- Author:
- Soroush Safaei <ssaf006@aucklanduni.ac.nz>
- Date:
- 2019-03-14 13:40:39+13:00
- Desc:
- restructuring
- Permanent Source URI:
- http://models.cellml.org/workspace/4bd/rawfile/8e9f1939f29abbc0acf4eda45d6836503466f20d/bondgraph/Neurotransmitter_module_Mn1.cellml
<?xml version='1.0'?>
<model name="Neurotransmitter_module" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:xlink="http://www.w3.org/1999/xlink">
<import xlink:href="Units.cellml">
<units name="amount" units_ref="amount"/>
<units name="per_sec" units_ref="per_sec"/>
<units name="amount_per_sec" units_ref="amount_per_sec"/>
</import>
<component name="Neuron">
<variable name="t" public_interface="in" units="second"/>
<variable name="glu" public_interface="in" units="amount"/>
<variable initial_value="0" name="Ca_Neuro" units="amount"/>
<variable initial_value="0" name="NO" public_interface="out" units="amount"/>
<variable initial_value="0" name="cGMP" public_interface="out" units="amount"/>
<variable initial_value="0" name="S1_cGMP" units="amount"/>
<variable initial_value="0" name="S2_cGMP" units="amount"/>
<variable initial_value="0" name="S3_cGMP" units="amount"/>
<variable name="Glutamate_N" units="amount_per_sec"/>
<variable name="calcium_Neuro1" units="amount_per_sec"/>
<variable name="calcium_Neuro2" units="amount_per_sec"/>
<variable name="NO_cGMP" units="amount_per_sec"/>
<variable name="sink_NO" units="amount_per_sec"/>
<variable name="v1_cGMP" units="amount_per_sec"/>
<variable name="v2_cGMP" units="amount_per_sec"/>
<variable name="v3_cGMP" units="amount_per_sec"/>
<variable name="cGMP_sink" units="amount_per_sec"/>
<!-- parameters-->
<variable initial_value="3.3634" name="k_3" public_interface="out" units="per_sec"/>
<variable initial_value="1.0993" name="k_10" public_interface="out" units="per_sec"/>
<variable initial_value="4.8221e5" name="k_11" public_interface="out" units="per_sec"/>
<variable initial_value="2.5067" name="k_21" public_interface="out" units="per_sec"/>
<variable initial_value="1.7921" name="k_22" public_interface="out" units="per_sec"/>
<variable initial_value="1.5562e5" name="k_23" public_interface="out" units="per_sec"/>
<variable initial_value="1.4943" name="Ca_Nbas" public_interface="out" units="amount_per_sec"/>
<variable initial_value="1.0735" name="NO_sink" public_interface="out" units="per_sec"/>
<variable initial_value="0.9493" name="sink_N" public_interface="out" units="per_sec"/>
<variable initial_value="6.7692e5" name="sink_C" public_interface="out" units="per_sec"/>
<!-- calcium influx in the neuron-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>Glutamate_N</ci>
<apply>
<times/>
<ci>k_3</ci>
<ci>glu</ci>
</apply>
</apply>
<!-- calcium outflux in the neuron-->
<apply>
<eq/>
<ci>calcium_Neuro1</ci>
<apply>
<times/>
<ci>Ca_Neuro</ci>
<ci>sink_N</ci>
</apply>
</apply>
<!-- calcium induced NO-->
<apply>
<eq/>
<ci>calcium_Neuro2</ci>
<apply>
<times/>
<ci>k_10</ci>
<ci>Ca_Neuro</ci>
</apply>
</apply>
<!-- NO induced cGMP-->
<apply>
<eq/>
<ci>NO_cGMP</ci>
<apply>
<times/>
<ci>k_11</ci>
<ci>NO</ci>
</apply>
</apply>
<!-- NO breakdown-->
<apply>
<eq/>
<ci>sink_NO</ci>
<apply>
<times/>
<ci>NO_sink</ci>
<ci>NO</ci>
</apply>
</apply>
<!-- delay state reactions-->
<apply>
<eq/>
<ci>v1_cGMP</ci>
<apply>
<times/>
<ci>k_21</ci>
<ci>S1_cGMP</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v2_cGMP</ci>
<apply>
<times/>
<ci>k_22</ci>
<ci>S2_cGMP</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v3_cGMP</ci>
<apply>
<times/>
<ci>k_23</ci>
<ci>S3_cGMP</ci>
</apply>
</apply>
<!-- cGMP breakdown-->
<apply>
<eq/>
<ci>cGMP_sink</ci>
<apply>
<times/>
<ci>cGMP</ci>
<ci>sink_C</ci>
</apply>
</apply>
<!-- calcium influx in the neuron-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>Ca_Neuro</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>Glutamate_N</ci>
<ci>calcium_Neuro1</ci>
</apply>
<ci>Ca_Nbas</ci>
</apply>
</apply>
<!-- change in NO level-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>NO</ci>
