INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING

Int. J. Numer. Meth. Engng 2014; 100:277299

Published online 28 July 2014 in Wiley Online Library (wileyonlinelibrary.com). DOI: 10.1002/nme.4735

A combined fluidstructure interaction and multifield scalar

transport model for simulating mass transport in biomechanics
L. Yoshihara*, , M. Coroneo, A. Comerford, G. Bauer, T. Klppel and W. A. Wall
Institute for Computational Mechanics, Technische Universitt Mnchen, Boltzmannstr. 15, 85747 Garching b.,
Munich, Germany

SUMMARY
Mass transport processes are known to play an important role in many fields of biomechanics such as respiratory, cardiovascular, and biofilm mechanics. In this paper, we present a novel computational model
considering the effect of local solid deformation and fluid flow on mass transport. As the transport processes are assumed to influence neither structure deformation nor fluid flow, a sequential one-way coupling
of a fluidstructure interaction (FSI) and a multi-field scalar transport model is realized. In each time step,
first the non-linear monolithic FSI problem is solved to determine current local deformations and velocities.
Using this information, the mass transport equations can then be formulated on the deformed fluid and solid
domains. At the interface, concentrations are related depending on the interfacial permeability. First numerical examples demonstrate that the proposed approach is suitable for simulating convective and diffusive
scalar transport on coupled, deformable fluid and solid domains. Copyright 2014 John Wiley & Sons, Ltd.
Received 13 June 2013; Revised 14 February 2014; Accepted 8 June 2014
KEY WORDS:

mass transport; fluidstructure interaction; cardiovascular mechanics; respiratory mechanics; biofilm mechanics

1. INTRODUCTION
Transport of substances through biological fluids and solids plays an essential role in many fields
of biomechanics. For instance, understanding particle transport in the lungs is essential for the optimization of targeted drug delivery. Another application in respiratory mechanics is the improvement
of blood oxygenation during mechanical ventilation. In this case, the transport and exchange of
oxygen and carbon dioxide between air, tissue, and blood have to be studied. In biofilm mechanics, a proper understanding of nutrient transport and uptake is indispensable to enable the control of
biofilm formation and development. While being mostly detrimental in the health sector, biofilms
can also be beneficial in a wide range of applications, such as waste water treatment. A prominent
example in cardiovascular mechanics is atherosclerosis, a prevalent disease of the large arteries that
involves an accumulation of lipoproteins in the arterial wall [1].
Computational models can fundamentally contribute to the understanding of involved phenomena and, as a consequence, to the improvement of therapeutical approaches. However, establishing
reasonable numerical models is very challenging because the interaction of various physical fields
such as fluid, solid, and transported species has to be considered. In addition, most of the transport
processes take place in a highly deforming environment. For instance, gas transport in the lungs is
affected by the periodic expansion and contraction of the organ during breathing.
Previous studies have been predominantly confined to passive transport processes in fluids. Corresponding computational approaches are based on a one-way coupling of a computational fluid
*Correspondence to: L. Yoshihara, Institute for Computational Mechanics, Technische Universitt Mnchen,
Boltzmannstr. 15, 85747 Garching b., Munich, Germany.
E-mail: yoshihara@lnm.mw.tum.de
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L. YOSHIHARA ET AL.

dynamics (CFD) and a scalar transport model. Hence, information on the flow field obtained from
the CFD simulation is utilized to formulate the convectiondiffusion equation for the mass transfer.
Applications of this methodology include the transport of (macro-)molecules in both blood [25]
and air [6, 7]. In addition, there have been a number of approaches considering also the coupling of
macromolecule transport in the arterial lumen to transport within the wall [812]. To model interstitial flow within the immovable wall, either Darcys law or Brinkmans equation has been utilized
in this context.
More complex models also include fluidstructure interaction (FSI) effects. For instance, it was
demonstrated in [13] that wall compliance affects the transport of oxygen to the arterial wall in the
carotid bifurcation. Mass transport within the wall, though, was ignored in this study. By contrast,
the approach proposed in [14] considers macro-molecule transport in both the lumen and the wall of
a coronary artery. The tissue was modeled as a poroelastic material, allowing the expression of the
interstitial velocity via Darcys equation. Subsequent to the FSI analysis, macro-molecule transport
was simulated based on the computed velocity and deformation field. However, transport processes
in the wall and in the lumen were considered in a decoupled manner. After having calculated the
concentration field within the fluid, interfacial lumen concentrations were utilized as a boundary
condition to the transport simulations within the wall. As a consequence, mass transfer was only
possible in one direction, that is, from fluid to tissue.
While the models mentioned so far have been concerned with rather basic transport processes,
there have also been a number of studies looking specifically at drug release from stents into the
arterial wall and lumen [1517]. Again, a convectiondiffusion equation was utilized to model the
transport of the drug through the different wall layers. In [16], the deformation of the wall following
stent deployment was considered simply by remeshing both the wall and the stent structure. Hence,
wall deformation and mass transport were essentially uncoupled. In [17], a structural simulation of
stent deployment was utilized to calculate the interstitial water velocity from the deformation field.
This was achieved by means of a decomposition of the total stress into the effective stress of the
tissue matrix and the pore pressure. The latter component was then used to calculate the interstitial
velocity via Darcys equation. However, the mass transfer problem was again formulated on the final
deformed structure. This methodology is suitable for drug eluting stent deployment simulations, but
not for more dynamically moving structures.
In addition to the 3D finite element (FE) based approaches discussed earlier, there have been a
number of studies utilizing a combination of 1D transport models and Ficks law to describe the
diffusion through the tissue (see, for instance, [18]). The major disadvantage of these reduceddimensional models is that no information is available about local transport processes.
To overcome the drawbacks of previous approaches, we have developed a novel computational
approach based on the sequential one-way coupling of a monolithic FSI model and a monolithic
multi-field transport model. The proposed methodology enables the consideration of (i) the effect of
local tissue deformation and fluid flow on mass transport and (ii) the mutual interaction of transport
processes in the lumen and the wall.
The remainder of this paper is organized as follows. After having summarized the governing
equations of the FSI and the multi-field transport subproblem in Sections 2 and 3, the coupling of
subproblems will be discussed in Section 4. The general validity and versatility of the proposed
model will be illustrated by selected numerical examples in Section 5. Finally, concluding remarks
and a brief outlook will be provided in Section 6.
2. FLUIDSTRUCTURE INTERACTION
FSI problems can formally be described as three-field problems. To begin with, there are two physical fields, fluid and structure, which share a common FSI interface . Furthermore, to account for
deformations of the fluid domain, an arbitrary LagrangianEulerian (ALE) approach is employed,
constituting a third, non-physical mesh field.
In the following, the governing equations for each field will be summarized. A definition of
the individual domains and the partitions of boundaries is given in Figure 1. In this context,
Copyright 2014 John Wiley & Sons, Ltd.

