Methods allowing to achieve thatgoal are numerous and mathematically deep. Some examples studied in BANG are

    Coupled multiscale modelling (description of tumors and tissues from the sub-cellular level to theorgan scale).

    Description of cell movement from the individual to the collective scales. Reduction of full 3d Navier-Stokes system to 2d or 1d hyperbolic equations by a section average

    (derivation of Saint-Venant system for shallow water).

    3.4. Numerical AlgorithmsVarious numerical methods are used in BANG. They may be based on finite elements or finite volume methods,or stochastic methods for individual agents. Algorithmic improvments are needed in order to take into accountthe specificity of each model, of their coupling, or their 3D features. Among them we can mention

    Well-balanced schemes for shallow water system. Free-surface Navier-Stokes solvers based on a multilayer St-Venant approach. Mixed finite elements for problems with large density variations (semi-conductors, chemotaxis). Description of tumor growth and tissue regeneration are based on systems of stochastic equations of

    motion for individual cells or Monte-Carlo simulations of multi-cellular configurations.

  • Project-Team Bang 3

    4. Application Domains

    4.1. PanoramaBANG has decided to develop new biomedical applications and focusses its know-how in these directions,while keeping more classical industrial relations. These are developed in relation with other INRIA projects:GAMMA, REO.

    4.2. Tissue growth and cell movmentThis research activity aims at studying mathematical models related to tumors developments and the controlof therapy. Among the many biological aspects let us mention

    cell movments (chemotaxis, vasculogenesis, angiogenesis), cell cycle, immune reaction and adaptive dynamics (structured population dynamics), modelling and optimization of chemotherapy through differential systems, tissue growth and regeneration, and biomechanical aspects of cell interaction, migration and growth

    control.

    4.3. Free surface flowsSeveral industrial applications require to solve fluid flows with a free surface. BANG develops algorithmsin two directions. Firstly flows in rivers and coastal areas using Saint-Venant model with applications todam break and pollution problems in averaged shallow water systems. Secondly, 3D hydrostatic flows bya multilayer Saint-Venant approach and 3D Navier-Stokes flows.

    4.4. SemiconductorsMathematical models based on drift-diffusion systems or energy transport systems are solved using mixedfinite elements methods. BANG has developed a highly sophisticated code which is able to simulate very stiffsemiconductor devices.

    5. Software

    5.1. IntroductionSoftwares initiated and developped within former projects (Menusin, M3N) and currently in use in the presentproject.

    5.2. OPTMTRGeneration of metric maps for use with adapted meshes generator (with Gamma project)

    5.3. EMC2Interactive 2D mesh generator (with Gamma project)

    5.4. HET_2DParti

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