arXiv subjects

Marie Doumic

Publications and source records attributed to Marie Doumic.

At least 19 recordsLinked to original sources

arXiv2026

Steady States of Transport-Coagulation-Nucleation Models

To model the dynamics of polymers formed through nucleation, elongated by polymerisation, shortened by depolymerisation and subject to aggregation reactions, we study a nonlinear integro-differential equation. Growth and shrinkage are described by transport terms, nucleation by a positive boundary condition, and aggregation by a Smoluchowski coagulation kernel. Our main result is the existence of steady states for the multiplicative coagulation kernel despite this kernel producing gelation in finite time for the pure coagulation equation. This is made possible by a sufficiently strong decay rate for large polymers. Beyond the existence result, the qualitative properties of the steady states are illustrated through explicit examples and numerical experiments. The analytical results connect the growth behaviour of the transport velocity and of the coagulation kernel to the decay properties of steady states.

math.AP↗

arXiv2025

Comparison Between Effective and Individual Growth Rates in a Heterogeneous Population

Is there an advantage to heterogeneity in a population where individuals grow and divide by fission? This is a broad question, to which there is no easy universal answer. This article aims to provide a quantitative answer in the specific context of growth rate heterogeneity by comparing the fitness of homogeneous versus heterogeneous populations. We focus on size-structured populations, where the growth rate of each individual is set at birth by heredity and/or random mutations. The fitness (or Malthus parameter, or effective fitness) of such heterogeneous population is defined by its long-term behaviour, and we introduce the effective growth rate as the individual growth rate in the homogeneous population with the same fitness. We derive analytical formulae linking effective and individual growth rates in two paradigmatic cases: first, constant growth and division rates, second, linear growth rates and uniform fragmentation. Surprisingly, these two cases yield similar expressions. Then, by comparing the fitness and the effective growth rates of populations with different degrees of heterogeneity or different laws of heredity/mutation to those of average homogeneous populations, we quantitatively investigate the combined influence of heredity and heterogeneity, and revisit previous results stating that heterogeneity is beneficial in the case of strong heredity.

math.AP↗

arXiv2024

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↗

arXiv2024

Asymptotic approaches in inverse problems for depolymerization estimation

Depolymerization reactions constitute frequent experiments, for instance in biochemistry for the study of amyloid fibrils. The quantities experimentally observed are related to the time dynamics of a quantity averaged over all polymer sizes, such as the total polymerised mass or the mean size of particles. The question analysed here is to link this measurement to the initial size distribution. To do so, we first derive, from the initial reaction system $$\mathcal{C}_i \stackrel{b}{\longrightarrow} \mathcal{C}_{i-1} + \mathcal{C}_1,\qquad i\geq i_0\geq 2,$$ two asymptotic models: at first order, a backward transport equation, and at second order, an advection-diffusion/Fokker-Planck equation complemented with a mixed boundary condition at $x = 0$. We estimate their distance to the original system solution. We then turn to the inverse problem, i.e., how to estimate the initial size distribution from the time measurement of an average quantity, given by a moment of the solution. This question has been already studied for the first order asymptotic model, and we analyse here the second order asymptotic. Thanks to Carleman inequalities and to log-convexity estimates, we prove observability results and error estimates for a Tikhonov regularization. We then develop a Kalman-based observer approach, and implement it on simulated observations. Despite its severely ill-posed character, the second-order approach appears numerically more accurate than the first-order one.

math.AP↗

arXiv2024

Moments approaches for asymptotic inverse problems of depolymerisation and fragmentation systems

Shrinkage of large particles, either through depolymerisation (i.e. progressive shortening) or through fragmentation (breakage into smaller pieces) may be modelled by discrete equations, of Becker-D\''oring type, or by continuous ones. In this note, we review two kinds of inverse problems: the first is the estimation of the initial size-distribution from moments measurements in a depolymerising system, in collaboration with Philippe Moireau and inspired by experiments carried out by Human Rezaei's team; the second is the inference of fragmentation characteristics from size distribution samples, in collaboration with Miguel Escobedo and Magali Tournus, based on biological questions and experiments of Wei-Feng Xue's team.

