arXiv subjects

Diane Peurichard

Publications and source records attributed to Diane Peurichard.

15 recordsLinked to original sources

arXiv2025

Scaling limits for a population model with growth, division and cross-diffusion

Originally motivated by the morphogenesis of bacterial microcolonies, the aim of this article is to explore models through different scales for a spatial population of interacting, growing and dividing particles. We start from a microscopic stochastic model, write the corresponding stochastic differential equation satisfied by the empirical measure, and rigorously derive its mesoscopic (mean-field) limit. Under smoothness and symmetry assumptions for the interaction kernel, we then obtain entropy estimates, which provide us with a localization limit at the macroscopic level. Finally, we perform a thorough numerical study in order to compare the three modeling scales.

math.AP↗

arXiv2023

Fiber crosslinking drives the emergence of order in a 3D dynamical network model

The Extra-Cellular-Matrix (ECM) is a complex interconnected 3D network that provides structural support for the cells and tissues and defines organ architecture key for their healthy functioning. However, the intimate mechanisms by which ECM acquire their 3D architecture are still largely unknown. In this paper, we address this question by means of a 3D individual based model of interacting fibers able to spontaneously crosslink or unlink to each other and align at the crosslinks. We show that such systems are able to spontaneously generate different types of architectures. We provide a thorough analysis of the emerging structures by an exhaustive parametric analysis and the use of appropriate visualization tools and quantifiers in 3D. The most striking result is that the emergence of ordered structures can be fully explained by a single emerging variable : the proportion of crosslinks in the network. This simple variable becomes an important putative target to control and predict the structuring of biological tissues, to suggest possible new therapeutic strategies to restore tissue functions after disruption, and to help in the development of collagen-based scaffolds for tissue engineering. Moreover, the model reveals that the emergence of architecture is a spatially homogeneous process following a unique evolutionary path, and highlights the essential role of dynamical crosslinking in tissue structuring.

physics.bio-ph↗

arXiv2023

Multispecies cross-diffusions: from a nonlocal mean-field to a porous medium system without self-diffusion

Systems describing the long-range interaction between individuals have attracted a lot of attention in the last years, in particular in relation with living systems. These systems are quadratic, written under the form of transport equations with a nonlocal self-generated drift. We establish the localisation limit, that is the convergence of nonlocal to local systems, when the range of interaction tends to 0. These theoretical results are sustained by numerical simulations. The major new feature in our analysis is that we do not need diffusion to gain compactness, at odd with the existing literature. The central compactness result is provided by a full rank assumption on the interaction kernels. In turn, we prove existence of weak solutions for the resulting system, a cross-diffusion system of quadratic type.

math.AP↗

arXiv2022

Asymptotic preserving schemes for nonlinear kinetic equations leading to volume-exclusion chemotaxis in the diffusive limit

In this work we first prove, by formal arguments, that the diffusion limit of nonlinear kinetic equations, where both the transport term and the turning operator are density-dependent, leads to volume-exclusion chemotactic equations. We generalise an asymptotic preserving scheme for such nonlinear kinetic equations based on a micro-macro decomposition. By properly discretizing the nonlinear term implicitly-explicitly in an upwind manner, the scheme produces accurate approximations also in the case of strong chemosensitivity. We show, via detailed calculations, that the scheme presents the following properties: asymptotic preserving, positivity preserving and energy dissipation, which are essential for practical applications. We extend this scheme to two dimensional kinetic models and we validate its efficiency by means of 1D and 2D numerical experiments of pattern formation in biological systems.