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279

Figure 1. FSI subproblem: definition of domains F ; S ; G , and their boundaries. The boundaries of solid
and fluid domains are partitioned in the form @K D DK [ NK [  with K 2 F; S, whereas the boundary
of G is given by @G D EG [ .

fluid, structure, and mesh (or grid) quantities are denoted by the superscripts ./F ; ./S , and ./G ,
respectively.
In order to enable the numerical solution of the field equations, discretization in space and time is
necessary. In this work, we utilize FEs and implicit time integration schemes for all fields, leading
to a set of non-linear algebraic equations, which is solved using a Newton-type method. It has to
be noted, though, that the algorithms discussed here are not restricted to any specific discretization
scheme.
After having reviewed the individual field equations, the coupling of fields will be discussed in
detail at the close of this section.
2.1. Structure field
In this work, the structure field is modeled by the non-linear elastodynamics equation
S

d2 dS
D r  .F  S/ C S bS
dt 2

in S  .0; T /;

(1)

where dS is the unknown structural displacement, S is the structural density, S denotes the undeformed domain, and bS represents the external body forces. In Equation (1), the internal forces are
expressed in terms of the second PiolaKirchhoff stress tensor S and the deformation gradient F. To
relate stresses and strains, a suitable constitutive model needs to be formulated.
At the Dirichlet and Neumann boundaries, DS and NS , boundary conditions have to be defined,
that is,
dS D dN S

on

DS  .0; T /

(2)

.F  S/  nS D hN S

on

NS  .0; T /;

(3)

where nS refers to the outward-pointing normal vector. To complete the initial boundary value
problem, the following initial conditions need to be specified:
dS .x; 0/ D dS0 .x/
ddS
.x; 0/ D dP S0 .x/
dt

for

x 2 S ;

(4)

for

x 2 S :

(5)

The weak form of the structure problem stated earlier is the starting point for the spatial discretization. Details about the FE method for structure fields can be found, for example, in [1921].
Although mixed or hybrid FE are equally suitable, a displacement-based FE formulation is considered exclusively in this work for the sake of simplicity. In this case, the weak form is obtained by
multiplication of Equation (1) with the virtual displacements dS followed by integration by parts,
that is,

2 S






S Sd d
0 D d ; 
C r dS ; F  S S  dS ; S bS S  dS ; hN S  S :
(6)
2
N
dt
S
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L. YOSHIHARA ET AL.

Here, .; /S and .; /NS denote the L2 inner products on S and NS , respectively. Equation (6) can
now be discretized in space and time. In the following, the residual of the discrete weak form is
denoted by rS D rS .dS /, where dS is from now on the vector of discretized nodal displacements.
After consistent linearization, the system to be solved in every iteration step i of the non-linear
algorithm reads
"

S II S I
S I S 

#i

"

dSI
dS

nC1

"

#i C1
D
nC1

rSI
rS

#i
(7)
nC1

for time step n C 1. In preparation of the coupling of fields introduced in Section 2.4, the set
of equations is already split into interior quantities identified by ./I and those defined at the FSI
interface denoted by ./ , that is,
S D

@rS
;
@dS

(8)

with ; 2 I; .
2.2. Fluid field
The considered flow problem is assumed to be governed by the instationary, incompressible Navier
Stokes equations for a Newtonian fluid on a deformable fluid domain F . The deformation of the
fluid domain dG is defined by a unique, arbitrary mapping ' given by


dG .x; t / D ' dG
for .x; t / 2 F  .0; T /;
(9)
 ; x; t
where dG
 represents the mesh interface displacement that will later be related to the structure
interface displacement dS . The grid velocity uG is then defined by
uG D

@'
@t

in F  .0; T /:

(10)

Equation (10) allows for the definition of the ALE convective velocity
cF D uF  uG

(11)

representing the fluid velocity uF relative to the arbitrarily moving fluid domain. Hence, the
convective formulation of the ALE form of the NavierStokes equations reads
F



 
@uF
C F cF  r uF  2r  " uF C r p F D F bF ;
@t
r  uF D 0;

(12)

(13)

where the fluid velocity uF and the fluid pressure p F are the unknown physical fields.In the momentum Equation (12), bF denotes a prescribed body force, ".uF / D 12 r uF C .r uF /T the strain rate
tensor of the Newtonian fluid, and  its dynamic viscosity. Equation (13) states the conservation of
mass given that the fluid density F is constant.
At the Dirichlet boundary DF and the Neumann boundary NF , the following conditions are set:
uF D uN on DF  .0; T /;
 F  nF D hN on
Copyright 2014 John Wiley & Sons, Ltd.

