Action potential propagation example
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Description
- This example simulates action potential propagation across a 4 mm by 5 mm piece of tissue.
- A 50 mA stimulus with user-defined start time and duration parameters is applied along the center of the tissue. The start time and duration may be altered by the user in the stimulus form. The stimulus strength can be altered in the node form.
- This simulation will make use of the MFHN Ionic model, so we need to load and compile that model.
- Connect to the database from File→Library→Search
At the top of the search form search for a Title containing mfhn
Right-click on EP_MFHN_sympy and select Load
You will get a warning window, select Reset (without save) then proceed
- Edit the model Electrophysiology→Edit→Ionic Model
Set Parameters stim_start to 1.0 , stim_dur to 10.0 next to Value and stim_mag to Field1 next to For default values use
Click on the Set initial values tab
Click on ug under Variable List and select Field2 next to For default values use
- Compile the model from Electrophysiology→Edit→Ionic Model
Under the Compile button near the bottom, select Compile Code as: C Double Precision. That will compile the model and should display a message saying that compilation was successful.
- We need to define a Conductivity model
- Electrophysiology→Edit→Conductivity Model
Change the following: f11 to have Value of 24.0e-4 and f22 and f33 have Value of 23.0e-4
Change the name of the model, by clicking on 'New_Model' and define the name to be Conductivity and hit return
Under the Compile button near the bottom, select Compile Code as: C Double Precision.
- It would be a good time to save the model: File→Save→Save model as... and save it as 2d_ep.cont6
Select rectangular Cartesian in the Global Coordinates: pop-up menu
Click OK to submit Coordinate Form
Choose Hermite Basis Function→2D→Cubic-Cubic with 4 integration/collocation points for Xi 1 and Xi 2
Click Add
Choose Lagrange Basis Function→2D→Linear-Linear with 4 integration/collocation points for Xi 1 and Xi 2
Click Add
- Verify that the list of basis functions now contains:
- Cubic-Cubic Hermite 4*4
- Linear-Linear Lagrange 4*4
Click OK to submit Basis Form
Click Import/Export/Graph button to open Continuity Table Manager
Continuity Table Manager→File→Open...
Select tab-delimited nodes file ( 2d_class_nodes.xls )
- You should now have nodes numbered 1-484
Select Linear-Linear Lagrange under Coordinate 1, Coordinate 2, and Coordinate 3
Click on the Fiber Angles tab
Select Linear-Linear Lagrange under Fiber Angle, Transverse Angle and Sheet Angle
Click on the Field Vector 1 tab
Select Linear-Linear Lagrange under Field Variable 1 and Cubic-Cubic Hermite Field Variable 2
Click OK to submit Node Form
Click Import/Export button to open Continuity Table Manager
Continuity Table Manager→File→Open...
Select tab-delimited elements file ( 2d_class_elems.xls )
- You should now have 441 elements in the list
Click OK to submit Element Form
Make sure to send data to the server: File->Send
Mesh→Edit→Material Coordinates...
Click OK
Select the OpenMesh radio button
Click OK
- Enter a file name and browse to a location to save your current problem as a cont6 file
Click Save
Click the surfaces radio button
Click Render to display mesh surface
Solve for action potential propagation
- Electrophysiology→Solve→Initialize...
Electrophysiology→Calculate→Constraints
Make sure the Fix out-of-plane boundary node derivatives check-box is checked
Make sure the Automatically update constraints form from table check-box is checked
Click OK
- Electriophysiology→Solve→Initialize...
Electriophysiology→Solve→Integration...
Verify that Start Time is 0.0
Set Duration to 30
Set Step Size to 0.1
In the Filename distinction box type 2D_mfhn or something similar. The files that will have the action potentials and ECG will be saved in the user temp directory as AP_out_2D_mfhn.txt and ECG_2D_mfhn.txt
Go to the Output tab
For Display solution every, choose 20 steps
Go to the APs tab
Make sure Write APs to file is checked and specify At nodes: to be all
Click OK and wait for the solver to complete its job (observe progress in the Python shell)
Rendering and output
Electriophysiology→Render→Render Solution...
Verify that Min Value is 0.0 and Max Value is 1.0
Click OK
- Wait for the rendering to complete all frames before proceeding (observe status in Python shell)
- When the 300 animation frames have been computed, you should see an animation in Continuity of the action propagation.
- See the screen shots above for sample snapshots of the animation
- Exporting the individual frames as bmps (for single frame shots or for movie making)
- Pause the movie after all frames are rendered (blue pause sign near right hand end on upper row of command icons)
View->Snapshot->Save Animation Frames...
- Choose element surfaces0
- Save As test.bmp
- Make sure no window is covering the main window at this point
- Note: The export process will take a couple of minutes to complete
- Enter a file name and browse to a location to save the solution
Click Save
- Select the file you saved in the previous step
- Open your favorite plotting program (Excel or Matlab) and plot the action potentials
- The first column is time, the second should all be zeros, and the subsequent columns the nodal output
- Open your favorite plotting program (Excel or Matlab) and plot the ECG
- The first column is time, the second is the ECG
Pre-built model
This cont6 file contains all data and parameters for this problem, before the Electrophysiology solve: elec1.cont6