## Publications

301 results found

Aceves-Sanchez P, Aymard B, Peurichard D, et al., 2021, A NEW MODEL FOR THE EMERGENCE OF BLOOD CAPILLARY NETWORKS, Publisher: AMER INST MATHEMATICAL SCIENCES-AIMS

Aceves Sanchez P, Aymard B, Peurichard D,
et al., 2021, A new model for the emergence of blood capillary networks, *Networks and Heterogeneous Media*, Vol: 16, Pages: 91-138, ISSN: 1556-1801

We propose a new model for the emergence of blood capillary networks. We assimilate the tissue and extra cellular matrix as a porous medium, using Darcy's law for describing both blood and interstitial fluid flows. Oxygen obeys a convection-diffusion-reaction equation describing advection by the blood, diffusion and consumption by the tissue. Discrete agents named capillary elements and modelling groups of endothelial cells are created or deleted according to different rules involving the oxygen concentration gradient, the blood velocity, the sheer stress or the capillary element density. Once created, a capillary element locally enhances the hydraulic conductivity matrix, contributing to a local increase of the blood velocity and oxygen flow. No connectivity between the capillary elements is imposed. The coupling between blood, oxygen flow and capillary elements provides a positive feedback mechanism which triggers the emergence of a network of channels of high hydraulic conductivity which we identify as new blood capillaries. We provide two different, biologically relevant geometrical settings and numerically analyze the influence of each of the capillary creation mechanism in detail. All mechanisms seem to concur towards a harmonious network but the most important ones are those involving oxygen gradient and sheer stress. A detailed discussion of this model with respect to the literature and its potential future developments concludes the paper.

Barker M, Degond P, Martin R, et al., 2021, A mean field game model of firm-level innovation, Publisher: arXiv

Knowledge spillovers occur when a firm researches a new technology and thattechnology is adapted or adopted by another firm, resulting in a social valueof the technology that is larger than the initially predicted private value. Asa result, firms systematically under--invest in research compared with thesocially optimal investment strategy. Understanding the level ofunder--investment, as well as policies to correct it, is an area of activeeconomic research. In this paper, we develop a new model of spillovers, takinginspiration from the available microeconomic data. We prove existence anduniqueness of solutions to the model, and we conduct some initial simulationsto understand how indirect spillovers contribute to the productivity of asector.

Barker M, Degond P, Wolfram M-T, 2020, Comparing the best reply strategy and mean field games: the stationary case, *European Journal of Applied Mathematics*, Pages: 1-32, ISSN: 0956-7925

Mean-field games (MFGs) and the best-reply strategy (BRS) are two methods of describing competitive optimisation of systems of interacting agents. The latter can be interpreted as an approximation of the respective MFG system. In this paper, we present an analysis and comparison of the two approaches in the stationary case. We provide novel existence and uniqueness results for the stationary boundary value problems related to the MFG and BRS formulations, and we present an analytical and numerical comparison of the two paradigms in some specific modelling situations.

Degond P, Merino-Aceituno S, 2020, Nematic alignment of self-propelled particles: from particle to macroscopic dynamics, *Mathematical Models and Methods in Applied Sciences (M3AS)*, Vol: 30, Pages: 1935-1986, ISSN: 0218-2025

Starting from a particle model describing self-propelled particles interacting through nematic alignment, we derive a macroscopic model for the particle density and mean direction of motion. We first propose a mean-field kinetic model of the particle dynamics. After diffusive rescaling of the kinetic equation, we formally show that the distribution function converges to an equilibrium distribution in particle direction, whose local density and mean direction satisfies a cross-diffusion system. We show that the system is consistent with symmetries typical of a nematic material. The derivation is carried over by means of a Hilbert expansion. It requires the inversion of the linearized collision operator for which we show that the generalized collision invariants, a concept introduced to overcome the lack of momentum conservation of the system, plays a central role. This cross-diffusion system poses many new challenging questions.