NF  .0; T /;

(14)
(15)

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MODEL FOR SIMULATING MASS TRANSPORT IN BIOMECHANICS

where nF denotes the outward-pointing normal vector. The Cauchy stress tensor  F for a Newtonian
fluid is given by
 
 F D p F I C 2" uF ;
(16)
with I denoting the second-order identity tensor. To complete the initial boundary value problem, a
divergence-free initial velocity field uF .x; 0/ D uF0 .x/ has to be specified for all x 2 F .
The weak form of the incompressible NavierStokes Equations (12) and (13) is obtained by
multiplying these equations with test functions uF for velocity and p F for pressure and integrating
by parts, that is,

F
 F F F

 

F F @u
0 D  u ;  b F C u ; 
C uF ; F cF  r uF F
@t F
(17)








F
F
C r u ; 2".u / F  r  uF ; p F F  p F ; r  uF F C uF ; hN  F :
N

In this work, an implicit time integration method is utilized in combination with stabilized FEs to
discretize the fluid problem (17). Stabilization terms are applied to account for instabilities arising
from equal-order discretization of fluid and pressure fields as well as for convection-dominated
problems. For details on the FE discretization of the fluid field and stabilization methods we refer,
for example, to [2224].
In the following, the residual of the discrete weak form is denoted by rF D rF .uF ; pF ; dG /.
Again, uF ; pF , and dG now represent the vectors of discretized nodal unknowns. The total residual
differential then reads
drF D

@rF F
@rF
@rF
du C F dpF C G ddG :
F
@u
@p
@d

(18)

The resulting set of linear equations can again be split into interior quantities and those defined at
the FSI interface, yielding the following system of equations
2
"

#i

G
F II F I F G
II F I
G
F I F  F G
I F 

uFI

3i C1
"

6
7
6 uF 7
6
7
6
G7
d
4
I 5
nC1
dG


D

rFI
rF

#i
(19)
nC1

nC1

with F ; F G
.; 2 I; / denoting the matrix representations of the partial derivatives
introduced in Equation (18), that is,
F D

@rF
;
@uF

FG
D

@rF
:
@dG

(20)

For ease of notation, the vector pF of nodal pressure values has been merged with the vector of the
interior fluid unknowns uFI . A detailed description of the so-called shape derivatives F G
can be
found, for instance, in [25, 26].
2.3. ALE field
The ALE formulation of the incompressible NavierStokes equations necessitates the definition of
the mapping ' introduced in Equation (9). In case of the FSI problems considered here, the boundary
of the ALE mesh is coupled to the Lagrangian mesh of the flanking structures (cf. also Section 2.4)
and an Eulerian mesh at the inflow and outflow portions denoted by E , that is,
dG D 0 on
dG D d S
Copyright 2014 John Wiley & Sons, Ltd.

EG  .0; T /;

(21)

on   .0; T /:

(22)

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L. YOSHIHARA ET AL.

Within the domain, the ALE mesh is allowed to deform arbitrarily. In this study, the ALE field is
treated as a quasi-elastostatic pseudo-structure following [27]. In this case, the ALE equation of
motion reads
r  G D 0

in G  .0; T /

(23)

with
 
 G D G tr G I C 2G G ;

G D

1  G  G T 
:
rd C rd
2

(24)

In this context, tr./ represents the trace operator and G ; G denote the Lam constants of the
pseudo-structure, which can be chosen arbitrarily.
The procedure for setting up the linearized discrete weak form associated with Equation (23) is
comparable to those presented in the previous sections. As the mesh movement is not allowed to
influence the interface, the resulting set of linear equations reduces to
"
#i C1
dG

i
I
G II G I nC1
D 0:
(25)
dG
 nC1
2.4. FSI coupling
At the fluidstructure interface , different kinematic and dynamic constraints have to be fulfilled.
Equilibrium of forces requires the surface tractions of fluid and structure to be equal, yielding
hS D hF

on

  .0; T /:

(26)

F
In addition, the grid velocity uG
 has to match the fluid velocity u at the interface:

uF D uG


on

  .0; T /:

(27)

Usually, both a mass flow across and a relative tangential movement of fluid and structure at  are
prohibited, that is,
@dS
D uF
@t

on

  .0; T /:

(28)

In combination with Equation (27), this condition is equivalent to

dS D dG


on

  .0; T /;

(29)

at least in the continuous setting. Hence, structural deformation and fluid movement (represented by
the ALE-based fluid domain deformation dG
 ) must match at .
The fully coupled non-linear FSI problem is solved within one global Newton loop. Consequently,
the individual field variables, that is, solid displacements, ALE mesh displacements, fluid velocities,
and pressure fields, are determined simultaneously. For complex biological problems involving the
coupling of incompressible flows and soft tissue, these so-called monolithic schemes were found
to be the best (and sometimes even the only feasible) alternative [28, 29]. As a matter of fact, the
similar densities of fluid and structure and the incompressible flow constitute a very challenging
scenario for coupling schemes, and partitioned schemes were found to be less robust and inefficient
in these conditions. In the following, it is assumed that fluid and solid FE discretizations coincide
at the interface, although the extension to non-conforming meshes is straightforward (cf., e.g., [30]
for a novel coupling algorithm based on a dual mortar method). In this case, there is only one
independent set of degrees of freedom at the interface as a consequence of the kinematic constraints
(27)(29). Thus, either interface displacements or velocities are retained in the monolithic system of
equations. In the following, the monolithic FSI problem will be derived for the latter case, although
Copyright 2014 John Wiley & Sons, Ltd.

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MODEL FOR SIMULATING MASS TRANSPORT IN BIOMECHANICS

both alternatives are in general equivalent. For the coupling of discrete mesh displacements and fluid
velocities at the interface, the following relation was derived in [31]

t  F
G
(30)
dG
uInC1 C uFIn :
InC1 D dIn C
2
This trapezoidal rule correctly preserves the size of the fluid domain and is exact for every fluid time
integration scheme that assumes constant accelerations within the time step t . Rearrangement of
Equation (30) yields the subsequent expression for the increments of interface displacements
t
C1
F
uFIi
InC1 C .i/t uIn ;
2
where i again denotes the iteration step, and we have introduced the mapping

1; i D 0
.i/ D
:
0; i > 0
C1
dGIi
InC1 D

(31)

(32)

Based on the linearized problems of the individual fields and the constraint conditions discussed
earlier, the monolithic FSI problem to be solved at time tnC1 , and iteration step i C 1 finally reads
2
3i 2
2 S 3i
3i C1
t
S II
S I
0
0
fI
dSI
2
6
7
7
6


