Simulation of action potential propagation based on the ghost structure method

In this paper, a ghost structure (GS) method is proposed to simulate the monodomain model in irregular computational domains using finite difference without regenerating body-fitted grids. In order to verify the validity of the GS method, it is first used to solve the Fitzhugh-Nagumo monodomain model in rectangular and circular regions at different states (the stationary and moving states). Then, the GS method is used to simulate the propagation of the action potential (AP) in transverse and longitudinal sections of a healthy human heart, and with left bundle branch block (LBBB). Finally, we analyze the AP and calcium concentration under healthy and LBBB conditions. Our numerical results show that the GS method can accurately simulate AP propagation with different computational domains either stationary or moving, and we also find that LBBB will cause the left ventricle to contract later than the right ventricle, which in turn affects synchronized contraction of the two ventricles

An unstructured mesh control volume method for two-dimensional space fractional diffusion equations with variable coefficients on convex domains

In this paper, we propose a novel unstructured mesh control volume method to deal with the space fractional derivative on arbitrarily shaped convex domains, which to the best of our knowledge is a new contribution to the literature. Firstly, we present the finite volume scheme for the two-dimensional space fractional diffusion equation with variable coefficients and provide the full implementation details for the case where the background interpolation mesh is based on triangular elements. Secondly, we explore the property of the stiffness matrix generated by the integral of space fractional derivative. We find that the stiffness matrix is sparse and not regular. Therefore, we choose a suitable sparse storage format for the stiffness matrix and develop a fast iterative method to solve the linear system, which is more efficient than using the Gaussian elimination method. Finally, we present several examples to verify our method, in which we make a comparison of our method with the finite element method for solving a Riesz space fractional diffusion equation on a circular domain. The numerical results demonstrate that our method can reduce CPU time significantly while retaining the same accuracy and approximation property as the finite element method. The numerical results also illustrate that our method is effective and reliable and can be applied to problems on arbitrarily shaped convex domains.Comment: 18 pages, 5 figures, 9 table

Differential quadrature method for space-fractional diffusion equations on 2D irregular domains

In mathematical physics, the space-fractional diffusion equations are of particular interest in the studies of physical phenomena modelled by L\'{e}vy processes, which are sometimes called super-diffusion equations. In this article, we develop the differential quadrature (DQ) methods for solving the 2D space-fractional diffusion equations on irregular domains. The methods in presence reduce the original equation into a set of ordinary differential equations (ODEs) by introducing valid DQ formulations to fractional directional derivatives based on the functional values at scattered nodal points on problem domain. The required weighted coefficients are calculated by using radial basis functions (RBFs) as trial functions, and the resultant ODEs are discretized by the Crank-Nicolson scheme. The main advantages of our methods lie in their flexibility and applicability to arbitrary domains. A series of illustrated examples are finally provided to support these points.Comment: 25 pages, 25 figures, 7 table

A Virtual Element Method for a Nonlocal FitzHugh-Nagumo Model of Cardiac Electrophysiology

We present a Virtual Element Method (VEM) for a nonlocal reaction-diffusion system of the cardiac electric field. To this system, we analyze an $H^1(\Omega)$-conforming discretization by means of VEM which can make use of general polygonal meshes. Under standard assumptions on the computational domain, we establish the convergence of the discrete solution by considering a series of a priori estimates and by using a general $L^p$ compactness criterion. Moreover, we obtain optimal order space-time error estimates in the $L^2$ norm. Finally, we report some numerical tests supporting the theoretical results

A Conservative Scheme with Optimal Error Estimates for a Multidimensional Space-Fractional Gross-Pitaevskii Equation

