CHAPTER I

FINITE ELEMENT METHODS: FUNDAMENTALS AND

APPLICATIONS IN BIOMEDICAL ENGINEERING

P. E. McHugh, D. O’Mahoney

Department of Mechanical and Biomedical Engineering, and National Centre

for Biomedical Engineering Science, National University of Ireland, Galway,
Ireland.

In this chapter an introduction to the finite element method, and

how it relates to biomechanics and biomedical engineering, is
presented. The chapter includes reviews of continuum mechanics
and finite element theory, necessary for the understanding of the
finite element formulation. The chapter highlights the important
aspects of the finite element method that must be kept in mind
when one is using it to solve boundary value problems, especially
for non-linear problems that frequently occur in biomechanics. The
chapter closes with a discussion of two case study applications.

1. Continuum Mechanics

Vectors (e.g., displacement and velocity) are represented using three

components in 3D. The structure presented in equation (1.1) below applies
when we are considering components referred to an orthonormal set of
basis vectors, e1, e2, e3. Note also the definition of the summation
convention, identified by repeated indices
v = vi e i = v1e1 + v2e 2 + v3e 3 (1.1)
The dot product of two vectors is defined as follows
v ⋅ u = vi ui = v1u1 + v2u 2 + v3u3 (1.2)
Second order tensors (e.g., stress and strain) are represented using
nine components in 3D. The components of a tensor A with respect to an
P.J. Prendergast and P.E. McHugh (Eds.), Topics in Bio-Mechanical Engineering, pp. 1-40.
© 2004 Trinity Centre for Bioengineering & National Centre for Biomedical Engineering Science.
1
2 Topics in Bio-Mechanical Engineering

orthonormal basis are given by the following two equivalent expressions

Aij = ei ⋅ A ⋅ e j
(1.3)
A = Aij ei e j
The second of equation (1.3) illustrates the definition of a dyadic or
tensor product of two vectors, ei and ej in this case. In general second order
tensors are linear vector functions of vectors, e.g.
v = A ⋅u
(1.4)
vi = Aij u j
Fourth order tensors represent linear tensor functions of second order
tensors, e.g. the tensor of linear elasticity, L, relating strain, ε , to stress, σ .
σ = L:ε
(1.5)
σ ij = Lijkl εlk = Lijkl εkl
For a fourth order tensor, major symmetry means that Lijkl = Lklij and minor
symmetry means that Lijkl = Ljikl and Lijkl = Lijlk.

1.1 Large Deformation Kinematics

Large (finite) deformation kinematics is usually addressed in terms of

considering the deformation of a reference configuration into a current (or
deformed) configuration. The position vector of a material point in the
reference configuration is given by the vector x and the position of this
point in the current configuration by the vector y(x). The displacement
vector for the point is u(x) = y(x) – x. The velocity vector of the material
point is v(x) = du/dt and the surface traction distribution on the current
configuration is given by t, as shown in Fig. 1 below.

Fig. 1. Illustration of finite deformation kinematics.

 Finite Elements in Biomedical Engineering 3

Also in Fig. 1, an infinitesimal material “fibre” is described by dx in

the reference configuration and by dy in the current configuration. The
deformation gradient tensor F relates the two
∂y ∂y
dy = F ⋅ dx ⇔ F = = ∇y ⇔ Fij = i = yi, j (1.6)
∂x ∂x j
The right-most term in equation (1.6) presents the “shorthand” method of
representing gradients in index notation. Also we can say
∂y ∂u
F= =I+ = I + ∇u ⇔ Fij = δ ij + ui, j (1.7)
∂x ∂x
where I is the identity tensor, whose components are δ ij , the Kronecker
delta function. A quantity that is usually of considerable interest is the
~
spatial velocity gradient L , defined as
~ ∂v & −1
L= = F⋅F (1.8)
∂y

1.2 Strain Measures

Consider the stretching of the material fibre dx from the point of view of
change in magnitude. Consider, in particular, the difference of the square
of the fibre length:
dy − dx = (F ⋅ dx ) ⋅ (F ⋅ dx ) − dx ⋅ dx
2 2

( )
= dx ⋅ F T ⋅ F ⋅ dx − dx ⋅ dx (1.9)
= dx ⋅ (F )
⋅ F − I ⋅ dx
T

= 2dx ⋅ E ⋅ dx
which allows the Lagrangian Strain tensor, E, to be defined
E= 1
2 (F T
⋅F − I ) (1.10)
This is demonstartes a non-linear relationship between strain and the
displacement gradient. The Lagrangian strain rate is given by
E 2 (
& = 1 F& T ⋅ F + F T ⋅ F& ) (1.11)
4 Topics in Bio-Mechanical Engineering

Another very important strain rate measure, normally associated with the
~
current configuration, is the Rate of Deformation tensor, D , derived
from the spatial velocity gradient as
~ ~
~
~ ~
() (
D = sym L = 12 LT + L ) ~ ~T
(1.12)
Both E and D are symmetric tensors, i.e., E = E , and D = D . Under
T

the assumption of infinitesimal (small) deformations and starting with the

definition of Lagrangian strain, the strain-displacement gradient
relationship expands as follows
E= 1
2 (F T
⋅F − I )
= 1
2 ((I + ∇u ) T
⋅ (I + ∇u ) − I ) (1.13)
= 1
2 (∇u + ∇u T
+ ∇u ⋅ ∇u T
)
Assuming that the product of infinitesimals is negligible we can say
(
E ≅ 12 ∇u + ∇u T = ε ) (1.14)
and we are left with the definition of the infinitesimal (small) strain tensor,
ε, which represents a linear relationship between strain and displacement
gradient. Allied to this is the definition of the infinitesimal spin tensor, ω
ω = ∇u − ε = 12 ∇u − ∇u T ( ) (1.15)

1.3 Stress Measures

Cauchy (true) Stress is given the symbol σ and describes the force per unit
area on the current configuration. It is a symmetric tensor and is related to
the traction t on a surface (internal or external) in the current configuration
and a unit normal vector to the surface n ~,
t = σ⋅n ~
(1.16)
ti = σ ij n~j
Other important stress tensors are the following:
Kirchhoff Stress (symmetric), τ = Jσ , where J = dV(x)/dV0(x), is the
Jacobian of the deformation, i.e., the ratio of local infinitesimal volumes in
the neighbourhood of a material point x, between the current configuration
(dV(x)) and the reference configuration (dV0(x))
 Finite Elements in Biomedical Engineering 5

Nominal Stress (unsymmetric), n = F −1 ⋅ τ , which is the force per unit

area on reference configuration; Second Piola Kirchhoff Stress
(symmetric), S = F −1 ⋅ τ ⋅ F − T .
These different quantities satisfy work conjugacy rules;
~ ~
σ : D = σ ij Dij = W&C is the rate of work per unit current volume and
~ & = W& is the rate of work per unit reference volume. In the
τ:D = S:E R
small deformation case we can assume that deviations from the reference
configuration are negligible, which means that F is approximated by I, and
all definitions of stress collapse onto one, usually denoted by σ .

