- Author:
- neilstephen2001 <npar276@aucklanduni.ac.nz>
- Date:
- 2021-01-26 14:35:03+13:00
- Desc:
- modifying rdf files
- Permanent Source URI:
- http://models.cellml.org/workspace/7f1/rawfile/4d6408caaf3e7b1b86d33d53d26105360ef95347/nagerl_novo_mody_vergara_2000/model/nagerl_novo_mody_vergara_2000.cellml
<?xml version="1.0" encoding="UTF-8"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:semsim="http://www.bhi.washington.edu/SemSim#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" name="nagerl_novo_mody_vergara_2000" cmeta:id="nagerl_model_2000_version02">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Ca2+ Binding Kinetics of Calbindin-D28k</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
Rapid changes in intracellular calcium concentration ([Ca
<superscript>2+</superscript>
]
<subscript>i</subscript>
) are characteristic of Ca
<superscript>2+</superscript>
signalling. Following a stimulus, Ca
<superscript>2+</superscript>
flows into the cytoplasm through channels in the cell membrane, and it's released from intracellular stores such as the endoplasmic reticulum. Normal [Ca
<superscript>2+</superscript>
] is resumed by the actions of Ca
<superscript>2+</superscript>
pumps, exchangers, binding proteins (CBPs) and other buffers. Calbindin-D
<subscript>28k</subscript>
is a CBP which is present at high cytosolic concentrations in neurons such as cerebellar Purkinje cells and hippocampal granule cells. Together with its high cytosolic concentration, the ability of calbindin-D
<subscript>28k</subscript>
to bind up to four Ca
<superscript>2+</superscript>
ions at any one time suggests that it plays an important role in Ca
<superscript>2+</superscript>
buffering.
</para>
<para>
Little is known about the Ca
<superscript>2+</superscript>
binding kinetics of calbindin-D
<subscript>28k</subscript>
, or of CBPs in general. In their 2000 paper, Nagerl
<emphasis>et al.</emphasis>
describe a new method to measure the binding kinetics of calbindin-D
<subscript>28k</subscript>
, which involves flash photolysis of DM-nitrophen (DM-n), a caged Ca
<superscript>2+</superscript>
compound. A mathematical model, which included the Ca
<superscript>2+</superscript>
binding reactions of all the species in the solution (see
<xref linkend="fig_reaction_diagram" />
below), was fitted to the experimental data in order to determine realistic kinetic parameters. The results of their experiments suggested that calbindin-D
<subscript>28k</subscript>
has two kinetically distinct types of Ca
<superscript>2+</superscript>
binding sites, one high- and one low-affinity. This heterogeneity was captured by their mathematical model.
</para>
<para>The complete original paper reference is cited below:</para>
<para>
<ulink url="http://www.biophysj.org/cgi/content/abstract/79/6/3009">
Binding Kinetics of Calbindin-D
<subscript>28k</subscript>
Determined by Flash Photolysis of Caged Ca
<superscript>2+</superscript>
</ulink>
, U. Valentin Nagerl, David Novo, Istvan Mody and Julio L. Vergara, 2000,
<ulink url="http://www.biophysj.org/">
<emphasis>Biophysical Journal</emphasis>
</ulink>
, 79, 3009-3018. (
<ulink url="http://www.biophysj.org/cgi/content/full/79/6/3009">Full text</ulink>
and
<ulink url="http://www.biophysj.org/cgi/reprint/79/6/3009.pdf">PDF versions</ulink>
of the article are available to subscribers on the Biophysical Journal website.)
<ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11106608&dopt=Abstract">PubMed ID: 11106608</ulink>
</para>
<para>
The raw CellML descriptions of the model can be downloaded in various formats as described in
<xref linkend="sec_download_this_model" />
.
