Example i51: 1D Small Intestine - Slow Wave and Dipole Source

This example simulates the slow wave activity in the 1D small intestine (Longitudinal muscle (LM) and Interstitial Cells of Cajal (ICC)) and generate a single dipole from the transmembrane potential gradients at each element (refer Master Thesis Section 5.3 - A. Lin (2003)).

The cell model is based on Aliev et al. (2000) except for the excitation parameter to create a decreasing frequency, conduction velocity and wavelength profile. However, the transmembrane potential solution doesn't reach a steady state which is a limitation of the cell model. An example of the transmembrane potentials at two specific times is given below. The left figures are longitudinal muscle and the right figures are ICC layers.

LM                ICC

LM                ICC

t=5s

t=160s

The comfile run by this example is as follows:

set Num_threads 1


# Set up region
$intestine = 1;
# Set up class
$active = 1;

# Define the geometry of the small intestine
fem define para;r;$example/intestine
fem de coor 3,1
fem define nodes;r;$example/intestine reg $intestine
fem de base;r;$example/intestine
fem define elements;r;$example/intestine reg $intestine

# Group different cell types
fem group node 1..111 as ICC reg $intestine 
fem group elem 1..110 as ICC reg $intestine 
fem group node 112..222 as LM reg $intestine 
fem group elem 111..220 as LM reg $intestine 

# Group elements which have similar length to apply different grid scheme later
fem group elem 27 as grid15 reg $intestine 
fem group elem 137 as grid15_LM reg $intestine 
fem group elem 44,40,67,39,43,28,38,46,45,18,31 as grid20 reg $intestine 
fem group elem 154,150,177,149,153,138,148,156,155,128,141 as grid20_LM reg $intestine 
fem group elem 80,58,53,68,91,29,62,25,49,84,19,77,66,61,72,57,41 as grid25 reg $intestine 
fem group elem 190,168,163,178,201,139,172,135,159,194,129,187,176,171,182,167,151 as grid25_LM reg $intestine 
fem group elem 33,51,52,36,64,23,83,82,17,10,69,75,26,47,86,79,107,42 as grid30 reg $intestine 
fem group elem 143,161,162,146,174,133,193,192,127,120,179,185,136,157,196,189,107,217,42,152 as grid30_LM reg $intestine 
fem group elem 74,13,16,65,59,104,50,87,54,21,94,73,92,32,76,102,12,35,109,100,48 as grid35 reg $intestine 
fem group elem 184,123,126,175,169,104,214,160,197,164,131,204,183,202,142,186,212,122,145,219,210,158 as grid35_LM reg $intestine 
fem group elem 37,63,93,95,105,34,101,14,2,7,60,78,56,90,4,20,99,70,71,11 as grid40 reg $intestine 
fem group elem 147,173,203,205,215,144,211,124,112,117,170,188,166,200,114,130,209,180,181,121 as grid40_LM reg $intestine 
fem group elem 110,30,89,108,55,96,97,15,5,3 as grid45 reg $intestine 
fem group elem 220,140,199,108,218,165,206,207,125,115,113 as grid45_LM reg $intestine 
fem group elem 1,103,88,6,81,85 as grid50 reg $intestine 
fem group elem 111,213,198,116,191,195 as grid50_LM reg $intestine 
fem group elem 98,106,9,24 as grid55 reg $intestine 
fem group elem 208,216,119,134 as grid55_LM reg $intestine 
fem group elem 22,8 as grid60 reg $intestine 
fem group elem 132,118 as grid60_LM reg $intestine 

# Apply different grid schemes to have the same spatial resolution
fem define grid;r;$example/intestine reg $intestine 
fem update grid geometry reg $intestine
fem update grid metri reg $intestine

# Group the grids for one-to-one mapping later
fem group grid grid 1..3716 as ICC_grid reg $intestine
fem group grid grid 3717..7432 as LM_grid reg $intestine