1.4 Equilibrium

The basic concept of static equilibrium is that the sum of external forces
and moments on a body is zero. It is useful to have point-wise version of
this concept, expressing equilibrium at (in the neighbourhood of) a
material point x. Such an expression can be written in terms of the
divergence of the stress, for the case of small deformations as
∂σ ij
= σ ij,j = 0
∂x j (1.17)
∇⋅σ = 0
For large deformation, we can say, in terms of quantities in the current
configuration,
∂σ ij
= σ ij,j = 0
∂y j (1.18)
∇⋅σ = 0
where σ is the Cauchy stress in this case and gradients are taken to be
spatial gradients. If the body is subject to a body force distribution, e.g., as
might come from gravity or a magnetic field, we can say
∂σ ij
+ fi = 0 (1.19)
∂y j
where f i is known as the body force density. For dynamic situations, an
inertia force density can be included
6 Topics in Bio-Mechanical Engineering

∂σ ij
+ f i − ρu&&i = 0 (1.20)
∂y j
Equilibrium at a point on the surface of body can be expressed in terms of
the relationship between stress and surface traction using equation (1.16).

1.5 Boundary Conditions

For the purposes of dealing with boundary conditions (BCs) on the surface
of a body or region, the surface S can be divided into the displacement
oundary S1 and the traction boundary S2 as indicated in Fig. 2 below.

Fig. 2. Specification of displacement and traction boundaries.

The surface S is given by S = S1 U S2, where S1 is the displacement

boundary, where the kinematic boundary conditions, i.e., displacements
and velocities, are prescribed, and S2 is the traction boundary, where the
traction boundary conditions, i.e., the surface forces are prescribed.

1.6 Boundary Value Problems

Problems in solid mechanics usually require that for a given body one can
determine the complete mechanical state for any point in time. This means
that (assuming small deformation terminology for convenience) we can
determine ε(x), σ(x), u(x) and t(x), plus rates of these quantities for rate
dependent or dynamic problems, plus other state variables (e.g., a strain
 Finite Elements in Biomedical Engineering 7

hardening parameter for a plastic material) and their rates, for any time t.
To do this we are usually required to solve the following
Equilibrium equation (conditions on σ )
Constitutive equation ( σ − ε relationship)
Compatibility equation ( ε − u relationship)
Together, these form a set of partial differential equations (PDEs). We
must also consider the boundary conditions. Combining the PDE and BC,
we are presented with a Boundary Value Problem (BVP) to solve. This
concept readily extends to heat flow, diffusion problems, etc.

1.7 Virtual Work

The Principle of Virtual Work (PVW), or in rate form the Principle of

Virtual Power, can be written on either the reference or current
configuration. It is an expression of the conservation of energy. Below, for
example, we write it in terms of power on the current configuration with
volume V and surface S (assuming zero body force f i ); the left hand side
represents internal virtual power and the right hand side represents external
virtual power.
~
∫ σ : δDdV = ∫ t ⋅ δvdS
V S
(1.21)

Here, σ and t are the real stress and surface traction, respectively,
~
and δD and δv are the virtual rate of deformation and surface velocity,
respectively. The fundamental point is that the relationship is true even
when the virtual quantities (deformation rate and velocity) are not due to
the real quantities (stress and traction). The virtual velocities (or
displacements) must satisfy the kinematic (velocity or displacement)
boundary conditions. Kinematic boundary conditions are also known as
essential boundary conditions. A commonly used form of the PVW is the
one used in small deformation analysis
∫ σ : δεdV = ∫ t ⋅ δudS
V S
(1.22)
8 Topics in Bio-Mechanical Engineering

2. Finite Element Analysis for Linear Elasticity

2.1 Introduction

The assumption of linear elasticity is intimately linked with small

displacement finite element analysis. Therefore in this section we use
linear elasticity to explain the finite element method and illustrate its
logical and elegant simplicity. First stated by Robert Hooke in 1678 as,
‘The power of any springy body is in the same proportion with the
extension’, the fundamental expression of linear elasticity can be written
simply as F = Ku . A graph of force (F) with extension (u) for a spring of
stiffness K undergoing small deflection is linear, as shown below in Fig. 3.

Fig. 3. Force deflection graph for a linear spring.

The strain energy stored (Ψ) in the spring stretched by an amount u is

given by the area under the graph, that is:
1 1 1
Ψ= Fu = K u 2 = u K u (2.1)
2 2 2
For a one dimensional solid body the strain energy per unit volume
becomes:
1 1 1
Ψ= σε = Eε 2 = εEε (2.2)
2 2 2
Here E is the Young’s modulus, σ is stress, and ε is strain. In general, for a
three dimensional solid body, the strain energy per unit volume is given in
matrix notation by Ψ = ½ ε Dε , where ε is a “vector” of strain
T
 Finite Elements in Biomedical Engineering 9

components (see equation 2.4 below) and D is the material stiffness

matrix; D is essentially the tensor L of equation (1.5) expressed in matrix
form. The simplest form of linear elasticity is isotropic linear elasticity
where the material constitutive behaviour is completely described by two
elastic constants; the most commonly used elastic constants in this regard
are E and ν (Poisson’s ratio). To find D from “first principles”, the general
isotropic linear elastic stress strain relations are used, these are:
σ 11
v
ε11 = (σ 22 + σ 33 )
−
E E
σ v
ε 22 = 22 − (σ 11 + σ 33 )
E E
(2.3)
σ v
ε 33 = 33 − (σ 11 + σ 22 )
E E
σ 12 σ 23 σ 13
γ12 = ; γ23 = ; γ13 =
G G G
Here, G is the Shear Modulus, given by G = E/2(1+ν), and the
engineering shear strain γij = 2εij. This can be organised into the following
matrix equation in terms of “vectors” σ and ε and the matrix D:
σ11 1−ν ν ν 0 0 0 ε11
σ   1−ν ν 0 0 0 ε22
 22 
σ33 E  1−ν 0 0 0 ε33
 =    (2.4)
σ12  (1+ν )(1− 2ν )  0 γ12 
1−2ν
2 0
σ23  SYMM 1−2ν
0 γ 23
  
2
 
σ13  γ13
1−2ν
 2 

or, σ = Dε . Very often, plane stress and plane strain assumptions are
used to simplify problems from 3D to 2D. If we assume plane strains
conditions, that is ε 33 = 0 , then equation (2.4) simplifies to:
σ 11  1 − ν ν 0   ε11 
σ  = E  ν  ε 
 22  (1 + ν )(1 − 2ν )  1 −ν 0   22  (2.5)
σ 12   0 0 1− 2ν 
γ 
2   12 
10 Topics in Bio-Mechanical Engineering

For the plane stress case, σ 33 = 0 , equation (2.4) simplifies to:

σ 11  1 ν 0  ε11 
σ  = E ν 1 0 ε  (2.6)
 22  1 − ν 2    22 
σ 12   0 0 1− 2ν 
γ 
2   12 

So what is the strain εij? For the general 3D case the infinitesimal
strains are given by equation (1.14). It is instructive to look at the
individual terms in this general expression. Assume that at an arbitrary
position x1, a slice of material of length ∆x1 is deformed a very small
amount ∆u1, the strain component ε11 is given by:
∂u1
ε11 = (2.7)
∂x1
∂u2 ∂u3
Similarly, ε 22 = and ε 33 = , where u2 and u3 are the
∂x2 ∂x3
deformations in the x2 and x3 directions, respectively. The shear strains
∂u1 ∂u2 ∂u2 ∂u3
are given as follows γ 12 = + , γ 23 = + and
∂x2 ∂x1 ∂x3 ∂x2
∂u1 ∂u3
γ 13 = + . For the 2D plane problems we are directly interested
∂x3 ∂x1
in ε11 , ε 22 and γ 12 , and in order to find these strain components we
need to have u1(x1, x2) and u2(x1, x2).