Aceves-Sanchez P, Degond P, Keaveny EE,
et al., 2020, Large-Scale Dynamics of Self-propelled Particles Moving Through Obstacles: Model Derivation and Pattern Formation, *BULLETIN OF MATHEMATICAL BIOLOGY*, Vol: 82, ISSN: 0092-8240

Degond P, Herda M, Mirrahimi S, 2020, A Fokker-Planck approach to the study of robustness in gene expression, *Mathematical Biosciences and Engineering*, ISSN: 1547-1063

We study several Fokker-Planck equations arising from a stochastic chemical kinetic system modeling a gene regulatory network in biology. Thedensities solving the Fokker-Planck equations describe the joint distribution ofthe mRNA and µRNA content in a cell. We provide theoretical and numericalevidence that the robustness of the gene expression is increased in the presenceof µRNA. At the mathematical level, increased robustness shows in a smallercoefficient of variation of the marginal density of the mRNA in the presenceof µRNA. These results follow from explicit formulas for solutions. Moreover,thanks to dimensional analyses and numerical simulations we provide qualitative insight into the role of each parameter in the model. As the increase ofgene expression level comes from the underlying stochasticity in the models,we eventually discuss the choice of noise in our models and its influence on ourresults.

Aceves Sanchez P, Degond P, Keaveny E,
et al., 2020, Large-scale dynamics of self-propelled particles moving through obstacles: model derivation and pattern formation, *Bulletin of Mathematical Biology*, ISSN: 0092-8240

We model and study the patterns created through the interactionof collectively moving self-propelled particles (SPPs) and elastically tetheredobstacles. Simulations of an individual-based model reveal at least three distinct large-scale patterns: travelling bands, trails and moving clusters. Thismotivates the derivation of a macroscopic partial differential equations modelfor the interactions between the self-propelled particles and the obstacles, forwhich we assume large tether stiffness. The result is a coupled system of non linear, non-local partial differential equations. Linear stability analysis showsthat patterning is expected if the interactions are strong enough and allowsfor the predictions of pattern size from model parameters. The macroscopicequations reveal that the obstacle interactions induce short-ranged SPP aggregation, irrespective of whether obstacles and SPPs are attractive or repulsive.

Degond P, Merino-Aceituno S, Vergnet F,
et al., 2020, Coupled Self-Organized Hydrodynamics and Stokes Models for Suspensions of Active Particles (vol 21, 6, 2019), *JOURNAL OF MATHEMATICAL FLUID MECHANICS*, Vol: 22, ISSN: 1422-6928

Barré J, Degond P, Peurichard D,
et al., 2020, Modelling pattern formation through diﬀerential repulsion, *Networks and Heterogeneous Media*, Vol: 15, Pages: 307-352, ISSN: 1556-1801

Motivated by experiments on cell segregation, we present a twospeciesmodel of interacting particles, aiming at a quantitative description ofthis phenomenon. Under precise scaling hypothesis, we derive from the microscopicmodel a macroscopic one and we analyze it. In particular, we determinethe range of parameters for which segregation is expected. We compare ouranalytical results and numerical simulations of the macroscopic model to directsimulations of the particles, and comment on possible links with experiments.

Degond P, Jin S, Zhu Y, 2020, An uncertainty quantification approach to the study of gene expression robustness, *Methods and Applications of Analysis*, ISSN: 1073-2772

We study a chemical kinetic system with uncertainty modeling a gene regulatorynetwork in biology. Specifically, we consider a system of two equations for the messengerRNA and micro RNA content of a cell. Our target is to provide a simple framework for noisebuffering in gene expression through micro RNA production. Here the uncertainty, modeledby random variables, enters the system through the initial data and the source term. Weobtain a sharp decay rate of the solution to the steady state, which reveals that the biologysystem is not sensitive to the initial perturbation around the steady state. The sharpregularity estimate leads to the stability of the generalized Polynomial Chaos stochasticGalerkin (gPC-SG) method. Based on the smoothness of the solution in the random spaceand the stability of the numerical method, we conclude the gPC-SG method has spectralaccuracy. Numerical experiments are conducted to verify the theoretical findings.

