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Reaction-Eikonal model experiment

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-:

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.

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05E_Smooth_Gradient_Heterogeneities 07A_augmentation