2.2 Element Formulation

In order to simplify the problem of finding the strain energy for an

arbitrary shaped body, let us first restrict our attention to 2D (this is for
illustrative purposes only – the principles also directly apply to 3D). Let
us assume we have a triangular piece (an element) of material ∆abc (see
Fig. 4) with forces acting at the vertices (the nodes). Let us also assume
that the deformations u1 and u2 are known at each of the vertices.
At any point P(x1,x2) within the element the deformation could
reasonably be assumed to be a “weighted average” of the displacements
 Finite Elements in Biomedical Engineering 11

of the nodes. So we need a formula to get the deformation at P in terms

of the nodal displacements. We can express this as:
∑ ∑
u1 ( x1 , x2 ) = N i ( x1 , x2 ) u1i and u2 ( x1 , x2 ) = N i ( x1 , x2 ) u2i , (2.8)
where the summation is made over the nodes on the triangle. In equation
(2.8) the Ni are the weights, which vary depending on where P is in the
element, and u1i and u2i are the two displacement components for node i.
So in the case of u1, for example, we have
u1 ( x1 , x2 ) = N a ( x1 , x2 )u1a + N b ( x1 , x2 )u1b + N c ( x1 , x2 )u1c .

x2

x1
Fig. 4. Prototype triangular element in 2D.

So what do the functions Ni look like? Well given that they are in fact
an “average” we must have for all points inside ∆abc that all Ni are
valued between zero and one. Also, the sum ∑Ni must be equal to one.
Finally, each Ni(x1k,x2k), where x1k and x2k are the two coordinates of
node k, is equal to one when i is equal k, and is zero otherwise, i.e. at
each of the other nodes.
A solution to this is to use ‘area co-ordinates’ first put forward by the
Polish mathematician Courant in 1943. If we assume we have a
triangular element as shown above, the weighting functions (or shape
functions) Ni can be defined as follows:
12 Topics in Bio-Mechanical Engineering

∆pbc ∆pca ∆pab

Na = = 1 − x1 − x2 , N b = = x1 , N c = = x2 (2.9)
∆abc ∆abc ∆abc
It can be easily shown for the triangular element defined above that the
conditions imposed on Ni hold.
We wish to also define the strain in a similar form to that of
deformation; let us assume the existence of coefficients Bαβ linking strain
component α with nodal displacement component β. For example,

ε11 ( x1 , x2 ) = ∑ B1i ( x1 , x2 )u1i , (2.10)

where the i is summed over the three nodes. We know that
u1 ( x1 , x2 ) = (1 − x1 − x2 )u1a + x1u1b + x2u1c
and (2.11)
u2 ( x1 , x2 ) = (1 − x1 − x2 )u2 a + x1u2b + x2u2c
Using the definition of strain given above we get
∂u1 ∂u2
ε11 = = − u1a + u1b ε 22 = = − u2 a + u2 c
∂x1 ∂x2
and (2.12)
∂u ∂u
γ 12 = 1 + 2 = −u1a + u1c − u 2 a + u 2 b .
∂x2 ∂x1
Rewriting this is in matrix-vector form we have:
 u1a 
u 
 ε11  − 1 0 1 0 0 0  
2a

ε  =  0 − 1 0 0 0 1 1b   u
 22    u  (2.13)
γ 12  − 1 − 1 0 1 1 0  2b 
 u1c 
 
u2c 
This equation illustrates that the equations emanating from the finite
element formulation are most conveniently expressed in matrix-vector
form. The Bαβ coefficients, which are spatial gradients of the weighting
functions (equation 2.10), generate a matrix B (on the rhs of equation
2.13). The nodal displacement components can be organised into a vector
 Finite Elements in Biomedical Engineering 13

ue (on the far rhs of equation 2.10). On this basis, equation (2.13) can be
written simply as
ε = Bu e (2.14)
As the strain energy per unit volume is Ψ = ½ ε T D ε , the strain
energy stored in the element, Φe, of volume Ve must be given
by Φ e = Ψ V e = ½ ε T D ε V e . This leads to the definition of the
element stiffness matrix, K, by substituting for the strain (equation 2.14)
Φ e = ½ ε T D ε V e = ½ ( Bu e ) T D ( Bu e )V e
(2.15)
T
= ½ u e B T DBu e V e
Comparing this with the expression for the strain energy of a spring,
involving the stiffness of the spring K and its displacement u, (equation
2.1) we can define K as
K = B T DB V e (2.16)
and hence Φ e = ½ u e T Ku e .
Bringing the spring analogy further, the displacement of the spring
can be determined from an inversion of Hooke’s equation (2.1),
u = F / K = FK −1 . Similarly, if a vector of nodal forces, Fe, is known,
and when K can be inverted (see section 2.3 below), the nodal
displacements can be determined through u e = K −1Fe . This is the
situation that normally pertains in solid mechanics problems to be solved
by the finite element method; one seeks the unknown displacements of a
body under known applied loads.
As regards the convenience of matrix notation for finite element
formulations, we note that equations (2.8) can be neatly expressed in the
following form using the shape function matrix N

u  N 0 Nb 0 Nc 0
u = Nu e , u =  1 , N =  a
N c 
(2.17)
u2  0 Na 0 Nb 0
14 Topics in Bio-Mechanical Engineering

2.3 Calculation of K for Prototype Element

If we take for example E = 250 Pa and ν = 0.2 under plane stress

conditions and with the triangle abc as described above, and assuming
unit thickness, we get for K:
T
−1 0 1 0 0 0 260 52 0  −1 0 1 0 0 0
K =  0 −1 0 0 0 1  52 260 0   0 − 1 0 0 0 1[0.5]
−1 −1 0 1 1 0  0 0 104 −1 − 1 0 1 1 0

The volume is given by area (0.5) times a unit thickness (1). This gives:
 182 78 − 130 − 52 − 52 26 
 78 182 − 26 − 52 − 52 − 130 

 − 130 − 26 130 0 0 26 
K =  (2.18)
 − 52 − 52 0 52 52 0 
 − 52 − 52 0 52 52 0 
 
 26 − 130 26 0 0 130 
The entries in K have the units of N/m. Some properties of K are
worth noting. The first is that K is symmetric (although this may not be
generally the case). To see why we can argue as follows:
K = B T DB
⇒ K T = [B T DB] T
⇒ K T = B T D T B TT
⇒ K T = B TDTB
Q D = DT ⇒ K = K T
The second is that the matrix is not of full rank, actually it has rank
N-3. In other words it is singular, and so does not have a regular inverse.
To have full rank, K in equation (2.18) must have six independent rows
(or columns). However, firstly note that row 4 (R4) and R5 are the same
so R4 - R5 = 0. Also, R1 + R3 + R5 = 0, and finally R2 + (R5 + R6) =
0. Performing these elementary row operations we get K’ as:
 Finite Elements in Biomedical Engineering 15

 0 0 0 0 0 0 
 0 0 0 0 0 0 

 − 130 − 26 130 0 0 26 
K' =  
 0 0 0 0 0 0 
 − 52 − 52 0 52 52 0 
 
 − 26 − 130 26 0 0 130 
The significance of this is that at least three displacement boundary
conditions must be specified in order to obtain a unique solution to
Hooke’s equation Fe = Kue. These three displacement boundary
conditions relate to the three rigid body modes of deformation in 2D.
These must be eliminated before the finite element solution for the
deformation of the body can be determined. Lastly we see from equation
(2.18) that all row and column sums are equal to zero. This is because K
is formed from a derivative, i.e. K= dFe/due. All differential operators
have this property.

