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Register a new userSynchrony and Oscillatory Dynamics for a 2-D PDE-ODE Model of Diffusion-Sensing with Small Signaling Compartments
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Added by
Sarafa Adewale Iyaniwura
Publication date
2020
fields
Physics
and research's language is
English
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We analyze a class of cell-bulk coupled PDE-ODE models, motivated by quorum and diffusion sensing phenomena in microbial systems, that characterize communication between localized spatially segregated dynamically active signaling compartments that have a permeable boundary. Each cell secretes a signaling chemical into the bulk region at a constant rate and receives a feedback of the bulk chemical from the entire collection of cells. This global feedback, which activates signaling pathways within the cells, modifies the intracellular dynamics according to the external environment. The cell secretion and global feedback are regulated by permeability parameters across the cell membrane. For arbitrary reaction-kinetics within each cell, the method of matched asymptotic expansions is used in the limit of small cell radius to construct steady-state solutions of the PDE-ODE model, and to derive a globally coupled nonlinear matrix eigenvalue problem (GCEP) that characterizes the linear stability properties of the steady-states. In the limit of large bulk diffusivity an asymptotic analysis of the PDE-ODE model leads to a limiting ODE system for the spatial average of the concentration in the bulk region that is coupled to the intracellular dynamics within the cells. Results from the linear stability theory and ODE dynamics are illustrated for Selkov reaction-kinetics, where the kinetic parameters are chosen so that each cell is quiescent when uncoupled from the bulk medium. For various specific spatial configurations of cells, the linear stability theory is used to construct phase diagrams in parameter space characterizing where a switch-like emergence of intracellular oscillations can occur through a Hopf bifurcation.
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Motivated by engineering applications of subsea installation by deepwater construction vessels in oil drilling, and of aid delivery by unmanned aerial vehicles in disaster relief, we develop output-feedback boundary control of heterodirectional coupled hyperbolic PDEs sandwiched between two ODEs, where the measurement is the output state of one ODE and suffers a time delay. After rewriting the time-delay dynamics as a transport PDE of which the left boundary connects with the sandwiched system, a state observer is built to estimate the states of the overall system of ODE-heterodirectional coupled hyperbolic PDEs-ODE-transport PDE using the right boundary state of the last transport PDE. An observer-based output-feedback controller acting at the first ODE is designed to stabilize the overall system using backstepping transformations and frequency-domain designs. The exponential stability results of the closed-loop system, boundedness and exponential convergence of the control input are proved. The obtained theoretical result is applied to control of a deepwater oil drilling construction vessel as a simulation case, where the simulation results show the proposed control design reduces cable oscillations and places the oil drilling equipment to be installed in the target area on the sea floor. Performance deterioration under extreme and unmodeled disturbances is also illustrated.
Localized spot patterns, where one or more solution components concentrates at certain points in the domain, are a common class of localized pattern for reaction-diffusion systems, and they arise in a wide range of modeling scenarios. In an arbitrary bounded 3-D domain, the existence, linear stability, and slow dynamics of localized multi-spot patterns is analyzed for the well-known singularly perturbed Gierer-Meinhardt (GM) activator-inhibitor system in the limit of a small activator diffusivity $varepsilon^2ll 1$. Our main focus is to classify the different types of multi-spot patterns, and predict their linear stability properties, for different asymptotic ranges of the inhibitor diffusivity $D$. For the range $D={mathcal O}(varepsilon^{-1})gg 1$, although both symmetric and asymmetric quasi-equilibrium spot patterns can be constructed, the asymmetric patterns are shown to be always unstable. On this range of $D$, it is shown that symmetric spot patterns can undergo either competition instabilities or a Hopf bifurcation, leading to spot annihilation or temporal spot amplitude oscillations, respectively. For $D={mathcal O}(1)$, only symmetric spot quasi-equilibria exist and they are linearly stable on ${mathcal O}(1)$ time intervals. On this range, it is shown that the spot locations evolve slowly on an ${mathcal O}(varepsilon^{-3})$ time scale towards their equilibrium locations according to an ODE gradient flow, which is determined by a discrete energy involving the reduced-wave Greens function. The central role of the far-field behavior of a certain core problem, which characterizes the profile of a localized spot, for the construction of quasi-equilibria in the $D={mathcal O}(1)$ and $D={mathcal O}(varepsilon^{-1})$ regimes, and in establishing some of their linear stability properties, is emphasized.
