SUMMARY

Book Modelling

A simplified model of cardiac ventricular electrical activity, based on the cellular automata
model of Mitchell et al. [15], consists of a 50 × 50 square grid, each square representing a small 2 × 2
mm2 region of electrical activity in the heart. The grid is wrapped around into a cylinder, so that the left
and right edges are assumed to be in contact. Every region has exactly eight neighbours, with the
exception of those squares on the top and bottom edges alone. Each square in the grid can be in one of
four states: 0 (quiescent), 1 (relative refractory), 2 (absolute refractory) and 3 (excited). Once a region is
excited, it will move through states 3 → 2 → 1 → 0 in that order, unless it is prematurely excited again.

The duration of the excited state is fixed at Tex and the duration of the relative refractory period
is fixed at 50 ms. To account for the inhomogeneous refractory properties of the tissue, the duration of
the total refractory period (absolute + relative) is a random variable for each region, drawn from a
normal distribution of mean Trp and standard deviation σrp. The ventricles are excited by a periodic
impulse from the atrioventricular (AV) node, of period T, located in a small square on the top border of
the grid one quarter of the way in from the left edge. Whenever applied, this impulse can only excite the
small square if its current state is not absolute refractory. All state behaviours and parameter values are
given on the following page.

4.2.2 Finite Difference Method

The finite difference (FD) method is a relatively simple approach for numerically solving PDEs. In
this method, the underlying PDE is discretized into a regular grid covering the PDE domain, and partial
derivatives are approximated from the discretized grid variables. Consider a quantity u(x), a function of
the 1D spatial position x. We can discretize the 1D spatial domain into a regularly-spaced set of nodes in
x, given by x1, x2,... xj,... , each spaced a distance h apart, as shown in Fig. 4.11. If we denote the value of
u at node j by uj, then we can use Taylor’s theorem (Eq. 3.1) to obtain

4.2.3 Method of Lines

Another common numerical technique used to solve time-dependent PDEs is the method of
lines, in which the spatial domain is discretized into a regular grid to form a system of ODEs in the grid
variables, as illustrated in Fig. 4.14. For example, to solve our familiar diffusion PDE:

over the interval x ∈ [0, 1] subject to zero-flux boundary conditions, we let cj be the value of c at
the nodes xj = (j − 1)h, j = 1 ··· M, where M = (1/h) + 1. The above PDE can then be replaced by a coupled
ODE system in M − 2 variables, by using a FD difference approximation to the second-order spatial
derivative as follows:

fig 4.4. Method of lines for numerically solving a PDE in the dependent variable u(x, t). u(x, t) is
discretized in the spatial domain using a regular grid-spacing of h, to obtain a series of time-dependent
state variables uj at each node. The PDE is thereby transformed into a regular ODE system in the nodal
variables u.
 The Finite Element Method

The finite element method (FEM) represents a well-established and widespread numerical
approach for solving partial differential equations in physics and engineering. The basics of the method
were first published in 1943 in seminal paper by Richard Courant [4], who solved 2D plate and plane
torsion problems by discretizing the spatial domain into triangular “elements”, resulting in piecewise
approximations of the displacements to be solved for. In the early years, the main application of FEM
was in the area of structural mechanics [12], but its use quickly spread to other engineering applications,
including electromagnetics [5, 10], and fluid dynamics. Today, the method is used in a numerous range
of physics applications, including bioengineering [8]. A major advantage of FEM over the finite difference
method is that irregular geometries can be readily accommodated. This feature is particularly is useful
for bioengineering, in which organs, tissues and other structures of the body typically exhibit complex
anatomies.

5.1 Finite Elements for 1D Systems

The finite element method is based on two important concepts: 1. Formulation of the
underlying PDE in terms of its so-called weak form. 2. Approximating the dependent variable in the weak
form using a finite sum of basis functions. Both of these concepts will be illustrated using our familiar
example of 1D diffusion, represented by the PDE. defined over the domain x ∈ [0, 1], where D is a fixed
parameter denoting the diffusion coefficient. We assume an initial value of c0(x) at t = 0, where c0 is a
given function. Furthermore, we impose a Dirichlet boundary condition at x = 0
 5.1.2 Basis Function Approximation

To solve the PDE equivalent weak form using the method of finite elements, the next step is to
approximate the dependent variable using a finite sum of basis functions. For our weak form example of
Eq. 5.2 the variable c(x, t) is approximated by.

5.2 Finite Elements for 2D/3D Systems

We can implement the finite element method for higher dimensional systems by using the same
concepts we employed for 1D, namely:

1. Formulate the underlying PDE in its weak form.

2. Approximate the dependent variable using a finite sum of basis functions. Substituting this
approximation into the weak form will lead to a matrix system of equations for the dependent variable
that can be solved for. For simplicity, we will illustrate these concepts using the following time-
independent PDE, written in strong form as.