Reaction-Eikonal model experiment

Module: tutorials.02_EP_tissue.06_eikonal.run

Section author: Aurel Neic <aurel.neic@medunigraz.at>

Introduction

This experiment is designed to show how to switch from the default Reaction-Diffusion propagation driver to a Reaction-Eikonal one and to demonstrate the differences between the drivers w.r.t. the computed potentials.

A small tissue strand (dim 30 x 0.5 x 0.5 mm) is excited in its center by a transmembrane current. Excitation then propagates towards both outer sides. The propagation driver can be selected to be either the diffusion term of the Monodomain / Bidomain model, or one based on the solution of an associated eikonal model.

Usage

The experiment-specific options are:

--sourceModel {monodomain,bidomain,pseudo_bidomain}
                      pick type of electrical source model (default is
                      monodomain)
--propagation {R-D,R-E+,R-E-,AP-E}
                      pick propagation driver, either R-D (reaction-
                      diffusion), R-E (+) with (-) without diffusion or AP-E
                      (prescribed AP without diffusion) shape with trigger
                      instant(default is R-E+)
--duration DURATION   duration of experiment, typically 25. ms for
                      activation only, 400 ms to include repolarization
                      (default is 25.)
--tag TAG             add tag to simulation ID

Using the --propagation argument, the user can select the propagation driver. The choices are:

  • R-D: Ionic reaction term with the Mono-/Bidomain diffusion term.
  • R-E-: Ionic reaction term with Eikonal-based propagation driver.
  • R-E+: Ionic reaction term with the Mono-/Bidomain diffusion term and an additional Eikonal-based propagation driver to enforce conduction velocity.
  • AP-E: Prescribed Action-Potential functions with Eikonal-based propagation driver.

Using the --dry option, one can observe which command-line options are added/removed when switching, propagation drivers.

In a nutshell, R-E propagation is activated by adding the -stimulus[1].stimtype 8 option. The difference between R-E+ and R-E- is that R-E+ includes diffusion via the -diffusionOn 1 option. As a consequence, in experiments featuring spatially heterogeneous ionic models, R-E- shows significant artificial potential gradients at the interfaces between regions with different models. The following picture shows Vm at 7 and 112 ms for R-D, R-E+ and R-E-:

../../_images/06Eikonal_R-E.vs.R-D.png

Tissue strand after 7 and 112 milliseconds using different propagation drivers.

Example

To run the example and visualize output, run:

./run.py --np NP --propagation PROP --visualize

Where NP denotes the desired number of processes and PROP the propagation mode.