## Search

Now showing items 1-10 of 21

JavaScript is disabled for your browser. Some features of this site may not work without it.

AuthorByrne, Helen M. (3)Harrington, Heather A. (3)MacLean, Adam L. (2)Aarts, Dirk G A L (1)Abate, Antonio (1)View MoreJournalJournal of Computational Physics (2)Nature Communications (2)SIAM Journal on Applied Mathematics (2)Communications in Applied Mathematics and Computational Science (1)IMA Journal of Numerical Analysis (1)View MoreKAUST Grant Number

KUK-C1-013-04 (21)

PublisherSociety for Industrial & Applied Mathematics (SIAM) (4)Springer Nature (4)Elsevier BV (3)American Chemical Society (ACS) (2)Cambridge University Press (CUP) (2)View MoreSubjectAdaptive step-size control (1)Adsorption kinetics (1)Algebraic methods (1)Asymptotic analysis (1)Bayesian inference (1)View MoreTypeArticle (20)Book Chapter (1)Year (Issue Date)
2015 (21)

Item AvailabilityMetadata Only (18)Open Access (3)

Now showing items 1-10 of 21

- List view
- Grid view
- Sort Options:
- Relevance
- Title Asc
- Title Desc
- Issue Date Asc
- Issue Date Desc
- Submit Date Asc
- Submit Date Desc
- Results Per Page:
- 5
- 10
- 20
- 40
- 60
- 80
- 100

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.

Controlled Topological Transitions in Thin-Film Phase Separation

Hennessy, Matthew G.; Burlakov, Victor M.; Goriely, Alain; Wagner, Barbara; Münch, Andreas (SIAM Journal on Applied Mathematics, Society for Industrial & Applied Mathematics (SIAM), 2015-01) [Article]

© 2015 Society for Industrial and Applied Mathematics. In this paper the evolution of a binary mixture in a thin-film geometry with a wall at the top and bottom is considered. By bringing the mixture into its miscibility gap so that no spinodal decomposition occurs in the bulk, a slight energetic bias of the walls toward each one of the constituents ensures the nucleation of thin boundary layers that grow until the constituents have moved into one of the two layers. These layers are separated by an interfacial region where the composition changes rapidly. Conditions that ensure the separation into two layers with a thin interfacial region are investigated based on a phase-field model. Using matched asymptotic expansions a corresponding sharp-interface problem for the location of the interface is established. It is then argued that this newly created two-layer system is not at its energetic minimum but destabilizes into a controlled self-replicating pattern of trapezoidal vertical stripes by minimizing the interfacial energy between the phases while conserving their area. A quantitative analysis of this mechanism is carried out via a thin-film model for the free interfaces, which is derived asymptotically from the sharp-interface 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.

Saffman-Taylor fingers with kinetic undercooling

Gardiner, Bennett P. J.; McCue, Scott W.; Dallaston, Michael C.; Moroney, Timothy J. (Physical Review E, American Physical Society (APS), 2015-02-23) [Article]

© 2015 American Physical Society. The mathematical model of a steadily propagating Saffman-Taylor finger in a Hele-Shaw channel has applications to two-dimensional interacting streamer discharges which are aligned in a periodic array. In the streamer context, the relevant regularization on the interface is not provided by surface tension but instead has been postulated to involve a mechanism equivalent to kinetic undercooling, which acts to penalize high velocities and prevent blow-up of the unregularized solution. Previous asymptotic results for the Hele-Shaw finger problem with kinetic undercooling suggest that for a given value of the kinetic undercooling parameter, there is a discrete set of possible finger shapes, each analytic at the nose and occupying a different fraction of the channel width. In the limit in which the kinetic undercooling parameter vanishes, the fraction for each family approaches 1/2, suggesting that this "selection" of 1/2 by kinetic undercooling is qualitatively similar to the well-known analog with surface tension. We treat the numerical problem of computing these Saffman-Taylor fingers with kinetic undercooling, which turns out to be more subtle than the analog with surface tension, since kinetic undercooling permits finger shapes which are corner-free but not analytic. We provide numerical evidence for the selection mechanism by setting up a problem with both kinetic undercooling and surface tension and numerically taking the limit that the surface tension vanishes.

Strongly coupled interaction between a ridge of fluid and an inviscid airflow

Paterson, C.; Wilson, S. K.; Duffy, B. R. (Physics of Fluids, AIP Publishing, 2015-07) [Article]

© 2015 AIP Publishing LLC. The behaviour of a steady thin sessile or pendent ridge of fluid on an inclined planar substrate which is strongly coupled to the external pressure gradient arising from an inviscid airflow parallel to the substrate far from the ridge is described. When the substrate is nearly horizontal, a very wide ridge can be supported against gravity by capillary and/or external pressure forces; otherwise, only a narrower (but still wide) ridge can be supported. Classical thin-aerofoil theory is adapted to obtain the governing singular integro-differential equation for the profile of the ridge in each case. Attention is focused mainly on the case of a very wide sessile ridge. The effect of strengthening the airflow is to push a pinned ridge down near to its edges and to pull it up near to its middle. At a critical airflow strength, the upslope contact angle reaches the receding contact angle at which the upslope contact line de-pins, and continuing to increase the airflow strength beyond this critical value results in the de-pinned ridge becoming narrower, thicker, and closer to being symmetric in the limit of a strong airflow. The effect of tilting the substrate is to skew a pinned ridge in the downslope direction. Depending on the values of the advancing and receding contact angles, the ridge may first de-pin at either the upslope or the downslope contact line but, in general, eventually both contact lines de-pin. The special cases in which only one of the contact lines de-pins are also considered. It is also shown that the behaviour of a very wide pendent ridge is qualitatively similar to that of a very wide sessile ridge, while the important qualitative difference between the behaviour of a very wide ridge and a narrower ridge is that, in general, for the latter one or both of the contact lines may never de-pin.

