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AuthorPestana, Jennifer (2)Alarcon, T. (1)Bueno-Orovio, Alfonso (1)Burrage, Kevin (1)Byrne, H. M. (1)View MoreJournalBulletin of Mathematical Biology (2)Journal of Mathematical Biology (2)Annals of Biomedical Engineering (1)BIT Numerical Mathematics (1)IFIP Advances in Information and Communication Technology (1)View MoreKAUST Grant Number

KUK-C1-013-04 (10)

Publisher
Springer Nature (10)

SubjectAngiogenesis (1)Compartment-based models (1)Constitutive law (1)Contact mechanics (1)Convergence (1)View MoreTypeArticle (9)Book Chapter (1)Year (Issue Date)
2014 (10)

Item AvailabilityMetadata Only (9)Open Access (1)

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Helical Birods: An Elastic Model of Helically Wound Double-Stranded Rods

Prior, Christopher (Journal of Elasticity, Springer Nature, 2014-03-11) [Article]

© 2014, Springer Science+Business Media Dordrecht. We consider a geometrically accurate model for a helically wound rope constructed from two intertwined elastic rods. The line of contact has an arbitrary smooth shape which is obtained under the action of an arbitrary set of applied forces and moments. We discuss the general form the theory should take along with an insight into the necessary geometric or constitutive laws which must be detailed in order for the system to be complete. This includes a number of contact laws for the interaction of the two rods, in order to fit various relevant physical scenarios. This discussion also extends to the boundary and how this composite system can be acted upon by a single moment and force pair. A second strand of inquiry concerns the linear response of an initially helical rope to an arbitrary set of forces and moments. In particular we show that if the rope has the dimensions assumed of a rod in the Kirchhoff rod theory then it can be accurately treated as an isotropic inextensible elastic rod. An important consideration in this demonstration is the possible effect of varying the geometric boundary constraints; it is shown the effect of this choice becomes negligible in this limit in which the rope has dimensions similar to those of a Kirchhoff rod. Finally we derive the bending and twisting coefficients of this effective rod.

Fourier spectral methods for fractional-in-space reaction-diffusion equations

Bueno-Orovio, Alfonso; Kay, David; Burrage, Kevin (BIT Numerical Mathematics, Springer Nature, 2014-04-01) [Article]

© 2014, Springer Science+Business Media Dordrecht. Fractional differential equations are becoming increasingly used as a powerful modelling approach for understanding the many aspects of nonlocality and spatial heterogeneity. However, the numerical approximation of these models is demanding and imposes a number of computational constraints. In this paper, we introduce Fourier spectral methods as an attractive and easy-to-code alternative for the integration of fractional-in-space reaction-diffusion equations described by the fractional Laplacian in bounded rectangular domains of ℝ. The main advantages of the proposed schemes is that they yield a fully diagonal representation of the fractional operator, with increased accuracy and efficiency when compared to low-order counterparts, and a completely straightforward extension to two and three spatial dimensions. Our approach is illustrated by solving several problems of practical interest, including the fractional Allen–Cahn, FitzHugh–Nagumo and Gray–Scott models, together with an analysis of the properties of these systems in terms of the fractional power of the underlying Laplacian operator.

Mesoscopic and continuum modelling of angiogenesis

Spill, F.; Guerrero, P.; Alarcon, T.; Maini, P. K.; Byrne, H. M. (Journal of Mathematical Biology, Springer Nature, 2014-03-11) [Article]

Angiogenesis is the formation of new blood vessels from pre-existing ones in response to chemical signals secreted by, for example, a wound or a tumour. In this paper, we propose a mesoscopic lattice-based model of angiogenesis, in which processes that include proliferation and cell movement are considered as stochastic events. By studying the dependence of the model on the lattice spacing and the number of cells involved, we are able to derive the deterministic continuum limit of our equations and compare it to similar existing models of angiogenesis. We further identify conditions under which the use of continuum models is justified, and others for which stochastic or discrete effects dominate. We also compare different stochastic models for the movement of endothelial tip cells which have the same macroscopic, deterministic behaviour, but lead to markedly different behaviour in terms of production of new vessel cells. © 2014 Springer-Verlag Berlin Heidelberg.