2.4 Quadrilateral Elements

For four node quadrilateral elements things are not quite so

straightforward. Let us assume we have an element such as that in Fig. 5,
and we wish to calculate K assuming the material matrix D is the same.

x2

x1

Fig. 5. Prototype quadrilateral element on [-1, 1] x [-1, 1]

16 Topics in Bio-Mechanical Engineering

The first problem is that area co-ordinates which we used for triangular
elements are not useful here. Instead we use the following weighting (or
shape) functions:
1
N a = ( 1 - x1 )( 1 - x2 )
4
1
N b = ( 1 + x1 )( 1 - x2 )
4 (2.19)
1
N c = ( 1 + x1 )( 1 + x2 )
4
1
N d = ( 1 - x1 )( 1 + x2 )
4
It can be easily shown that these Ni meet the same requirements as those
for the triangular element. Again we wish to find an expression for the
strain within the element in terms of the nodal displacements, e.g. we
wish to have
∑
ε11 ( x1 , x2 ) = B1i ( x1 , x2 )u1i (2.20)
Starting with the shape functions, as before, we can say
∑ ∑
u1 ( x1 , x2 ) = N i ( x1 , x2 ) u1i and u2 ( x1 , x2 ) = N i ( x1 , x2 ) u2i (2.21)
By substituting these definitions into the definition of strain we generate
a result similar to that given in equation (2.13) but where this time the B
matrix has the form:
−1+ x2 0 1− x2 0 1+ x2 0 −1− x2 0 
1
B=  0 −1+ x1 0 −1− x1 0 1+ x1 0 1− x1 
4
 −1+ x1 −1+ x2 −1− x1 1− x2 1+ x1 1+ x2 1− x1 −1− x2 
(2.22)
It is worth noting that the matrix B is not a constant. Instead it varies
according to the position within the element. Therefore, the strain varies
across the element in a linear fashion. So, the product BTDB gives a
matrix which varies across the element. So K cannot be found directly.
In order to find an overall value for K we assume that for a small
element of volume dV (= dx1 x dx2 x 1), at a position (x1,x2), the elemental
stiffness matrix is dK, so we have:
 Finite Elements in Biomedical Engineering 17

d K = B T
DB dV
= ∫ (2.23)
T
K B DB dV
1 1
= ∫ ∫
T
K B DB dx 1 dx 2
−1 −1

2.5 Integration of Stiffness Matrices and Gaussian Quadrature

In order to evaluate the last integral (equation 2.23) one could simply use
Maple or Mathematica to get:
113 33 − 74 −7 − 56 − 33 17 7 
 113 7 17 − 33 − 56 −7− 74

 113 − 33 17 − 7 − 56 33 
 
113 7 − 74 33 − 56
K= (2.24)
 113 33 − 74 − 7 
 
 SYMM 113 7 17 
 113 − 33
 
 113 
However, this is obviously not practical when using a programming
language such as Fortran or Pascal. Instead Gaussian integration is
commonly used. In this approximation the integrand is evaluated at
special points on [−1,1]x[−1,1] called Gauss points. In this case the
integrand is simply a matrix, containing functions as entries, rather than
constants. On [−1,1] x [−1,1] the four Gauss points ξi(x1,x2) are at
[0.577, ± 0.577] and [−0.577, ± 0.577] . The integral is then evaluated
as a weighted sum:
4
(2.25)
K = ∑ H i B T ( ξ i ) DB ( ξ i )
i =1
In this case the weights Hi are all equal to 1, although this is not
generally the case. A more general treatment of this method can be found
in most numerical methods text books.
18 Topics in Bio-Mechanical Engineering

2.6 Worked Example

To see how the finite element method works in practice, let us look at the
following example. Consider the structure shown below, which is hinged
at a and is only allowed to move in the x1 direction at b. We wish to find
all remaining displacements and reaction forces.

Fig. 6. Structure for FE analysis

Expanding Hooke’s equation Fe = Kue, and substituting in the known

values for force and displacement, we get

 F1a   182 78 − 130 − 52 − 52 26   u1a 

 F   78 182 − 26 − 52 − 52 − 130 u2 a 
 2a  
 F1b  − 130 − 26 130 0 0 26   u1b 
 =  
 F2b   − 52 − 52 0 52 52 0  u 2 b 
 F1c   − 52 − 52 0 52 52 0   u1c 
    
 F2 c   26 − 130 26 0 0 130  u2 c 
 Finite Elements in Biomedical Engineering 19

Inserting the prescribed force and displacement B.C.’s gives:

 F1a   182 78 − 130 − 52 − 52 26   0 

 F   78
 2a   182 − 26 − 52 − 52 − 130  0 
 1  − 130 − 26 130 0 0 26   u1b 
 =  
 F2b   − 52 − 52 0 52 52 0  0 
 1   − 52 − 52 0 52 52 0   u1c 
    
 1   26 − 130 26 0 0 130  u2c 

This system of equations can now be easily solved to determine the

unknown displacements as: u1b = u2c = 0.0064 m and u1c = 0.0192 m.

2.7 Generalisations

The fundamentals of the finite element method have been presented in

this section. The details on how the method is directly formulated and
used to solve mechanics problems using linear elasticity have been
given. To keep the presentation simple, the focus has been on a single
element; of course in practice many finite elements are typically used to
discretise the geometry of a given body, i.e. a finite element mesh is
generated (in 2D or 3D). Linear or quadrilateral element types are
typically used; in 2D 3-noded linear triangles (as detailed above) or 6-
noded quadratic triangles are quite common, also 4-noded bi-linear quads
(as detailed above) and 8-noded bi-quadratic quads are common; in 3D
8-noded and 20-noded brick elements are common. In all of these cases,
except for the 3-noded triangle, the element stiffness matrices are
computed using Gaussian integration, as illustrated in equation (2.25).
For a mesh of inter-connected finite elements the Hooke’s equation for a
single element ( Ku e = Fe ) is generalised into a global form that
represents the discretised elastic response of the complete body. This can
be written as K gu g = Fg . Here ug and Fg are global nodal displacement
and nodal force vectors and Kg is the global stiffness matrix that is
20 Topics in Bio-Mechanical Engineering

generated by direct superposition of the individual element stiffness

matrices that form the mesh (the generation of Kg is known as the
“assembly” process). Once appropriate boundary conditions and nodal
forces are applied, the unknown nodal displacements (the primary
−1
solution variables) can be determined through u g = K g Fg . Once these
are determined, back at the individual element level, strains can be
determined through ε = Bu e and hence the stresses through σ = Dε .
The inversion of Kg is a major computational task for very large meshes,
especially in 3D. Methods are continually being developed to improve
the efficiency of the inversion and equation solving process.
It is important to realise that for linear BVPs a solution can be
obtained via a single inversion of Kg and multiplication by Fg. From a
computational resource perspective this is highly desirable but it is not
however the most common situation encountered in practice. Non-
linearities can arise for many reasons and when they do the BVP cannot
be represented by a simple expression such as Hooke’s equation and
solutions cannot be obtained using a single matrix inversion. Instead
incremental and/or iterative solution procedures are adopted, normally
requiring numerous sequential matrix inversions. These non-linear
solution procedures will be discussed in the next section.
Non-linearities can arise under three main headings:
• Constitutive equation: a non-linear σ − ε relationship, such as would
be the case for an elastic-plastic material, as shown in Figure 7 below.
• Compatibility equation: a non-linear ε − u relationship, as arises
under assumptions of finite deformation kinematics. This can clearly
be seen in the form of the Lagrangian strain tensor in equation (1.13)
which involves a product of displacement gradients.
• Boundary conditions: Non-linear boundary conditions that evolve
with the deformation, such as surface contact.
All of these can introduce considerable complexities into the
achievement of a finite element solution. All of these are relevant in the
biomechanics area, for example in terms of large deformations and non-
linear material response of soft tissue.
 Finite Elements in Biomedical Engineering 21