6
7
6 S I F  C t S  C F G F I F G 7
6 fSF 7
6 uF 7

I 7
6
6  7
2
6
7
D6
(33)
6
7
7
6
7
6 0
7
6 fF 7
F I C t
FG
F II F G
4 uFI 5
II 5
I
4
4 I 5
2
t
G I
2

0
with

fSI

3i

6
7
6 fSF 7
6  7
6 F 7
6f 7
4 I 5
fG
I

nC1

G II

rSI

dG
I

nC1

fG
I

nC1

3i

7
6 S
6 r C rF 7
 7
6 
D 6
7
7
6 rFI
5
4
rG
I
nC1
2
S I
6
6 0 S 
6
C .i/ t 6
6 0
4
0

C FG

0
0

3i

uF

nC1

dG
I

7
6 F7
0 7
6 u 7
7
6
7
7
6 F7 :
G
u
F I 0 7
4
 5
5
0 G I nC1 uF n

dG
I

nC1

(34)

After solution of Equation (33), the vector of unknowns is updated as follows:

2 S 3i C1
2 S 3i
2
3i C1
dI
dI
dSI
6 F7
6 F7
6
7
6 u 7
6 u 7
6 uF 7
6
7
7
7
D6
C6
:
6 F7
6 F7
6
7
4 uI 5
4 uI 5
4 uFI 5
dG
I

nC1

(35)

nC1

The iterative procedure is aborted when a convergence criterion is met, for example,

2
3

fS i

6 SF 7

FSI i

6 f 7

r nC1
D
6 F 7

< FSI ;

6 fI 7

4
5

fI

(36)

nC1

where

FSI

is a problem-specific tolerance.

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L. YOSHIHARA ET AL.

Figure 2. Multi-field scalar transport subproblem: Definition of domains K and boundary partitions
@IK D DIK [ NIK [  with K 2 F; S.

3. MULTI-FIELD SCALAR TRANSPORT

To study passive transport phenomena in biological systems, a multi-field scalar transport model
is established. On each domain K (with K 2 F; S, cf. also Figure 2), the temporal and
spatial variation of the scalar concentration field K is governed by the following partial
differential equation




@K
C cK  rK C K r  uK  r  D K rK C RK D 0:
@t

(37)

Here, D K denotes the domain-specific diffusion coefficient, uK the velocity, RK the reaction
term, and cK the convective velocity. The latter has already been introduced for the fluid field in
S
and the grid velocity are identical, and,
Equation (11). On the solid domain, the velocity uS D @d
@t
hence, the convective velocity vanishes. In contrast to the momentum equation for the incompressible fluid (12), a conservative formulation needs to be chosen for the mass transport because, in
general, r  uS 0.
Essential (or Dirichlet) boundary conditions are defined by
NK
K D

on DIK  .0; T /:

(38)

A typical example is an inflow boundary where the mass concentration entering the domain is
known. At the Neumann boundary NIK , the negative normal flux is prescribed as follows:
D K rK  nK D hN K

on

NIK  .0; T /:

At the interface  between the domains F and S , the mass fluxes are given by




on   .0; T /;
hS D P S  F ; hF D P F  S

(39)

(40)

where P denotes the interface permeability. The initial boundary value problem is completed by the
definition of appropriate initial concentration fields reading
K .x; 0/ D K
0 .x/

for x 2 K :

(41)

For each domain K , the weak form is obtained by multiplying Equation (37) with the virtual
concentrations K and integrating by parts, yielding






@K
C rK ; DrK K
0 D K ;
C cK  rK C K r  uK
@t
K
(42)
 K K
 K K
 K  K
N
C ; R K  ; h  IK  ; h  :
N

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MODEL FOR SIMULATING MASS TRANSPORT IN BIOMECHANICS

After discretization in space and time, the discrete form of Equation (42) reads


0 D K tIK C hIK ;

(43)

which has to hold for arbitrary virtual concentrations K . The discrete vectors tIK and hIK
arise from the first four summands and the last term of the right hand side of (42), respectively. In
case of a linear reaction term, the transport problem is completely linear. Hence, the system to be
solved in every time step tnC1 can be formulated in terms of either absolute concentrations K
nC1 or
.
If,
however,
the
reaction
term
is
nonlinear,
Equation
(43)
has to
concentration increments  K
nC1
be solved iteratively. Hence, we restrict ourselves to the more general incremental formulation here.
In this case, the monolithic system of equations reads
2

T FII

T FI

6 F
6T T F CH 0
6 I 
6
6 0
0
T SII
4
0

H

H
T SI

T SI T S C H

3i

7
7
7
7
7
5

6
7
6  F 7
 7
6
6
7
6  S 7
I
4
5

nC1

 FI

 S

3i C1

nC1

tIF
I

3i

(44)

7
6
7
6 IF
6 t C hIF 7
7
6
D 6
;
7
7
6
tIS
I
5
4
IS
tIS
C
h

nC1
IK
where T K
with respect to the nodal
is the matrix representation of the partial derivatives of t
concentrations K
.;

2
I;
/.
The
coupling
matrix
H
arises
from
the
discrete flux condition

hIK and has a mass matrix like structure. For the sake of clarity, the set of Equations (44) has
again been split into interior and boundary quantities. After solution of Equation (44), the vector of
unknowns is updated as follows:

FI

3i C1

6 F7
6 7
6 7
6 S7
6 7
4 I 5
S

nC1

FI

3i

6 F7
6 7
6 7
D6 S7
6 7
4 I 5
S

 FI

3i C1

7
6
6  F 7
 7
6
C6
7
6  S 7
I 5
4

nC1

 S

(45)

nC1

The iterative procedure is aborted when a convergence criterion is met, for example,

2
3i

tIF

6
7
6

6 tIF C hIF 7

mass i

6 

< mass ;
7

.r /nC1
D
6

7
IS

6
7
tI

4
5

IS

t C hIS

nC1

(46)

where mass is a problem-specific tolerance.

In the limiting case of an infinite permeability, the interfacial concentrations are equal, that is,
S D F :
Copyright 2014 John Wiley & Sons, Ltd.

