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AuthorByrne, Helen M. (7)Goriely, Alain (6)Whiteley, Jonathan P. (5)Gaffney, E.A. (4)Maini, Philip K. (4)View MoreJournalJournal of Theoretical Biology (12)Journal of Computational Physics (9)International Journal of Non-Linear Mechanics (3)Applied Mathematics Letters (2)Journal of Non-Newtonian Fluid Mechanics (2)View MoreKAUST Grant Number

KUK-C1-013-04 (50)

Publisher
Elsevier BV (50)

SubjectMorphoelasticity (3)Acidity (2)Asymptotic analysis (2)Cancer (2)Cardiac electrophysiology (2)View MoreTypeArticle (50)Year (Issue Date)2015 (3)2014 (5)2013 (15)2012 (10)2011 (9)View MoreItem AvailabilityMetadata Only (49)Open Access (1)

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Hybrid approaches for multiple-species stochastic reaction-diffusion models.

Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K; Byrne, Helen M. (Journal of Computational Physics, Elsevier BV, 2015-10-01) [Article]

Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.

A spatially-averaged mathematical model of kidney branching morphogenesis

Zubkov, V.S.; Combes, A.N.; Short, K.M.; Lefevre, J.; Hamilton, N.A.; Smyth, I.M.; Little, M.H.; Byrne, H.M. (Journal of Theoretical Biology, Elsevier BV, 2015-08) [Article]

© 2015 Published by Elsevier Ltd. Kidney development is initiated by the outgrowth of an epithelial ureteric bud into a population of mesenchymal cells. Reciprocal morphogenetic responses between these two populations generate a highly branched epithelial ureteric tree with the mesenchyme differentiating into nephrons, the functional units of the kidney. While we understand some of the mechanisms involved, current knowledge fails to explain the variability of organ sizes and nephron endowment in mice and humans. Here we present a spatially-averaged mathematical model of kidney morphogenesis in which the growth of the two key populations is described by a system of time-dependant ordinary differential equations. We assume that branching is symmetric and is invoked when the number of epithelial cells per tip reaches a threshold value. This process continues until the number of mesenchymal cells falls below a critical value that triggers cessation of branching. The mathematical model and its predictions are validated against experimentally quantified C57Bl6 mouse embryonic kidneys. Numerical simulations are performed to determine how the final number of branches changes as key system parameters are varied (such as the growth rate of tip cells, mesenchyme cells, or component cell population exit rate). Our results predict that the developing kidney responds differently to loss of cap and tip cells. They also indicate that the final number of kidney branches is less sensitive to changes in the growth rate of the ureteric tip cells than to changes in the growth rate of the mesenchymal cells. By inference, increasing the growth rate of mesenchymal cells should maximise branch number. Our model also provides a framework for predicting the branching outcome when ureteric tip or mesenchyme cells change behaviour in response to different genetic or environmental developmental stresses.

Convergence of methods for coupling of microscopic and mesoscopic reaction–diffusion simulations

Flegg, Mark B.; Hellander, Stefan; Erban, Radek (Journal of Computational Physics, Elsevier BV, 2015-05) [Article]

© 2015 Elsevier Inc. In this paper, three multiscale methods for coupling of mesoscopic (compartment-based) and microscopic (molecular-based) stochastic reaction-diffusion simulations are investigated. Two of the three methods that will be discussed in detail have been previously reported in the literature; the two-regime method (TRM) and the compartment-placement method (CPM). The third method that is introduced and analysed in this paper is called the ghost cell method (GCM), since it works by constructing a "ghost cell" in which molecules can disappear and jump into the compartment-based simulation. Presented is a comparison of sources of error. The convergent properties of this error are studied as the time step δ. t (for updating the molecular-based part of the model) approaches zero. It is found that the error behaviour depends on another fundamental computational parameter h, the compartment size in the mesoscopic part of the model. Two important limiting cases, which appear in applications, are considered:. (i)δt→0 and h is fixed;(ii)δt→0 and h→0 such that δt/h is fixed. The error for previously developed approaches (the TRM and CPM) converges to zero only in the limiting case (ii), but not in case (i). It is shown that the error of the GCM converges in the limiting case (i). Thus the GCM is superior to previous coupling techniques if the mesoscopic description is much coarser than the microscopic part of the model.