It is important to realise that, at the fundamental level, the finite

element method is a means of obtaining approximate numerical solutions
to boundary value problems. The quality of the approximation depends
on many factors. For linear problems one of the most important of these
is the quality of the finite element mesh. It is usually best to use regular
element shapes because element distortion causes errors in the Gaussian
integration process. In general, higher mesh densities mean greater
accuracy, but this must usually be balanced by the higher computational
resources required by dense meshes. For non-linear problems both the
mesh quality and the accuracy of the non-linear equation solution
procedure used (to be discussed below) are of critical importance.
Checking the suitability of the mesh is ideally done by a mesh
convergence study, where meshes of increasing density are used until the
difference in the solution between any two is less than some chosen
tolerance. In practice this may not always be possible to do for a very
complex problem where the converged mesh may be denser that what is
practical to use, based on normal computational resources. In such cases
the approximate nature of the mesh that is used must always be kept in
mind when interpreting the results. At the very least, in dealing with any
BVP, the sensitivity of the result to the mesh density should be assessed,
by comparing the results of at least two different meshes, and the
sensitivity should be kept in mind, should one never be able to use a fully
converged mesh. There are situations where it is fundamentally
impossible to achieve a converged mesh and these include fracture
mechanics problems where one might try to resolve an infinite stress
concentration at a crack tip or a crack growth problem where one might
try to model crack growth using direct element removal or node release.
In such cases, where the processes controlling the overall behaviour of
the system are localised to a particular region (e.g. the crack tip), the
model predictions are directly dependent on the mesh size and will show
differences no matter how much the element size is reduced. Problems
like this can often be dealt with by “calibrating” or fixing the element
size, usually to be representative of some microstructural length scale in
the material or system. This removes the mesh size variability and other
model parameters can then be adjusted until the model gives reasonably
22 Topics in Bio-Mechanical Engineering

Fig. 7. Stress-strain curve for an elastic-plastic material. Based on elastic unloading, the
strain can be decomposed into elastic and plastic parts.

accurate quantitative results. However, mesh dependence remains a very

important issue in finite element analysis of problems involving localised
phenomena, and much work is being done to develop generalised
formulations that account for the effect and eliminate the problem, e.g.,
Gasser and Holzapfel (2).

3. Conventional Finite Element Formulation

In this section we build on the fundamentals presented in the previous

section and consider a general formulation of the finite element method
 Finite Elements in Biomedical Engineering 23

that has the potential to deal with both linear and non-linear problems. A
very good reference on finite element formulations of the “conventional
form” is Zienkiewicz and Taylor (8). Consider a BVP, assuming small
deformation kinematics, posed in terms of the PVW, where t is the surface
traction vector and the δ refers to virtual quantities
∫ σ : δεdV = ∫ t ⋅ δudS
V S
(3.1)

Rewrite this in matrix/vector form

∫ δε σdV = ∫ δu T tdS
T
(3.2)
V S
For example in 2D we would have:
δε σ
δu t
 δε11   σ11 
     δu1   t1  (3.3)
 δε 22   σ 22     
 2δε  σ   δu 2   t2 
 12   12 

Using the definition of the infinitesimal strain tensor and inserting the
finite element interpolation as illustrated in equations (2.14 and 2.17) we
can say
ε = 12 (∇u + ∇u T ) = B e u e and δε = B e δu e (3.4)
Here Be is the matrix of shape function gradients for element “e” in the
finite element mesh. For a material with a non-linear constitutive response
we can say
σ = σ (ε) → σ = σ (u e ) (3.5)
Substitution into the PVW and summation over all the elements “e” in a
finite element mesh, each with a volume Ve and a surface Se, yields
∑ ∫ δu
e Ve
T
e B Te σ (u e )dV = ∑ ∫ δu Te N Te tdS
e Se
(3.6)

If we drop the summation notation and the subscripts for convenience and
eliminate or “cancel” the arbitrary virtual displacements we get
∫B σ (u)dV = ∫ N T tdS
T
(3.7)
V S

If we rearrange this we get

24 Topics in Bio-Mechanical Engineering

G (u) = ∫ B T σ (u)dV − ∫ N T tdS = 0 (3.8)

V S

G is a set of non-linear equations in u, where u now means the vector of

nodal displacements and G is the residual force vector. The solution of this
set of equations is usually achieved by incremental methods, i.e., applying
load in increments/steps and stepping to final time tfinal in time steps ∆t.
Numerous algorithms have been developed to solve the equations for the
increment and these can be generally classified under the headings of
Implicit or Explicit methods.
Considering an increment in time, t → t+∆t, implicit methods involve
determining the state at t+∆t based on information at time t and t+∆t,
whereas explicit methods involve determining the state at t+∆t based on
information at time t alone. In implicit methods iteration is usually
required to obtain the solution for an increment. Generally, for reasonable
accuracy, ∆t values for implicit methods can be an order of magnitude
greater than ∆t values for explicit methods. In the following, we consider a
very common implicit method, the Newton-Raphson method.

3.1 Newton-Raphson Method

Assume that we have solved for state at time t and we wish to update state
to t+∆t. The ut+∆t are considered as main solution variables and we must
solve the following non-linear set of equations for ut+∆t
( )
G u t + ∆t = 0 (3.9)
The Newton-Raphson (NR) method can be applied to determine the ut+∆t
by iteration. Let’s first look at a 1D analogy. Suppose we wish to solve f(x)
= 0 by NR. If we have a guess at the root xi, a better guess xi+1 given by the
NR formula
−1
 df 
xi+1 = xi −   ⋅ f ( xi ) (3.10)
 dx  xi
The method is applied iteratively, i.e., xi+1 is substituted for xi and the NR
formula is reapplied. This process is continued until a convergence
criterion is satisfied
 Finite Elements in Biomedical Engineering 25

xi+1 − xi < Tolerance

(3.11)
f ( xi +1 ) < Tolerance
If we apply the same concept to our non-linear finite element equations
(3.9) we can say for the ith iteration

u ti ++1∆t = u ti + ∆t − 
(
 ∂G u ti + ∆t  ) −1
t + ∆t
( )
 G ui (3.12)
 ∂u 
If we reorganise this in terms of the change in incremental displacement
we get
 ∂G u ti + ∆t 
δu i +1 = u ti ++1∆t − u ti + ∆t = − 
( )
t + ∆t
−1

( )
 G ui (3.13)
 ∂u 
The partial derivative term on the right hand side of equation (3.13) is the
Jacobian of the governing equations. We can identify this as the Tangent
Stiffness matrix, K. Using this we can say
(
δu i +1 = −K u ti + ∆t ) G (u )
−1 t + ∆t
i (3.14)
and hence by inversion
( ) (
K u ti + ∆t δu i +1 = −G u ti + ∆t ) (3.15)
The matrix equation (3.15) represents a set of linear algebraic equations in
the δu i +1 . It has the same form as for a linear problem (Ku = F). It must be
solved, for each iteration, for the change in incremental displacements. The
matrix K and vector G (the residual force vector) are different for each
iteration. At any particular iteration, the current increment in
displacements is given by
i
u ti + ∆t − u t = ∆u i = ∑ δu k (3.16)
k =1
The convergence criterion can be expressed in terms of G as follows
( )
G u ti ++1∆t < Tolerance (3.17)
It is important to note that the method requires accurate evaluation of
( ) ( )
K u ti + ∆t and G u ti + ∆t for each iteration i. G requires accurate evaluation
of the stress σ at the current estimate of ut+∆t. This can be seen from the
form of G,
26 Topics in Bio-Mechanical Engineering

( )
G u ti + ∆t = ∫ B T σ (u ti + ∆t )dV − ∫ N T t t + ∆t dS (3.18)
V S

which in turn means that a stress update algorithm is required. Next, look
at structure of K.

