Mathematical models for cellular aggregation: the chemotactic instability and clustering formation

In this thesis we present a mathematical formulation of the interaction between microorganisms such as bacteria or amoebae and chemicals, often produced by the organisms themselves. This interaction is called chemotaxis and leads to cellular aggregation. We derive some models to describe chemotaxis. The first is the pioneristic Keller-Segel parabolic-parabolic model and it is derived by two different frameworks: a macroscopic perspective and a microscopic perspective, in which we start with a stochastic differential equation and we perform a mean-field approximation. This parabolic model may be generalized by the introduction of a degenerate diffusion parameter, which depends on the density itself via a power law. Then we derive a model for chemotaxis based on Cattaneo's law of heat propagation with finite speed, which is a hyperbolic model. The last model proposed here is a hydrodynamic model, which takes into account the inertia of the system by a friction force. In the limit of strong friction, the model reduces to the parabolic model, whereas in the limit of weak friction, we recover a hyperbolic model. Finally, we analyze the instability condition, which is the condition that leads to aggregation, and we describe the different kinds of aggregates we may obtain: the parabolic models lead to clusters or peaks whereas the hyperbolic models lead to the formation of network patterns or filaments. Moreover, we discuss the analogy between bacterial colonies and self gravitating systems by comparing the chemotactic collapse and the gravitational collapse (Jeans instability).

Symbolic dynamics generated by a hybrid chaotic systems

We consider piecewise defined differential dynamical systems which can be analysed through symbolic dynamics and transition matrices. We have a continuous regime, where the time flow is characterized by an ordinary differential equation (ODE) which has explicit solutions, and the singular regime, where the time flow is characterized by an appropriate transformation. The symbolic codification is given through the association of a symbol for each distinct regular system and singular system. The transition matrices are then determined as linear approximations to the symbolic dynamics. We analyse the dependence on initial conditions, parameter variation and the occurrence of global strange attractors.

Unbounded solutions for functional problems on the half-line

This paper presents an existence and localization result of unbounded solutions for a second-order differential equation on the half-line with functional boundary conditions. By applying unbounded upper and lower solutions, Green's functions and Schauder fixed point theorem, the existence of at least one solution is shown for the above problem. One example and one application to an Emden-Fowler equation are shown to illustrate our results.

Unbounded solutions for functional problems on the half-line

This paper presents an existence and localization result of unbounded solutions for a second-order differential equation on the half-line with functional boundary conditions. By applying unbounded upper and lower solutions, Green's functions and Schauder fixed point theorem, the existence of at least one solution is shown for the above problem. One example and one application to an Emden-Fowler equation are shown to illustrate our results.

A staggered approach for the coupling of Cahn–Hilliard type diffusion and finite strain elasticity

We develop an algorithm and computational implementation for simulation of problems that combine Cahn–Hilliard type diffusion with finite strain elasticity. We have in mind applications such as the electro-chemo- mechanics of lithium ion (Li-ion) batteries. We concentrate on basic computational aspects. A staggered algorithm is pro- posed for the coupled multi-field model. For the diffusion problem, the fourth order differential equation is replaced by a system of second order equations to deal with the issue of the regularity required for the approximation spaces. Low order finite elements are used for discretization in space of the involved fields (displacement, concentration, nonlocal concentration). Three (both 2D and 3D) extensively worked numerical examples show the capabilities of our approach for the representation of (i) phase separation, (ii) the effect of concentration in deformation and stress, (iii) the effect of Electronic supplementary material The online version of this article (doi:10.1007/s00466-015-1235-1) contains supplementary material, which is available to authorized users. B P. Areias pmaa@uevora.pt 1 Department of Physics, University of Évora, Colégio Luís António Verney, Rua Romão Ramalho, 59, 7002-554 Évora, Portugal 2 ICIST, Lisbon, Portugal 3 School of Engineering, Universidad de Cuenca, Av. 12 de Abril s/n. 01-01-168, Cuenca, Ecuador 4 Institute of Structural Mechanics, Bauhaus-University Weimar, Marienstraße 15, 99423 Weimar, Germany strain in concentration, and (iv) lithiation. We analyze con- vergence with respect to spatial and time discretization and found that very good results are achievable using both a stag- gered scheme and approximated strain interpolation.

Uso do R-shiny para execução de modelos matemáticos via web: estudo de caso sobre a dinâmica de propagação do HLB do citros.

RESUMO - O Huanglongbing (HLB ou Greening) é a doença mais importante e destrutiva da citricultura mundial. Presente de forma endêmica nos continentes asiático e africano há várias décadas, essa doença foi constatada no Brasil em 2004, sendo transmitida pelo psilídeo Diaphorina citri e causada por bactérias de floema Candidatus Liberibacter spp. Para auxiliar o estudo da doença, foram desenvolvidos modelos matemáticos para avaliação da propagação do HLB Citros. Este trabalho tem por objetivo a criação de um sistema para execução via web de um destes modelos, permitindo aos profissionais de diversas formações, em especial os das áreas biológicas, que são os especialistas do domínio em estudo, acesso rápido aos resultados fornecidos pelo modelo matemático, eliminando ainda a necessidade de conhecimento prévio em alguma linguagem de programação ou de métodos de resolução de equações diferenciais. O sistema foi completamente implementado em R, tendo sido o pacote deSolve usado para solução do modelo matemático e o framework web Shiny para a interface com usuário, sendo todos open source.

