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S ur f a c e Re a c t i ons i n a Bi os e ns or
This example illustrates how to use the Surface Reactions physics interface, the
Transport of Diluted Species physics interface, and the Laminar Flow physics interface
to set up a model of a biosensor application. Combining these physics interfaces makes
it straightforward to couple surface reactions to mass transport in a fluid stream.
Introduction
A flow cell in a biosensor contains an array of micropillars. The curved side of the pillars
are coated with an active material that allows for the selective adsorption of analyte
species in the sample stream. The adsorbed species produce a signal that is dependent
upon the local concentration at the pillar surfaces. This example investigates the
surface concentration distribution in the cell while an analyte pulse is transported
through it. It also studies the effect of a quenching surface reaction where adsorbed
species are converted into an inactive state.
Model Definition
G E O ME T R Y
The flow cell contains seven rows containing four pillars each. The curved surfaces of
the pillars are the only active surfaces for adsorbing the analyte molecules. The flow
cell has two planes of symmetry that allow for reduction of the modeling domain to
one fourth of the full geometry.
Outlet
Inlet
Active surface
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Figure 1: The flow cell holds seven rows of pillars with four pillars in each row. The curved
pillar surface is the only surface that allows the adsorption of analyte molecules. The
modeling geometry can be reduced to one fourth of the full geometry due to mirror
symmetry.
S U R F A C E R E A C T I O N S
Analyte molecules (P) can adsorb and desorb from surface sites (S) on the micropillar
surfaces according to
(1)
The adsorbed analyte (PS) can transform into a quenched state (QS) that does not
contribute to the sensor signal. The quenching reaction is reversible:
(2)
The rate of adsorption is
(3)
where c
p
is the concentration of P in the stream. The desorption rate is linear in the
concentration of surface adsorbed species, c
PS
:
+ P S PS
k
ads
k
des
PS QS
k
1
k
2
r
ads
k
ads
c
P
=
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(4)
The rate of the reversible quenching reaction is given by
(5)
MA S S TR A N S P O R T I N T H E A N A L Y T E S T R E A M
The equations in the Transport of Diluted Species interface describe the transport of
the species, P, in the analyte stream according to
(6)
Here D
P
denotes the diffusion coefficient (m
2
/s), c
P
the species concentration (mol/
m
3
), and u the velocity vector (m/s).
The sample pulse that enters the sensor array is described by a Gaussian distribution at
flow cell inlet with a maximum concentration of 80 mol/m
3
.
At the outlet, the Outflow condition is used:
(7)
The adsorption and desorption of analyte at the active pillar surfaces give rise to a net
flux at the corresponding boundaries:
(8)
The mass flux due to desorption is dependent upon local concentration of adsorbed
surface species and is hence coupled to the equations in the Surface Reactions
interface, described next.
MA S S TR A N S P O R T A N D R E A C T I O N S O N T H E A C T I V E S U R F A C E S
Transport of adsorbed species occurs in the tangential direction along the surface. The
Surface Reactions interface models the tangential flux in the along the surface, the
surface molar flux, N
t,i
(mol/(ms)), according to
where D
s,i
(m
2
/s) is the surface diffusion coefficient for species i.
The governing equation for the surface concentrations is written as
r
des
k
des
c
PS
=
r
quench
k
1
c
PS
k
2
c
QS
+ =
c
P
t
--------- + D
P
c
P
( ) u c
P
+ 0 =
n D c ( ) 0 =
N
p
r
ads
r
des
+ =
N
t i ,
D
s i ,

t
c
s i ,
=
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where R
s,i
(mol/(m
2
s)) is the sum of all sources due to surface reactions and
adsorption/desorption phenomena.
In this example, surface diffusion is ignored. Using the reactions described by
Equation 3 through Equation 5, the balances equation for the surface species P and Q
become:
The rate of adsorption depends on the concentration of the P species in the analyte
stream and is therefore coupled to the equations in the Surface Reactions interface to
those provided by the Transport of Diluted Species interface.
