A one-dimensional Keller-Segel equation with a drift issued from the boundary

We investigate in this note the dynamics of a one-dimensional Keller-Segel type model on the half-line. On the contrary to the classical configuration, the chemical production term is located on the boundary. We prove, under suitable assumptions, the following dichotomy which is reminiscent of the two-dimensional Keller-Segel system. Solutions are global if the mass is below the critical mass, they blow-up in finite time above the critical mass, and they converge to some equilibrium at the critical mass. Entropy techniques are presented which aim at providing quantitative convergence results for the subcritical case. This note is completed with a brief introduction to a more realistic model (still one-dimensional).Comment: short version, 8 page

A stochastic model for protrusion activity

In this work we approach cell migration under a large-scale assumption, so that the system reduces to a particle in motion. Unlike classical particle models, the cell displacement results from its internal activity: the cell velocity is a function of the (discrete) protrusive forces exerted by filopodia on the substrate. Cell polarisation ability is modeled in the feedback that the cell motion exerts on the protrusion rates: faster cells form preferentially protrusions in the direction of motion. By using the mathematical framework of structured population processes previously developed to study population dynamics [Fournier and M{\'e}l{\'e}ard, 2004], we introduce rigorously the mathematical model and we derive some of its fundamental properties. We perform numerical simulations on this model showing that different types of trajectories may be obtained: Brownian-like, persistent, or intermittent when the cell switches between both previous regimes. We find back the trajectories usually described in the literature for cell migration

Numerical simulation of the dynamics of molecular markers involved in cell polarisation

A cell is polarised when it has developed a main axis of organisation through the reorganisation of its cytosqueleton and its intracellular organelles. Polarisation can occur spontaneously or be triggered by external signals, like gradients of signaling molecules ... In this work, we study mathematical models for cell polarisation. These models are based on nonlinear convection-diffusion equations. The nonlinearity in the transport term expresses the positive loop between the level of protein concentration localised in a small area of the cell membrane and the number of new proteins that will be convected to the same area. We perform numerical simulations and we illustrate that these models are rich enough to describe the apparition of a polarisome.Comment: 15 page

Proving the Turing Universality of Oritatami Co-Transcriptional Folding (Full Text)

We study the oritatami model for molecular co-transcriptional folding. In oritatami systems, the transcript (the "molecule") folds as it is synthesized (transcribed), according to a local energy optimisation process, which is similar to how actual biomolecules such as RNA fold into complex shapes and functions as they are transcribed. We prove that there is an oritatami system embedding universal computation in the folding process itself. Our result relies on the development of a generic toolbox, which is easily reusable for future work to design complex functions in oritatami systems. We develop "low-level" tools that allow to easily spread apart the encoding of different "functions" in the transcript, even if they are required to be applied at the same geometrical location in the folding. We build upon these low-level tools, a programming framework with increasing levels of abstraction, from encoding of instructions into the transcript to logical analysis. This framework is similar to the hardware-to-algorithm levels of abstractions in standard algorithm theory. These various levels of abstractions allow to separate the proof of correctness of the global behavior of our system, from the proof of correctness of its implementation. Thanks to this framework, we were able to computerize the proof of correctness of its implementation and produce certificates, in the form of a relatively small number of proof trees, compact and easily readable and checkable by human, while encapsulating huge case enumerations. We believe this particular type of certificates can be generalized to other discrete dynamical systems, where proofs involve large case enumerations as well

A congestion model for cell migration

This paper deals with a class of macroscopic models for cell migration in a saturated medium for two-species mixtures. Those species tend to achieve some motion according to a desired velocity, and congestion forces them to adapt their velocity. This adaptation is modelled by a correction velocity which is chosen minimal in a least-square sense. We are especially interested in two situations: a single active species moves in a passive matrix (cell migration) with a given desired velocity, and a closed-loop Keller-Segel type model, where the desired velocity is the gradient of a self-emitted chemoattractant. We propose a theoretical framework for the open-loop model (desired velocities are defined as gradients of given functions) based on a formulation in the form of a gradient flow in the Wasserstein space. We propose a numerical strategy to discretize the model, and illustrate its behaviour in the case of a prescribed velocity, and for the saturated Keller-Segel model

Numerical solutions of a 2D fluid problem coupled to a nonlinear non-local reaction-advection-diffusion problem for cell crawling migration in a discoidal domain

In this work, we present a numerical scheme for the approximate solutions of a 2D crawling cell migration problem. The model, defined on a non-deformable discoidal domain, consists in a Darcy fluid problem coupled with a Poisson problem and a reaction-advection-diffusion problem. Moreover, the advection velocity depends on boundary values, making the problem nonlinear and non local. \parFor a discoidal domain, numerical solutions can be obtained using the finite volume method on the polar formulation of the model. Simulations show that different migration behaviours can be captured

The "strange term" in the periodic homogenization for multivalued Leray-Lions operators in perforated domains

International audienceUsing the periodic unfolding method of Cioranescu, Damlamian and Griso, we study the homogenization for equations of the form -\Div d_\varepsilon=f,\text{ with }\bigl(\nabla u_{\varepsilon , \delta }(x),d_{\varepsilon , \delta }(x)\bigr) \in A_\varepsilon(x) in a perforated domain with holes of size $\varepsilon \delta$ periodically distributed in the domain, where $A_\varepsilon$ is a function whose values are maximal monotone graphs (on $\R^{N})$. Two different unfolding operators are involved in such a geometric situation. Under appropriate growth and coercivity assumptions, if the corresponding two sequences of unfolded maximal monotone graphs converge in the graph sense to the maximal monotone graphs $A(x,y)$ and $A_0(x,z)$ for almost every $(x,y,z)\in \Omega \times Y \times \R^N$, as $\varepsilon \to 0$, then every cluster point $(u_0,d_0)$ of the sequence $(u_{\varepsilon , \delta }, d_{\varepsilon , \delta } )$ for the weak topology in the naturally associated Sobolev space is a solution of the homogenized problem which is expressed in terms of $u_0$ alone. This result applies to the case where $A_{\varepsilon}(x)$ is of the form $B(x/\varepsilon)$ where $B(y)$ is periodic and continuous at $y=0$, and, in particular, to the oscillating $p$-Laplacian

Numerical simulation on a cell polarisation model: the polar case

20 pagesWhen it is polarised, a cell develops an asymmetric distribution of specific molecular markers, cytoskeleton and cell membrane shape. Polarisation can occur spontaneously or be triggered by external signals, like gradients of signalling molecules... In this work, we use the published models of cell polarisation and we set a numerical analysis for these models. They are based on nonlinear convection-diffusion equations and the nonlinearity in the transport term expresses the positive loop between the level of protein concentration localised in a small area of the cell membrane and the number of new proteins that will be convected to the same area. We perform numerical simulations and we illustrate that these models are rich enough to describe the apparition of a polarisome

Elastic limit of square lattices with three point interactions

26 pagesInternational audienceWe derive the equivalent energy of a square lattice that either deforms into the three-dimensional Euclidean space or remains planar. Interactions are not restricted to pairs of points and take into account changes of angles. Under some relationships between the local energies associated with the four vertices of an elementary square, we show that the limit energy can be obtained by mere quasiconvexification of the elementary cell energy and that the limit process does not involve any relaxation at the atomic scale. In this case, it can be said that the Cauchy-Born rule holds true. Our results apply to classical models of mechanical trusses that include torques between adjacent bars and to atomic models