</para>
<informalfigure float="0" id="fig_reaction_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>reaction_diagram</title>
</objectinfo>
<imagedata fileref="nagerl_2000.png" />
</imageobject>
</mediaobject>
<caption>
Schematic diagram of the mathematical model used to simulate the dynamic redistribution of Ca
<superscript>2+</superscript>
generated by flash photolysis of DM-n. CaDM1, CaDM2, CaD and CaB represent the concentration of Ca
<superscript>2+</superscript>
bound to DM-n, dye and buffer, respectively. Alpha models the fraction of Ca
<superscript>2+</superscript>
-bound DM-n1 that is photolysed by the UV laser flash.
</caption>
</informalfigure>
</sect1>
</article>
</documentation>
<units name="millisecond">
<unit prefix="milli" units="second" />
</units>
<units name="second_order_rate_constant">
<unit exponent="-1.0" units="millisecond" />
<unit exponent="-1.0" units="micromolar" />
</units>
<units name="microsecond">
<unit prefix="micro" units="second" />
</units>
<units name="first_order_rate_constant">
<unit exponent="-1.0" units="millisecond" />
</units>
<units name="flux">
<unit exponent="-1.0" units="millisecond" />
<unit units="micromolar" />
</units>
<units name="millimolar">
<unit exponent="-1.0" units="litre" />
<unit prefix="milli" units="mole" />
</units>
<units name="micromolar">
<unit exponent="-1.0" units="litre" />
<unit prefix="micro" units="mole" />
</units>
<component name="environment">
<variable cmeta:id="environment.time" name="time" public_interface="out" units="millisecond" />
</component>
<component name="Ca" cmeta:id="Ca">
<variable cmeta:id="Ca.Ca" initial_value="1.5" name="Ca" public_interface="out" units="micromolar" />
<variable cmeta:id="Ca.CaD" name="CaD" public_interface="in" units="micromolar" />
<variable cmeta:id="Ca.CaDM1" name="CaDM1" public_interface="in" units="micromolar" />
<variable cmeta:id="Ca.CaDM2" name="CaDM2" public_interface="in" units="micromolar" />
<variable cmeta:id="Ca.CaBi" name="CaBi" public_interface="in" units="micromolar" />
<variable cmeta:id="Ca.Ca_T" name="Ca_T" units="micromolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML" id="1">
<apply>
<eq />
<ci>Ca</ci>
<apply>
<minus />
<ci>Ca_T</ci>
<apply>
<plus />
<ci>CaD</ci>
<ci>CaDM1</ci>
<ci>CaDM2</ci>
<ci>CaBi</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="DM_T" cmeta:id="DM_T">
<variable cmeta:id="DM_T.DM_T" initial_value="5.0" name="DM_T" public_interface="out" units="millimolar" />
</component>
<component name="DM1" cmeta:id="DM1">
<variable cmeta:id="DM1.DM1" name="DM1" public_interface="out" units="millimolar" />
<variable cmeta:id="DM1.alpha" name="alpha" public_interface="in" units="dimensionless" />
<variable cmeta:id="DM1.DM_T" name="DM_T" public_interface="in" units="millimolar" />
<variable cmeta:id="DM1.CaDM1" name="CaDM1" public_interface="in" units="micromolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML" id="3">
<apply>
<eq />
<ci>DM1</ci>
<apply>
<minus />
<apply>
<times />
<ci>DM_T</ci>
<ci>alpha</ci>
</apply>
<ci>CaDM1</ci>
</apply>
</apply>
</math>
</component>
<component name="DM1_T" cmeta:id="DM1_T">
<variable cmeta:id="DM1_T.DM1_T" name="DM1_T" public_interface="out" units="millimolar" />
<variable cmeta:id="DM1_T.DM1" name="DM1" public_interface="in" units="millimolar" />
<variable cmeta:id="DM1_T.CaDM1" name="CaDM1" public_interface="in" units="micromolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML" id="4">
<apply>
<eq />
<ci>DM1_T</ci>
<apply>
<plus />
<ci>DM1</ci>
<ci>CaDM1</ci>
</apply>
</apply>
</math>
</component>
<component name="DM2" cmeta:id="DM2">
<variable cmeta:id="DM2.DM2" name="DM2" public_interface="out" units="micromolar" />
<variable cmeta:id="DM2.alpha" name="alpha" public_interface="in" units="dimensionless" />
<variable cmeta:id="DM2.DM_T" name="DM_T" public_interface="in" units="millimolar" />
<variable cmeta:id="DM2.CaDM2" name="CaDM2" public_interface="in" units="micromolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML" id="5">
<apply>
<eq />
<ci>DM2</ci>
<apply>
<minus />
<apply>
<times />
<ci>DM_T</ci>
<apply>
<minus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1.0</cn>
<ci>alpha</ci>
</apply>
</apply>
<ci>CaDM2</ci>
</apply>
</apply>
</math>
</component>
<component name="DM2_T" cmeta:id="DM2_T">
<variable cmeta:id="DM2_T.DM2_T" name="DM2_T" public_interface="out" units="millimolar" />
<variable cmeta:id="DM2_T.DM2" name="DM2" public_interface="in" units="millimolar" />
<variable cmeta:id="DM2_T.CaDM2" name="CaDM2" public_interface="in" units="micromolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML" id="6">
<apply>
<eq />
<ci>DM2_T</ci>
<apply>
<plus />
<ci>DM2</ci>
<ci>CaDM2</ci>
</apply>
</apply>
</math>
</component>
<component name="D" cmeta:id="D">
<variable cmeta:id="D.D_T" initial_value="100.0" name="D_T" units="micromolar" />
<variable cmeta:id="D.D" name="D" public_interface="out" units="micromolar" />
<variable cmeta:id="D.CaD" name="CaD" public_interface="in" units="micromolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML" id="7">
<apply>
<eq />
<ci>D</ci>
<apply>
<minus />
<ci>D_T</ci>
<ci>CaD</ci>
</apply>
</apply>
</math>
</component>
<component name="Bi" cmeta:id="Bi">
<variable cmeta:id="Bi.Bi_T" initial_value="1.0" name="Bi_T" units="micromolar" />
<variable cmeta:id="Bi.Bi" name="Bi" public_interface="out" units="micromolar" />
<variable cmeta:id="Bi.CaBi" name="CaBi" public_interface="in" units="micromolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML" id="8">