(47)
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L. YOSHIHARA ET AL.

As a consequence, the concentration increments are also identical, and, hence, the discrete multifield scalar transport problem simplifies to
2

T FII

T FI

3i

 FI

3i C1

tIF
I

3i

6 IF
7
6
7
7
6 F
IS 7
6  F 7
6T T F CT S T S 7
D 6
 5

I 5
4 t C t 5
4
4 I 
0
T SI
T SII nC1  SI nC1
tIS
I

(48)

nC1

As it is well-known, for convectiondiffusionreaction problems in convection-dominated

regimes, the standard Galerkin FE method is potentially unstable. It is possible to avoid such instabilities through the use of very fine spatial resolutions. This strategy, however, usually becomes
prohibitively expensive in terms of computational costs for most examples. As a consequence,
stabilized FE formulations for the numerical solution of convectiondiffusionreaction equations
were introduced. The proposed stabilization technique, which basically is a streamline upwind
Petrov/Galerkin method [32], accounts for spurious oscillations of the standard Galerkin FE method
when convection dominates. Details of the stabilized FE formulation implemented in the present
approach are provided in [33].

4. COUPLING OF FSI AND MASS TRANSPORT SUBPROBLEMS

In most cases, it can be assumed that fluid flow and structural deformation are not influenced by
mass transport processes. In line with this supposition, a one-way coupling of CFD and transport
models has been proposed in the past, for example, to study multi-ion transport in electrochemical
systems [34] or nanoparticle transport in the lung [7]. A sequential procedure also seems suitable for
the coupling of the FSI and multi-field scalar transport models discussed in Sections 2 and 3. Hence,
in each time step, the non-linear FSI problem is solved first. In the present study, the same spatial
discretization for the FSI and the mass transport equations is utilized. Hence, local deformations and
velocities obtained from the FSI calculation can be transferred directly (i.e., without necessitating
any interpolation) to the mass transport subproblem. Using this information, the multi-field scalar
transport equations can then be solved on the deforming fluid and solid domains. The proposed
procedure is summarized in Algorithm 1 and Figure 3. It is, however, important to highlight that
there are some specific applications in which the scalar transport has an influence on the fluid flow.
In these cases, a two-way coupling between the FSI and the scalar transport subproblems has to be
employed [34, 35].
Algorithm 1 Coupling of FSI and mass transport subproblems
while t <
tmax
do
while
rFSI
> FSI do
Set up and solve (33)
Update dS ; uF , and dG (35)
Check convergence (36)
end while
Transfer dS ; dG ; uS ; uF , and cF to mass transport subproblem
while krmass k > mass do
Set up and solve (44) or (48)
Update F and S (45)
Check convergence (46)
end while
Update t
end while
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Figure 3. Schematic of the one-way coupling of FSI and mass transport subproblems.

5. NUMERICAL EXAMPLES
To demonstrate that the presented approach is suitable for simulating multi-field scalar transport on
deformable domains, selected numerical examples will be provided in the following. All simulations
are based on a parallel implementation of the algorithms discussed earlier in our in-house multiphysics research code BACI [36]. For time discretization of fluid, solid, and transport equations, a
one-step-
time integration scheme is utilized. For the purpose of increasing the numerical robustness, a slight shift of
towards higher values as compared to the trapezoidal rule is chosen, and in
all the examples,
D 0:66 is always used. For the first four examples, trilinear hexahedral FE are
used. Hence, they are based on three-dimensional models and discretizations, albeit a pseudo-twodimensional deformation and flow state are enforced by prescribing specific boundary conditions
in most simulations considered. However, for the last example, a two-dimensional model is chosen to reduce computational costs. As quantitative results are of minor importance for the first four
examples, details on material parameters and others are provided only where they seem to be helpful for a better understanding. Besides, instead of computing absolute concentrations (i.e., the total
mass of a substance), we confine ourselves to calculate the spatial and temporal development of
concentrations relative to an arbitrarily chosen prescribed value. Hence, K is dimensionless in
these cases. By contrast, the last example accurately reproduces a real application. Therefore, all
details regarding material parameters and operating conditions are reported, and K is given in
absolute values.
In Sections 5.1 and 5.2, conservation of mass will be proven for structural and FSI problems,
respectively. The influence of the permeability on the coupling of interfacial concentrations will be
addressed in Section 5.3. Afterwards, a possible application of the proposed methodology to oxygen
transport in an idealized alveolus will be discussed in Section 5.4. Finally, the importance of the
proposed model is highlighted in Section 5.5 using the example of a real biofilm structure.
5.1. Mass conservation for solid problems
In the first numerical example, a cube of lung tissue (edge length L D 100 m) compressed to half
its original volume. The chosen initial distribution of oxygen concentrations in the cube is given by
S .x; y; z/ D 2:0 C cos.0:02x/ cos.0:02y/ cos.0:02z/
with 50 m 6 x; y; z 6 50 m (cf. also Figure 4). In line with [37], the diffusivity of oxygen
in lung tissue is assumed to be D S D 1:0 m2 =ms. At the boundary @S of the cube, zero-flux
conditions are prescribed. In each time step tnC1 , the transport equation
T SnC1  SnC1 D tIS
nC1

(49)

is solved on the deforming solid domain S .

In Figure 5, simulated concentration profiles are plotted at different points in time. Owing to the
diffusion processes within the cube, the initial gradient of the concentration field gradually reduces
to zero. At the same time, the concentration increases owing to the prescribed compression of
the cube.
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Figure 4. Initial concentration field.

Figure 5. Simulated concentration profiles along the x-axis at different points in time.

