- Author:
- pmr2.import <nobody@models.cellml.org>
- Date:
- 2008-03-25 03:42:26+13:00
- Desc:
- committing version02 of faville_pullan_sanders_smith_2008
- Permanent Source URI:
- https://models.fieldml.org/workspace/faville_pullan_sanders_smith_2008/rawfile/19e3365b8f8cee2041ce1cfd1e61d690416d9d9b/faville_pullan_sanders_smith_2008.cellml
<?xml version='1.0' encoding='utf-8'?>
<!-- FILE : faville_model_2008.xml
CREATED : 4th October 2007
LAST MODIFIED : 20th March 2008
AUTHOR : Catherine Lloyd
Bioengineering Institute
The University of Auckland
MODEL STATUS : This model conforms to the CellML 1.1 Specification.
DESCRIPTION : This file contains a CellML description of Richard Faville et al.'s 2008 biophysically based mathematical model of unitary potential activity in interstitial cells of Cajal.
CHANGES:
--><model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" cmeta:id="faville_model_2008" name="faville_model_2008">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>A Biophysically Based Mathematical Model of Unitary Potential Activity in Interstitial Cells of Cajal</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>
This CellML model is known to run in both COR and PCEnv to replicate the published results. The units have been checked and are consistent. We'd like to acknowledge Richard Faville for his help in getting the CellML model to replicate his published model.
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
Phasic gastrointestinal (GI) muscle is able to autonomously generate rhythmic contractions independent of the enteric nervous system. The electrical activity that generates these rhythmic contractions are called slow waves, or pacemaker potentials (PP), and they are produced by a specialised group of pacemaker cells called Interstitial Cells of Cajal (ICC). They pass via gap junctions from the ICC to smooth muscle cells (SMC), activating L-type Ca2+ channels, Ca2+ influx and the contraction of the SMC. Full slow waves result from the summation of a large number of localised cellular membrane fluctuations, and are know as unitary potentials (UPs). These are generated at intracellular sites called pacemaker units, and are known to play an essential role in driving the coordinated contraction of GI muscles.
</para>
<para>
In the study described here, Richard Faville <emphasis>et al.</emphasis> have developed a mathematical model which quantitatively describes the transmembrane ion flows and intracellular Ca2+ dynamics from a single ICC pacemaker unit. They have combined experimental data with a theoretical hypothesis to produce a biophysically-based computational modelling framework that simulates ICC pacemaker activity on the pacemaker unit spatial scale.
</para>
<informalfigure float="0" id="fig_reaction_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>model diagram</title>
</objectinfo>
<imagedata fileref="faville_2008.png"/>
</imageobject>
</mediaobject>
<caption>A schematic diagram of the pacemaker unit illustrating all the compartmental volumes and ionic conductances, together with their interactions.</caption>
</informalfigure>
<para>
The complete original paper reference is cited below:
</para>
<para>
<ulink url="http://www.springerlink.com/content/652t4456624w2502/">A Biophysically Based Mathematical Model of Unitary Potential Activity in Interstitial Cells of Cajal</ulink>, R.A. Faville, A.J. Pullan, K.M. Sanders, and N.P. Smith, 2008, <ulink url="http://www.biophysj.org/">
<emphasis>Biophysical Journal</emphasis>
</ulink>. (A <ulink url="http://www.biophysj.org/cgi/rapidpdf/biophysj.107.122507v1">PDF</ulink> version of the article are available to journal subscribers on the <emphasis>Biophysical Journal</emphasis> website.) <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=18339738&query_hl=1&itool=pubmed_docsum">PubMed ID: 18339738</ulink>
</para>
</sect1>
</article>
</documentation>
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<unit units="second" exponent="-1"/>
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<variable units="second" public_interface="out" name="time"/>
</component>
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<variable units="picoampere" public_interface="in" name="I_NSCC_Na"/>
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<rdf:Description rdf:about="I_Ca">
<dc:title>I_Ca</dc:title>
<dcterms:alternative>calcium current</dcterms:alternative>
</rdf:Description>
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<times/>
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<divide/>
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<ci> T </ci>
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<apply>
<times/>
<cn cellml:units="dimensionless"> 2.0 </cn>
<ci> F </ci>
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<apply>
<ln/>
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<divide/>
<ci> CO </ci>
<ci> CS1 </ci>
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<apply>
<eq/>
<ci> I_Ca </ci>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="I_NSCC_Ca">
<dc:title>I_NSCC_Ca</dc:title>
<dcterms:alternative>non-selective calcium conductance</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
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<eq/>
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<ci> gNSCC_Ca_ </ci>
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<divide/>