<apply>
<eq />
<ci>Bi_T</ci>
<apply>
<plus />
<ci>Bi</ci>
<ci>CaBi</ci>
</apply>
</apply>
</math>
</component>
<component name="CaDM1" cmeta:id="CaDM1">
<variable cmeta:id="CaDM1.CaDM1" name="CaDM1" public_interface="out" units="micromolar" />
<variable cmeta:id="CaDM1.Ca" name="Ca" public_interface="in" units="micromolar" />
<variable cmeta:id="CaDM1.DM1" name="DM1" public_interface="in" units="micromolar" />
<variable cmeta:id="CaDM1.kon_DM" name="kon_DM" public_interface="in" units="second_order_rate_constant" />
<variable cmeta:id="CaDM1.koff_DM" name="koff_DM" public_interface="in" units="first_order_rate_constant" />
<variable cmeta:id="CaDM1.k_trans" name="k_trans" public_interface="in" units="first_order_rate_constant" />
<variable cmeta:id="CaDM1.t_pulse" name="t_pulse" public_interface="in" units="millisecond" />
<variable cmeta:id="CaDM1.time" name="time" public_interface="in" units="millisecond" />
<math xmlns="http://www.w3.org/1998/Math/MathML" id="9">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>CaDM1</ci>
</apply>
<piecewise>
<piece>
<apply>
<minus />
<apply>
<times />
<ci>kon_DM</ci>
<ci>Ca</ci>
<ci>DM1</ci>
</apply>
<apply>
<times />
<ci>koff_DM</ci>
<ci>CaDM1</ci>
</apply>
</apply>
<apply>
<eq />
<ci>t_pulse</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">0.0</cn>
</apply>
</piece>
<otherwise>
<apply>
<minus />
<apply>
<times />
<ci>kon_DM</ci>
<ci>Ca</ci>
<ci>DM1</ci>
</apply>
<apply>
<times />
<ci>k_trans</ci>
<ci>CaDM1</ci>
</apply>
</apply>
</otherwise>
</piecewise>
</apply>
</math>
</component>
<component name="CaDM2" cmeta:id="CaDM2">
<variable cmeta:id="CaDM2.CaDM2" name="CaDM2" public_interface="out" units="micromolar" />
<variable cmeta:id="CaDM2.Ca" name="Ca" public_interface="in" units="micromolar" />
<variable cmeta:id="CaDM2.DM2" name="DM2" public_interface="in" units="micromolar" />
<variable cmeta:id="CaDM2.kon_DM" name="kon_DM" public_interface="in" units="second_order_rate_constant" />
<variable cmeta:id="CaDM2.koff_DM" name="koff_DM" public_interface="in" units="first_order_rate_constant" />
<variable cmeta:id="CaDM2.time" name="time" public_interface="in" units="millisecond" />
<math xmlns="http://www.w3.org/1998/Math/MathML" id="10">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>CaDM2</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>kon_DM</ci>
<ci>Ca</ci>
<ci>DM2</ci>
</apply>
<apply>
<times />
<ci>koff_DM</ci>
<ci>CaDM2</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="CaD" cmeta:id="CaD">
<variable cmeta:id="CaD.CaD" name="CaD" public_interface="out" units="micromolar" />
<variable cmeta:id="CaD.Ca" name="Ca" public_interface="in" units="micromolar" />
<variable cmeta:id="CaD.D" name="D" public_interface="in" units="micromolar" />
<variable cmeta:id="CaD.kon_D" name="kon_D" public_interface="in" units="second_order_rate_constant" />
<variable cmeta:id="CaD.koff_D" name="koff_D" public_interface="in" units="first_order_rate_constant" />
<variable cmeta:id="CaD.time" name="time" public_interface="in" units="millisecond" />
<math xmlns="http://www.w3.org/1998/Math/MathML" id="11">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>CaD</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>kon_D</ci>
<ci>Ca</ci>
<ci>D</ci>
</apply>
<apply>
<times />
<ci>koff_D</ci>
<ci>CaD</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="CaBi" cmeta:id="CaBi">
<variable cmeta:id="CaBi.CaBi" name="CaBi" public_interface="out" units="micromolar" />
<variable cmeta:id="CaBi.Ca" name="Ca" public_interface="in" units="micromolar" />
<variable cmeta:id="CaBi.Bi" name="Bi" public_interface="in" units="micromolar" />
<variable cmeta:id="CaBi.kon_Bi" name="kon_Bi" public_interface="in" units="second_order_rate_constant" />
<variable cmeta:id="CaBi.koff_Bi" name="koff_Bi" public_interface="in" units="first_order_rate_constant" />
<variable cmeta:id="CaBi.time" name="time" public_interface="in" units="millisecond" />
<math xmlns="http://www.w3.org/1998/Math/MathML" id="12">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>CaBi</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>kon_Bi</ci>
<ci>Ca</ci>
<ci>Bi</ci>
</apply>
<apply>
<times />
<ci>koff_Bi</ci>
<ci>CaBi</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="constants">
<variable cmeta:id="constants.kon_DM" initial_value="0.03" name="kon_DM" public_interface="out" units="second_order_rate_constant" />
<variable cmeta:id="constants.koff_DM" initial_value="0.00006" name="koff_DM" public_interface="out" units="first_order_rate_constant" />
<variable cmeta:id="constants.kon_D" initial_value="0.124" name="kon_D" public_interface="out" units="second_order_rate_constant" />
<variable cmeta:id="constants.koff_D" initial_value="5.6" name="koff_D" public_interface="out" units="first_order_rate_constant" />
<variable cmeta:id="constants.kon_Bi" initial_value="1.0" name="kon_Bi" public_interface="out" units="second_order_rate_constant" />
<variable cmeta:id="constants.koff_Bi" initial_value="1.0" name="koff_Bi" public_interface="out" units="first_order_rate_constant" />
<variable cmeta:id="constants.k_trans" name="k_trans" public_interface="out" units="first_order_rate_constant" />
<variable cmeta:id="constants.t_pulse" initial_value="1.0" name="t_pulse" public_interface="out" units="millisecond" />
<variable cmeta:id="constants.alpha" initial_value="0.5" name="alpha" public_interface="out" units="dimensionless" />