Degond P, Diez A, Frouvelle A, et al., 2020, Phase Transitions and Macroscopic Limits in a BGK Model of Body-Attitude Coordination, Publisher: SPRINGER

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Degond P, Diez A, Frouvelle A,
et al., 2020, Phase transitions and macroscopic limits in a BGK model of body-attitude coordination, *Journal of Nonlinear Science*, ISSN: 0938-8974

In this article we investigate the phase transition phenomena that occur in a model of self-organisation through body-attitude coordination. Here, the body attitude of an agent is modelled by a rotation matrix in R3 as in Degond et al. (Math Models Methods Appl Sci 27(6):1005–1049, 2017). The starting point of this study is a BGK equation modelling the evolution of the distribution function of the system at a kinetic level. The main novelty of this work is to show that in the spatially homogeneous case, self-organisation may appear or not depending on the local density of agents involved. We first exhibit a connection between body-orientation models and models of nematic alignment of polymers in higher-dimensional space from which we deduce the complete description of the possible equilibria. Then, thanks to a gradient-flow structure specific to this BGK model, we are able to prove the stability and the convergence towards the equilibria in the different regimes. We then derive the macroscopic models associated with the stable equilibria in the spirit of Degond et al. (Arch Ration Mech Anal 216(1):63–115, 2015, Math Models Methods Appl Sci 27(6):1005–1049, 2017).

Degond P, Engel M, Liu J-G,
et al., 2020, A Markov jump process modelling animal group size statistics, *Communications in Mathematical Sciences*, Vol: 18, Pages: 55-89, ISSN: 1539-6746

We translate a coagulation-framentation model, describing the dynamics of animal group size distributions, into a model for the population distribution and associate the nonlinear evolution equation witha Markov jump process of a type introduced in classic work of H. McKean. In particular this formalizesa model suggested by H.-S. Niwa [J. Theo. Biol. 224 (2003)] with simple coagulation and fragmentationrates. Based on the jump process, we develop a numerical scheme that allows us to approximate the equilibrium for the Niwa model, validated by comparison to analytical results by Degond et al. [J. NonlinearSci. 27 (2017)], and study the population and size distributions for more complicated rates. Furthermore,the simulations are used to describe statistical properties of the underlying jump process. We additionally discuss the relation of the jump process to models expressed in stochastic differential equations anddemonstrate that such a connection is justified in the case of nearest-neighbour interactions, as opposedto global interactions as in the Niwa model.

Degond P, Hecht S, Vauchelet N, 2020, Incompressible limit of a continuum model of tissue growth for two cell populations, *Networks and Heterogeneous Media*, Vol: 15, Pages: 57-85, ISSN: 1556-1801

This paper investigates the incompressible limit of a system modelling the growth oftwo cells population. The model describes the dynamics of cell densities, driven by pressureexclusion and cell proliferation. It has been shown that solutions to this system of partialdifferential equations have the segregation property, meaning that two population initiallysegregated remain segregated. This work is devoted to the incompressible limit of suchsystem towards a free boundary Hele Shaw type model for two cell populations.

Degond P, Ferreira M, Merino-Aceituno S,
et al., 2020, A new continuum theory for incompressible swelling materials, *SIAM: Multiscale Modeling and Simulation*, Vol: 18, Pages: 163-197, ISSN: 1540-3459

Swelling media (e.g. gels, tumors) are usually described by mechanical constitutive laws (e.g. Hooke or Darcy laws). However, constitutive relations of real swelling media are not well-known. Here, we take an opposite route and consider a simple packing heuristics, i.e. the particles can’t overlap. We deduce a formula for the equilibrium density under a confining potential. We then consider its evolution when the average particle volume and confining potential depend on time under two additional heuristics: (i) any two particles can’t swap their position; (ii) motion should obey some energy minimization principle. These heuristics determine the medium velocity consistently with the continuity equation. In the direction normal to the potential level sets the velocity is related with that of the level sets while in the parallel direction, it is determined by a Laplace-Beltrami operator on these sets. This complex geometrical feature cannot be recovered using a simple Darcy law.