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<ci> hNSCC </ci>
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<ci> KNSCC </ci>
<ci> hNSCC </ci>
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</apply>
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<eq/>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="I_NSCC_Na">
<dc:title>I_NSCC_Na</dc:title>
<dcterms:alternative>non-selective sodium conductance</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
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<variable units="micromolar" public_interface="in" name="CS1"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> gNSCC_Na_ </ci>
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<eq/>
<ci> I_NSCC_Na </ci>
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<rdf:Description rdf:about="I_PM">
<dc:title>I_PM</dc:title>
<dcterms:alternative>plasma membrane Ca2+-ATPase current</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
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<variable units="femtoampere" name="gPM" initial_value="420.0"/>
<variable units="micromolar" name="KPM" initial_value="1.0"/>
<variable units="micromolar" public_interface="in" name="CS1"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
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<eq/>
<ci> I_PM </ci>
<apply>
<times/>
<ci> gPM </ci>
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<divide/>
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<power/>
<ci> CS1 </ci>
<cn cellml:units="dimensionless"> 2.0 </cn>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci> KPM </ci>
<cn cellml:units="dimensionless"> 2.0 </cn>
</apply>
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<power/>
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<cn cellml:units="dimensionless"> 2.0 </cn>
</apply>
</apply>
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<rdf:Description rdf:about="I_Na">
<dc:title>I_Na</dc:title>
<dcterms:alternative>sodium current</dcterms:alternative>
</rdf:Description>
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<variable units="micromolar" name="KNa" initial_value="1.0E4"/>
<variable units="dimensionless" name="hNa" initial_value="4.0"/>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> I_Na </ci>
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<ci> hNa </ci>
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<ci> hNa </ci>
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<dc:title>JSERCA</dc:title>
<dcterms:alternative>SERCA pump</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
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<dc:title>JMCU</dc:title>
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<ci> hINH </ci>
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<ci> KINH </ci>
<ci> hINH </ci>
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<ci> hINH </ci>
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<dc:title>JNCX</dc:title>
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<ci> JNCX </ci>
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<ci> CMT </ci>
<ci> KNCX </ci>
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<variable units="micromolar" public_interface="in" name="CS2"/>
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<ci> JS1S2 </ci>
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<ci> mu_S1S2 </ci>
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<dc:title>JIPR</dc:title>
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<variable units="flux" public_interface="out" name="JIPR"/>
<variable units="first_order_rate_constant" name="kIPR" initial_value="2000.0"/>
<variable units="flux" name="k_1" initial_value="6.4"/>
<variable units="first_order_rate_constant" name="k1" initial_value="0.0"/>
<variable units="first_order_rate_constant" name="k2" initial_value="4.0"/>
<variable units="first_order_rate_constant" name="r2" initial_value="200.0"/>
<variable units="flux" name="r_2" initial_value="0.0"/>
<variable units="first_order_rate_constant" name="r4" initial_value="750.0"/>
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<variable units="micromolar" name="R3" initial_value="300.0"/>
<variable units="first_order_rate_constant" name="phi1"/>
<variable units="flux" name="phi_1"/>
<variable units="first_order_rate_constant" name="phi2"/>
<variable units="first_order_rate_constant" name="phi3" initial_value="0.306"/>
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<variable units="first_order_rate_constant" name="g_beta" initial_value="300.0"/>
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<variable units="micromolar" name="K_beta" initial_value="2.0"/>
<variable units="per_second_squared" name="alpha_phi3"/>
<variable units="first_order_rate_constant" name="beta_phi3"/>
<variable units="micromolar" public_interface="in" name="CER"/>
<variable units="micromolar" public_interface="in" name="CS2"/>
<variable units="micromolar" public_interface="in" name="P"/>
<variable units="second" public_interface="in" name="time"/>
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<ci>time</ci>
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Richard Faville et al.'s 2008 biophysically based mathematical model of unitary potential activity in interstitial cells of Cajal.
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