<variable cmeta:id="constants.koff_DM_" initial_value="75.0" name="koff_DM_" units="first_order_rate_constant" />
<variable cmeta:id="constants.tau_photolysis" initial_value="20.0" name="tau_photolysis" units="microsecond" />
<variable cmeta:id="constants.time" name="time" public_interface="in" units="millisecond" />
<math xmlns="http://www.w3.org/1998/Math/MathML" id="13">
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<eq />
<ci>k_trans</ci>
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<apply>
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<apply>
<exp />
<apply>
<divide />
<apply>
<minus />
<apply>
<minus />
<ci>time</ci>
<ci>t_pulse</ci>
</apply>
</apply>
<ci>tau_photolysis</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="CaDM1" component_2="DM1" />
<map_variables variable_1="CaDM1" variable_2="CaDM1" />
</connection>
<connection>
<map_components component_1="Ca" component_2="CaDM1" />
<map_variables variable_1="Ca" variable_2="Ca" />
</connection>
<connection>
<map_components component_1="DM2" component_2="DM2_T" />
<map_variables variable_1="DM2" variable_2="DM2" />
</connection>
<connection>
<map_components component_1="environment" component_2="CaDM1" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="constants" component_2="CaD" />
<map_variables variable_1="kon_D" variable_2="kon_D" />
<map_variables variable_1="koff_D" variable_2="koff_D" />
</connection>
<connection>
<map_components component_1="environment" component_2="CaDM2" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="Ca" component_2="CaD" />
<map_variables variable_1="Ca" variable_2="Ca" />
</connection>
<connection>
<map_components component_1="CaDM1" component_2="DM1_T" />
<map_variables variable_1="CaDM1" variable_2="CaDM1" />
</connection>
<connection>
<map_components component_1="constants" component_2="CaDM2" />
<map_variables variable_1="kon_DM" variable_2="kon_DM" />
<map_variables variable_1="koff_DM" variable_2="koff_DM" />
</connection>
<connection>
<map_components component_1="CaBi" component_2="Bi" />
<map_variables variable_1="CaBi" variable_2="CaBi" />
</connection>
<connection>
<map_components component_1="environment" component_2="constants" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="environment" component_2="CaD" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="DM1" component_2="DM1_T" />
<map_variables variable_1="DM1" variable_2="DM1" />
</connection>
<connection>
<map_components component_1="CaDM2" component_2="DM2_T" />
<map_variables variable_1="CaDM2" variable_2="CaDM2" />
</connection>
<connection>
<map_components component_1="Bi" component_2="CaBi" />
<map_variables variable_1="Bi" variable_2="Bi" />
</connection>
<connection>
<map_components component_1="Ca" component_2="CaDM2" />
<map_variables variable_1="Ca" variable_2="Ca" />
</connection>
<connection>
<map_components component_1="CaDM2" component_2="DM2" />
<map_variables variable_1="CaDM2" variable_2="CaDM2" />
</connection>
<connection>
<map_components component_1="constants" component_2="DM1" />
<map_variables variable_1="alpha" variable_2="alpha" />
</connection>
<connection>
<map_components component_1="constants" component_2="CaDM1" />
<map_variables variable_1="kon_DM" variable_2="kon_DM" />
<map_variables variable_1="t_pulse" variable_2="t_pulse" />
<map_variables variable_1="k_trans" variable_2="k_trans" />
<map_variables variable_1="koff_DM" variable_2="koff_DM" />
</connection>
<connection>
<map_components component_1="CaDM1" component_2="Ca" />
<map_variables variable_1="CaDM1" variable_2="CaDM1" />
</connection>
<connection>
<map_components component_1="constants" component_2="CaBi" />
<map_variables variable_1="koff_Bi" variable_2="koff_Bi" />
<map_variables variable_1="kon_Bi" variable_2="kon_Bi" />
</connection>
<connection>
<map_components component_1="CaD" component_2="D" />
<map_variables variable_1="CaD" variable_2="CaD" />
</connection>
<connection>
<map_components component_1="CaD" component_2="Ca" />
<map_variables variable_1="CaD" variable_2="CaD" />
</connection>
<connection>
<map_components component_1="environment" component_2="CaBi" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="Ca" component_2="CaBi" />
<map_variables variable_1="Ca" variable_2="Ca" />
</connection>
<connection>
<map_components component_1="CaDM2" component_2="Ca" />
<map_variables variable_1="CaDM2" variable_2="CaDM2" />
</connection>
<connection>
<map_components component_1="CaBi" component_2="Ca" />
<map_variables variable_1="CaBi" variable_2="CaBi" />
</connection>
<connection>
<map_components component_1="D" component_2="CaD" />
<map_variables variable_1="D" variable_2="D" />
</connection>
<connection>
<map_components component_1="DM_T" component_2="DM1" />
<map_variables variable_1="DM_T" variable_2="DM_T" />
</connection>
<connection>
<map_components component_1="DM1" component_2="CaDM1" />
<map_variables variable_1="DM1" variable_2="DM1" />
</connection>
<connection>
<map_components component_1="DM_T" component_2="DM2" />
<map_variables variable_1="DM_T" variable_2="DM_T" />
</connection>
<connection>
<map_components component_1="DM2" component_2="CaDM2" />
<map_variables variable_1="DM2" variable_2="DM2" />
</connection>
<connection>
<map_components component_1="constants" component_2="DM2" />
<map_variables variable_1="alpha" variable_2="alpha" />
</connection>
<rdf:RDF xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:ro="http://www.obofoundry.org/ro/ro.owl#" xmlns:opb="http://bhi.washington.edu/OPB#">