Degond P, Herda M, Mirrahimi S, 2020, A Fokker-Planck approach to the study of robustness in gene expression, *MATHEMATICAL BIOSCIENCES AND ENGINEERING*, Vol: 17, Pages: 6459-6486, ISSN: 1547-1063

Ferreira M, Despin-Guitard E, Duarte F,
et al., 2019, Interkinetic nuclear movements promote apical expansion in pseudostratified epithelia at the expense of apicobasal elongation, *PLoS Computational Biology*, ISSN: 1553-734X

Pseudostratified epithelia (PSE) are a common type of columnar epithelia found in a wealth of embryonic and adult tissues such as ectodermal placodes, the trachea, the ureter, the gut and the neuroepithelium. PSE are characterized by the choreographed displacement of cells’ nuclei along the apicobasal axis according to phases of their cell cycle. Such movements, called interkinetic movements (INM) have been proposed to influence tissue expansionand shape and suggested as culprit in several congenital diseases such as CAKUT(Congenital anomalies of kidney and urinary tract)and esophageal atresia. INM rely on cytoskeleton dynamics just as adhesion, contractility and mitosis do. Therefore, long term impairment of INM without affecting proliferation and adhesion is currently technically unachievable. Here we bypassed this hurdle by generating a 2D agent-based model of a proliferating PSE and compared its output to the growth of the chick neuroepitheliumto assess the interplay between INM and these other importantcell processes during growth of a PSE. We found that INM directly generates apical expansion and apical nuclear crowding. In addition, our data strongly suggest that apicobasal elongation of cells is not an emerging property of a proliferative PSE but rather requires a specific elongation program. We then discuss how such program might functionally link INM, tissue growth and differentiation.

Aceves Sanchez P, Bostan M, Carrillo de la Plata JA,
et al., 2019, Hydrodynamic limits for kinetic ﬂocking models of Cucker-Smale type, *Mathematical Biosciences and Engineering*, Vol: 16, Pages: 7883-7910, ISSN: 1547-1063

We analyse the asymptotic behavior for kinetic models describing the collective behavior of animal populations. We focus on models for self-propelled individuals, whose velocity relaxes toward the mean orientation of the neighbors. The self-propelling and friction forces together with the alignment and the noise are interpreted as a collision/interaction mechanism acting with equal strength. We show that the set of generalized collision invariants, introduced in [39], is equivalent in our setting to the more classical notion of collision invariants, i.e., the kernel of a suitably linearized collision operator. After identifying these collision invariants, we derive the fluid model, by appealing to the balances for the particle concentration and orientation. We investigate the main properties of the macroscopic model for a general potential with radial symmetry.

Degond P, Pulvirenti M, 2019, Propagation of chaos for topological interactions, *Annals of Applied Probability*, Vol: 29, Pages: 2594-2612, ISSN: 1050-5164

We consider aN-particle model describing an alignment mechanism due to a topolog-ical interaction among the agents. We show that the kinetic equation, expected to holdin the mean-field limitN→∞, as following from the previous analysis in Ref. [3] can berigorously derived. This means that the statistical independence (propagation of chaos)is indeed recovered in the limit, provided it is assumed at time zero.

Chertock A, Degond P, Hecht S,
et al., 2019, Incompressible limit of a continuum model of tissue growth with segregation for two cell populations, *Mathematical Biosciences and Engineering*, Vol: 16, Pages: 5804-5835, ISSN: 1547-1063

This paper proposes a model for the growth of two interacting populations of cells that do not mix. The dynamics is driven by pressure and cohesion forces on the one hand and proliferation on the other hand. Contrasting with earlier works which assume that the two populations are initially segregated, our model can deal with initially mixed populations as it explicitly incorporates a repul-sion force that enforces segregation. To balance segregation instabilities potentially triggered by the repulsion force, our model also incorporates a fourth order diffusion. In this paper, we study the influ-ence of the model parameters thanks to one-dimensional simulations using a finite-volume method for a relaxation approximation of the fourth order diffusion. Then, following earlier works on the single population case, we provide formal arguments that the model approximates a free boundary Hele Shaw type model that we characterise using both analytical and numerical arguments.

Ferreira MA, Despin-Guitard E, Duarte F, et al., 2019, Interkinetic nuclear movements promote apical expansion in pseudostratified epithelia at the expense of apicobasal elongation, Publisher: Cold Spring Harbor Laboratory

