See code in GitLab.
Author: Jason Bayer jason.bayer@ihu-liryc.fr

This tutorial demonstrates how to adjust ionic model parameters to generate a specific action potential duration in your simulations. To run the experiments of this tutorial change directories as follows:

## Ionic model

For this example, we use the most recent version of the ten Tusscher ionic model for human ventricular myocytes [#Tusscher2006]. This ionic model is labeled TT2 in openCARP's LIMPET library.

## 1D cable model

For this exercise we compute APD in a 1.5 cm cable of epicardial ventricular myocytes. The model domain was discretized with linear finite elements with an average edge length of 0.02 cm.

## Pacing protocol

The left side of the 1D cable model is paced with 5-ms-long stimuli at twice capture amplitude for a basic cycle length and number of beats chosen by the user.

## Action potential duration

Activation potential duration is computed at 80% repolarization ($$APD_{80}$$) according to [Bayer2016]. This is achieved by using the igbutils function igbapd as illustrated below. See the igbutils tutorial for more information on using igbapd.

./igbapd -t nbeats-1*bcl --repol=80 --vup=-10 --peak-value=plateau --plateau-start=15 ./vm.igb

## Usage

The following optional arguments are available (default values are indicated):

./run.py --help
When in adjust mode, will use im_param options by user
--im_param          Is a string for which you can input operations to
perform to specific variables in a chosen ionic model.
For example, 'Gmax_1*0.4,Gmax_2=0.4'
--IMP               Ionic model name from LIMPET library.
--nbeats            Default: 2
Number of beats to perform before APD computation. In
reality, this should be much larger to reach
steady-state. Due to tutorial time constraints, it is
very small.
--bcl               Default: 700
Basic cycle length of pacing

1. List all of the ionic channel conductances in the ten tusscher model by running the command below
bench --imp-info -I TT2
1. Determine the baseline APD by running the following command.
./run.py --Mode default --IMP TT2

Note, you can look at the values for the APD on each node of the cable by scrolling through the vertex values under the Highlight tab in meshalyzer.

1. Shorten APD by >30 milliseconds by adjusting the maximal conductance for the slow outward potassium current (Iks). What is the name of the variable from the output in task 1? Did you have to increase or decrease the value?
2. This time, prolong APD by >30 altering the plateau of the action potential by modifying the maximal conductance of the L-type calcium channel current (ICaL).

In the future, you will want to run many more beats than 2. Also, the process can be automated similar to tuneCV.

References

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