The effect of boundaries on the asymptotic wavenumber of spiral wave solutions of the complex Ginzburg–Landau equation

Aguareles, M. (Physica D: Nonlinear Phenomena, Elsevier BV, 2014-06) [Article]

In this paper we consider an oscillatory medium whose dynamics are modeled by the complex Ginzburg-Landau equation. In particular, we focus on n-armed spiral wave solutions of the complex Ginzburg-Landau equation in a disk of radius d with homogeneous Neumann boundary conditions. It is well-known that such solutions exist for small enough values of the twist parameter q and large enough values of d. We investigate the effect of boundaries on the rotational frequency of the spirals, which is an unknown of the problem uniquely determined by the parameters d and q. We show that there is a threshold in the parameter space where the effect of the boundary on the rotational frequency switches from being algebraic to exponentially weak. We use the method of matched asymptotic expansions to obtain explicit expressions for the asymptotic wavenumber as a function of the twist parameter and the domain size for small values of q. © 2014 Elsevier B.V. All rights reserved.

Fast solution of Cahn–Hilliard variational inequalities using implicit time discretization and finite elements

Bosch, Jessica; Stoll, Martin; Benner, Peter (Journal of Computational Physics, Elsevier BV, 2014-04) [Article]

We consider the efficient solution of the Cahn-Hilliard variational inequality using an implicit time discretization, which is formulated as an optimal control problem with pointwise constraints on the control. By applying a semi-smooth Newton method combined with a Moreau-Yosida regularization technique for handling the control constraints we show superlinear convergence in function space. At the heart of this method lies the solution of large and sparse linear systems for which we propose the use of preconditioned Krylov subspace solvers using an effective Schur complement approximation. Numerical results illustrate the competitiveness of this approach. © 2014 Elsevier Inc.

Singular inextensible limit in the vibrations of post-buckled rods: Analytical derivation and role of boundary conditions

Neukirch, Sébastien; Goriely, Alain; Thomas, Olivier (Journal of Sound and Vibration, Elsevier BV, 2014-02) [Article]

In-plane vibrations of an elastic rod clamped at both extremities are studied. The rod is modeled as an extensible planar Kirchhoff elastic rod under large displacements and rotations. Equilibrium configurations and vibrations around these configurations are computed analytically in the incipient post-buckling regime. Of particular interest is the variation of the first mode frequency as the load is increased through the buckling threshold. The loading type is found to have a crucial importance as the first mode frequency is shown to behave singularly in the zero thickness limit in the case of prescribed axial displacement, whereas a regular behavior is found in the case of prescribed axial load. © 2013 Elsevier Ltd.

Adaptive approximation of higher order posterior statistics

Lee, Wonjung (Journal of Computational Physics, Elsevier BV, 2014-02) [Article]

Filtering is an approach for incorporating observed data into time-evolving systems. Instead of a family of Dirac delta masses that is widely used in Monte Carlo methods, we here use the Wiener chaos expansion for the parametrization of the conditioned probability distribution to solve the nonlinear filtering problem. The Wiener chaos expansion is not the best method for uncertainty propagation without observations. Nevertheless, the projection of the system variables in a fixed polynomial basis spanning the probability space might be a competitive representation in the presence of relatively frequent observations because the Wiener chaos approach not only leads to an accurate and efficient prediction for short time uncertainty quantification, but it also allows to apply several data assimilation methods that can be used to yield a better approximate filtering solution. The aim of the present paper is to investigate this hypothesis. We answer in the affirmative for the (stochastic) Lorenz-63 system based on numerical simulations in which the uncertainty quantification method and the data assimilation method are adaptively selected by whether the dynamics is driven by Brownian motion and the near-Gaussianity of the measure to be updated, respectively. © 2013 Elsevier Inc.

