Velocity-induced numerical solutions of reaction-diffusion systems on continuously growing domains

Reaction-diffusion systems have been widely studied in developmental biology, chemistry and more recently in financial mathematics. Most of these systems comprise nonlinear reaction terms which makes it difficult to find closed form solutions. It therefore becomes convenient to look for numerical solutions: finite difference, finite element, finite volume and spectral methods are typical examples of the numerical methods used. Most of these methods are locally based schemes. We examine the implications of mesh structure on numerically computed solutions of a well-studied reaction-diffusion model system on two-dimensional fixed and growing domains. The incorporation of domain growth creates an additional parameter – the grid-point velocity – and this greatly influences the selection of certain symmetric solutions for the ADI finite difference scheme when a uniform square mesh structure is used. Domain growth coupled with grid-point velocity on a uniform square mesh stabilises certain patterns which are however very sensitive to any kind of perturbation in mesh structure. We compare our results to those obtained by use of finite elements on unstructured triangular elements

Stability analysis of non-autonomous reaction-diffusion systems: the effects of growing domains

By using asymptotic theory, we generalise the Turing diffusively-driven instability conditions for reaction-diffusion systems with slow, isotropic domain growth. There are two fundamental biological differences between the Turing conditions on fixed and growing domains, namely: (i) we need not enforce cross nor pure kinetic conditions and (ii) the restriction to activator-inhibitor kinetics to induce pattern formation on a growing biological system is no longer a requirement. Our theoretical findings are confirmed and reinforced by numerical simulations for the special cases of isotropic linear, exponential and logistic growth profiles. In particular we illustrate an example of a reaction-diffusion system which cannot exhibit a diffusively-driven instability on a fixed domain but is unstable in the presence of slow growth

Analysis and simulations of coupled bulk-surface reaction-diffusion systems on exponentially evolving volumes

In this article we present a system of coupled bulk-surface reaction-diffusion equations on exponentially evolving volumes. Detailed linear stability analysis of the homogeneous steady state is carried out. It turns out that due to the nature of the coupling (linear Robin-type boundary conditions) the characterisation of the dispersion relation in the absence and presence of spatial variation (i.e. diffusion), can be decomposed as a product of the dispersion relation of the bulk and surface models thereby allowing detailed analytical tractability. As a result we state and prove the conditions for diffusion-driven instability for systems of coupled bulk-surface reaction-diffusion equations. Furthermore, we plot explicit evolving parameter spaces for the case of an exponential growth. By selecting parameter values from the parameter spaces, we exhibit pattern formation in the bulk and on the surface in complete agreement with theoretical predictions

Characterization of Turing diffusion-driven instability on evolving domains

In this paper we establish a general theoretical framework for Turing diffusion-driven instability for reaction-diffusion systems on time-dependent evolving domains. The main result is that Turing diffusion-driven instability for reaction-diffusion systems on evolving domains is characterised by Lyapunov exponents of the evolution family associated with the linearised system (obtained by linearising the original system along a spatially independent solution). This framework allows for the inclusion of the analysis of the long-time behavior of the solutions of reaction-diffusion systems. Applications to two special types of evolving domains are considered: (i) time-dependent domains which evolve to a final limiting fixed domain and (ii) time-dependent domains which are eventually time periodic. Reaction-diffusion systems have been widely proposed as plausible mechanisms for pattern formation in morphogenesis

A parallel and adaptive multigrid solver for the solutions of the optimal control of geometric evolution laws in two and three dimensions

We present a problem concerning the optimal control of geometric evolution laws. This is a minimisation problem that aims to find a control η which minimises the objective functional J subject to some imposed constraints. We apply this methodology to an application of whole cell tracking. Given two sets of data of cell morphologies, we may solve the optimal control problem to dynamically reconstruct the cell movements between the time frame of these two sets of data. This problem is solved in two and three space dimensions, using a state-of-the-art numerical method, namely multigrid, with adaptivity and parallelism

Global existence for semilinear reaction-diffusion systems on evolving domains

We present global existence results for solutions of reaction-diffusion systems on evolving domains. Global existence results for a class of reaction-diffusion systems on fixed domains are extended to the same systems posed on spatially linear isotropically evolving domains. The results hold without any assumptions on the sign of the growth rate. The analysis is valid for many systems that commonly arise in the theory of pattern formation. We present numerical results illustrating our theoretical findings.Comment: 24 pages, 3 figure