( )
K uti+∆t =
( )
∂G uti+∆t
= ∫ BT
∂σ
dV = ∫ BT
∂σ ∂ε
dV = ∫ BT
∂σ
BdV
∂u V
∂u (uti+∆t ) V
∂ε (uti+∆t ) ∂u V
∂ε (uti+∆t )
(3.19)
The partial derivative in the right-most term in equation (3.19) is the
Jacobian of the constitutive law and can be identified as the Tangent
matrix, Dtan.
∂σ
D tan =
∂ε (uti + ∆t )
( )
⇒ K u ti + ∆t = ∫ B T Dtan BdV (3.20)
V

The tangent stiffness matrix K has the same form as for linear problems,
i.e., the classic “BTDB” structure. However here K is different for each
iteration. This can lead to problems since the tangent matrix can be
difficult to evaluate for very non-linear materials.
The NR method is accurate and displays rapid convergence. However
sometimes it is modified, e.g.,
• use of a constant K, from the first iteration in the increment (or even
the first increment in the loading history – initial stress method) which
means we avoid having to recalculate K for each iteration
• use of a symmetric K if the problem generates an unsymmetric K,
otherwise we must use unsymmetric solvers
• more complex versions of the algorithm: BFGS method (Broyden-
Fletcher-Goldfarb-Shanno).
These and other methods can work well. They sometimes result in slower
convergence, but they can actually increase the radius of convergence. It
is important to note that it is acceptable to modify K but we always must
calculate G correctly and since G depends directly on the stress this
means that we must have a stress update algorithm that is accurate:
 Finite Elements in Biomedical Engineering 27

u ti + ∆t = u t + ∆u i
G (u ti + ∆t ) = ∫ B T σ (u ti + ∆t )dV − ∫ N T t t + ∆t dS (3.21)
V S

σ (u ti + ∆t ) = σ (u t + ∆u i ) = σ (u t ) + ∆σ i
From equation (3.21) we must determine ∆σ i accurately, given ∆ui. This
can be quite difficult for complex non-linear constitutive laws.

3.2 Explicit Stress Update Algorithms

Explicit algorithms use information at time t to get to time t+∆t directly.

Perhaps the simplest explicit method is the Simple/Forward Euler method
which is based on a linearisation of the constitutive law about time t. It is
usually easy to implement but it is not very accurate unless very small time
steps are used. Another explicit method is the Runge Kutta method. This is
a multi-step explicit method based on subdivision of the time step. The
Rate Tangent method (6) is also an explicit method. For the general case of
a rate dependent elastic-plastic constitutive law, the method is based on
linearising the non-linear expression for plastic strain rate, using a Taylor
expansion about time t to estimate the plastic strain rate at t+∆t. Since it
involves this estimation of the state at t+∆t, it is also sometimes called a
“semi-implicit” method.

3.3 Implicit Stress Update Algorithms

For an implicit algorithm the state at time t+∆t is determined from

information at time t and t+∆t. An example of a “fully” implicit method is
the Backward Euler method which is based on a linearisation of the
constitutive law about time t+∆t. Since the state at t+∆t is unknown, the
method usually produces a system of coupled non-linear equations in the
stress/state variables at t+∆t that must be solved to perform the stress/state
variable update. The equations can usually be solved using a NR iteration.
The Backward Euler method is very accurate.
There are many other forms of explicit and implicit stress update
algorithms presented in the literature. Implicit algorithms usually allow
28 Topics in Bio-Mechanical Engineering

bigger time increments to be taken than explicit formulations, from the

point of view of accuracy and stability, due to the iteration and the
shooting for convergence at the end of the time step. Factors of at least 10
in time step size difference between implicit and explicit are possible.
Remember that we are still discussing stress update algorithms within
the context of the implicit NR (or similar) solution of the overall system
equations G(u) = 0. The implication of this is that we can have explicit or
implicit stress update algorithm operating within each NR iteration. For
example, if using Backward Euler method we would have a series of
iterations to update stresses and state variables within each element, and in
fact a series of iterations at each Gaussian integration point within each
element, and this is done for each iteration of the NR solution of the
governing equations for each increment.
It is interesting to note that people commonly write user material
subroutines for implicit commercial finite element codes, such as
ABAQUS/Standard (UMAT). Usually these routines implement a stress
update algorithm. It should be realised that it is up to the user to write a
UMAT that produces a sufficiently accurate stress update based on the
time and strain increments provided by ABAQUS. For a given iteration
within a given increment, ABAQUS will provide the UMAT with a
number of quantities, including the time step and the current estimate of
the strain increment (ABAQUS → UMAT: ∆t, ∆ε,…). Based on these, the
UMAT increments and updates the stress and the other state variables and
calculates the Jacobian of the constitutive law (UMAT → ABAQUS: ∆σ,
dσ/dε,…). The important issue to consider is whether the stress
increment/updated stress is accurate based on the ABAQUS ∆t. ABAQUS
assumes that it is and if the overall NR iteration converges then it will
assume that equilibrium has been achieved for t+∆t. But just because
convergence has been reached doesn’t mean that the solution is correct. It
will only be correct if the stress increment/updated stress provided by the
UMAT is correct. Therefore, care must be taken in writing UMATs, and
for a given ∆t, in order to ensure accuracy, it might be necessary to modify
or reduce ∆t within the UMAT. Fortunately, this can readily be done.
 Finite Elements in Biomedical Engineering 29

3.4 Dynamical Solution Methods

Since we have used the word explicit above, it is important to distinguish

the above approach from the dynamic explicit approach that is also
commonly (and therefore confusingly) referred to as explicit.
First of all, consider including inertia and formulating the BVP
dynamically as expressed by the following
Mu&& + G (u, v ) = 0 (3.22)
Here, M is a mass matrix, u && is the nodal acceleration vector, and G is now
a function of the nodal displacements u and the nodal velocities v. This is a
general form valid for non-linear materials, finite deformation kinematics,
etc. Both implicit and explicit methods have been developed to solve such
equations. In the dynamic context the terms implicit and explicit usually
have the following meanings.
• Explicit: no matrix inversion is required and there is usually no need to
form a tangent stiffness matrix K from G. A popular explicit method
is the Central Difference Method.
• Implicit: matrix inversion/equation solution is required, and this can be
iterative. A popular implicit method is Newmark’s Algorithm.
Let us consider the central difference method. A good description of the
method in the finite element context is given in the ABAQUS Theory
manual (4). The central difference method is a fully explicit method,
involving no matrix inversion and no formation of a stiffness matrix, K. M
must be in diagonal or “lumped” mass form. The method works in terms
of “half” increments: i-1/2, i, i+1/2, i+1, etc. The algorithm works in terms
of first evaluating accelerations by solving the first of equation (3.23),
which is trivial since M is diagonal, and then solving for velocities and
displacements.
&& i = −M −1G i
u
∆ti+1 + ∆ti
v i+ 1 = v i− 1 + u
&& i (3.23)
2 2 2
u i +1 = u i + ∆ti +1 v i + 1
2

This is a very computationally efficient method for updating the state

variables. It integrates through time using many small times increments for
30 Topics in Bio-Mechanical Engineering

accuracy. It is conditionally stable and the time step must be kept within
stability limit. Algorithms have been developed to evaluate this limit.
Explicit methods are becoming more popular since there are no iteration
and no convergence difficulties. They are suited to large deformation
problems and highly non-linear problems that might arise due to material
constitutive law complexity and surface contact, for example. The main
down side it the necessity to use a very small time step size that can slow
down computation. Time step size can be increased using mass scaling,
i.e., artificially factoring-up the mass. However this has to be carefully
monitored to avoid the introduction of artificially high kinetic energy
effects.