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#DM_T.DM_T">
<bqbiol:isPropertyOf>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#entity_0">
<bqbiol:is rdf:resource="http://identifiers.org/fma/FMA:84663" />
</rdf:Description>
</bqbiol:isPropertyOf>
<dcterms:description>total concentration of DM-nitrophen complex</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Ca.CaDM1">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_2">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_3">
<ro:part_of>
<rdf:Description rdf:about="#entity_1">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/fma/FMA:226054" />
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/chebi/CHEBI:26714" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-bound DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Ca.CaBi">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_4">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_4">
<ro:part_of rdf:resource="#entity_1" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/chebi/CHEBI:30741" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-bound buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaDM1.koff_DM">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>dissociation rate constant of DM-nitrophen</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#environment.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#CaBi.koff_Bi">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>dissociation rate constant of buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#DM2.DM2">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of free DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.kon_DM">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>binding rate constant of DM-nitrophen</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#constants.kon_Bi">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>binding rate constant of buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaD.D">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of free calcium indicator dye</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#Bi.Bi">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of free buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#DM2.DM2">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_13">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of free DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Ca.CaD">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_1">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_2">
<ro:part_of rdf:resource="#entity_1" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/chebi/CHEBI:37958" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-dye complex</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#Ca.CaBi">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium-bound buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Bi.CaBi">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_24">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-bound buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#DM2_T.DM2_T">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>total concentration of DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#DM2_T.CaDM2">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium-bound DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaDM1.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#constants.t_pulse">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
<dcterms:description>point of flash pulse delivery</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaD.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#DM1.alpha">
<dcterms:description>fraction of DM-nitrophen photolysed by flash</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaDM1.Ca">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of free calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#DM1_T.CaDM1">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium-bound DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#constants.koff_DM">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>dissociation rate constant of DM-nitrophen</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#DM1_T.DM1">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of free DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#DM2_T.DM2">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of free DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#DM2.DM_T">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_14">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>total concentration of DM-nitrophen complex</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaD.Ca">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_32">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_0">
<ro:part_of rdf:resource="#entity_1" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/chebi/CHEBI:29108" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of free calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaD.Ca">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of free calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#D.CaD">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium-dye complex</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaDM2.Ca">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_29">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of free calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#DM1.alpha">