On a poroviscoelastic model for cell crawling

Kimpton, L. S.; Whiteley, J. P.; Waters, S. L.; Oliver, J. M. (Journal of Mathematical Biology, Springer Nature, 2014-02-08) [Article]

In this paper a minimal, one-dimensional, two-phase, viscoelastic, reactive, flow model for a crawling cell is presented. Two-phase models are used with a variety of constitutive assumptions in the literature to model cell motility. We use an upper-convected Maxwell model and demonstrate that even the simplest of two-phase, viscoelastic models displays features relevant to cell motility. We also show care must be exercised in choosing parameters for such models as a poor choice can lead to an ill-posed problem. A stability analysis reveals that the initially stationary, spatially uniform strip of cytoplasm starts to crawl in response to a perturbation which breaks the symmetry of the network volume fraction or network stress. We also demonstrate numerically that there is a steady travelling-wave solution in which the crawling velocity has a bell-shaped dependence on adhesion strength, in agreement with biological observation.

Irreversible energy flow in forced Vlasov dynamics

Plunk, Gabriel G.; Parker, Joseph T. (The European Physical Journal D, Springer Nature, 2014-10) [Article]

© EDP Sciences, Società Italiana di Fisica, Springer-Verlag. The recent paper of Plunk [G.G. Plunk, Phys. Plasmas 20, 032304 (2013)] considered the forced linear Vlasov equation as a model for the quasi-steady state of a single stable plasma wavenumber interacting with a bath of turbulent fluctuations. This approach gives some insight into possible energy flows without solving for nonlinear dynamics. The central result of the present work is that the forced linear Vlasov equation exhibits asymptotically zero (irreversible) dissipation to all orders under a detuning of the forcing frequency and the characteristic frequency associated with particle streaming. We first prove this by direct calculation, tracking energy flow in terms of certain exact conservation laws of the linear (collisionless) Vlasov equation. Then we analyze the steady-state solutions in detail using a weakly collisional Hermite-moment formulation, and compare with numerical solution. This leads to a detailed description of the Hermite energy spectrum, and a proof of no dissipation at all orders, complementing the collisionless Vlasov result.

Some observations on weighted GMRES

Güttel, Stefan; Pestana, Jennifer (Numerical Algorithms, Springer Nature, 2014-01-10) [Article]

We investigate the convergence of the weighted GMRES method for solving linear systems. Two different weighting variants are compared with unweighted GMRES for three model problems, giving a phenomenological explanation of cases where weighting improves convergence, and a case where weighting has no effect on the convergence. We also present a new alternative implementation of the weighted Arnoldi algorithm which under known circumstances will be favourable in terms of computational complexity. These implementations of weighted GMRES are compared for a large number of examples. We find that weighted GMRES may outperform unweighted GMRES for some problems, but more often this method is not competitive with other Krylov subspace methods like GMRES with deflated restarting or BICGSTAB, in particular when a preconditioner is used. © 2014 Springer Science+Business Media New York.

Stochastic simulations of normal aging and Werner's syndrome.

Qi, Qi; Wattis, Jonathan A D; Byrne, Helen M. (Bulletin of Mathematical Biology, Springer Nature, 2014-04-26) [Article]