<jats:title>Abstract</jats:title><jats:p>Pseudostratified epithelia (PSE) are a common type of columnar epithelia found in a wealth of embryonic and adult tissues such as ectodermal placodes, the trachea, the ureter, the gut and the neuroepithelium. PSE are characterized by the choreographed displacement of cells’ nuclei along the apicobasal axis according to phases of their cell cycle. Such movements, called interkinetic movements (INM) have been proposed to influence tissue expansion and shape and suggested as culprit in several congenital diseases such as CAKUT and esophageal atresia. INM rely on cytoskeleton dynamics just as adhesion, contractility and mitosis do. Therefore, longer term impairment of INM without affecting proliferation and adhesion is currently technically unachievable. Here we bypassed this hurdle by generating a 2D agent-based model of a proliferating PSE and compared its output to the growth of the chick neuroepithelium to assess the interplay between INM and these other important cell processes during growth of a PSE. We found that INM directly generates apical expansion and apical nuclear crowding. In addition, our data strongly suggest that apicobasal elongation of cells is not an emerging property of a proliferative PSE but rather requires a specific elongation program. We then discuss how such program might functionally link INM, tissue growth and differentiation.</jats:p><jats:sec><jats:title>Authors Summary</jats:title><jats:p>Pseudostratified epithelia (PSE) are a common type of epithelia characterized by the choreographed displacement of cells’ nuclei along the apicobasal axis during proliferation. These so-called interkinetic movements (INM) were proposed to influence tissue expansion and suggested as culprit in several congenital diseases. INM rely on cytoskeleton dynamics. Therefore, longer term impairment of INM without affecting proliferation and adhesion is currently t

Peurichard D, Ousset M, Paupert J,
et al., 2019, Extra-cellular matrix rigidity may dictate the fate of injury outcome, *Journal of Theoretical Biology*, Vol: 469, Pages: 127-136, ISSN: 0022-5193

After injury, while regeneration can be observed in hydra, planaria and some vertebrates, regeneration is rare in mammals and particularly in humans. In this paper, we investigate the mechanisms by which biological tissues recover after injury. We explore this question on adipose tissue, using the mathematical framework recently developed in Peurichard et al., J. Theoret. Biol. 429 (2017), pp. 61-81. Our assumption is that simple mechanical cuesbetween the Extra-Cellular Matrix (ECM) and differentiated cells can explain adipose tissue morphogenesis and that regeneration requires after injury the same mechanisms. We validate this hypothesis by means of a two-dimensional Individual Based Model (IBM) of interacting adipocytes and ECM fiber elements. The model successfully generates regeneration or scar formation as functions of few key parameters, and seems to indicate that the fate of injury outcome could be mainly due to ECM rigidity

Degond P, Merino Aceituno S, Vergnet F,
et al., 2019, Coupled Self-Organized Hydrodynamics and Stokes models for suspensions of active particles, *Journal of Mathematical Fluid Mechanics*, Vol: 21, ISSN: 1422-6928

We derive macroscopic dynamics for self-propelled particles in a fluid. The starting point is a coupled Vicsek–Stokes system. The Vicsek model describes self-propelled agents interacting through alignment. It provides a phenomenological description of hydrodynamic interactions between agents at high density. Stokes equations describe a low Reynolds number fluid. These two dynamics are coupled by the interaction between the agents and the fluid. The fluid contributes to rotating the particles through Jeffery’s equation. Particle self-propulsion induces a force dipole on the fluid. After coarse-graining we obtain a coupled Self-Organised Hydrodynamics–Stokes system. We perform a linear stability analysis for this system which shows that both pullers and pushers have unstable modes. We conclude by providing extensions of the Vicsek–Stokes model including short-distance repulsion, finite particle inertia and finite Reynolds number fluid regime.

Singh K, Muljadi B, Raeini AQ,
et al., 2019, The architectural design of smart ventilation and drainage systems in termite nests, *Science Advances*, Vol: 5, ISSN: 2375-2548

Termite nests have been widely studied as effective examples for ventilation and thermoregulation;however, the mechanisms by which the nest properties are controlled by the micro-structure of the outer walls remain unclear. Here, we combine multi-scale X-ray imaging with three-dimensional flow field simulations to investigate the impact of the architectural design of nest walls on CO2and heat transport as well as on water drainage. We show that termites construct an outer wall that contains both small and percolating large pores at the micro-scale. The network of larger micro-scale pores in the outer wall provides a permeability that is 1-2 orders of magnitude greater than that of the smaller pores, andaCO2diffusivitythat is a factor of up to eight times larger. The largerpores and resultant high porosity also reduce the solid mass required for nest construction by ~11-14%. This is energetically favorable and reduces the overall weight of the nest, thus lowering the risk of collapse. In addition, the pore network offers enhanced thermal insulation to the inner parts of the nest and allows quick drainage ofrainwater thereby restoring the ventilation and providing structural stability to the wet nest.