Spiral and antispiral waves are studied numerically in two examples of oscillatory reaction-diffusion media and analytically in the corresponding complex Ginzburg-Landau equation (CGLE). We argue that both these structures are sources of waves in oscillatory media, which are distinguished only by the sign of the phase velocity of the emitted waves. Using known analytical results in the CGLE, we obtain a criterion for the CGLE coefficients that predicts whether antispirals or spirals will occur in the corresponding reaction-diffusion systems. We apply this criterion to the FitzHugh-Nagumo and Brusselator models by deriving the CGLE near the Hopf bifurcations of the respective equations. Numerical simulations of the full reaction-diffusion equations confirm the validity of our simple criterion near the onset of oscillations. They also reveal that antispirals often occur near the onset and turn into spirals further away from it. The transition from antispirals to spirals is characterized by a divergence in the wavelength. A tentative interpretaion of recent experimental observations of antispiral waves in the Belousov-Zhabotinsky reaction in a microemulsion is given.
A hybrid asymptotic-numerical theory is developed to analyze the effect of different types of localized heterogeneities on the existence, linear stability, and slow dynamics of localized spot patterns for the two-component Schnakenberg reaction-diffusion model in a 2-D domain. Two distinct types of localized heterogeneities are considered: a strong localized perturbation of a spatially uniform feed rate and the effect of removing a small hole in the domain, through which the chemical species can leak out. Our hybrid theory reveals a wide range of novel phenomena such as, saddle-node bifurcations for quasi-equilibrium spot patterns that otherwise would not occur for a homogeneous medium, a new type of spot solution pinned at the concentration point of the feed rate, spot self-replication behavior leading to the creation of more than two new spots, and the existence of a creation-annihilation attractor with at most three spots. Depending on the type of localized heterogeneity introduced, localized spots are either repelled or attracted towards the localized defect on asymptotically long time scales. Results for slow spot dynamics and detailed predictions of various instabilities of quasi-equilibrium spot patterns, all based on our hybrid asymptotic-numerical theory, are illustrated and confirmed through extensive full PDE numerical simulations.
We analyze a coupled bulk-membrane PDE model in which a scalar linear 2-D bulk diffusion process is coupled through a linear Robin boundary condition to a two-component 1-D reaction-diffusion (RD) system with Gierer-Meinhardt (nonlinear) reaction kinetics defined on the domain boundary. For this coupled model, in the singularly perturbed limit of a long-range inhibition and short-range activation for the membrane-bound species, asymptotic methods are used to analyze the existence of localized steady-state multi-spike membrane-bound patterns, and to derive a nonlocal eigenvalue problem (NLEP) characterizing $mathcal{O}(1)$ time-scale instabilities of these patterns. A central, and novel, feature of this NLEP is that it involves a membrane Greens function that is coupled nonlocally to a bulk Greens function. When the domain is a disk, or in the well-mixed shadow-system limit corresponding to an infinite bulk diffusivity, this Greens function problem is analytically tractable, and as a result we will use a hybrid analytical-numerical approach to determine unstable spectra of this NLEP. This analysis characterizes how the 2-D bulk diffusion process and the bulk-membrane coupling modifies the well-known linear stability properties of steady-state spike patterns for the 1-D Gierer-Meinhardt model in the absence of coupling. In particular, phase diagrams in parameter space for our coupled model characterizing either oscillatory instabilities due to Hopf bifurcations, or competition instabilities due to zero-eigenvalue crossings are constructed. Finally, linear stability predictions from the NLEP analysis are confirmed with full numerical finite-element simulations of the coupled PDE system.
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