F L U I D F L OW
The flow in the flow cell is laminar and given by the Navier-Stokes equations:
(9)
where denotes density (kg/m
3
), u represents the velocity (m/s), denotes viscosity
(kg/(m s)), and p equals the pressure in the tubes (Pa).
The calculated flow field serves as input to the Transport of Diluted Species interface,
to describe the convective mass transport.
The boundary conditions are
(10)
At the outlet, viscous stresses are ignored and the pressure is set to 1 atmosphere.
t

c
s i ,

t
D
s i ,

t
c
s i ,
( ) + R
s i ,
=
dc
s P ,
dt
-------------- r
ads
r
des
r
quench
=
dc
s Q ,
dt
-------------- r
quench
=
u u pI u u ( )
T
+ ( ) 2 3 ( ) u ( )I + [ ] =
u ( ) 0 =
u n v
0
=
u 0 =
p p
ref
=
inlet
walls
outlet
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Results and Discussion
Figure 2 shows the magnitude of the laminar velocity field in the flow cell.
Figure 2: The velocity magnitude of the laminar flow field in the biosensor flow cell
Figure 3 through Figure 6 show the concentration of the species, P, in the stream as
well the relative coverage of surface adsorbed species, PS, as the analyte pulse passes
through the flow cell.
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Figure 3: Concentration distribution in the analyte stream and surface coverage of
adsorbed species at t = 35 s.
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Figure 4: Concentration distribution in the analyte stream and surface coverage of
adsorbed species at t = 45 s.
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Figure 5: Concentration distribution in the analyte stream and surface coverage of
adsorbed species at t = 55 s.
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Figure 6: Concentration distribution in the analyte stream and surface coverage of
adsorbed species at t = 75 s.
The velocity distribution of the flow field will cause pillars near the wall to reach their
maximum adsorption level at a later time compared to pillars in the center of the
stream. Pillars near the wall will also take longer to release adsorbed analyte. The
position of a pillar in a row also has an effect on the maximum adsorption level, and
the time at which it is reached. This effect is highlighted in Figure 7. These geometrical
effects will cause the sensor signal to become relatively diffuse.
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Figure 7: Average fractional surface coverage of adsorbed analyte PS.
Figure 8 shows the relative surface concentration of the quenched surface species QS
for the same pillar positions. The geometrical effect is once again evident yet more
importantly, the plot shows that a relatively long time is required to purge the reactive
sites in preparation for a new analysis.
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Figure 8: Average fractional surface coverage of adsorbed quenched species QS.
Notes About the COMSOL Implementation
In this example, there is a one-way coupling between the stationary flow field and the
mass transport equations. This means that the equations for the laminar flow need only
be solved once, and that the results can be used for calculating the transient mass
transport problem. This is accomplished by using two study steps when setting up and
solving the model. The first step solves for the stationary flow field. The solution is
then used in the second step where the transient mass balance equations are solved.
Model Library path: Chemical_Reaction_Engineering_Module/
Surface_Reactions_and_Deposition_Processes/reacting_pillars
Modeling Instructions
From the File menu, choose New.
N E W
1 In the New window, click the Model Wizard button.
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MO D E L WI Z A R D
1 In the Model Wizard window, click the 3D button.
2 In the Select physics tree, select Fluid Flow>Single-Phase Flow>Laminar Flow (spf).
3 Click the Add button.
4 In the Select physics tree, select Chemical Species Transport>Transport of Diluted
Species (chds).
5 Click the Add button.
6 In the Concentrations table, enter the following settings:
7 In the Select physics tree, select Chemical Species Transport>Surface Reactions (chsr).
8 Click the Add button.
9 In the Number of surface species edit field, type 2.
10 In the Surface (adsorbed) species concentrations table, enter the following settings:
11 Click the Study button.
12 In the tree, select Preset Studies for Selected Physics>Stationary.
13 Click the Done button.
G E O ME T R Y 1
Start by creating the geometry. To simplify this step, insert a prepared geometry
sequence from file. After insertion you can study each geometry step in the sequence.