3.5 Quasi-static Formulation: Implicit Solution for Finite Deformation

Kinematics

Let us now return to considering the quasi-static formulation of the BVP

expressed in equation (3.8), and introduce finite deformation kinematics.
Let us look at the complexities this can introduce. A good discussion on
this is also presented in the ABAQUS Theory Manual (4). Consider now
the PVW expressed in rate form on the current configuration with volume
V and surface S. In this case t is the surface traction vector in the deformed
configuration
∫ δD σdV = ∫ δv
T T
tdS (3.24)
V S

For small elastic strains and incompressible plasticity, the Jacobian of the
mapping J is approximately equal to 1, and hence the Cauchy stress is
approximately equal to the Kirchhoff stress. Referring the PVW back to
the reference configuration, V0 and S0, we can say

∫ δD σdV = ∫ δv tℜdS
T T
(3.25)
V0 S0

Here, ℜ is the infinitesimal surface area ratio between the current and the
reference configurations. Introducing the finite element interpolation as
before we can say u = N e u e , δu = N e δu e , v = N e v e and δv = N e δv e .
~
The rate of deformation tensor D is linearly related to ve at any instant in
time through the matrix of shape function spatial gradients, Be, as follows
 Finite Elements in Biomedical Engineering 31

 ∂v ∂v 
( )
T
~ ~ ~
D= 1
L + LT = 12  +  = Be ve
 (3.26)
 ∂y ∂y
2

In contrast to the small deformation case, here the shape functions and
hence the shape function gradients can be functions of the deformation y
and the displacements u. This means that Be can be different at each
instant in time. The linear relationship is only true instantaneously and is
not true in a time integrated form, i.e., the strain and displacement are not
linearly related. In an incremental form over a time step ∆t the linear
relationship is approximately true and we can say the following
∆ε = D∆t = B e v e ∆t = B e ∆u e (3.27)
In this case, ∆ε is the increment in logarithmic strain. Substituting into the
PVW, equation (3.25), summing over all the elements “e” in a finite
element mesh and dropping the summation notation and the subscripts for
convenience we get
∫ δv B(u) T σ (u)dV = ∫ δv T N T tℜdS
T
(3.28)
V0 S0

Eliminating or “cancelling” the arbitrary virtual velocities we get

∫ B(u) σ (u)dV = ∫ N T tℜdS
T
(3.29)
V0 S0

This has a similar structure to equation (3.7) except for complexity of B.

Finally, we can define G as before
G (u) = ∫ B(u) T σ(u)dV − ∫ N T tℜdS = 0 (3.30)
V0 S0

For solution of these equations using and implicit NR based method an

accurate stress update algorithm required, as before. Let us consider the
form of the Jacobian of governing equilibrium equations (tangent stiffness
matrix) for an NR solution scheme in this case. Referring back to equation
(3.19) we can say
32 Topics in Bio-Mechanical Engineering

( )
K u ti + ∆t =
(
∂G u ti + ∆t
=∫
∂BT) σdV + ∫ BT
∂σ
dV
∂u V0
∂u (u t + ∆t ) V0
∂u (u t + ∆t
i )
i
(3.31)
∂t ∂ℜ
− ∫N T
ℜdS − ∫ N T t dS
S0
∂u (u ti + ∆t ) S0
∂u (u ti + ∆t )

However, as before,

∂σ ∂σ ∂ε
= = Dtan B (3.32)
∂u (uti + ∆t ) ∂ε ∂u (uti + ∆t )

so that

( ) ∫ ∂∂Bu ∂t
T
K u ti + ∆t = σdV + ∫ BT D tan BdV − ∫ N T ℜdS
V0 (u )
t + ∆t V0 S0
∂u (u ti + ∆t )
i

∂ℜ
− ∫ NT t dS
S0
∂u (u ti + ∆t )
(3.33)
Here we see that finite deformation kinematics have introduced
considerable complexities. In the first instance B will be different at each
point in time in the evaluation of G, from equation (3.30). More
significantly however, K is quite complicated, being composed of the
familiar term involving the material tangent matrix (second term on right
in equation 3.33) and other terms coming from the variation in B, t and
ℜ, due to large deformations. A finite element programme written to
implement this method must keep track of all these variations to generate
an accurate G and an accurate K. As part of this, the stress update
algorithm is specifically required to generate an accurate σ and an
accurate Dtan. K will in general be an un-symmetric matrix, requiring the
use of un-symmetric solvers when implemented in a computer
programme.
 Finite Elements in Biomedical Engineering 33

4. Applications in Biomechanics and Biomedical Engineering

4.1 Introduction

As can clearly be seen from the previous sections the finite element
method can be developed to deal with a range of boundary value
problems, both linear to non-linear. The presentation above is concerned
with solid mechanics only, however the principles and method are also
applicable to problems involving temperature/heat flow, diffusion,
chemical reactions, electromagnetism and, or course, biological
processes. The applications of computational methods in the
biomechanics and biomedical engineering fields have grown enormously
in recent years. Many advances have been made in applying them to the
analysis and design of medical devices, and this endeavour, on the
whole, has proved extremely successful – indeed finite element analysis
is a required part of the US FDA certification process for certain classes
of medical devices. More challenging is the application of computational
methods to tissue and to the representation of biological processes; this is
a very exciting and rapidly developing area at the forefront of modern
engineering science. In this new realm, there is tremendous scope for the
enhancement of existing computational methods and for the development
of new methods, based on alternative paradigms, that more completely
capture the physical nature of the problems to be addressed. In this
context, “cellular automata” approaches, and the combination of such
approaches with continuum mechanics, may prove extremely useful in
the future.
In the following we present two examples of the finite element
method, (i) modelling deformation of trabecular bone and (ii) modelling
failure of cardiovascular stent struts. Both examples can be classified
under the heading of micromechanics, where computational mechanics is
applied to physical problems at the micron size scale. Micromechanics
has been very successfully used in the past to deal with the mechanics of
multiphase materials and advanced metal-ceramic composites, and is
now finding increased application in the biomedical area.
Micromechanical models are usually based on the concept of the periodic
or repeating “unit cell”, whereby a macroscale material or system is
34 Topics in Bio-Mechanical Engineering

considered to be built up of identical unit cells, each cell having a

structure representative of the microstructure of the system. This is a
powerful technique; analysis of the cell itself allows the small scale
physical processes in the material or system microstructure to be
resolved, and since the overall system is assumed periodic, the average
response of any one cell is equivalent to the overall response of the
complete macroscale system, i.e. one is provided with a micro-macro
link relating microscale processes to macroscale behaviour. A good
review of the principles of micromechanical modelling of this type is
presented in Böhm (1). The types of boundary conditions applied to the
unit cell are an important aspect of this modelling approach. Boundary
conditions can either by “symmetric” or “periodic” (1), the former is
simpler to apply but the latter is more accurate for general loading
conditions. The size of the unit cell is also critical, the more
microstructural features that can be included the better – what we really
want is a Representative Volume Element (RVE). Current estimates
suggest that for a purely linear elastic material in 3D a unit cell/RVE
must have on the order of at least 10 microstructural features (reinforcing
particles, pores, grains, trabeculae….) to be reasonable accurate. When
we move to attempting to represent material non-linearity (plasticity,
damage, microcracking…) at least 50 features per unit cell/RVE are
required.

