COMSOL 6.4 - Isoelectric Focusing

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Isoelectric Focusing

This model simulates the separation phase during isoelectric focusing of seven carrier ampholytes in a closed column. Isoelectric focusing is a technique used to separate ampholytes (molecules with both acidic and basic functional groups) based on their isoelectric point (pI)—the pH at which the molecule has no net charge. The pI of the ampholytes uniformly span the interval 3.5–9.5, with ΔpK of 2 for each ampholyte The model reproduces results reported by Thormann and others (Ref. 1).

Model Definition

The model is set up in 1D using the Electrophoretic Transport interface, using seven Ampholyte domain nodes to define the transported species. The same mobility and the same uniform initial concentration values are used for all ampholytes.

The problem is solved in a time-dependent study for the time range 0 to 4 minutes.

Results and Discussion

Figure 1 shows the pH in the column for different times during the simulation. After four minutes the pH profile features seven different plateaus.

Figure 1: pH of the separation column for various times.

Figure 2 shows the corresponding conductivities in the column. The conductivity decreases as the separation process proceeds.

Figure 2: Electrolyte conductivity of the separation column at various times.

Figure 3 shows the current density vs time. The cell is operated at constant voltage conditions, and hence the current density decreases over time as a result of the lowered conductivity.

Figure 3: Anode current density (in A/m2) versus time.

Figure 4 shows the concentration of the seven different ampholytes at t = 4 min. At this time, the sample has separated into seven well-separated regions, each one containing one ampholyte only. Steady-state has however not yet been reached (increase the simulation tome to 3000 s to reach the final concentration profile).

Figure 4: Concentration of the seven ampholytes at t = 4 min.

1. W. Thormann, M. Breadmore, J. Caslavska, and R. Mosher, “Dynamic computer simulations of electrophoresis: A versatile research and teaching tool,” Electrophoresis, vol. 31, pp. 726–754, 2010.

Electrochemistry_Module/Electrochemical_Engineering/isoelectric_focusing_1d

Modeling Instructions

From the menu, choose .

In the window, click

.

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In the window, click

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In the tree, select > .

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In the tree, select > .

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Global Definitions

Load the model parameters from a text file.

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In the window, under click .

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In the window for , locate the section.

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Browse to the model’s Application Libraries folder and double-click the file isoelectric_focusing_1d_parameters.txt.

Interval 1 (i1)

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In the window, under right-click and choose .

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In the window for , locate the section.

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In the table, enter the following settings:


Coordinates (m)
0
L

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Electrophoretic Transport (el)

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In the toolbar, click

and choose .

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Select Boundary 1 only.

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In the toolbar, click

and choose .

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Select Boundary 2 only.

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In the window for , locate the section.

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In the ϕl,bnd text field, type dV*L.

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In the toolbar, click

and choose .

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In the window for , locate the section.

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In the table, enter the following settings:


Dissociation step (1)	pKa (1)
1	pI_start-1
2	pI_start+1

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Locate the section. In the um text field, type mob.

Initial Concentration 1

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In the window, expand the node, then click .

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In the window for , locate the section.

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In the c text field, type c0.

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In the window, under > right-click and choose .

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In the window for , locate the section.

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In the table, enter the following settings:


Dissociation step (1)	pKa (1)
1	pI_start-1+1
2	pI_start+1+1

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Right-click and choose .

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In the window for , locate the section.

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In the table, enter the following settings:


Dissociation step (1)	pKa (1)
1	pI_start-1+2
2	pI_start+1+2

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Right-click and choose .

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In the window for , locate the section.

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In the table, enter the following settings:


Dissociation step (1)	pKa (1)
1	pI_start-1+3
2	pI_start+1+3

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Right-click and choose .

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In the window for , locate the section.

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In the table, enter the following settings:


Dissociation step (1)	pKa (1)
1	pI_start-1+4
2	pI_start+1+4

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Right-click and choose .

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In the window for , locate the section.

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In the table, enter the following settings:


Dissociation step (1)	pKa (1)
1	pI_start-1+5
2	pI_start+1+5

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Right-click and choose .

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In the window for , locate the section.

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In the table, enter the following settings:


Dissociation step (1)	pKa (1)
1	pI_start-1+6
2	pI_start+1+6

Global Definitions

Default Model Inputs

Set up the temperature value used in the entire model.

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In the window, under click .

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In the window for , locate the section.

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In the tree, select > .

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Find the subsection. In the text field, type T.

Proceed as follows to create a user-defined mesh with a higher resolution toward the end boundaries:

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In the window, under click .

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In the window for , locate the section.

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From the list, choose .

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In the window, under > click .

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In the window for , locate the section.

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Click the button.

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Locate the section. In the text field, type 4e-6.

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In the window, right-click and choose .

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In the window for , locate the section.

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From the list, choose .

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From the list, choose .

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Locate the section. Click the button.

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Locate the section.

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Select the checkbox. In the associated text field, type 1e-6.

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The model is now ready for solving. Add a probe to monitor the current density for each time step during the simulation.

Domain Point Probe 1

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In the toolbar, click

and choose .

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In the window for , locate the section.

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Select the checkbox.

Point Probe Expression 1 (ppb1)

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In the window, expand the node, then click .

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In the window for , locate the section.

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In the text field, type -el.nIl.

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Select the checkbox. In the associated text field, type Current density probe.

Step 2: Time Dependent

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In the window, under click .

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In the window for , locate the section.

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From the list, choose .

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In the text field, type 0 0.4 4.

The initial transients of the focusing process will be very short. Modify the default solver to set a small initial time step as follows:

Solution 1 (sol1)

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In the toolbar, click

.

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In the window, expand the node, then click .

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In the window for , click to expand the section.

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Select the checkbox. In the associated text field, type 1e-5.

The model will take a few hours to solve.

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In the toolbar, click

.

A number of plots are created by default.

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In the window for , click to expand the section.

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From the list, choose .

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Locate the section. From the list, choose .

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In the toolbar, click

.

Electrolyte Conductivity (el)

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In the window, click .

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In the window for , locate the section.

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From the list, choose .

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In the toolbar, click

.

Current Density vs. Time

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In the window, under click .

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In the window for , type Current Density vs. Time in the text field.

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Locate the section. Clear the checkbox.

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In the toolbar, click

.

Molar Concentration - S (el)

Proceed as follows to create a plot of all ampholyte concentrations in the same figure:

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In the window, right-click and choose .

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In the window for , type Concentrations in the text field.

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Locate the section. From the list, choose .

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Click to expand the section. From the list, choose .

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In the window, expand the node, then click .

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In the window for , click to expand the section.

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Clear the checkbox.

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Right-click > > and choose .

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In the window for , locate the section.

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In the text field, type el.c_S1.

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Right-click and choose .

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In the window for , locate the section.

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In the text field, type el.c_S2.

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Right-click and choose .

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In the window for , locate the section.

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In the text field, type el.c_S3.

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Right-click and choose .

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In the window for , locate the section.

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In the text field, type el.c_S4.

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Right-click and choose .

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In the window for , locate the section.

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In the text field, type el.c_S5.

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Right-click and choose .

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In the window for , locate the section.

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In the text field, type el.c_S6.

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In the toolbar, click

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Your final plot should look something like this: