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Turing patterns in reaction-diffusion (RD) systems have classically been studied only in RD systems which do not explicitly depend on independent variables such as space. In practise, many systems for which Turing patterning is important are not homogeneous with ideal boundary conditions. In heterogeneous systems with stable steady states, the steady states are also necessarily heterogeneous which is problematic for applying the classical analysis. Whilst there has been some work done to extend Turing analysis to some heterogeneous systems, for many systems it is still difficult to determine if a stable patterned state is driven purely by system heterogeneity or if a Turing instability is playing a role. In this work, we try to define a framework which uses numerical continuation to map heterogeneous RD systems onto a sensible nearby homogeneous system. This framework may be used for discussing the role of Turing instabilities in establishing patterns in heterogeneous RD systems. We study the Schnakenberg and Gierer-Meinhardt models with spatially heterogeneous production as test problems. It is shown that for sufficiently large system heterogeneity (large amplitude spatial variations in morphogen production) it is possible that Turing-patterned and base states become coincident and therefore impossible to distinguish. Other exotic behaviour is also shown to be possible. We also study a novel scenario in which morphogen is produced locally at levels that could support Turing patterning but on intervals/patches which are on the scale of classical critical domain lengths. Without classical domain boundaries, Turing patterns are allowed to bleed through; an effect noted by other authors. In this case, this phenomena effectively changes the critical domain length. Indeed, we even note that this phenomena may also effectively couple local patches together and drive instability in this way., 10 figures

Enzyme-catalysed reactions involve two distinct timescales. There is a short timescale on which enzymes bind to substrate molecules to produce bound complexes, and a comparatively long timescale on which the complex is transformed into a product. The rate at which the substrate is converted into product is characteristically non-linear and is traditionally derived by applying of singular perturbation theory to the system's governing equations. Central to this analysis is the assumption that complex formation is effectively instantaneous on the timescale over which significant substrate degradation occurs. This prevents many particle-based simulations of reaction-diffusion systems from accurately modelling enzyme kinetics since they rely on proximity based reaction conditions that do not correctly model the fast reactions associated with the complex on the long timescale. In this paper we derive a new proximity based reaction condition that correctly incorporates the reactions that occur on the short timescale for a specific enzymatic system. We present proof of concept particle-based simulations that demonstrate that non-linear reaction rates typical of enzyme kinetics can be reproduced without needing to explicitly simulate reactions on the short timescale., Comment: 18 pages, 6 figures

Spatial reaction-diffusion models have been employed to describe many emergent phenomena in biological systems. The modelling technique most commonly adopted in the literature implements systems of partial differential equations (PDEs), which assumes there are sufficient densities of particles that a continuum approximation is valid. However, due to recent advances in computational power, the simulation, and therefore postulation, of computationally intensive individual-based models has become a popular way to investigate the effects of noise in reaction-diffusion systems in which regions of low copy numbers exist. The stochastic models with which we shall be concerned in this manuscript are referred to as `compartment-based'. These models are characterised by a discretisation of the computational domain into a grid/lattice of `compartments'. Within each compartment particles are assumed to be well-mixed and are permitted to react with other particles within their compartment or to transfer between neighbouring compartments. We develop two hybrid algorithms in which a PDE is coupled to a compartment-based model. Rather than attempting to balance average fluxes, our algorithms answer a more fundamental question: `how are individual particles transported between the vastly different model descriptions?' First, we present an algorithm derived by carefully re-defining the continuous PDE concentration as a probability distribution. Whilst this first algorithm shows strong convergence to analytic solutions of test problems, it can be cumbersome to simulate. Our second algorithm is a simplified and more efficient implementation of the first, it is derived in the continuum limit over the PDE region alone. We test our hybrid methods for functionality and accuracy in a variety of different scenarios by comparing the averaged simulations to analytic solutions of PDEs for mean concentrations., MAIN - 24 pages, 10 figures, 1 supplementary file - 3 pages, 2 figures