Heat or mass transfer at low Péclet number for Brinkman and Darcy flow round a sphere

Bell, Christopher G.; Byrne, H.M.; Whiteley, J.P.; Waters, S.L. (International Journal of Heat and Mass Transfer, Elsevier BV, 2014-01) [Article]

Prior research into the effect of convection on steady-state mass transfer from a spherical particle embedded in a porous medium has used the Darcy model to describe the flow. However, a limitation of the Darcy model is that it does not account for viscous effects near boundaries. Brinkman modified the Darcy model to include these effects by introducing an extra viscous term. Here we investigate the impact of this extra viscous term on the steady-state mass transfer from a sphere at low Péclet number, Pe 1. We use singular perturbation techniques to find the approximate asymptotic solution for the concentration profile. Mass-release from the surface of the sphere is described by a Robin boundary condition, which represents a first-order chemical reaction. We find that a larger Brinkman viscous boundary layer renders mass transport by convection less effective, and reduces the asymmetry in the peri-sphere concentration profiles. We provide simple analytical expressions that can be used to calculate the concentration profiles, as well as the local and average Sherwood numbers; and comparison to numerical simulations verifies the order of magnitude of the error in the asymptotic expansions. In the appropriate limits, the asymptotic results agree with solutions previously obtained for Stokes and Darcy flow. The solution for Darcy flow with a Robin boundary condition has not been considered previously in the literature and is a new result. Whilst the article has been formulated in terms of mass transfer, the analysis is also applicable to heat transfer, with concentration replaced by temperature and the Sherwood number by the Nusselt number. © 2013 Elsevier Ltd. All rights reserved.

Homogenization via formal multiscale asymptotics and volume averaging: How do the two techniques compare?

Davit, Yohan; Bell, Christopher G.; Byrne, Helen M.; Chapman, Lloyd A.C.; Kimpton, Laura S.; Lang, Georgina E.; Leonard, Katherine H.L.; Oliver, James M.; Pearson, Natalie C.; Shipley, Rebecca J.; Waters, Sarah L.; Whiteley, Jonathan P.; Wood, Brian D.; Quintard, Michel (Advances in Water Resources, Elsevier BV, 2013-12) [Article]

A wide variety of techniques have been developed to homogenize transport equations in multiscale and multiphase systems. This has yielded a rich and diverse field, but has also resulted in the emergence of isolated scientific communities and disconnected bodies of literature. Here, our goal is to bridge the gap between formal multiscale asymptotics and the volume averaging theory. We illustrate the methodologies via a simple example application describing a parabolic transport problem and, in so doing, compare their respective advantages/disadvantages from a practical point of view. This paper is also intended as a pedagogical guide and may be viewed as a tutorial for graduate students as we provide historical context, detail subtle points with great care, and reference many fundamental works. © 2013 Elsevier Ltd.

Growth-induced axial buckling of a slender elastic filament embedded in an isotropic elastic matrix

O'Keeffe, Stephen G.; Moulton, Derek E.; Waters, Sarah L.; Goriely, Alain (International Journal of Non-Linear Mechanics, Elsevier BV, 2013-11) [Article]

We investigate the problem of an axially loaded, isotropic, slender cylinder embedded in a soft, isotropic, outer elastic matrix. The cylinder undergoes uniform axial growth, whilst both the cylinder and the surrounding elastic matrix are confined between two rigid plates, so that this growth results in axial compression of the cylinder. We use two different modelling approaches to estimate the critical axial growth (that is, the amount of axial growth the cylinder is able to sustain before it buckles) and buckling wavelength of the cylinder. The first approach treats the filament and surrounding matrix as a single 3-dimensional elastic body undergoing large deformations, whilst the second approach treats the filament as a planar, elastic rod embedded in an infinite elastic foundation. By comparing the results of these two approaches, we obtain an estimate of the foundation modulus parameter, which characterises the strength of the foundation, in terms of the geometric and material properties of the system. © 2013 Elsevier Ltd. All rights reserved.

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