1 On the Geometry toolbar, click Insert Sequence.
2 Browse to the models Model Library folder and double-click the file
reacting_pillars_geom_sequence.mph.
3 On the Geometry toolbar, click Build all.
4 Click the Zoom Extents button on the Graphics toolbar.
G L O B A L D E F I N I T I O N S
Read in a text file with model parameters such as model rate constants and diffusion
coefficients.
c_P
cs_P
cs_Q
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Parameters
1 On the Home toolbar, click Parameters.
2 In the Parameters settings window, locate the Parameters section.
3 Click Load from File.
4 Browse to the models Model Library folder and double-click the file
reacting_pillars_parameters.txt.
D E F I N I T I O N S
Variables 1
1 In the Model Builder window, under Component 1 right-click Definitions and choose
Variables.
2 In the Variables settings window, locate the Variables section.
3 Click Load from File.
4 Browse to the models Model Library folder and double-click the file
reacting_pillars_variables.txt.
Gaussian Pulse 1
1 On the Home toolbar, click Functions and choose Global>Gaussian Pulse.
2 In the Gaussian Pulse settings window, locate the Parameters section.
3 In the Location edit field, type 20.
4 In the Standard deviation edit field, type 2.
Note that you can plot the Gaussian function by clicking the Plot button on the
Settings toolbar.
Explicit 1
1 On the Definitions toolbar, click Explicit.
2 In the Explicit settings window, locate the Input Entities section.
3 From the Geometric entity level list, choose Boundary.
4 Click the Wireframe Rendering button on the Graphics toolbar.
You can select the surfaces boundary by boundary according to the list below.
Alternatively, click the Go to YZ View button on the Graphics toolbar and then click
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the Select Box button. Enclose the concave pillar surfaces with the rubber band box
and right-click the selection to confirm.
5 Select Boundaries 8, 9, 12, 13, 15, 16, 19, 20, 23, 2628, 31, 32, 37, 38, 41, 42,
44, 45, 48, 49, 52, 5557, 60, 61, 66, 67, 70, 71, 73, 74, 77, 78, 81, 8486, 89,
90, 95, 96, 99, 100, 102, 103, 106, 107, 110, 113115, 118, and 119 only.
6 Right-click Component 1>Definitions>Explicit 1 and choose Rename.
7 Go to the Rename Explicit dialog box and type Reacting surface in the New name
edit field.
8 Click OK.
Create a number of operators features that calculate the surface average.
Average 1
1 On the Definitions toolbar, click Component Couplings and choose Average.
2 In the Average settings window, locate the Source Selection section.
3 From the Geometric entity level list, choose Boundary.
4 Select Boundaries 23 and 28 only.
5 Locate the Operator Name section. In the Operator name edit field, type
ave_center_1.
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Average 2
1 On the Definitions toolbar, click Component Couplings and choose Average.
2 In the Average settings window, locate the Source Selection section.
3 From the Geometric entity level list, choose Boundary.
4 Select Boundaries 110 and 115 only.
5 Locate the Operator Name section. In the Operator name edit field, type
ave_center_4.
Average 3
1 On the Definitions toolbar, click Component Couplings and choose Average.
2 In the Average settings window, locate the Source Selection section.
3 From the Geometric entity level list, choose Boundary.
4 Select Boundaries 12, 13, 19, and 20 only.
5 Locate the Operator Name section. In the Operator name edit field, type
ave_wall_1.
Average 4
1 On the Definitions toolbar, click Component Couplings and choose Average.
2 In the Average settings window, locate the Source Selection section.
3 From the Geometric entity level list, choose Boundary.
4 Select Boundaries 99, 100, 106, and 107 only.
5 Locate the Operator Name section. In the Operator name edit field, type
ave_wall_4.
MA T E R I A L S
Select water as the material in the flow cell.
