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:

Testing status by file:

• cmiss_test.log
  

  i686-linux
  Success	cm:	cmiss_test.log.retain.
  Success	cm-debug:	cmiss_test.log.retain.
  mips-irix
  Success	cm:	cmiss_test.log.retain.
  Success	cm-debug:	cmiss_test.log.retain.
  Success	cm-debug-clear-malloc:	cmiss_test.log.retain.
  Success	cm-debug-clear-malloc7:	cmiss_test.log.retain.
  Success	cm64:	cmiss_test.log.retain.
  Success	cm64-debug:	cmiss_test.log.retain.
  Success	cm64-debug-clear-malloc:	cmiss_test.log.retain.
  rs6000-aix
  Success	cm:	cmiss_test.log.retain.
  Success	cm-debug:	cmiss_test.log.retain.
  Success	cm64:	cmiss_test.log.retain.
  Success	cm64-debug:	cmiss_test.log.retain.
  x86_64-linux
  Success	cm:	cmiss_test.log.retain.
  Success	cm-debug:	cmiss_test.log.retain.

  
  
• cmiss_test.out
  

  i686-linux
  Success	cm:	ndiff test: no significant differences with generic answer.
  Success	cm-debug:	ndiff test: no significant differences with generic answer.
  mips-irix
  Success	cm:	ndiff test: no significant differences with generic answer.
  Success	cm-debug:	ndiff test: no significant differences with generic answer.
  Success	cm-debug-clear-malloc:	ndiff test: no significant differences with generic answer.
  Success	cm-debug-clear-malloc7:	ndiff test: no significant differences with generic answer.
  Success	cm64:	ndiff test: no significant differences with generic answer.
  Success	cm64-debug:	ndiff test: no significant differences with generic answer.
  Success	cm64-debug-clear-malloc:	ndiff test: no significant differences with generic answer.
  rs6000-aix
  Success	cm:	ndiff test: no significant differences with generic answer.
  Success	cm-debug:	ndiff test: no significant differences with generic answer.
  Success	cm64:	ndiff test: no significant differences with generic answer.
  Success	cm64-debug:	ndiff test: no significant differences with generic answer.
  x86_64-linux
  Success	cm:	ndiff test: no significant differences with generic answer.
  Success	cm-debug:	ndiff test: no significant differences with generic answer.

  
  
• test.binsig
  

  i686-linux
  Success	cm:	diff test: no differences with generic answer.
  Success	cm-debug:	diff test: no differences with generic answer.
  mips-irix
  Success	cm:	diff test: no differences with generic answer.
  Success	cm-debug:	diff test: no differences with generic answer.
  Success	cm-debug-clear-malloc:	diff test: no differences with generic answer.
  Success	cm-debug-clear-malloc7:	diff test: no differences with generic answer.
  Success	cm64:	diff test: no differences with generic answer.
  Success	cm64-debug:	diff test: no differences with generic answer.
  Success	cm64-debug-clear-malloc:	diff test: no differences with generic answer.
  rs6000-aix
  Success	cm:	diff test: no differences with generic answer.
  Success	cm-debug:	diff test: no differences with generic answer.
  Success	cm64:	diff test: no differences with generic answer.
  Success	cm64-debug:	diff test: no differences with generic answer.
  x86_64-linux
  Success	cm:	diff test: no differences with generic answer.
  Success	cm-debug:	diff test: no differences with generic answer.

  
  
• test.signal
  

  i686-linux
  Success	cm:	diff test: no differences with generic answer.
  Success	cm-debug:	diff test: no differences with generic answer.
  mips-irix
  Success	cm:	diff test: no differences with generic answer.
  Success	cm-debug:	diff test: no differences with generic answer.
  Success	cm-debug-clear-malloc:	diff test: no differences with generic answer.
  Success	cm-debug-clear-malloc7:	diff test: no differences with generic answer.
  Success	cm64:	diff test: no differences with generic answer.
  Success	cm64-debug:	diff test: no differences with generic answer.
  Success	cm64-debug-clear-malloc:	diff test: no differences with generic answer.
  rs6000-aix
  Success	cm:	diff test: no differences with generic answer.
  Success	cm-debug:	diff test: no differences with generic answer.
  Success	cm64:	diff test: no differences with generic answer.
  Success	cm64-debug:	diff test: no differences with generic answer.
  x86_64-linux
  Success	cm:	diff test: no differences with generic answer.
  Success	cm-debug:	diff test: no differences with generic answer.

  
  

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

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