<dcterms:description>fraction of DM-nitrophen photolysed by flash</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#DM1.CaDM1">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium-bound DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#constants.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#CaBi.kon_Bi">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>binding rate constant of buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#nagerl_model_2000_version02" semsim:modelName="nagerl_novo_mody_vergara_2000" bqmodel:isDescribedBy="11106608">
<semsim:unknown>Nagerl et al's 2000 study of the binding kinetics of calbindin-D28k.</semsim:unknown>
<semsim:modelName>nagerl_novo_mody_vergara_2000_version01</semsim:modelName>
</rdf:Description>
<rdf:Description rdf:about="#constants.k_trans">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>transitional dissociation rate constant of photolysis reaction</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaDM1.t_pulse">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
<dcterms:description>point of flash pulse delivery</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#constants.kon_D">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>binding rate constant of OGB-5N indicator</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaDM1.t_pulse">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
<dcterms:description>point of flash pulse delivery</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaDM2.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#CaDM2.DM2">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_30">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of free DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaDM1.k_trans">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>transitional dissociation rate constant of photolysis reaction</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaBi.Ca">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of free calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaDM1.koff_DM">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>dissociation rate constant of DM-nitrophen</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaDM1.CaDM1">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_25">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-bound DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#Ca.CaD">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium-dye complex</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#DM2.DM_T">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>total concentration of DM-nitrophen complex</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#DM1.DM_T">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_8">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>total concentration of DM-nitrophen complex</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaDM2.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#DM2.CaDM2">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium-bound DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaBi.Ca">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_35">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of free calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaD.koff_D">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>dissociation rate constant of OGB-5N indicator</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#D.D_T">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>total concentration of calcium indicator dye</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#DM1.CaDM1">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_9">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-bound DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaBi.Bi">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of free buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#DM1.DM1">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of free DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaBi.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#nagerl_model_2000_version02" bqmodel:isDescribedBy="11106608" />
<rdf:Description rdf:about="#CaDM1.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#Ca.CaDM2">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium-bound DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#constants.alpha">
<dcterms:description>fraction of DM-nitrophen photolysed by flash</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#DM1.DM1">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_7">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of free DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaDM2.CaDM2">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_28">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-bound DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaDM2.CaDM2">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium-bound DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#D.D_T">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_19">