math.AP↗

arXiv2022

How environment affects active particle swarms: a case study

We investigate the collective motion of self-propelled agents in an environment filled with obstacles that are tethered to fixed positions via springs. The active particles are able to modify the environment by moving the obstacles through repulsion forces. This creates feedback interactions between the particles and the obstacles from which a breadth of patterns emerges (trails, band, clusters, honey-comb structures,...). We will focus on a discrete model first introduced in [Aceves2020] and derived into a continuum PDE model. As a first major novelty, we perform an in-depth investigation of pattern formation of the discrete and continuum models in 2D: we provide phase-diagrams and determine the key mechanisms for bifurcations to happen using linear stability analysis. As a result, we discover that the agent-agent repulsion, the agent-obstacle repulsion and the obstacle's spring stiffness are the key forces in the appearance of patterns, while alignment forces between the particles play a secondary role. The second major novelty lies in the development of an innovative methodology to compare discrete and continuum models that we apply here to perform an in-depth analysis of the agreement between the discrete and continuum models.

math-ph↗

arXiv2021

Treatment-induced shrinking of tumour aggregates: A nonlinear volume-filling chemotactic approach

Motivated by experimental observations in 3D/organoid cultures derived from glioblastoma, we develop a mathematical model where tumour aggregate formation is obtained as the result of nutrient-limited cell proliferation coupled with chemotaxis-based cell movement. The introduction of a chemotherapeutic treatment induces mechanical changes at the cell level, with cells undergoing a transition from rigid bodies to semi-elastic entities. We analyse the influence of these individual mechanical changes on the properties of the aggregates obtained at the population level by introducing a nonlinear volume-filling chemotactic system of partial differential equations. The elastic properties of the cells are taken into account through the so-called squeezing probability, which allows us to change the packing capacity of the aggregates, depending on the concentration of the treatment in the extracellular microenvironment. We explore two scenarios for the effect of the treatment: firstly, the treatment acts only on the mechanical properties of the cells and, secondly, we assume it also prevents cell proliferation. A linear stability analysis enables us to study the ability of the system to create patterns. We provide numerical simulations in 1D and 2D that illustrate the shrinking of the aggregates due to the presence of the treatment.

nlin.PS↗

arXiv2020

A purely mechanical model with asymmetric features for early morphogenesis of rod-shaped bacteria micro-colony

To model the morphogenesis of rod-shaped bacterial micro-colony, several individual-based models have been proposed in the biophysical literature. When studying the shape of micro-colonies, most models present interaction forces such as attraction or filial link. In this article, we propose a model where the bacteria interact only through non-overlapping constraints. We consider the asymmetry of the bacteria, and its influence on the friction with the substrate. Besides, we consider asymmetry in the mass distribution of the bacteria along their length. These two new modelling assumptions allow us to retrieve mechanical behaviours of micro-colony growth without the need of interaction such as attraction. We compare our model to various sets of experiments, discuss our results, and propose several quantifiers to compare model to data in a systematic way.

q-bio.CB↗

arXiv2020

Large-scale dynamics of self-propelled particles moving through obstacles: model derivation and pattern formation

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

math.AP↗

arXiv2020

Modelling adhesion-independent cell migration

A two-dimensional mathematical model for cells migrating without adhesion capabilities is presented and analyzed. Cells are represented by their cortex, which is modelled as an elastic curve, subject to an internal pressure force. Net polymerization or depolymerization in the cortex is modelled via local addition or removal of material, driving a cortical flow. The model takes the form of a fully nonlinear degenerate parabolic system. An existence analysis is carried out by adapting ideas from the theory of gradient flows. Numerical simulations show that these simple rules can account for the behavior observed in experiments, suggesting a possible mechanical mechanism for adhesion-independent motility.

math.AP↗

arXiv2019

Extra-cellular matrix rigidity may dictate the fate of injury outcome

After injury, if 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 cues between 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.

q-bio.TO↗

arXiv2018

Modelling cell-cell collision and adhesion with the Filament Based Lamellipodium Model

We extend the live-cell motility Filament Based Lamellipodium Model to incorporate the forces exerted on the lamellipodium of the cells due to cell-cell collision and cadherin induced cell-cell adhesion. We take into account the nature of these forces via physical and biological constraints and modelling assumptions. We investigate the effect these new components have in the migration and morphology of the cells through particular experiments. We exhibit moreover the similarities between our simulated cells and HeLa cancer cells.