Figure 6 shows the time-dependent course of the cubes volume, the mean oxygen concentration,
and the overall mass of oxygen. Clearly, the mean concentration increases to the same extent as the
volume of the cube decreases. Hence, the overall mass of oxygen remains constant at all times.
5.2. Mass conservation for FSI problems
The previous example demonstrated the validity of the proposed approach for mass transport in
solids. Next, a simple FSI example will be considered. On the left hand side of Figure 7, the general
set-up of the problem is shown. The fluid domain F (dimensions 100 m  80 m  5 m) is
bound by a rigid wall at the bottom (indicated by DF ) and a movable, nearly rigid solid cuboid
(dimensions 100 m  20 m  5 m) at the top. The interface between the cuboid and the fluid
domain is again denoted by . At NF , zero-traction boundary conditions are defined for the fluid
field. By prescribing the following Dirichlet condition



.t  250:0 ms/
S
on DS  .0; T D 500 ms/;
(50)
dy .t / D 15 m 1:0 C sin
500:0 ms
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R S S 
R

d
,
Figure 6. Time-dependent course of the cubes volume dS , the mean oxygen concentration Rd
S
R S S
and the overall mass of oxygen d during compression of the cube. All quantities are referred to their
respective initial values.

Figure 7. Left: general set-up of the FSI validation example. Right: fluid flow at t D 250 ms, that is, at the
time of maximum flow. Colors and vector lengths indicate local velocity magnitudes.

Figure 8. Distribution of concentrations K at t D 0 ms, t D 250 ms, and t D 500 ms (from left to right).

the solid cuboid is forced to move downwards, thereby decreasing the volume of the fluid domain.
Consequently, flow through NF is induced (cf. also the right hand side of Figure 7).
The initial configuration of the mass transport problem is defined by a linear concentration gradient in vertical direction. The permeability of the interface is assumed to be infinite, and, thus,
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concentrations at  are identical in both fields. The diffusivities are chosen to be D F D 1:6 m2 =ms
and D S D 1:0 m2 =ms, corresponding to the diffusivity of oxygen in blood and lung tissue, respectively. In Figure 8, the distribution of concentrations is shown at different points in time. As a
consequence of the convective and diffusive transport processes, the concentrations in both fields
again gradually equalize.
At the boundaries NF , mass is transported out of the computational domain. Hence, in contrast
to the example discussed in Section 5.1, the overall mass within the domain changes with time. As
can
seen
 F be clearly
 in Figure 9, this change in mass equals the mass flux out of the domain given by
c  D F rF  nF . Hence, conservation of mass also holds in case of FSI problems.
5.3. Coupling of concentrations at the interface
So far, the permeability of the interface between fluid and solid domains was assumed to be infinite.
In practice, however, this presumption is unlikely to hold. The following example serves to provide
an insight into how permeability affects the distribution of concentrations within both domains.
For this purpose, mass transport is studied in a channel of fluid .100 m  20 m  2 m/ and
an adjacent solid structure (dimensions 100 m  6 m  2 m/, which is fixed at DS . A detailed
overview on the respective domains and boundaries is given in Figure 10. The fluid is loaded by a
body force in the x-direction with


 50 ms 
for t < 100 ms
100:0 m=ms2 1:0 C sin  t100
F
ms
bx D
(51)
2
for 100 ms 6 t 6 300 ms;
200:0 m=ms
yielding a maximum velocity of uFxImax D 0:64 m=ms. The diffusivities of the substance under
consideration are chosen to be D F D 1:6 m2 =ms and D S D 0:5 m2 =ms on the fluid and solid

Figure 9. Time-dependent course of the change in overall

domain K  t d , the mass
 F mass within the
F
F
F
F
flux out of the domain c  D r  n computed at N , and the sum of both.

Figure 10. Coupling of concentrations at the interface: definition of domains and boundaries. For the sake
of simplicity, Neumann boundaries are not explicitly marked.
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Figure 11. Concentration fields at t D 300ms for P D 0:0 ms1 ; P D 0:05 ms1 ; P D 0:2 ms1 ; P D
1:0 ms1 , and the limiting case P ! 1 (from top to bottom). Fluid flows from left to right. For the sake
of a better perceptibility of the concentration differences, the interface  between fluid and solid domains is
not explicitly marked.

domain, respectively. In the beginning, the concentration is zero throughout both domains except
for the boundaries DIF and DIS , where F D S D 1:0 is prescribed. Depending on whether a
finite or infinite permeability of the interface is assumed, either the weakly coupled problem (44) or
the simplified, strongly coupled system (48) is solved.
In Figure 11, the computed concentration fields at t D 300:0 ms can be compared for different permeabilities of the interface. Owing to the pronounced convective transport in the fluid phase
in combination with the different diffusivities in both domains, an uneven distribution of concentrations develops in all cases. However, the actual dispersion strongly depends on the interfacial
permeability. If P D 0:0 ms1 (cf. the top of Figure 11), concentrations at the interface are completely decoupled. With increasing permeability, interfacial concentrations gradually equalize, and,
hence, transport processes in both domains affect each other more and more. In the limiting case of
an infinite permeability (cf. the bottom of Figure 11), concentrations on both sides of the interface
are identical.
Exemplarily, the difference in interfacial concentrations at the outlet of the fluid and solid domain,
respectively, is plotted in Figure 12. Starting from  D 0:14, the difference drops quickly with
increasing permeability, thereby asymptotically approaching the limiting case  D 0:0.
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Figure 12. Magnitude of the difference in interfacial concentrations  at the outlet of the fluid and solid
domain, respectively, for different surface permeabilities P .