Human cells typically consist of 23 pairs of chromosomes. Telomeres are repetitive sequences of DNA located at the ends of chromosomes. During cell replication, a number of basepairs are lost from the end of the chromosome and this shortening restricts the number of divisions that a cell can complete before it becomes senescent, or non-replicative. In this paper, we use Monte Carlo simulations to form a stochastic model of telomere shortening to investigate how telomere shortening affects normal aging. Using this model, we study various hypotheses for the way in which shortening occurs by comparing their impact on aging at the chromosome and cell levels. We consider different types of length-dependent loss and replication probabilities to describe these processes. After analyzing a simple model for a population of independent chromosomes, we simulate a population of cells in which each cell has 46 chromosomes and the shortest telomere governs the replicative potential of the cell. We generalize these simulations to Werner's syndrome, a condition in which large sections of DNA are removed during cell division and, amongst other conditions, results in rapid aging. Since the mechanisms governing the loss of additional basepairs are not known, we use our model to simulate a variety of possible forms for the rate at which additional telomeres are lost per replication and several expressions for how the probability of cell division depends on telomere length. As well as the evolution of the mean telomere length, we consider the standard deviation and the shape of the distribution. We compare our results with a variety of data from the literature, covering both experimental data and previous models. We find good agreement for the evolution of telomere length when plotted against population doubling.

Transmural Variation and Anisotropy of Microvascular Flow Conductivity in the Rat Myocardium

Smith, Amy F.; Shipley, Rebecca J.; Lee, Jack; Sands, Gregory B.; LeGrice, Ian J.; Smith, Nicolas P. (Annals of Biomedical Engineering, Springer Nature, 2014-05-28) [Article]

Transmural variations in the relationship between structural and fluid transport properties of myocardial capillary networks are determined via continuum modeling approaches using recent three-dimensional (3D) data on the microvascular structure. Specifically, the permeability tensor, which quantifies the inverse of the blood flow resistivity of the capillary network, is computed by volume-averaging flow solutions in synthetic networks with geometrical and topological properties derived from an anatomically-detailed microvascular data set extracted from the rat myocardium. Results show that the permeability is approximately ten times higher in the principal direction of capillary alignment (the "longitudinal" direction) than perpendicular to this direction, reflecting the strong anisotropy of the microvascular network. Additionally, a 30% increase in capillary diameter from subepicardium to subendocardium is shown to translate to a 130% transmural rise in permeability in the longitudinal capillary direction. This result supports the hypothesis that perfusion is preferentially facilitated during diastole in the subendocardial microvasculature to compensate for the severely-reduced systolic perfusion in the subendocardium.

Stochastic Turing Patterns: Analysis of Compartment-Based Approaches

Cao, Yang; Erban, Radek (Bulletin of Mathematical Biology, Springer Nature, 2014-11-25) [Article]

© 2014, Society for Mathematical Biology. Turing patterns can be observed in reaction-diffusion systems where chemical species have different diffusion constants. In recent years, several studies investigated the effects of noise on Turing patterns and showed that the parameter regimes, for which stochastic Turing patterns are observed, can be larger than the parameter regimes predicted by deterministic models, which are written in terms of partial differential equations (PDEs) for species concentrations. A common stochastic reaction-diffusion approach is written in terms of compartment-based (lattice-based) models, where the domain of interest is divided into artificial compartments and the number of molecules in each compartment is simulated. In this paper, the dependence of stochastic Turing patterns on the compartment size is investigated. It has previously been shown (for relatively simpler systems) that a modeler should not choose compartment sizes which are too small or too large, and that the optimal compartment size depends on the diffusion constant. Taking these results into account, we propose and study a compartment-based model of Turing patterns where each chemical species is described using a different set of compartments. It is shown that the parameter regions where spatial patterns form are different from the regions obtained by classical deterministic PDE-based models, but they are also different from the results obtained for the stochastic reaction-diffusion models which use a single set of compartments for all chemical species. In particular, it is argued that some previously reported results on the effect of noise on Turing patterns in biological systems need to be reinterpreted.

Right-Hand Side Dependent Bounds for GMRES Applied to Ill-Posed Problems

Pestana, Jennifer (IFIP Advances in Information and Communication Technology, Springer Nature, 2014) [Book Chapter]

© IFIP International Federation for Information Processing 2014. In this paper we apply simple GMRES bounds to the nearly singular systems that arise in ill-posed problems. Our bounds depend on the eigenvalues of the coefficient matrix, the right-hand side vector and the nonnormality of the system. The bounds show that GMRES residuals initially decrease, as residual components associated with large eigenvalues are reduced, after which semi-convergence can be expected because of the effects of small eigenvalues.

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