# Define the monodomain equation
fem define equ;r;$example/ICCcmiss reg $intestine class $active
# Use Aliev cell model 
fem define cell;r;$example/ICCcmiss reg $intestine class $active 
# The parameters are based on Aliev (2000) except the excitation parameters
fem define mate;r;$example/ICCcmiss cell reg $intestine class $active 
# Define the conductivity based on Aliev (2000)
fem define mate;r;$example/ICCcmiss reg $intestine class $active 
fem update grid material reg $intestine class $active 
# Define initial problem
fem define init;r;$example/ICCcmiss reg $intestine class $active 
# Define solver
fem define solv;r;$example/ICCcmiss reg $intestine class $active 

# Initial solve
fem solve to 0 reg $intestine class $active 

# Exporting...
fem export nodes;LM no LM as LM reg $intestine
fem export nodes;ICC no ICC as ICC reg $intestine
fem export element;LM ele LM as LM reg $intestine
fem export element;ICC ele ICC as ICC reg $intestine
fem export ele;grid_ICC ele ICC as ICC grid_numbers reg $intestine
fem export ele;grid_LM ele LM as LM grid_numbers reg $intestine
fem export no;intestine reg $intestine as intestine
fem export ele;intestine reg $intestine as intestine
fem export ele;coupling_field_0 reg $intestine class $active field as intestine;

# Solve with a time step of 0.02s and output every 1s
$counter=50;
$over_time=5;
$step=0.02;
$endloop=$over_time/$step;
for $M ( 0..$endloop) 
{
    $time=$M*$step;
    # one-to-one mapping
    fem update grid stimulus grid ICC_grid map_grid LM_grid diffusion 0.3 reg $intestine class $active 
    fem solve restart to $time reg $intestine class $active 
    if ($counter>=49) {
                print $time
                # Calculate the dipole sources (per element) and output electrical field
		fem define sour;c grid grregion $intestine grclass $active time $time     
		fem export ele;coupling_field_$time reg $intestine class $active field as intestine; 
	 	$counter=0;
    } else {
		$counter++;
	}
}

# Write out all the dipole source in one ipsour file
fem define sour;w;dipole_elem grid grregion $intestine grclass $active
fem export sour;dipole_all as dipole

Files used by this example are:

Name              Modified     Size


example_i51.com   28-Oct-2005  4.6k
ICCcmiss.ipcell   28-Oct-2005  3.5k
ICCcmiss.ipequa   27-Oct-2005  1.5k
ICCcmiss.ipinit   27-Oct-2005  214 
ICCcmiss.ipmatc   27-Oct-2005  333k
ICCcmiss.ipmate   27-Oct-2005  1.9k
ICCcmiss.ipsolv   27-Oct-2005  900 
ICCcmiss_new.cml  27-Oct-2005  8.9k
intestine.ipbase  27-Oct-2005  5.6k
intestine.ipelem  27-Oct-2005   68k
intestine.ipgrid  27-Oct-2005  3.3k
intestine.ipnode  27-Oct-2005   95k
intestine.ippara  01-Nov-2005  5.9k

Download the entire example:

Name                      Modified     Size


examples_i_i5_i51.tar.gz  19-Aug-2006  286k

Testing status by version:

StatusTestedReal time (s)
i686-linux
cmSuccessSun Mar 6 00:04:16 20163
cm-debugSuccessSat Mar 5 00:18:57 201610
mips-irix
cmSuccessSun Aug 19 02:30:15 200756
cm-debugSuccessWed Aug 15 04:00:52 2007344
cm-debug-clear-mallocSuccessSat Aug 18 04:35:37 2007355
cm-debug-clear-malloc7SuccessMon Aug 20 04:37:32 2007351
cm64SuccessSun Aug 19 02:31:16 200758
cm64-debugSuccessTue Aug 21 04:58:13 2007308
rs6000-aix
cmSuccessWed Mar 4 01:11:15 20094
cm-debugSuccessMon Mar 2 01:24:51 200953
cm64SuccessWed Mar 4 01:11:16 20094
cm64-debugSuccessTue Mar 3 01:27:39 200958
x86_64-linux
cmSuccessSun Mar 6 00:01:10 20162
cm-debugSuccessSat Mar 5 00:02:07 20166

Testing status by file:

Graphical output from this problem is given here.

Html last generated: Sun Mar 6 05:51:39 2016

Input last modified: Tue Feb 21 11:04:21 2006

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