The present work departs from an extended form of the classical multi-dimensional Gross-Pitaevskii equation, which considers fractional derivatives of the Riesz type in space, a generalized potential function and angular momentum rotation. It is well known that the classical system possesses functionals which are preserved throughout time. It is easy to check that the generalized fractional model considered in this work also possesses conserved quantities, whence the development of conservative and efficient numerical schemes is pragmatically justified. Motivated by these facts, we propose a finite-difference method based on weighted-shifted Grünwald differences to approximate the solutions of the generalized Gross-Pitaevskii system. We provide here a discrete extension of the uniform Sobolev inequality to multiple dimensions, and show that the proposed method is capable of preserving discrete forms of the mass and the energy of the model. Moreover, we establish thoroughly the stability and the convergence of the technique, and provide some illustrative simulations to show that the method is capable of preserving the total mass and the total energy of the generalized system. © 2019 Ahmed S. Hendy et al., published by Sciendo 2019

Numerical methods for simulation of electrical activity in the myocardial tissue

Mathematical models of electric activity in cardiac tissue are becoming increasingly powerful tools in the study of cardiac arrhythmias. Considered here are mathematical models based on ordinary differential equations (ODEs) and partial differential equations (PDEs) that describe the behaviour of this electrical activity. Generating an efficient numerical solution of these models is a challenging task, and in fact the physiological accuracy of tissue-scale models is often limited by the efficiency of the numerical solution process. In this thesis, we discuss two sets of experiments that test ideas for making the numerical solution process more efficient. In the first set of experiments, we examine the numerical solution of four single cell cardiac electrophysiological models, which consist solely of ODEs. We study the efficiency of using implicit-explicit Runge-Kutta (IMEX-RK) splitting methods to solve these models. We find that variable step-size implementations of IMEX-RK methods (ARK3 and ARK5) that take advantage of Jacobian structure clearly outperform most methods commonly used in practice for two of the models, and they outperform all methods commonly used in practice for the remaining models. In the second set of experiments, we examine the solution of the bidomain model, a model consisting of both ODEs and PDEs that are typically solved separately. We focus these experiments on numerical methods for the solution of the two PDEs in the bidomain model. The most popular method for this task, the Crank-Nicolson method, produces unphysical oscillations; we propose a method based on a second-order L-stable singly diagonally implicit Runge-Kutta (SDIRK) method to eliminate these oscillations. We find that although the SDIRK method is able to eliminate these unphysical oscillations, it is only more efficient for crude error tolerances

Numerical Methods for Solving Space Fractional Partial Differential Equations Using Hadamard Finite-Part Integral Approach

From Springer Nature via Jisc Publications RouterHistory: received 2018-09-29, rev-recd 2018-11-09, accepted 2018-11-10, registration 2019-06-11, epub 2019-07-26, online 2019-07-26, ppub 2019-12Publication status: PublishedAbstract: We introduce a novel numerical method for solving two-sided space fractional partial differential equations in two-dimensional case. The approximation of the space fractional Riemann–Liouville derivative is based on the approximation of the Hadamard finite-part integral which has the convergence order O(h3-α), where h is the space step size and α∈(1, 2) is the order of Riemann–Liouville fractional derivative. Based on this scheme, we introduce a shifted finite difference method for solving space fractional partial differential equations. We obtained the error estimates with the convergence orders O(τ+h3-α+hβ), where τ is the time step size and β>0 is a parameter which measures the smoothness of the fractional derivatives of the solution of the equation. Unlike the numerical methods for solving space fractional partial differential equations constructed using the standard shifted Grünwald–Letnikov formula or higher order Lubich’s methods which require the solution of the equation to satisfy the homogeneous Dirichlet boundary condition to get the first-order convergence, the numerical method for solving the space fractional partial differential equation constructed using the Hadamard finite-part integral approach does not require the solution of the equation to satisfy the Dirichlet homogeneous boundary condition. Numerical results show that the experimentally determined convergence order obtained using the Hadamard finite-part integral approach for solving the space fractional partial differential equation with non-homogeneous Dirichlet boundary conditions is indeed higher than the convergence order obtained using the numerical methods constructed with the standard shifted Grünwald–Letnikov formula or Lubich’s higher order approximation schemes