<semsim:physicalPropertyOf rdf:resource="#entity_2" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>total concentration of calcium indicator dye</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.koff_DM_">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>dissociation rate constant of DM-nitrophen after photolysis</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaD.kon_D">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>binding rate constant of OGB-5N indicator</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#DM2.CaDM2">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_15">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-bound DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.koff_D">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>dissociation rate constant of OGB-5N indicator</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaDM1.Ca">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_26">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of free calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaDM2.kon_DM">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>binding rate constant of DM-nitrophen</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#D.D">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of free calcium indicator dye</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#constants.koff_D">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>dissociation rate constant of OGB-5N indicator</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaDM1.k_trans">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>transitional dissociation rate constant of photolysis reaction</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaDM1.kon_DM">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>binding rate constant of DM-nitrophen</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#Ca.CaDM1">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium-bound DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Ca.Ca">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_0">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of free calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#DM2_T.DM2">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_17">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of free DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaBi.Bi">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_36">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of free buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaDM2.DM2">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of free DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaDM2.Ca">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of free calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaBi.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#CaBi.CaBi">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_34">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-bound buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaDM1.DM1">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of free DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Ca.Ca_T">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_5">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of total calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Bi.Bi">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_23">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of free buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.kon_D">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>binding rate constant of OGB-5N indicator</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaD.kon_D">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>binding rate constant of OGB-5N indicator</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#DM2_T.CaDM2">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_18">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-bound DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaDM1.CaDM1">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium-bound DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#DM1_T.DM1">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_11">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of free DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#D.CaD">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_21">
<semsim:physicalPropertyOf rdf:resource="#entity_2" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-dye complex</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#DM1_T.CaDM1">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_12">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-bound DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#DM1.DM_T">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>total concentration of DM-nitrophen complex</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#Bi.CaBi">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium-bound buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#environment.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#CaDM1.DM1">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_27">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of free DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaD.koff_D">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>dissociation rate constant of OGB-5N indicator</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaDM1.kon_DM">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>binding rate constant of DM-nitrophen</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaD.D">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_33">
<semsim:physicalPropertyOf rdf:resource="#entity_2" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of free calcium indicator dye</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaBi.kon_Bi">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>binding rate constant of buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#D.D">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_20">