1 On the Home toolbar, click Add Material.
A D D MA T E R I A L
1 Go to the Add Material window.
2 In the tree, select Liquids and Gases>Liquids>Water.
3 In the Add material window, click Add to Component.
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MA T E R I A L S
Water
Move on to set up the physics interfaces.
L A MI N A R F L OW
Inlet 1
1 On the Physics toolbar, click Boundaries and choose Inlet.
2 Select Boundary 1 only.
3 In the Inlet settings window, locate the Velocity section.
4 In the U
0
edit field, type u_in.
Outlet 1
1 On the Physics toolbar, click Boundaries and choose Outlet.
2 Select Boundary 122 only.
Symmetry 1
1 On the Physics toolbar, click Boundaries and choose Symmetry.
2 Select Boundaries 2, 4, 34, 63, 92, and 121 only.
TR A N S P O R T O F D I L U T E D S P E C I E S
Convection and Diffusion 1
1 In the Model Builder window, expand the Component 1>Transport of Diluted Species
node, then click Convection and Diffusion 1.
2 In the Convection and Diffusion settings window, locate the Model Inputs section.
3 From the u list, choose Velocity field (spf/fp1).
4 Locate the Diffusion section. In the D
cP
edit field, type D.
Inflow 1
1 On the Physics toolbar, click Boundaries and choose Inflow.
2 Select Boundary 1 only.
3 In the Inflow settings window, locate the Concentration section.
4 In the c
0,cP
edit field, type c0.
Outflow 1
1 On the Physics toolbar, click Boundaries and choose Outflow.
2 Select Boundary 122 only.
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Symmetry 1
1 On the Physics toolbar, click Boundaries and choose Symmetry.
2 Select Boundaries 2, 4, 34, 63, 92, and 121 only.
Flux 1
1 On the Physics toolbar, click Boundaries and choose Flux.
2 In the Flux settings window, locate the Boundary Selection section.
3 From the Selection list, choose Reacting surface.
4 Locate the Inward Flux section. Select the Species c_P check box.
5 In the N
0,cP
edit field, type -r_ads+r_des.
S U R F A C E R E A C T I O N S
1 In the Model Builder window, under Component 1 click Surface Reactions.
2 In the Surface Reactions settings window, locate the Boundary Selection section.
3 From the Selection list, choose Reacting surface.
Reactions 1
1 On the Physics toolbar, click Boundaries and choose Reactions.
2 In the Reactions settings window, locate the Boundary Selection section.
3 From the Selection list, choose Reacting surface.
4 Locate the Reaction Rate for Surface Species section. In the R
s,csP
edit field, type
r_ads-r_des-r_quench.
5 In the R
s,csQ
edit field, type r_quench.
ME S H 1
Free Triangular 1
1 In the Model Builder window, under Component 1 right-click Mesh 1 and choose Free
Triangular.
2 In the Free Triangular settings window, locate the Boundary Selection section.
3 From the Selection list, choose Reacting surface.
Size 1
1 Right-click Component 1>Mesh 1>Free Triangular 1 and choose Size.
2 In the Size settings window, locate the Element Size section.
3 Click the Custom button.
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4 Locate the Element Size Parameters section. Select the Maximum element size check
box.
5 In the associated edit field, type 5e-5.
Free Tetrahedral 1
In the Model Builder window, right-click Mesh 1 and choose Free Tetrahedral.
Size 1
1 In the Model Builder window, under Component 1>Mesh 1 right-click Free Tetrahedral
1 and choose Size.
2 In the Size settings window, locate the Element Size section.
3 Click the Custom button.
4 Locate the Element Size Parameters section. Select the Maximum element size check
box.
5 In the associated edit field, type 2e-4.
6 In the Model Builder window, right-click Mesh 1 and choose Build All.
This creates a better overview of the model tree as you move to set up the solvers and
work with results processing.
Solve the problems using two study steps. The first step solves for the stationary flow
field. In the second step, use the solution from the first step to solve the transient mass
balance equations.