math.AP↗

arXiv2024

Asymptotic Analysis of a bi-monomeric nonlinear Becker-D{\"o}ring system

To provide a mechanistic explanation of sustained {then} damped oscillations observed in a depolymerisation experiment, a bi-monomeric variant of the seminal Becker-D\"oring system has been proposed in \cite{DFMR}. When all reaction rates are constant, the equations are the following: \begin{align*}\frac{dv}{dt} & =-vw+v\sum_{j=2}^{\infty}c_{j}, \qquad \frac{dw}{dt} =vw-w\sum_{j=1}^{\infty}c_{j}, \\ \frac{dc_{j}}{dt} & =J_{j-1}-J_{j}\ \ ,\ \ j\geq1\ \ ,\ \ \ J_{j}=wc_{j}-vc_{j+1}\ \ ,\ \ j\geq1\ \ ,\ J_{0}=0, \end{align*} where $v$ and $w$ are two distinct unit species, and $c_i$ represents the concentration of clusters containing $i$ units. We study in detail the mechanisms leading to such oscillations and characterise the different phases of the dynamics, from the initial high-amplitude oscillations to the progressive damping leading to the convergence towards the unique positive stationary solution. We give quantitative approximations for the main quantities of interest: period of the oscillations, size of the damping (corresponding to a loss of energy), number of oscillations characterising each phase. We illustrate these results by numerical simulation, in line with the theoretical results, and provide numerical methods to solve the system.

math.AP↗

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↗

arXiv2021

An inverse problem: recovering the fragmentation kernel from the short-time behaviour of the fragmentation equation

The present paper provides a new representation of the solution to the fragmentation equation as a power series in the Banach space of Radon measures endowed with the total variation norm. This representation is used to justify how the fragmentation kernel, which is one of the two key parameters of the fragmentation equation, can be recovered from short-time experimental measurements of the particle size distributions when the initial condition is a delta function. A new stability result for this equation is also provided using a Wasserstein-type norm. We exploit this stability to prove the robustness of our reconstruction formula with respect to noise and initial data.

math.AP↗

arXiv2021

Individual and population approaches for calibrating division rates in population dynamics: Application to the bacterial cell cycle

Modelling, analysing and inferring triggering mechanisms in population reproduction is fundamental in many biological applications. It is also an active and growing research domain in mathematical biology. In this chapter, we review the main results developed over the last decade for the estimation of the division rate in growing and dividing populations in a steady environment. These methods combine tools borrowed from PDE's and stochastic processes, with a certain view that emerges from mathematical statistics. A focus on the application to the bacterial cell division cycle provides a concrete presentation, and may help the reader to identify major new challenges in the field.

math.AP↗

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

A mathematical model of p62-ubiquitin aggregates in autophagy

Aggregation of ubiquitinated cargo by oligomers of the protein p62 is an important preparatory step in cellular autophagy. In this work a mathematical model for the dynamics of these heterogeneous aggregates in the form of a system of ordinary differential equations is derived and analyzed. Three different parameter regimes are identified, where either aggregates are unstable, or their size saturates at a finite value, or their size grows indefinitely as long as free particles are abundant. The boundaries of these regimes as well as the finite size in the second case can be computed explicitly. The growth in the third case (quadratic in time) can also be made explicit by formal asymptotic methods. The qualitative results are illustrated by numerical simulations. A comparison with recent experimental results permits a partial parametrization of the model.

cond-mat.stat-mech↗

arXiv2019

Testing for high frequency features in a noisy signal

Given nonstationary data, one generally wants to extract the trend from the noise by smoothing or filtering. However, it is often important to delineate a third intermediate category, that we call high frequency (HF) features: this is the case in our motivating example, which consists in experimental measurements of the time-dynamics of depolymerising protein fibrils average size. One may intuitively visualise HF features as the presence of fast, possibly nonstationary and transient oscillations, distinct from a slowly-varying trend envelope. The aim of this article is to propose an empirical definition of HF features and construct estimators and statistical tests for their presence accordingly, when the data consists of a noisy nonstationary 1-dimensional signal. We propose a parametric characterization in the Fourier domain of the HF features by defining a maximal amplitude and distance to low frequencies of significant energy. We introduce a data-driven procedure to estimate these parameters, and compute a p-value proxy based on a statistical test for the presence of HF features. The test is first conducted on simulated signals where the ratio amplitude of the HF features to the level of the noise is controlled. The test detects HF features even when the level of noise is five times larger than the amplitude of the oscillations. In a second part, the test is conducted on experimental data from Prion disease experiments and it confirms the presence of HF features in these signals with significant confidence.

eess.SP↗

arXiv2019

Estimating the division rate from indirect measurements of single cells

Is it possible to estimate the dependence of a growing and dividing population on a given trait in the case where this trait is not directly accessible by experimental measurements, but making use of measurements of another variable? This article adresses this general question for a very recent and popular model describing bacterial growth, the so-called incremental or adder model. In this model, the division rate depends on the increment of size between birth and division, whereas the most accessible trait is the size itself. We prove that estimating the division 10 rate from size measurements is possible, we state a reconstruction formula in a deterministic and then in a statistical setting, and solve numerically the problem on simulated and experimental data. Though this represents a severely ill-posed inverse problem, our numerical results prove to be satisfactory.