<semsim:physicalPropertyOf rdf:resource="#entity_2" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of free calcium indicator dye</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaD.time">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaBi.CaBi">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium-bound buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#constants.koff_DM_">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>dissociation rate constant of DM-nitrophen after photolysis</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#constants.koff_Bi">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>dissociation rate constant of buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Bi.Bi_T">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_22">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>total concentration of buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.koff_Bi">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>dissociation rate constant of buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaDM2.kon_DM">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>binding rate constant of DM-nitrophen</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.tau_photolysis">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
<dcterms:description>time constant of photolysis reaction</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.alpha">
<dcterms:description>fraction of DM-nitrophen photolysed by flash</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#DM2_T.DM2_T">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_16">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>total concentration of DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#Ca.Ca_T">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of total calcium</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.koff_DM">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>dissociation rate constant of DM-nitrophen</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaBi.koff_Bi">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>dissociation rate constant of buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#constants.tau_photolysis">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
<dcterms:description>time constant of photolysis reaction</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#DM1_T.DM1_T">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_10">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>total concentration of DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaD.CaD">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of calcium-dye complex</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#constants.k_trans">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>transitional dissociation rate constant of photolysis reaction</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#DM1_T.DM1_T">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>total concentration of DM-nitrophen complex to be photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#DM2.alpha">
<dcterms:description>fraction of DM-nitrophen photolysed by flash</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Ca.CaDM2">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_3">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-bound DM-nitrophen complex not photolysed</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#DM_T.DM_T">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_6">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>total concentration of DM-nitrophen complex</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.t_pulse">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01023" />
<dcterms:description>point of flash pulse delivery</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#DM2.alpha">
<dcterms:description>fraction of DM-nitrophen photolysed by flash</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaDM2.koff_DM">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>dissociation rate constant of DM-nitrophen</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#constants.kon_Bi">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>binding rate constant of buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#constants.kon_DM">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>binding rate constant of DM-nitrophen</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#CaDM2.koff_DM">
<bqbiol:is rdf:resource="https://identifiers.org/opb/OPB_01296" />
<dcterms:description>dissociation rate constant of DM-nitrophen</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#Bi.Bi_T">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>total concentration of buffer</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#CaD.CaD">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_31">
<semsim:physicalPropertyOf rdf:resource="#entity_2" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of calcium-dye complex</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="nagerl_novo_mody_vergara_2000.cellml#Ca.Ca">
<bqbiol:isPropertyOf rdf:resource="nagerl_novo_mody_vergara_2000.cellml#entity_0" />
<dcterms:description>concentration of free calcium</dcterms:description>
</rdf:Description>
</rdf:RDF>
</model>