5.4. Oxygen transport in an idealized terminal lung unit

After the general validity of the combined FSI and multi-field scalar transport model has
been demonstrated, a potential application in the field of respiratory mechanics is discussed in
the following.
The primary function of the lung is to enable the transport of oxygen and carbon dioxide between
environment and blood. Efficient gas exchange requires that the bloodgas barrier possesses an
extremely large surface area combined with a small thickness, such that the passage of gas molecules
is impeded as slightly as possible. For serving this purpose, multiple thin interior walls are formed,
thereby subdividing the lung into a large number of small air chambers (also known as alveoli),
which are connected with the outside air through the airway tree. The pulmonary arteries and veins
form similar trees that finally converge in a dense capillary network wrapped around the alveoli.
Unfortunately, in vivo imaging techniques such as magnetic resonance tomography or computed
tomography are inapplicable to alveoli owing to their small characteristic size in combination with
the high water content of the tissue. Hence, realistic representations are only available for excised
small animal lungs (see, for instance, [38] for an imaging-based model of rat lung tissue). However,
the geometry of alveoli in the intact human lung is still unknown. Besides, many quantities such as
exact flow velocities or material parameters of the tissue are currently investigated (see, e.g., [39]).
Hence, at the moment, gas transport in the alveolus can only be simulated qualitatively at best. However, owing to the complex interplay of tissue deformation, air flow, blood flow, and gas transport,
this application is suited to demonstrate the general capabilities of the proposed methodology.
Details on the simplified configuration considered here are given in Figure 13. The lumen of a
single alveolus is approximated by a cuboid FIa (dimensions 100 m  30 m  1 m) filled with
FIa
FIa
air. On both sides of the cuboid DI1
, no-slip conditions are prescribed. Vis--vis of the inlet DI2
,
the alveolar wall S is situated. The wall itself consists of two layers of tissue (dimensions 100 m
5 m  1 m) surrounding a pulmonary capillary FIb (dimensions 100 m  5 m  1 m). In
fact, the upper tissue layer is of minor interest here and is introduced only to enable a reasonable
movement of the capillary by providing an FSI interface. At DS , deformations in the x- and zdirections are prohibited, whereas the wall is allowed to move freely in the y-direction. To describe
the material behavior of the tissue, a neo-Hookean constitutive model with Youngs modulus E S D
105 pN=m2 , Poissons ratio  S D 0:49, and density S D 0:001 ng=m3 is utilized. The material
parameters for air and blood are given by FIa D 0:01983 ng=.m ms/; FIa D 1:2  106 ng=m3
and FIb D 3:0 ng=.m ms/; FIb D 1:06  103 ng=m3 . In line with [37, 40], the diffusivities of
oxygen in tissue, air, and blood are chosen to be D S D 1:0 m2 =ms; D FIa D 2:0  104 m2 =ms, and
D FIb D 1:6 m2 =ms, respectively.
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Figure 13. Oxygen transport in an idealized terminal lung unit: definition of domains and boundaries. For
the sake of simplicity, Neumann boundaries are not explicitly marked.

Figure 14. Distribution of flow velocities in the capillary at t D 150 ms (left) and in the lumen at t D 650
ms (right). Owing to the different magnitudes of velocity, blood and air flow are displayed separately. Blood
flows from left to right.

In the first 150 ms of the simulation, a body force in the x-direction bFx D 1100:0 m=ms2 is gradually applied to the capillary, yielding a maximum blood velocity of 1:19 m=ms. Subsequently, air
flow and relative oxygen concentration at the inlet of the alveolus are prescribed as follows:
uFIa
y D 0:1 m=ms  C.x; t / on

FIa
DI2
;

FIa D 1:0  C.x; t /

on DIFIa

(52)

with


C.x; t / D 1:0  0:0004x


t  150:0 ms
:
sin 
1000:0 ms


(53)

To model the deoxygenated state of the blood entering the alveolus, FIb D 0:0 is chosen at the
inlet of the capillary DIFIb . As transport of oxygen from the blood to the upper tissue layer is not
assumed to occur, concentrations are decoupled at the interface 3 . At both 1 and 2 , the limiting
case of an infinite permeability is assumed.
In Figures 14 and 15, snapshots of the distribution of flow and relative oxygen concentration are
shown. As a consequence of the inflow, the volume of the air domain increases, thereby causing
an upward movement of the alveolar wall. Oxygen is transported through both the lumen of the
alveolus and the lower tissue layer into the capillary, where it is removed from the alveolus.
Although the presented example is still very simple, it clearly illustrates the suitability of
the presented approach to model complex multi-field transport processes on deforming domains.
It is moreover important to highlight that with a rigid model, there would not be any flow,
and consequently, mass transfer would not be properly calculated because only diffusion would
be present.
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Figure 15. Distribution of concentrations in all three fields at t D 350 ms, t D 450 ms, t D 650 ms (i.e., at
maximum inflow), t D 800 ms, t D 950 ms, and t D 1100 ms (from left top to right bottom).

Figure 16. Computational domain (a) and particular of the streamer (b).

5.5. Nutrient transport in a biofilm structure

The importance of coupling mass transfer with FSI can be particularly appreciated when modeling
the interaction of biofilms with the surrounding fluid. In this case, the coupled simulation highlights the beneficial effect of the structure motion on food supply, which plays an important role
for the formation and growth of biofilms. Among the several structures a biofilm can form, a filamentous shape in flow direction, usually called streamer, is selected for this example. This type of
biofilm architecture was experimentally studied by Stoodley et al. [41], who grew streamers in a
flow cell and observed their lateral oscillation, highlighting that their formation is due both to high
shear rates and to a limited nutrient availability [42]. Hence, to reproduce the macro-scale dynamics of this type of biofilm structures, it is essential to consider fluid flow, structure deformation, and
substrate transport.
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In the present example, a streamer located in a two-dimensional rectangular flow channel is considered as sketched in Figure 16. Streamer dimensions, flow conditions, and material properties are
assumed similar to those found experimentally in [41] and utilized in [43, 44] for biofilm simulations
(cf. Tables I and II, respectively).
The streamer consists of a head attached to the substratum and a tail free to move in the flow.
Hence, only the interface between the streamer tail and the fluid, , is considered as the FSI surface,
while the streamer head boundary, head , is fixed. At the inlet of the channel, a uniform horizontal
velocity profile and a constant substrate concentration are prescribed. At the upper and lower domain
boundaries, a slip condition is imposed on the fluid to avoid the development of any boundary layers.
For the scalar transport problem, an infinite permeability is assumed along the entire interface
between the fluid and the structure domain, that is, in both the tail and the head region. In the fluid
domain, substrate transport is modeled using a convectiondiffusion equation, whereas a diffusion
reaction equation is utilized to consider substrate transport and consumption within the streamer.
The corresponding reaction term is based on the non-linear Monod kinetic (cf. [44] for a comparison
of different reaction models for biofilm applications). In this case, the reaction term R is given by
RDk