q-bio.CB↗

arXiv2017

Simple mechanical cues could explain adipose tissue morphology

The mechanisms by which organs acquire their functional structure and realize its maintenance (or homeostasis) over time are still largely unknown. In this paper, we investigate this question on adipose tissue. Adipose tissue can represent 20 to 50% of the body weight. Its investigation is key to overcome a large array of metabolic disorders that heavily strike populations worldwide. Adipose tissue consists of lobular clusters of adipocytes surrounded by an organized collagen fiber network. By supplying substrates needed for adipogenesis, vasculature was believed to induce the regroupment of adipocytes near capillary extremities. This paper shows that the emergence of these structures could be explained by simple mechanical interactions between the adipocytes and the collagen fibers. Our assumption is that the fiber network resists the pressure induced by the growing adipocytes and forces them to regroup into clusters. Reciprocally, cell clusters force the fibers to merge into a well-organized network. We validate this hypothesis by means of a two-dimensional Individual Based Model (IBM) of interacting adipocytes and extra-cellular-matrix fiber elements. The model produces structures that compare quantitatively well to the experimental observations. Our model seems to indicate that cell clusters could spontaneously emerge as a result of simple mechanical interactions between cells and fibers and surprisingly, vasculature is not directly needed for these structures to emerge.

physics.med-ph↗

arXiv2017

Particle interactions mediated by dynamical networks: assessment of macroscopic descriptions

We provide a numerical study of the macroscopic model of [3] derived from an agent-based model for a system of particles interacting through a dynamical network of links. Assuming that the network remodelling process is very fast, the macroscopic model takes the form of a single aggregation diffusion equation for the density of particles. The theoretical study of the macroscopic model gives precise criteria for the phase transitions of the steady states, and in the 1-dimensional case, we show numerically that the stationary solutions of the microscopic model undergo the same phase transitions and bifurcation types as the macroscopic model. In the 2-dimensional case, we show that the numerical simulations of the macroscopic model are in excellent agreement with the predicted theoretical values. This study provides a partial validation of the formal derivation of the macroscopic model from a microscopic formulation and shows that the former is a consistent approximation of an underlying particle dynamics, making it a powerful tool for the modelling of dynamical networks at a large scale.

cond-mat.stat-mech↗

arXiv2017

From short-range repulsion to Hele-Shaw problem in a model of tumor growth

We investigate the large time behavior of an agent based model describing tumor growth. The microscopic model combines short-range repulsion and cell division. As the number of cells increases exponentially in time, the microscopic model is challenging in terms of computational time. To overcome this problem, we aim at deriving the associated macroscopic dynamics leading here to a porous media type equation. As we are interested in the long time behavior of the dynamics, the macroscopic equation obtained through usual derivation method fails at providing the correct qualitative behavior (e.g. stationary states differ from the microscopic dynamics). We propose a modified version of the macroscopic equation introducing a density threshold for the repulsion. We numerically validate the new formulation by comparing the solutions of the micro- and macro- dynamics. Moreover, we study the asymptotic behavior of the dynamics as the repulsion between cells becomes singular (leading to non-overlapping constraints in the microscopic model). We manage to show formally that such an asymptotic limit leads to a Hele-Shaw type problem for the macroscopic dynamics. The macroscopic model derived in this paper therefore enables to overcome the problem of large computational time raised by the microscopic model and stays closely linked to the microscopic dynamics.

cond-mat.soft↗

arXiv2015

Continuum model for linked fibers with alignment interactions

We introduce an individual-based model for fiber elements having the ability to cross-link or unlink each other and to align with each other at the cross links. We first formally derive a kinetic model for the fiber and cross-links distribution functions. We then consider the fast linking/unlinking regime in which the model can be reduced to the fiber distribution function only and investigate its diffusion limit. The resulting macroscopic model consists of a system of nonlinear diffusion equations for the fiber density and mean orientation. In the case of a homogeneous fiber density, we show that the model is elliptic.

math-ph↗