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Register a new userStationary peaks in a multivariable reaction--diffusion system: Foliated snaking due to subcritical Turing instability
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An activator-inhibitor-substrate model of side-branching used in the context of pulmonary vascular and lung development is considered on the supposition that spatially localized concentrations of the activator trigger local side-branching. The model consists of four coupled reaction-diffusion equations and its steady localized solutions therefore obey an eight-dimensional spatial dynamical system in one dimension (1D). Stationary localized structures within the model are found to be associated with a subcritical Turing instability and organized within a distinct type of foliated snaking bifurcation structure. This behavior is in turn associated with the presence of an exchange point in parameter space at which the complex leading spatial eigenvalues of the uniform concentration state are overtaken by a pair of real eigenvalues; this point plays the role of a Belyakov-Devaney point in this system. The primary foliated snaking structure consists of periodic spike or peak trains with $N$ identical equidistant peaks, $N=1,2,dots ,$, together with cross-links consisting of nonidentical, nonequidistant peaks. The structure is complicated by a multitude of multipulse states, some of which are also computed, and spans the parameter range from the primary Turing bifurcation all the way to the fold of the $N=1$ state. These states form a complex template from which localized physical structures develop in the transverse direction in 2D.
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An understanding of the underlying mechanism of side--branching is paramount in controlling and/or therapeutically treating mammalian organs, such as lungs, kidneys, and glands. Motivated by an activator-inhibitor-substrate approach that is conjectured to dominate the initiation of side--branching in pulmonary vascular pattern, I demonstrate a distinct transverse front instability in which new fingers grow out of an oscillatory breakup dynamics at the front line, without any typical length scale. These two features are attributed to unstable peak solutions in 1D that subcritically emanate from the Turing bifurcation and that exhibit repulsive interactions. The results are based on a bifurcation analysis and numerical simulations, and provide a potential strategy toward developing a framework of side--branching also of other biological systems, such as plant roots and cellular protrusions.
We derive a full 3-dimensional (3-D) model of inhomogeneous -- anisotropic diffusion in a tumor region coupled to a binary population model. The diffusion tensors are acquired using Diffusion Tensor Magnetic Resonance Imaging (DTI) from a patient diagnosed with glioblastoma multiform (GBM). Then we numerically simulate the full model with Finite Element Method (FEM) and produce drug concentration heat maps, apoptosis regions, and dose-response curves. Finally, predictions are made about optimal injection locations and volumes, which are presented in a form that can be employed by doctors and oncologists.
Realistic examples of reaction-diffusion phenomena governing spatial and spatiotemporal pattern formation are rarely isolated systems, either chemically or thermodynamically. However, even formulations of `open reaction-diffusion systems often neglect the role of domain boundaries. Most idealizations of closed reaction-diffusion systems employ no-flux boundary conditions, and often patterns will form up to, or along, these boundaries. Motivated by boundaries of patterning fields related to the emergence of spatial form in embryonic development, we propose a set of mixed boundary conditions for a two-species reaction-diffusion system which forms inhomogeneous solutions away from the boundary of the domain for a variety of different reaction kinetics, with a prescribed uniform state near the boundary. We show that these boundary conditions can be derived from a larger heterogeneous field, indicating that these conditions can arise naturally if cell signalling or other properties of the medium vary in space. We explain the basic mechanisms behind this pattern localization, and demonstrate that it can capture a large range of localized patterning in one, two, and three dimensions, and that this framework can be applied to systems involving more than two species. Furthermore, the boundary conditions proposed lead to more symmetrical patterns on the interior of the domain, and plausibly capture more realistic boundaries in developmental systems. Finally, we show that these isolated patterns are more robust to fluctuations in initial conditions, and that they allow intriguing possibilities of pattern selection via geometry, distinct from known selection mechanisms.
Reaction-diffusion processes across layered media arise in several scientific domains such as pattern-forming E. coli on agar substrates, epidermal-mesenchymal coupling in development, and symmetry-breaking in cell polarisation. We develop a modelling framework for bi-layer reaction-diffusion systems and relate it to a range of existing models. We derive conditions for diffusion-driven instability of a spatially homogeneous equilibrium analogous to the classical conditions for a Turing instability in the simplest nontrivial setting where one domain has a standard reaction-diffusion system, and the other permits only diffusion. Due to the transverse coupling between these two regions, standard techniques for computing eigenfunctions of the Laplacian cannot be applied, and so we propose an alternative method to compute the dispersion relation directly. We compare instability conditions with full numerical simulations to demonstrate impacts of the geometry and coupling parameters on patterning, and explore various experimentally-relevant asymptotic regimes. In the regime where the first domain is suitably thin, we recover a simple modulation of the standard Turing conditions, and find that often the broad impact of the diffusion-only domain is to reduce the ability of the system to form patterns. We also demonstrate complex impacts of this coupling on pattern formation. For instance, we exhibit non-monotonicity of pattern-forming instabilities with respect to geometric and coupling parameters, and highlight an instability from a nontrivial interaction between kinetics in one domain and diffusion in the other. These results are valuable for informing design choices in applications such as synthetic engineering of Turing patterns, but also for understanding the role of stratified media in modulating pattern-forming processes in developmental biology and beyond.
We revisit the problem of pinning a reaction-diffusion front by a defect, in particular by a reaction-free region. Using collective variables for the front and numerical simulations, we compare the behaviors of a bistable and monostable front. A bistable front can be pinned as confirmed by a pinning criterion, the analysis of the time independant problem and simulations. Conversely, a monostable front can never be pinned, it gives rise to a secondary pulse past the defect and we calculate the time this pulse takes to appear. These radically different behaviors of bistable and monostable fronts raise issues for modelers in particular areas of biology, as for example, the study of tumor growth in the presence of different tissues.
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