Mathematical Modelling of Surfactant Self-assembly at Interfaces

Morgan, C. E.; Breward, C. J. W.; Griffiths, I. M.; Howell, P. D. (SIAM Journal on Applied Mathematics, Society for Industrial & Applied Mathematics (SIAM), 2015-01) [Article]

© 2015 Society for Industrial and Applied Mathematics. We present a mathematical model to describe the distribution of surfactant pairs in a multilayer structure beneath an adsorbed monolayer. A mesoscopic model comprising a set of ordinary differential equations that couple the rearrangement of surfactant within the multilayer to the surface adsorption kinetics is first derived. This model is then extended to the macroscopic scale by taking the continuum limit that exploits the typically large number of surfactant layers, which results in a novel third-order partial differential equation. The model is generalized to allow for the presence of two adsorbing boundaries, which results in an implicit free-boundary problem. The system predicts physically observed features in multilayer systems such as the initial formation of smaller lamellar structures and the typical number of layers that form in equilibrium.

The Closest Point Method and Multigrid Solvers for Elliptic Equations on Surfaces

Chen, Yujia; Macdonald, Colin B. (SIAM Journal on Scientific Computing, Society for Industrial & Applied Mathematics (SIAM), 2015-01) [Article]

© 2015 Society for Industrial and Applied Mathematics. Elliptic partial differential equations are important from both application and analysis points of view. In this paper we apply the closest point method to solve elliptic equations on general curved surfaces. Based on the closest point representation of the underlying surface, we formulate an embedding equation for the surface elliptic problem, then discretize it using standard finite differences and interpolation schemes on banded but uniform Cartesian grids. We prove the convergence of the difference scheme for the Poisson's equation on a smooth closed curve. In order to solve the resulting large sparse linear systems, we propose a specific geometric multigrid method in the setting of the closest point method. Convergence studies in both the accuracy of the difference scheme and the speed of the multigrid algorithm show that our approaches are effective.

Revisionist integral deferred correction with adaptive step-size control

Christlieb, Andrew; Macdonald, Colin; Ong, Benjamin; Spiteri, Raymond (Communications in Applied Mathematics and Computational Science, Mathematical Sciences Publishers, 2015-03-27) [Article]

© 2015 Mathematical Sciences Publishers. Adaptive step-size control is a critical feature for the robust and efficient numerical solution of initial-value problems in ordinary differential equations. In this paper, we show that adaptive step-size control can be incorporated within a family of parallel time integrators known as revisionist integral deferred correction (RIDC) methods. The RIDC framework allows for various strategies to implement stepsize control, and we report results from exploring a few of them.

Rectangular spectral collocation

Driscoll, Tobin A.; Hale, Nicholas (IMA Journal of Numerical Analysis, Oxford University Press (OUP), 2015-02-06) [Article]

Boundary conditions in spectral collocation methods are typically imposed by removing some rows of the discretized differential operator and replacing them with others that enforce the required conditions at the boundary. A new approach based upon resampling differentiated polynomials into a lower-degree subspace makes differentiation matrices, and operators built from them, rectangular without any row deletions. Then, boundary and interface conditions can be adjoined to yield a square system. The resulting method is both flexible and robust, and avoids ambiguities that arise when applying the classical row deletion method outside of two-point scalar boundary-value problems. The new method is the basis for ordinary differential equation solutions in Chebfun software, and is demonstrated for a variety of boundary-value, eigenvalue and time-dependent problems.

Natural Preconditioning and Iterative Methods for Saddle Point Systems

Pestana, Jennifer; Wathen, Andrew J. (SIAM Review, Society for Industrial & Applied Mathematics (SIAM), 2015-01) [Article]

© 2015 Society for Industrial and Applied Mathematics. The solution of quadratic or locally quadratic extremum problems subject to linear(ized) constraints gives rise to linear systems in saddle point form. This is true whether in the continuous or the discrete setting, so saddle point systems arising from the discretization of partial differential equation problems, such as those describing electromagnetic problems or incompressible flow, lead to equations with this structure, as do, for example, interior point methods and the sequential quadratic programming approach to nonlinear optimization. This survey concerns iterative solution methods for these problems and, in particular, shows how the problem formulation leads to natural preconditioners which guarantee a fast rate of convergence of the relevant iterative methods. These preconditioners are related to the original extremum problem and their effectiveness - in terms of rapidity of convergence - is established here via a proof of general bounds on the eigenvalues of the preconditioned saddle point matrix on which iteration convergence depends.

The export option will allow you to export the current search results of the entered query to a file. Different formats are available for download. To export the items, click on the button corresponding with the preferred download format.

By default, clicking on the export buttons will result in a download of the allowed maximum amount of items. For anonymous users the allowed maximum amount is 50 search results.

To select a subset of the search results, click "Selective Export" button and make a selection of the items you want to export. The amount of items that can be exported at once is similarly restricted as the full export.

After making a selection, click one of the export format buttons. The amount of items that will be exported is indicated in the bubble next to export format.