Example b142: Coupled Noble '98 - HMT

This exmaple solves the coupled Noble '98 - HMT model for a single cell (grid point). It solves the standard Noble '98 membrane kinetics with the HMT troponin, tropomyosin, and cross-bridge kinetics.

Mechano-electric feedback is provided via tension dependent release of Ca++ from Tn-C.

A single step change in length is applied during an isometirc twitch.


The comfile run by this example is as follows:

#Example b142 - Coupled Noble 98 - HMT

# Set the signals we want to export - if you change these, need to
# update the ipexpo file.
# 	Vm = 1			Cai = 4
# 	CaTROP = 9		z = 26
# 	ExtensionRatio = 27	Tension = 28
# 	IsometricTension = 29


# Command updated by fixcom.sh on Wed Aug 23 17:49:43 NZT 2000
# Old command: assign variable SIGNALS 1,4,9,26,27,28,29
$SIGNALS = "1,4,9,26,27,28,29"


# Define the problem size
fem def para;r;n98_hmt;example

# Create a single node and element
fem def no;d
fem def base;d
fem def elem;d
# Create the single cell we want to use
fem def grid;d
fem update grid geom
fem update grid metric

# Define the equations we want to solve
fem def equa;r;n98_hmt;example

# Define the cellular material parameters
fem def cell;r;n98_hmt;example
fem def mate;r;n98_hmt;example cell
fem def mate;r;n98_hmt;example
fem update grid material

# Define a single step change
fem def time;r;step;example
# and set it to describe the extension ratio variable
fem def init;r;n98_hmt;example

# Define an explict, adaptive Adams-Moulton integration
fem def solv;r;n98_hmt;example

# Initialise the solve
fem solve to 0

# Create the history file to store the signals we want to export
fem open history;test write variables yqs niqslist $SIGNALS binary

# Loop through time (500 ms)

# Command updated by fixcom.sh on Wed Aug 23 17:49:43 NZT 2000
# Old command: DO TIME = 0..499
for $TIME ( 0..499 ) 
{


#  Solve for the current time
  fem solve restart to $TIME

#  Write the signals to the history file
  fem write history time $TIME variables yqs binary


# Command updated by fixcom.sh on Wed Aug 23 17:49:43 NZT 2000
# Old command: ENDDO
}


#  Close the history file
fem close history binary

# Generate a UnEMAP signal file
fem evaluate electrode;test history test from grid yqs iy $SIGNALS binary
fem define export;r;n98_hmt;example
fem export signal;test electrode signal test

# Tidy-up

# Command updated by fixcom.sh on Wed Aug 23 17:49:43 NZT 2000
# Old command: deassign variable SIGNALS
  






Additional testing commands:

#Testing example b142

fem list time
fem list signal signal test binary


Files used by this example are:

Name                Modified     Size

example_b142.com 05-Mar-2001 2.0k n98_hmt.ipcell 07-Oct-2000 11k n98_hmt.ipequa 26-May-2003 1.3k n98_hmt.ipexpo 19-May-2000 657 n98_hmt.ipinit 19-May-2000 650 n98_hmt.ipmatc 29-Jan-2003 379 n98_hmt.ipmate 19-May-2000 1.8k n98_hmt.ippara 12-Nov-2002 5.9k n98_hmt.ipsolv 21-Jan-2003 1.3k n98_hmt.ipsolv.old 19-May-2000 1.3k step.iptime 30-Jul-2001 1.0k test_output.com 20-Nov-2001 73

Download the entire example:

Name                           Modified     Size

examples_b_b1_b14_b142.tar.gz 19-Aug-2006 28k

Testing status by version:

StatusTestedReal time (s)
i686-linux
cmSuccessSun Mar 6 00:04:01 20163
cm-debugSuccessSat Mar 5 00:16:07 20168
mips-irix
cmSuccessSun Aug 19 02:02:09 200733
cm-debugSuccessWed Aug 15 02:02:01 200784
cm-debug-clear-mallocSuccessSat Aug 18 02:12:16 200786
cm-debug-clear-malloc7SuccessMon Aug 20 02:12:16 200791
cm64SuccessSun Aug 19 02:03:16 200733
cm64-debugSuccessTue Aug 21 02:01:21 200785
cm64-debug-clear-mallocSuccessThu Apr 1 11:10:13 200438
rs6000-aix
cmSuccessWed Mar 4 01:09:11 20093
cm-debugSuccessMon Mar 2 01:13:38 200920
cm64SuccessWed Mar 4 01:09:45 20092
cm64-debugSuccessTue Mar 3 01:18:09 200920
x86_64-linux
cmSuccessSun Mar 6 00:01:10 20162
cm-debugSuccessSat Mar 5 00:01:54 20164

Testing status by file:


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

Input last modified: Mon May 26 18:04:44 2003


CMISS Help / Examples / b / b1 / b14 / b142