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:
cd ${TUTORIALS}/02_EP_tissue/03_study_prep_APD
In mammalian hearts, cardiac repolarization varies between species, is spatially heterogeneous, and altered during disease. Thus, it is important to calibrate your ionic models to account for these repolarization differences. The easiest way to do this is to modify the maximum conductance for ionic currents known to alter action potential duration (APD), i.e., the time duration a cardiac myocyte repolarizes after excitation. Ideally, these values are obtained from experiments in the literature. In this exercise, you will learn how to look up the ionic current variables in your model that you can change to alter APD, and how to adjust in cable/tissue models.
For this example, we use the most recent version of the ten Tusscher-Panfilov ionic model for human ventricular myocytes 1 . This ionic model is labeled tenTusscherPanfilov in openCARP's LIMPET library.
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.
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.
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
The following optional arguments are available (default values are indicated):
./run.py --help
--Mode Options: {default,adjust}, Default: default
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
bench --imp-info -I tenTusscherPanfilov
./run.py --Mode default --IMP tenTusscherPanfilov
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.
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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