An optimal control approach to cell tracking

Cell tracking is of vital importance in many biological studies, hence robust cell tracking algorithms are needed for inference of dynamic features from (static) in vivo and in vitro experimental imaging data of cells migrating. In recent years much attention has been focused on the modelling of cell motility from physical principles and the development of state-of-the art numerical methods for the simulation of the model equations. Despite this, the vast majority of cell tracking algorithms proposed to date focus solely on the imaging data itself and do not attempt to incorporate any physical knowledge on cell migration into the tracking procedure. In this study, we present a mathematical approach for cell tracking, in which we formulate the cell tracking problem as an inverse problem for fitting a mathematical model for cell motility to experimental imaging data. The novelty of this approach is that the physics underlying the model for cell migration is encoded in the tracking algorithm. To illustrate this we focus on an example of Zebrafish (Danio rerio's larvae) Neutrophil migration and contrast an ad-hoc approach to cell tracking based on interpolation with the model fitting approach we propose in this study

Projected finite elements for reaction-diffusion systems on stationary closed surfaces

This paper presents a robust, efficient and accurate finite element method for solving reaction-diffusion systems on stationary spheroidal surfaces (these are surfaces which are deformations of the sphere such as ellipsoids, dumbbells, and heart-shaped surfaces) with potential applications in the areas of developmental biology, cancer research, wound healing, tissue regeneration, and cell motility among many others where such models are routinely used. Our method is inspired by the radially projected finite element method introduced by Meir and Tuncer (2009), hence the name ``projected'' finite element method. The advantages of the projected finite element method are that it is easy to implement and that it provides a conforming finite element discretization which is ``logically'' rectangular. To demonstrate the robustness, applicability and generality of this numerical method, we present solutions of reaction-diffusion systems on various spheroidal surfaces. We show that the method presented in this paper preserves positivity of the solutions of reaction-diffusion equations which is not generally true for Galerkin type methods. We conclude that surface geometry plays a pivotal role in pattern formation. For a fixed set of model parameter values, different surfaces give rise to different pattern generation sequences of either spots or stripes or a combination (observed as circular spot-stripe patterns). These results clearly demonstrate the need for detailed theoretical analytical studies to elucidate how surface geometry and curvature influence pattern formation on complex surfaces

A mathematical understanding of how cytoplasmic dynein walks on microtubules

Cytoplasmic dynein 1 (hereafter referred to simply as dynein) is a dimeric motor protein that walks and transports intracellular cargos towards the minus end of microtubules. In this article, we formulate, based on physical principles, a mechanical model to describe the stepping behaviour of cytoplasmic dynein walking on microtubules from the cell membrane towards the nucleus. Unlike previous studies on physical models of this nature, we base our formulation on the whole structure of dynein to include the temporal dynamics of the individual subunits such as the cargo ( for example, an endosome, vesicle or bead), two rings of six ATPase domains associated with diverse cellular activities (AAAþ rings) and the microtubule-binding domains which allow dynein to bind to microtubules. This mathematical framework allows us to examine experimental observations on dynein across a wide range of different species, as well as being able to make predictions on the temporal behaviour of the individual components of dynein not currently experimentally measured. Furthermore, we extend the model framework to include backward stepping, variable step size and dwelling. The power of our model is in its predictive nature; first it reflects recent experimental observations that dynein walks on microtubules using a weakly coordinated stepping pattern with predominantly not passing steps. Second, the model predicts that interhead coordination in the ATP cycle of cytoplasmic dynein is important in order to obtain the alternating stepping patterns and long run lengths seen in experiments

Pigmentation pattern formation in butterfly wigns: Global patterns on fore- and hind-wing

Pigmentation patterns in butterfly wings are one of the most spectacular & vivid examples of pattern formation in biology. In this chapter, we devote our attention to the mechanisms for generating global patterns. We focus on the relationship between pattern forming mechanisms for the fore- and hindwing patterns. Through mathematical modeling and computational analysis of Papilio dardanus and polytes, our results indicate that the patterns formed on the forewing need not correlate to those of the hindwing in the sense that the formation mechanism is the same for both patterns. The independence of pattern formation mechanisms means that the coordination of unified patterns of fore- and hindwings is accidental. This is remarkable, because from Oudeman's principle [10], patterns appearing on the exposed surface of fore-and hindwing at the natural resting position are often integrated to form a composite and unified adaptive pattern with their surrounding environment