Bailo R, Carrillo JA, Degond P, 2019, Pedestrian models based on rational behaviour, Crowd Dynamics, Volume 1, Editors: Bellomo, Gibelli, Publisher: Springer Nature, Pages: 259-292

Following the paradigm set by attraction-repulsion-alignment schemes, a myriad of individual-based models have been proposed to calculate the evolution of abstract agents. While the emergent features of many agent systems have been described astonishingly well with force-based models, this is not the case for pedestrians. Many of the classical schemes have failed to capture the fine detail of crowd dynamics, and it is unlikely that a purely mechanical model will succeed. As a response to the mechanistic literature, we will consider a model for pedestrian dynamics that attempts to reproduce the rational behaviour of individual agents through the means of anticipation. Each pedestrian undergoes a two-step time evolution based on a perception stage and a decision stage. We will discuss the validity of this game theoretical-based model in regimes with varying degrees of congestion, ultimately presenting a correction to the mechanistic model in order to achieve realistic high-density dynamics.

Degond P, Frouvelle A, Merino Aceituno S, et al., 2019, Alignment of self-propelled rigid bodies: from particle systems to macroscopic equations, Stochastic dynamics out of equilibrium, Publisher: Springer Nature, ISSN: 2194-1017

The goal of these lecture notes is to present in a unified wayvarious models for the dynamics of aligning self-propelled rigid bodiesat different scales and the links between them. The models and methodsare inspired from [17,18], but, in addition, we introduce a new modeland apply on it the same methods. While the new model has its owninterest, our aim is also to emphasize the methods by demonstratingtheir adaptability and by presenting them in a unified and simplifiedway. Furthermore, from the various microscopic models we derive thesame macroscopic model, which is a good indicator of its universality.

Aceves-Sanchez P, Bostan M, Carrillo J-A, et al., 2019, Hydrodynamic limits for kinetic flocking models of Cucker-Smale type, Publisher: AMER INST MATHEMATICAL SCIENCES-AIMS

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Motsch S, Moussaid M, Guillot E,
et al., 2018, Modeling crowd dynamics through coarse-grained data analysis, *Mathematical Biosciences and Engineering*, Vol: 15, Pages: 1271-1290, ISSN: 1547-1063

Understanding and predicting the collective behaviour of crowdsis essential to improve the efficiency of pedestrian flows in urban areas andminimize the risks of accidents at mass events. We advocate for the develop-ment of crowd traffic management systems, whereby observations of crowdscan be coupled to fast and reliable models to produce rapid predictions of thecrowd movement and eventually help crowd managers choose between tailoredoptimization strategies. Here, we propose a Bi-directional Macroscopic (BM)model as the core of such a system. Its key input is the fundamental diagramfor bi-directional flows, i.e. the relation between the pedestrian fluxes anddensities. We design and run a laboratory experiments involving a total of119 participants walking in opposite directions in a circular corridor and showthat the model is able to accurately capture the experimental data in a typicalcrowd forecasting situation. Finally, we propose a simple segregation strat-egy for enhancing the traffic efficiency, and use the BM model to determinethe conditions under which this strategy would be beneficial. The BM model,therefore, could serve as a building block to develop on the fly prediction ofcrowd movements and help deploying real-time crowd optimization strategies.

Degond PAA, Minakowski P, Zatorska E, 2018, Transport of congestion in two-phase compressible/incompressible flows, *Nonlinear Analysis: Real World Applications*, Vol: 42, Pages: 485-510, ISSN: 1468-1218

We study the existence of weak solutions to the two-phase fluid model with congestion constraint. The model encompasses the flow in the uncongested regime (compressible) and the congested one (incompressible) with the free boundary separating the two phases. The congested regime appears when the density in the uncongested regime achieves a threshold value that describes the comfort zone of individuals. This quantity is prescribed initially and transported along with the flow. We prove that this system can be approximated by the fully compressible Navier–Stokes system with a singular pressure, supplemented with transport equation for the congestion density. We also present the application of this approximation for the purposes of numerical simulations in the one-dimensional domain.

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