S T U D Y 1
Step 1: Stationary
1 In the Model Builder window, expand the Study 1 node, then click Step 1: Stationary.
2 In the Stationary settings window, locate the Physics and Variables Selection section.
3 In the table, enter the following settings:
Step 2: Time Dependent
1 On the Study toolbar, click Study Steps and choose Time Dependent>Time Dependent.
2 In the Time Dependent settings window, locate the Study Settings section.
3 In the Times edit field, type range(0,1,100).
Physics Solve for Discretization
Transport of Diluted Species physics
Surface Reactions physics
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4 Locate the Physics and Variables Selection section. In the table, enter the following
settings:
Solver 1
1 On the Study toolbar, click Show Default Solver.
The magnitude of the concentration in the analyte stream will be of many orders of
magnitude higher compared to the concentrations of the surface species. Providing
manual scales for the concentration variables will help convergence.
2 In the Model Builder window, expand the Study 1>Solver Configurations>Solver
1>Dependent Variables 2 node, then click Surface concentration (comp1.cs_Q).
3 In the Field settings window, locate the Scaling section.
4 From the Method list, choose Manual.
5 In the Scale edit field, type 1e-7.
6 In the Model Builder window, under Study 1>Solver Configurations>Solver
1>Dependent Variables 2 click Surface concentration (comp1.cs_P).
7 In the Field settings window, locate the Scaling section.
8 From the Method list, choose Manual.
9 In the Scale edit field, type 1e-7.
10 In the Model Builder window, under Study 1>Solver Configurations>Solver
1>Dependent Variables 2 click Concentration (comp1.c_P).
11 In the Field settings window, locate the Scaling section.
12 From the Method list, choose Manual.
13 In the Scale edit field, type 10.
14 In the Model Builder window, expand the Study 1>Solver Configurations>Solver
1>Time-Dependent Solver 1 node.
15 Right-click Study 1>Solver Configurations>Solver 1>Time-Dependent Solver 1 and
choose Fully Coupled.
16 In the Fully Coupled settings window, click to expand the Method and termination
section.
17 Locate the Method and Termination section. From the Jacobian update list, choose
Once per time step.
18 On the Home toolbar, click Compute.
Physics Solve for Discretization
Laminar Flow physics
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R E S U L T S
Velocity (spf)
Create Mirror 3D data sets to create plots for the full flow-cell geometry.
Data Sets
1 On the Results toolbar, click More Data Sets and choose Mirror 3D.
2 In the Mirror 3D settings window, locate the Plane Data section.
3 From the Plane list, choose xy-planes.
4 In the z-coordinate edit field, type 5e-4.
5 On the Results toolbar, click More Data Sets and choose Mirror 3D.
6 In the Mirror 3D settings window, locate the Plane Data section.
7 From the Plane list, choose xz-planes.
8 In the y-coordinate edit field, type -3e-3.
Velocity (spf)
1 In the Model Builder window, under Results click Velocity (spf).
2 In the 3D Plot Group settings window, locate the Data section.
3 From the Data set list, choose Mirror 3D 2.
4 In the Model Builder window, expand the Velocity (spf) node, then click Slice 1.
5 In the Slice settings window, locate the Plane Data section.
6 From the Plane list, choose xy-planes.
7 In the Planes edit field, type 1.
8 On the 3D plot group toolbar, click Plot.
Next create the plots shown in Figure 3 through Figure 6, illustrating the analyte
concentration and adsorbed species concentration as function of time.
3D Plot Group 6
1 On the Home toolbar, click Add Plot Group and choose 3D Plot Group.
2 In the 3D Plot Group settings window, locate the Data section.
3 From the Data set list, choose Mirror 3D 2.
4 From the Time (s) list, choose 35.
5 Right-click Results>3D Plot Group 6 and choose Slice.
6 In the Slice settings window, locate the Expression section.
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7 Click Concentration (c_P) in the upper-right corner of the section. Locate the Plane
Data section. From the Plane list, choose xy-planes.