S
K C S

(54)

where k denotes the reaction rate constant and K represents the half saturation constant.
Computations are run on a 2D mesh of 165.000 quad cells refined in the interface region. A
fixed time step of 0.01 ms is utilized. At first, a simulation with a completely fixed streamer, that
is, neglecting FSI effects, is run. Corresponding results are then used as initial condition for the
coupled simulation considering the combined FSI and multi-field mass transport. Simulation results
at different time steps for both the fixed and moving tail configuration are given in Figure 17.
By considering the coupling between FSI and mass transport, the effect of both the local biofilm
deformation and the fluid flow on the transport and reaction of nutrients can be analyzed. The scalar
Table I. Geometrical details.
Parameter

Symbol

Value (mm)

Tail length
Head diameter
Tip diameter
Distance from inlet
Domain length
Domain height

Ltail
Dhead
Dtip
Linlet
L
H

1.499
3:33  101
6:7  102
1.5
12
3

Table II. Material parameters and operating conditions.

Parameter

Symbol

Value

Unit

Liquid
Dynamic viscosity
Density
Inlet velocity

F
F
uFIN

103
103
3  101

kg m1 s1
kg m3
m s1

Biofilm
Density
Youngs modulus
Poisson ratio

S
ES
S

103
4  103
4  101

kg m3
kg m1 s2

Substrate
Diffusion coefficient
Uptake rate coefficient
Saturation coefficient
Inlet concentration

D
k
K
FIN

Copyright 2014 John Wiley & Sons, Ltd.

2:5  109
3  102
3  103
2:5  102

m2 s1
mol m3 s1
mol m3
mol m3

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Figure 17. Velocity (left) and concentration (right) maps for a fixed tail (top) and for a moving tail at three
different time steps (u in m/s; in mol/m3 ).

1.2

0.8

0.6

0.4
-1.5

-1

-0.5

Uncoupled
Coupled
0.5
1

Figure 18. Molar flux along the tail boundary for both the fixed and moving tail configuration.

field maps highlight an important concentration boundary layer on the tail surface. Hence, the substrate concentration at the interface is significantly lower than in the bulk of the fluid. The streamer
movement permits the tip to reach zones with higher substrate concentration, thereby causing an
increase of the mass transfer compared to the fixed tail configuration. In Figure 18, the molar flux
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along the interface between fluid and tail, , is reported for both the fixed and moving tail configuration. In the latter case, results are averaged in time because the flapping tail produces a time
dependent flux. In particular, reported results refer to the system condition 150 ms after the tail flapping starts. Without considering the tail movement, the positions of local maxima and minima of
mass flux cannot be predicted, which is a very important information when the local growth of the
biofilm structure is of interest. Besides, an overall higher mass flux can be observed for the moving
tail configuration, reaching a percentage increase of 39% at the tail tip. Hence, to enable a realistic determination of substrate uptake and consumption within the biofilm streamer, the presented
approach considering both FSI and multi-field mass transport effects is indispensable.

6. CONCLUSION AND OUTLOOK

To enable the investigation of transport processes in biomechanical applications, we have developed
an advanced computational model considering the effect of local structure deformation and fluid
flow on passive mass transport. For this purpose, a sequential one-way coupling of an FSI and a
multi-field scalar transport model has been realized. In each time step, the non-linear monolithic FSI
problem is solved first to determine local deformations and velocities. Using this information, the
monolithic multi-field transport problem can then be solved on the deforming domains. Depending
on the surface permeability P , concentrations at the interface between fluid and solid fields are
completely decoupled .P D 0:0/, coupled by means of a flux condition .P > 0:0/ or identical
.P ! 1/ in both domains.
Although the effect of structure deformation on mass transport has already been considered
before, previous approaches suffered from a number of limitations. For instance, in [14], the transport of macromolecules was considered separately on both domains. As a consequence, mass
transfer was only possible in one direction, that is, from fluid to tissue. In [17], the structural simulation was essentially decoupled. Hence, instead of solving the solid field equations in each time
step, the mass transfer problem was formulated on the final deformed structure. Although this simplification seems to be suitable in the realm of drug eluting stent modeling, it may be too restrictive
for other applications. All mentioned limitations are overcome by the new methodology presented
in this paper. The proposed combination of FSI and multi-field scalar transport models enables the
mutual coupling of (i) flow and solid deformation and (ii) transport processes on deforming fluid
and solid domains. Hence, our approach can provide insights into how local deformations influence
transport processes in both fluid and solid fields, which is of utmost importance in highly dynamic
structures such as alveoli during ventilation and biofilm structures under specific flow conditions.
Another major advantage of the proposed approach is the generality of its implementation. As
already mentioned before, the algorithms discussed in Sections 2 and 3 are by no means restricted
to any specific discretization scheme or solution technique. Furthermore, arbitrary constitutive laws
including poroelastic models (cf., for instance, [45]) and multi-scale approaches (see, e.g., [46])
may be utilized to describe the behavior of the tissue under consideration as accurately as possible.
The general validity and versatility of the proposed methodology was illustrated by selected
numerical examples. Conservation of mass was proven for both structural and FSI problems.
Besides, it was shown that a reasonable coupling of concentrations at the field interface has been
achieved. Finally, the application of the novel approach to oxygen transport in an idealized alveolus
and in a real biofilm application was discussed. It was successfully demonstrated that our approach
is in general suitable for modeling convective and diffusive scalar transport as well as reaction
processes on deformable, coupled fluid and solid domains for the first time.
Future work will be concerned with employing the proposed model to new realistic scenarios
from different fields of biomechanics. Planned applications include the optimization of targeted
drug delivery, the investigation of atherosclerosis, and the growth of biofilms. In the latter case,
flow and deformation states are affected by transport-mediated growth processes. Hence, ongoing
work focuses on extending the presented approach towards a mutual coupling of FSI, transport, and
biochemical models.
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DOI: 10.1002/nme