math.ST↗

arXiv2018

Explicit Solution and Fine Asymptotics for a Critical Growth-Fragmentation Equation

We give here an explicit formula for the following critical case of the growth-fragmentation equation $$\frac{\partial}{\partial t} u(t, x) + \frac{\partial}{\partial x} (gxu(t, x)) + bu(t, x) = bα^2 u(t, αx), \qquad u(0, x) = u\_0 (x),$$ for some constants $g > 0$, $b > 0$ and $α> 1$ - the case $α= 2$ being the emblematic binary fission case. We discuss the links between this formula and the asymptotic ones previously obtained in (Doumic, Escobedo, Kin. Rel. Mod., 2016), and use them to clarify how periodicity may appear asymptotically.

math.AP↗

arXiv2018

Long-time asymptotics for polymerization models

This study is devoted to the long-term behavior of nucleation, growth and fragmentation equations, modeling the spontaneous formation and kinetics of large polymers in a spatially homogeneous and closed environment. Such models are, for instance, commonly used in the biophysical community in order to model in vitro experiments of fibrillation. We investigate the interplay between four processes: nucleation, polymeriza-tion, depolymerization and fragmentation. We first revisit the well-known Lifshitz-Slyozov model, which takes into account only polymerization and depolymerization, and we show that, when nucleation is included, the system goes to a trivial equilibrium: all polymers fragmentize, going back to very small polymers. Taking into account only polymerization and fragmentation, modeled by the classical growth-fragmentation equation, also leads the system to the same trivial equilibrium, whether or not nucleation is considered. However, also taking into account a depolymer-ization reaction term may surprisingly stabilize the system, since a steady size-distribution of polymers may then emerge, as soon as polymeriza-tion dominates depolymerization for large sizes whereas depolymerization dominates polymerization for smaller ones-a case which fits the classical assumptions for the Lifshitz-Slyozov equations, but complemented with fragmentation so that " Ostwald ripening " does not happen.

math.AP↗

arXiv2018

Cyclic asymptotic behaviour of a population reproducing by fission into two equal parts

We study the asymptotic behaviour of the following linear growth-fragmentation equation$$\dfrac{\partial}{\partial t} u(t,x) + \dfrac{\partial}{\partial x} \big(x u(t,x)\big) + B(x) u(t,x) =4 B(2x)u(t,2x),$$ and prove that under fairly general assumptions on the division rate $B(x),$ its solution converges towards an oscillatory function,explicitely given by the projection of the initial state on the space generated by the countable set of the dominant eigenvectors of the operator. Despite the lack of hypo-coercivity of the operator, the proof relies on a general relative entropy argument in a convenient weighted $L^2$ space, where well-posedness is obtained via semigroup analysis. We also propose a non-dissipative numerical scheme, able to capture the oscillations.

math.AP↗

arXiv2018

Estimating the division rate and kernel in the fragmentation equation

We consider the fragmentation equation $\dfrac{\partial}{\partial t}f (t, x) = --B(x)f (t, x) + \int\_{ y=x}^{ y=\infty} k(y, x)B(y)f (t, y)dy,$ and address the question of estimating the fragmentation parameters-i.e. the division rate $B(x)$ and the fragmentation kernel $k(y, x)$-from measurements of the size distribution $f (t, $\times$)$ at various times. This is a natural question for any application where the sizes of the particles are measured experimentally whereas the fragmentation rates are unknown, see for instance (Xue, Radford, Biophys. Journal, 2013) for amyloid fibril breakage. Under the assumption of a polynomial division rate $B(x) = αx^γ$ and a self-similar fragmentation kernel $k(y, x) = \frac{1}{y} k\_0 (x/ y)$, we use the asymptotic behaviour proved in (Escobedo, Mischler, Rodriguez-Ricard, Ann. IHP, 2004) to obtain uniqueness of the triplet $(α, γ, k \_0)$ and a representation formula for $k\_0$. To invert this formula, one of the delicate points is to prove that the Mellin transform of the asymptotic profile never vanishes, what we do through the use of the Cauchy integral.

math.AP↗

arXiv2018

Relative Entropy Method for Measure Solutions of the Growth-Fragmentation Equation

The aim of this study is to generalise recent results of the two last authors on en-tropy methods for measure solutions of the renewal equation to other classes of structured population problems. Specifically, we develop a generalised relative entropy inequality for the growth-fragmentation equation and prove asymptotic convergence to a steady-state solution, even when the initial datum is only a non-negative measure.

math.AP↗