Extending BACOLI to solve multi-scale problems

The BACOLI package is a numerical software package for solving parabolic partial differential equations in one spatial dimension. It implements a B-spline collocation method for the spatial discretization of a system of partial differential equations. The resultant ordinary differential equations together with the boundary conditions form a system of differential-algebraic equations. The differential-algebraic equations are then solved using the DASSL solver. The BACOLI software package features adaptive error control in the temporal and spatial domains. The estimate of the temporal error is controlled through the DASSL solver. The estimate of the spatial error is controlled based on the difference between two solutions computed in the BACOLI software package. This difference gives an estimation of the error. If this error estimate does not meet the user-supplied tolerance, then the spatial mesh is changed. The BACOLI software package can only solve parabolic partial differential equations that depend on spatial derivatives. In this thesis, the BACOLI software package is modified to solve a broader spectrum of problems. In fact, after some modifications, the extended BACOLI software package can solve systems of parabolic partial differential equations and time-dependent equations that do not depend on spatial derivatives. We apply this extended software package to solve the monodomain model of cardiac electrophysiology. The monodomain model is a multi-scale mathematical model for the evolution of the electrical potential in cardiac tissue that couples the ionic currents at the cellular scale with their propagation at the tissue scale. Because of their local nature, the mathematical models of a single cell have no dependency on spatial derivatives whereas the models at the tissue level do. The heart models considered in our numerical experiments use various cardiac cell models. We find that solving the heart models through the extended BACOLI software package, in some cases, leads to a speed-up in comparison with the Chaste software package, which is a powerful, widely used, and well-respected software package for heart simulation

Almost Block Diagonal Linear Systems: Sequential and Parallel Solution Techniques, and Applications

Almost block diagonal (ABD) linear systems arise in a variety of contexts, specifically in numerical methods for two-point boundary value problems for ordinary differential equations and in related partial differential equation problems. The stable, efficient sequential solution of ABDs has received much attention over the last fifteen years and the parallel solution more recently. We survey the fields of application with emphasis on how ABDs and bordered ABDs (BABDs) arise. We outline most known direct solution techniques, both sequential and parallel, and discuss the comparative efficiency of the parallel methods. Finally, we examine parallel iterative methods for solving BABD systems. Copyright (C) 2000 John Wiley & Sons, Ltd

An Adaptive Method for Calculating Blow-Up Solutions

Reactive-diffusive systems modeling physical phenomena in certain situations develop a singularity at a finite value of the independent variable referred to as blow-up. The attempt to find the blow-up time analytically is most often impossible, thus requiring a numerical determination of the value. The numerical methods often use a priori knowledge of the blow-up solution such as monotonicity or self-similarity. For equations where such a priori knowledge is unavailable, ad hoc methods were constructed. The object of this research is to develop a simple and consistent approach to find numerically the blow-up solution without having a priori knowledge or resorting to other ad hoc methods. The proposed method allows the investigator the ability to distinguish whether a singular solution or a non-singular solution exists on a given interval. Step size in the vicinity of a singular solution is automatically adjusted. The programming of the proposed method is simple and uses well-developed software for most of the auxiliary routines. The proposed numerical method is mainly concerned with the integration of nonlinear integral equations with Abel-type kernels developed from combustion problems, but may be used on similar equations from other fields. To demonstrate the flexibility of the proposed method, it is applied to ordinary differential equations with blow-up solutions or to ordinary differential equations which exhibit extremely stiff structure

High order collocation software for the numerical solution of fourth order parabolic PDEs

viii, 114 leaves : ill. ; 29 cm.Includes abstract.Includes bibliographical references (leaves 109-114).BACOL is an efficient software package for solving systems of second order parabolic PDEs in one space dimension. A significant feature of the package is that it employs adaptive error control in both time and space. A second order PDE depends on the solution, u, and its first and second derivatives, ux and uxx. However, many applications lead to mathematical models which involve fourth order PDEs. Fourth order PDEs depend on u, ux, uxxx, and uxxxx. One contribution of the thesis is that it provides a survey of applications in which fourth order PDEs arise. The thesis focuses on how to extend BACOL so that it can handle fourth order PDEs. We have explored a somewhat novel approach that involves converting the fourth order PDE to a coupled system which contains one second order PDE and one second order PDE (in space). A careful investigation of the BACOL package is carried out in order to extend it so that it can treat this coupled PDE/ODE system directly; the new software is called BACOL42. For comparison purposes we have also considered an approximate form of the converted system that can be solved using the original BACOL software. Numerical results are provided to demonstrate the effectiveness of BACOL42. The thesis also provides a numerical study of two other PDE solvers, pdepe and MOVCOL4, that can be applied to solve fourth order PDEs