Commit 20761489 authored by lisapankewitz's avatar lisapankewitz
Browse files

Further updating the documentation.

parent 99868eee
......@@ -28,17 +28,13 @@ This tutorial aims to:
Setup
=====
A 2D tissue patch of size 5 cm x 5 cm and average edge length of 0.4 mm is
generated. We include a variant of the Courtemanche et al. ionic model
reflecting AF-induced remodeling [#loewe14a]_
to simulate the case of persistent AF. A conduction velocity of 0.3 m/s is
obtained by adjusting intra- and extracellular conductivities. A circular
fibrotic region of radius 1.42 cm is added at the center of the tissue.
To account for the presence of scar tissue, we set 30% of the elements in this
fibrotic region to almost non-conductive (1e-7 S/m).
In the other 70%, several ionic conductances were rescaled (50% ``gK1``,
60% ``gNa`` and 50% ``gCaL``) to consider effects of cytokines[#roneyfib]_.
A 3D mesh in shape of the (open)CARP logo of size 13 mm x 4.8 mm x 3 mm and average edge length of 0.2 mm is
generated.
We include three different ionic models, the TT2 (human), MurineMouse (mouse) and the
UCLA_RAB (rabbit) to simulate the response of different model organisms to
on the classical reentry protocol.
A conduction velocity of 0.3 m/s is
obtained by adjusting intra- and extracellular conductivities.
Protocols
=========
......@@ -58,12 +54,6 @@ The protocols included in this tutorial are:
#) at the end of the protocol (RP:math:`_E`)
#) after each beat (RP:math:`_B`).
* **Phase singularity distribution:**
consists of manually placing phase singularities on the geometrical model
and then solving the Eikonal equation to estimate the activation time map
[#PSD]_. Based on this initial state, you can simulate electrical wave
propagation by solving the monodomain equation.
* **Pacing at the end of the effective refractory period:**
triggers ectopic beats at the end of the effective refractory period,
automatically computed as the minimum coupling interval at which the
......@@ -81,9 +71,7 @@ Main Input Parameters
The following input parameters are exposed to steer the experiment:
::
--protocol {prepace,RP_E,RP_B,PSD,PEERP}
Protocol to run (default: PEERP)
--cv cv
conduction velocity in m/s (default: 0.3 m/s)
......@@ -108,7 +96,7 @@ during prepacing in :numref:`fig-tutorial-protocols-prepace`.
.. _fig-tutorial-protocols-prepace:
.. figure:: /images/02_21_prepace.gif
.. figure:: /images/02_23_prepace.gif
:width: 75%
:align: center
......@@ -117,56 +105,6 @@ during prepacing in :numref:`fig-tutorial-protocols-prepace`.
transmembrane voltage V:math:`_m`.
Phase singularity distribution experiment
=========================================
We place a phase singularity at the center of the tissue patch and solve the
monodomain system using the last activation time map obtained by solving the
Eikonal solution as initial state [#PSD]_].
.. code-block:: bash
./run.py --np 2 --protocol PSD --visualize
The phase map produced by solving the Laplace equation after placing a
phase singularity in the center is shown
in :numref:`fig-tutorial-protocols-laplace`.
.. _fig-tutorial-protocols-laplace:
.. figure:: /images/02_21_phase_laplace.png
:width: 75%
:align: center
The phase ranges from -pi to +pi.
The last activation time yielded by the Eikonal system is shown in
:numref:`fig-tutorial-protocols-LAT`.
.. _fig-tutorial-protocols-LAT:
.. figure:: /images/02_21_LAT.png
:width: 75%
:align: center
Last activation time map ranging from 0 to 168 ms.
The spread of activation in terms of transmembrane voltage V:math:`_m`
is shown in :numref:`fig-tutorial-protocols-PSD`. The activation time map
obtained by solving the Eikonal equation was used to initalize a mondomain
simulation.
.. _fig-tutorial-protocols-PSD:
.. figure:: /images/02_21_PSD.gif
:width: 75%
:align: center
The spread of activation and repolarization is shown in terms of
transmembrane voltage V:math:`_m`.
.. _RP_E:
Rapid pacing with arrhythmia checking at the end of the experiment
==================================================================
......
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