4.2 Trabecular Bone Modelling

Trabecular bone (TB) makes up the inner part of a typical skeletal bone,
consisting of a highly porous network of tiny plates and strands called
trabeculae. Accurate three-dimensional finite element models are the key
to fully understanding its mechanical properties and how it functions in-
vivo. The challenging shape and size scale necessitates micro-CT scans to
be used as starting point for the geometry of such finite element models.
Firstly, a 3D STL model is created from a set of TB µ-CT scans using
imaging processing software (such as MIMICS). This mesh can then be
improved using specialised finite element pre-processing software. The
finite element analysis can then be performed using a conventional solver.
 Finite Elements in Biomedical Engineering 35

However, modelling large samples of TB in this way can be impractical

due to the amount of manual effort required. Varying success can be found
between different commercial mesh generators. PATRAN for example can
be problematic when attempting to model trabeculae connections.
HYPERMESH can be used in modelling both single and small numbers of
connected trabeculae. Only models containing few or single trabeculae can
be made without extensive manual effort in mesh correction. Other models
can suffer with elements having very poor aspect ratio, leading to serious
element distortion under loading. These models, constructed of tetrahedral
elements that varied widely in size, shape and orientation, result in a high
CPU load and memory requirement.

Fig. 8. FE model of canine trabecular bone (3) – contour plot of von-Mises stress, computed
using ABAQUS/Standard.
36 Topics in Bio-Mechanical Engineering

The largest models currently run are based on a 3.5mm cube unit cell
created from canine femur bone µCT scans (see Fig. 8 (3)). The model
consists of 1.8 million 4-noded tetrahedral elements. Linear elastic
material behaviour has been assumed. Simple boundary conditions have
been applied here; the bottom surface is constrained and the top surface is
subjected to a uniform compressive displacement. A non-uniform stress
distribution in the microstructure is clearly evident. Solving takes in the
order of 4 hrs wall time on single processor of SGI Origin 3800. Many
elements have very poor aspect ratio leading to excessive element
distortion under loading. The considerable variation in element size and
shape required excessive CPU time because the stiffness matrix for each
element has to be computed.
Voxel mesh generation is also the currently used for this analysis of
trabecular bone. In this case an eight node brick element is placed at each
position where the CT scan detects bone. This results in a highly structured
mesh with a jagged irregular surface. However, the resulting system of
equations can be solved quickly as each element will have the same
stiffness matrix.

4.3 Cardiovascular Stents

Micromechanics has been used to study size effects in small scale metallic
medical devices, in particular vascular stents for the treatment of coronary
heart disease (7). Stents, when manufactured, typically take the form of
networks of thin stainless steel struts. The structure undergoes
considerable plastic deformation when the stent is being deployed in a
blocked artery. It is expanded into position in the artery by the inflation of
a balloon upon which it is mounted. Once deployed, the balloon is deflated
and removed. Since stent struts are quite small, on the order of 75 µm x 75
µm in cross-section, and may only have a few grains across the thickness
(on the order of 10), the issue of size effects on material properties arises.
In particular, Murphy et al. (5) studied the influence of strut size on
ductility, finding that thin strut tensile ductility was only on the order of
50% of the ductility of bulk material. In Savage et al. (7), crystal plasticity
polycrystalline models were used to study this effect in 2D generalised
 Finite Elements in Biomedical Engineering 37

plane strain deformation. ABAQUS/Standard was used for the

simulations. The crystal plasticity material description was introduced via
a UMAT. Grains were assumed to be regular hexagons in the plane with
random crystal lattice orientations (in 3D). A unit cell for a model with
three grains through the strut thickness is shown in Fig. 9. In this case
symmetric boundary conditions were applied at the left and right hand
ends of the unit cell. The properties of 316L austenitic (FCC) stainless
steel were assumed. Due to the inhomogeneous lattice orientations, plastic
strain localisation occurred, leading to necking and failure. An example of
this is shown in Fig. 10 for a model with nine grains through the thickness.
By considering models of different thicknesses, where the grain size was
kept constant, a clear relationship between failure strain and the thickness
was predicted, following the trend seen in the experiments. This is shown
in Fig. 11, where experimental and computed macroscopic failure strains
are compared. Failure strain was taken as the strain at the UTS point from
the macroscopic tensile stress-strain diagram in both cases. The results
show that the models predict the observed trend but that further refinement
is necessary to obtain full quantitative agreement.

Fig. 9. Example of 2D stent strut model with hexagonal grains. Reprinted from Savage et
al. (7) © Biomedical Engineering Society.
38 Topics in Bio-Mechanical Engineering

Fig. 10. Contour plot of accumulated plastic strain for a stent strut model with nine grains
across the thickness. Reprinted from Savage et al. (7) © Biomedical Engineering Society.

60
Failure Strain [%]

Computational
50
Experimental
40

30

20

10

0
0 100 200 300 400 500 600

Strut Size [µm]

Fig. 11. Comparison of experimental and computational failure strain for different stent
strut thicknesses. Reprinted from Savage et al. (7) © Biomedical Engineering Society.
 Finite Elements in Biomedical Engineering 39

5. Concluding Remarks

In this chapter we have reviewed the finite element method, exploring

the fundamental details in the context of linear elasticity and generalising
to full finite deformation non-linearity. For linear problems the
importance of mesh quality has been emphasised. For non-linear
problems, the importance of mesh quality and the accuracy of the
numerical integration scheme used have been discussed. Non-linear
formulations are very important for tackling problems in biomechanics
and biomedical engineering because tissues can exhibit large
deformation and non-linear material behaviour. In addition, surface
contact problems are common, for example in the context of implanted
devices: total hip replacements, catheter insertion and stent expansion in
arterial lesions. For solving BVPs in the continuum mechanics context,
the importance of finite element solution mesh dependence has been
discussed; the issue is of high importance for problem exhibiting strong
localisations. Computational mechanics applied at the micron size scale
(micromechanics) has been introduced and two examples from the
biomedical field have been presented.
The future is bright for applications of computational methods in
biomechanics and biomedical engineering, particularly in terms of
incorporating representations of biological processes. Cell mechanics,
where attempts are being made to represent the physical behaviour of
cells using computational methods, is especially exciting for the future.
To do so it may be necessary to go beyond the bounds of traditional
continuum mechanics perspectives and to incorporate discrete event
modelling. These indeed are very exciting challenges for the future.

Acknowledgements

The authors acknowledge the research collaboration with the Trinity

Centre for Bioengineering and research partners at The Royal College of
Surgeons in Ireland and University College Dublin, funded under the
Programme for Research in Third-Level Institutions (PRTLI),
administered by the HEA.
40 Topics in Bio-Mechanical Engineering

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