Created in COMSOL Multiphysics 5.
Biosensor Design
This Application is licensed under the COMSOL Application License 5.5.
All trademarks are the property of their respective owners. See [Link]/trademarks.
About the Application Biosensor Design
A flow cell in a biosensor contains an array of micropillars used to detect biomolecules, for
example antibodies in aqueous solutions. The pillars are coated with an active material that
selectively adsorbs biomolecules in the sample stream. These biomolecules then react on
the surface. A signal proportional to the surface coverage can be detected in a sensor, for
example through chemiluminescence. This app allows the user to change the design of the
sensor by altering parameters such as pillar diameter, grid spacing, and inlet velocity to
investigate how the design affects the detection results. The geometry and operating
conditions have impact on the signal strength and diffuseness which is visualized in plots.
Also, manufacturing constraints, set by a minimum distance between pillars, are reported
in the app.
The image below summarizes how to use the application.
Update Run Select result Animate Create Visualize
geometry simulation visualization report geometry and results
Reset
input
Set operating
conditions
and define
geometry
Check
geometry
Simulation
status
Select time
for 3D plots
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SUMMARY OF USER INPUT
The following parameters can be set in the app:
• Inlet velocity: Allowed values are between 0.5e-4 and 10e-4 m/s.
• Injection concentration: The sample concentration. The default is 400 mol/m3.
• Pillar radius: To manufacture the device, the pillar radius must not be smaller than
0.18 mm.
• Simulation time.
• Grid size: The number of pillar across and along the device.
Note that the grid size and the radius are used to determine if the geometry can be
manufactured. A warning is shown in the user interface if the pillars are too close.
The Embedded Model
A flow cell in a biosensor contains an array of micropillars. The curved sides 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.
GEOMETRY
The flow cell contains a number of rows containing pillars, see Figure 1. The geometry is
inspired by Ref. 1. The grid size is specified by the app user. 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 in the underlying model.
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Outlet
Inlet
Active surface
Figure 1: The flow cell holds different numbers of pillars depending on the user input. The
curved pillar surface is the only surface that allows the adsorption of analyte molecules. Before
computation, the modeling geometry is reduced to one fourth of the full geometry thanks to
mirror symmetry. The cell geometry is inspired by Ref. 1.
MODEL DEFINITION
Surface Reactions
Analyte molecules (P) can adsorb and desorb from surface sites (S) on the micropillar
surfaces according to
kads
P + S PS
kdes
The adsorbed analyte (PS) can transform into a quenched state (QS) that does not
contribute to the sensor signal. The quenching reaction is reversible:
k1
PS QS
k2
The rate of adsorption is
r ads = k ads c P (1)
where cp is the concentration of P in the stream. The desorption rate is linear in the
concentration of surface adsorbed species, cPS:
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r des = k des c PS (2)
The rate of the reversible quenching reaction is given by
r quench = – k 1 c PS + k 2 c QS (3)
Mass Transport in the Analyte Stream
The equations in the Transport of Diluted Species interface describe the transport of the
species, P, in the analyte stream according to
c
--------P- + – D P c P + u c P = 0 (4)
t
Here, DP denotes the diffusion coefficient (SI unit: m2/s), cP denotes the species
concentration (SI unit: mol/m3), and is u is the velocity vector (SI unit: m/s).
The injected sample concentration is given by the user and is 400 mol/m3as default
during 2.5 ms. Due to the diffusive spreading just before the inlet section, a smooth pulse
enters the sensor, which is described by a Gaussian distribution at the flow cell inlet with
a maximum concentration of 80 mol/m3 (at default input settings) and a standard
deviation of 2.
The adsorption and desorption of analyte at the active pillar surfaces give rise to a net flux
at the corresponding boundaries:
N p = – r ads + r des
The mass flux due to desorption is dependent upon the local concentration of adsorbed
surface species and is hence coupled to the equations in the Surface Reactions, described
next.
Mass Transport and Reactions on the Active Surfaces
In this example, surface diffusion is ignored on the active surfaces. Therefore, using the
reactions described by Equation 1, Equation 2, and Equation 3, the balance equations for
the surface species P and Q will be:
dc s P
-------------- = r ads – r des – r quench
dt
dc s Q
-------------- = r quench
dt
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The rate of adsorption depends on the concentration of the P species in the analyte stream
and therefore the equations describing the surface reactions (above) are coupled to that of
the free analyte flow, Equation 4.
Fluid Flow
The flow regime is laminar in the cell.
The calculated flow field serves as input to the Equation 4, to describe the convective mass
transport.
RESULTS AND DISCUSSION
Figure 2 shows the magnitude of the laminar velocity field in the flow cell and surface
concentration on the pillars.
Figure 2: The velocity magnitude of the laminar flow field and surface concentration 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 causes 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 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 cause the sensor signal to become relatively diffuse.
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Figure 7: Average fractional surface coverage of adsorbed analyte PS.
References
1. M. Weber, M. Reed, “Analyte Capture from Liquid Samples: Size Matters”,
Proceedings of the COMSOL Conference 2013, Boston, MA. Available from
[Link]/paper/analyte-capture-from-liquid-samples-size-matters-15985
Application Library path: Chemical_Reaction_Engineering_Module/
Applications/biosensor_design
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