||<< click on the image to enlarge!
|Example of region concept using an unstructured grid. FEīs are tagged with region IDīs which can be used subsequently to define regional properties of a model.
|:: Flexibility: Mixing Ionic Models in a Domain
|LIMPET is designed to set active tissue properties in a domain on a per region base.
In a finite element mesh, each element may be tagged. Such tags or arbitrary sets of
tags can be used to define a region. To every region an ionic models can be assigned,
each ionic model can be augmented with any of the available plugins, and almost any
default parameter in any ionic model or plugin can be overruled. A negotiation layer
between ionic model an plugin is required to determine whether an ionic model provides
proper support for a plugin. For instance, the plugin IA, a hypothetical potassium current
that activates at large positive polarizations, influences the potassium concentration of
the ionic model. For this sake, the plugin has to negotiate first whether the ionic model
keeps track of potassium or not. If so, the plugin needs to know how to update the
potassium concentration of the ionic model. A complex example showing most of the
LIMPET features is shown here:
num_regions = 3
This shows a practical example that demonstrates the flexibility of LIMPET.
The intracellular grid is subdivided into 3 regions (specified by num_regions).
Shown here is the con- figuration of the first region only. We name the
region ENDO and assign the UCLA_RAB model. We also would like to overrule
some of the default settings of the model (see reference xx). Here we increase the sodium conductivity
by 10 percent and we reduce gKs by 5 percent. Instead of using the default
initialization of state variables we use a different initial state vector
which we have generate with the single cell code bench where we paced a
single cell 100 times at a basic cycle length of 300 ms. Furthermore, besides
Vm and φe which are output by default we also output
dyadic space, (cp) the subsacrolemnal space and (Ca_i) the
cytosol. Several plugins are switched on, EP_RS (electroporation with resealing),
IA (hypothetical potassium current that activates at large depolarizations),
MusCon (the Hunter - McCulloch - terKeurs model to compute active mechanical
parameters) and SAC_KS (model of stretch activated channels). Several default
parameters of the electroporation models are overruled, whereas all other
plugins use the default values. We also output several state variables in
the plugins including the number of pores n formed due to electroporation
and several active mechanical parameters. The region to which we apply
all these settings is composed of 4 subregions where the subregions are
formed by finite elements that are either tagged with the IDs 1, 2, 3 or
region.description = "ENDO"
region.im = "UCLA_RAB"
region.im_param = "gNa+10%:gKs*0.95"
region.im_sv_init = "sCpacing_bcl_100x300ms"
region.im_sv_dumps = "cp:cs:ca_i"
region.plugins = "IA:EP_RS:Muscon:SAC_KS"
region.plug_param = ":q=2.71,N0=7.5e4:::"
region.plug_sv_dumps = ":n:olambda,z,Q1,Q2:"
region.num_IDs = 4
region.ID = 1
region.ID = 2
region.ID = 3
region.ID = 4
region.description = "EPI"
region.im = "PUG"
Calcium concentration in different cell components such as the dyadic.