Neurogeometry of stereo vision

This work aims to develop a neurogeometric model of stereo vision, based on cortical architectures involved in the problem of 3D perception and neural mechanisms generated by retinal disparities. First, we provide a sub-Riemannian geometry for stereo vision, inspired by the work on the stereo problem by Zucker (2006), and using sub-Riemannian tools introduced by Citti-Sarti (2006) for monocular vision. We present a mathematical interpretation of the neural mechanisms underlying the behavior of binocular cells, that integrate monocular inputs. The natural compatibility between stereo geometry and neurophysiological models shows that these binocular cells are sensitive to position and orientation. Therefore, we model their action in the space R3xS2 equipped with a sub-Riemannian metric. Integral curves of the sub-Riemannian structure model neural connectivity and can be related to the 3D analog of the psychophysical association fields for the 3D process of regular contour formation. Then, we identify 3D perceptual units in the visual scene: they emerge as a consequence of the random cortico-cortical connection of binocular cells. Considering an opportune stochastic version of the integral curves, we generate a family of kernels. These kernels represent the probability of interaction between binocular cells, and they are implemented as facilitation patterns to define the evolution in time of neural population activity at a point. This activity is usually modeled through a mean field equation: steady stable solutions lead to consider the associated eigenvalue problem. We show that three-dimensional perceptual units naturally arise from the discrete version of the eigenvalue problem associated to the integro-differential equation of the population activity.

Scale-invariant moving finite elements for nonlinear partial differential equations in two dimensions

A scale-invariant moving finite element method is proposed for the adaptive solution of nonlinear partial differential equations. The mesh movement is based on a finite element discretisation of a scale-invariant conservation principle incorporating a monitor function, while the time discretisation of the resulting system of ordinary differential equations is carried out using a scale-invariant time-stepping which yields uniform local accuracy in time. The accuracy and reliability of the algorithm are successfully tested against exact self-similar solutions where available, and otherwise against a state-of-the-art h-refinement scheme for solutions of a two-dimensional porous medium equation problem with a moving boundary. The monitor functions used are the dependent variable and a monitor related to the surface area of the solution manifold. (c) 2005 IMACS. Published by Elsevier B.V. All rights reserved.

Velocity-based moving mesh methods for nonlinear partial differential equations

This article describes a number of velocity-based moving mesh numerical methods formultidimensional nonlinear time-dependent partial differential equations (PDEs). It consists of a short historical review followed by a detailed description of a recently developed multidimensional moving mesh finite element method based on conservation. Finite element algorithms are derived for both mass-conserving and non mass-conserving problems, and results shown for a number of multidimensional nonlinear test problems, including the second order porous medium equation and the fourth order thin film equation as well as a two-phase problem. Further applications and extensions are referenced.

Nonlinear Time-Fractional Differential Equations in Combustion Science

MSC 2010: 34A08 (main), 34G20, 80A25

On Modified Method of Simplest Equation for Obtaining Exact Solutions of Nonlinear PDEs: Case of Elliptic Simplest Equation

2010 Mathematics Subject Classification: 74J30, 34L30.

Combining Legendre's Polynomials and Genetic Algorithm in the Solution of Nonlinear Initial-Value Problems

This work develops a method for solving ordinary differential equations, that is, initial-value problems, with solutions approximated by using Legendre's polynomials. An iterative procedure for the adjustment of the polynomial coefficients is developed, based on the genetic algorithm. This procedure is applied to several examples providing comparisons between its results and the best polynomial fitting when numerical solutions by the traditional Runge-Kutta or Adams methods are available. The resulting algorithm provides reliable solutions even if the numerical solutions are not available, that is, when the mass matrix is singular or the equation produces unstable running processes.

Nonlinear waves in a quark gluon plasma

We study the propagation of perturbations in the quark gluon plasma. This subject has been addressed in other works and in most of the theoretical descriptions of this phenomenon the hydrodynamic equations have been linearized for simplicity. We propose an alternative approach, also based on hydrodynamics but taking into account the nonlinear terms of the equations. We show that these terms may lead to localized waves or even solitons. We use a simple equation of state for the QGP and expand the hydrodynamic equations around equilibrium configurations. The resulting differential equations describe the propagation of perturbations in the energy density. We solve them numerically and find that localized perturbations can propagate for long distances in the plasma. Under certain conditions our solutions mimic the propagation of Korteweg-de Vries solitons.

On a class of abstract neutral functional differential equations

By using the theory of semigroups of growth a, we discuss the existence of mild solutions for a class of abstract neutral functional differential equations. A concrete application to partial neutral functional differential equations is considered. (C) 2011 Elsevier Ltd. All rights reserved.