8 In the Planes edit field, type 1.
9 Locate the Coloring and Style section. Clear the Color legend check box.
10 Right-click Results>3D Plot Group 6>Slice 1 and choose Deformation.
11 In the Deformation settings window, locate the Expression section.
12 In the z component edit field, type c_P.
13 On the 3D plot group toolbar, click Plot.
14 In the Model Builder window, click 3D Plot Group 6.
15 In the 3D Plot Group settings window, locate the Data section.
16 From the Time (s) list, choose 45.
17 On the 3D plot group toolbar, click Plot.
18 From the Time (s) list, choose 55.
19 On the 3D plot group toolbar, click Plot.
20 From the Time (s) list, choose 75.
21 On the 3D plot group toolbar, click Plot.
3D Plot Group 7
1 On the Home toolbar, click Add Plot Group and choose 3D Plot Group.
2 In the 3D Plot Group settings window, locate the Data section.
3 From the Data set list, choose Mirror 3D 2.
4 From the Time (s) list, choose 35.
5 Right-click Results>3D Plot Group 7 and choose Surface.
6 In the Surface settings window, locate the Expression section.
7 Click Surface coverage (chsr.theta_i_cs_P) in the upper-right corner of the section.
Locate the Coloring and Style section. Clear the Color legend check box.
8 On the 3D plot group toolbar, click Plot.
9 In the Model Builder window, click 3D Plot Group 7.
10 In the 3D Plot Group settings window, locate the Data section.
11 From the Time (s) list, choose 45.
12 On the 3D plot group toolbar, click Plot.
13 From the Time (s) list, choose 55.
14 On the 3D plot group toolbar, click Plot.
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15 From the Time (s) list, choose 75.
16 On the 3D plot group toolbar, click Plot.
Finally create line plots showing the average coverage of surface species as a function
of time and pillar position. Note how the Duplicate feature speeds up this
procedure.
1D Plot Group 8
1 On the Home toolbar, click Add Plot Group and choose 1D Plot Group.
2 In the 1D Plot Group settings window, click to expand the Title section.
3 From the Title type list, choose Manual.
4 Locate the Plot Settings section. Select the y-axis label check box.
5 In the associated edit field, type Surface Fraction P.
6 On the 1D plot group toolbar, click Point Graph.
7 Select Point 10 only.
8 In the Point Graph settings window, locate the y-Axis Data section.
9 In the Expression edit field, type ave_center_1(chsr.theta_i_cs_P).
10 Click to expand the Coloring and style section. Locate the Coloring and Style section.
Find the Line style subsection. From the Color list, choose Blue.
11 Click to expand the Legends section. Select the Show legends check box.
12 From the Legends list, choose Manual.
13 In the table, enter the following settings:
14 Right-click Results>1D Plot Group 8>Point Graph 1 and choose Duplicate.
15 In the Point Graph settings window, locate the y-Axis Data section.
16 In the Expression edit field, type ave_center_4(chsr.theta_i_cs_P).
17 Locate the Coloring and Style section. Find the Line markers subsection. From the
Line list, choose Dash-dot.
18 Locate the Legends section. In the table, enter the following settings:
19 Right-click Point Graph 1 and choose Duplicate.
Legends
Center row, first pillar
Legends
Center row, last pillar
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20 In the Point Graph settings window, locate the y-Axis Data section.
21 In the Expression edit field, type ave_wall_1(chsr.theta_i_cs_P).
22 Locate the Coloring and Style section. Find the Line style subsection. From the Color
list, choose Red.
23 Locate the Legends section. In the table, enter the following settings:
24 In the Model Builder window, under Results>1D Plot Group 8 right-click Point Graph
2 and choose Duplicate.
25 In the Point Graph settings window, locate the y-Axis Data section.
26 In the Expression edit field, type ave_wall_4(chsr.theta_i_cs_P).
27 Locate the Coloring and Style section. Find the Line style subsection. From the Color
list, choose Red.
28 Locate the Legends section. In the table, enter the following settings:
29 On the 1D plot group toolbar, click Plot.
Legends
Wall row, first pillar
Legends
Wall row, last pillar
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