</apply>
<apply>
<minus/>
<ci>calcium_Neuro2</ci>
<ci>sink_NO</ci>
</apply>
</apply>
<!-- cGMP effecting the blood vesels-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>cGMP</ci>
</apply>
<apply>
<minus/>
<ci>v3_cGMP</ci>
<ci>cGMP_sink</ci>
</apply>
</apply>
<!-- delay states-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>S1_cGMP</ci>
</apply>
<apply>
<minus/>
<ci>NO_cGMP</ci>
<ci>v1_cGMP</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>S2_cGMP</ci>
</apply>
<apply>
<minus/>
<ci>v1_cGMP</ci>
<ci>v2_cGMP</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>S3_cGMP</ci>
</apply>
<apply>
<minus/>
<ci>v2_cGMP</ci>
<ci>v3_cGMP</ci>
</apply>
</apply>
</math>
</component>
<component name="Astrocyte">
<variable name="t" public_interface="in" units="second"/>
<variable name="glu" public_interface="in" units="amount"/>
<variable initial_value="0" name="Ca_Astro" units="amount"/>
<variable initial_value="0" name="AA" units="amount"/>
<variable name="NO" public_interface="in" units="amount"/>
<variable initial_value="0" name="HETE" public_interface="out" units="amount"/>
<variable initial_value="0" name="S1_HETE" units="amount"/>
<variable initial_value="0" name="S2_HETE" units="amount"/>
<variable initial_value="0" name="S3_HETE" units="amount"/>
<variable initial_value="0" name="PG" public_interface="out" units="amount"/>
<variable initial_value="0" name="S1_PG" units="amount"/>
<variable initial_value="0" name="S2_PG" units="amount"/>
<variable initial_value="0" name="S3_PG" units="amount"/>
<variable initial_value="0" name="EET" public_interface="out" units="amount"/>
<variable initial_value="0" name="S1_EET" units="amount"/>
<variable initial_value="0" name="S2_EET" units="amount"/>
<variable initial_value="0" name="S3_EET" units="amount"/>
<variable name="Glutamate_A" units="amount_per_sec"/>
<variable name="calcium_Astro1" units="amount_per_sec"/>
<variable name="calcium_Astro2" units="amount_per_sec"/>
<variable name="AA_HETE" units="amount_per_sec"/>
<variable name="AA_PG" units="amount_per_sec"/>
<variable name="AA_EET" units="amount_per_sec"/>
<variable name="v1_HETE" units="amount_per_sec"/>
<variable name="v2_HETE" units="amount_per_sec"/>
<variable name="v3_HETE" units="amount_per_sec"/>
<variable name="HETE_sink" units="amount_per_sec"/>
<variable name="v1_PG" units="amount_per_sec"/>
<variable name="v2_PG" units="amount_per_sec"/>
<variable name="v3_PG" units="amount_per_sec"/>
<variable name="PG_sink" units="amount_per_sec"/>
<variable name="v1_EET" units="amount_per_sec"/>
<variable name="v2_EET" units="amount_per_sec"/>
<variable name="v3_EET" units="amount_per_sec"/>
<variable name="EET_sink" units="amount_per_sec"/>
<!-- parameters-->
<variable initial_value="0.053036" name="k_2" public_interface="out" units="per_sec"/>
<variable initial_value="1.6775" name="k_4" public_interface="out" units="per_amount_per_sec"/>
<variable initial_value="0.43467" name="k_5" public_interface="out" units="amount_per_sec"/>
<variable initial_value="5.892e7" name="k_6" public_interface="out" units="per_sec"/>
<variable initial_value="1.7891" name="k_7" public_interface="out" units="amount_per_sec"/>
<variable initial_value="1.0276" name="k_8" public_interface="out" units="dimensionless"/>
<variable initial_value="2.8976" name="k_9" public_interface="out" units="dimensionless"/>
<variable initial_value="6.3353e8" name="k_12" public_interface="out" units="per_sec"/>
<variable initial_value="0.87781" name="k_13" public_interface="out" units="per_sec"/>
<variable initial_value="1.0343" name="k_14" public_interface="out" units="per_sec"/>
<variable initial_value="2.1986" name="k_15" public_interface="out" units="per_sec"/>
<variable initial_value="0.8836" name="k_16" public_interface="out" units="per_sec"/>
<variable initial_value="1.2209" name="k_17" public_interface="out" units="per_sec"/>
<variable initial_value="0.6518" name="k_18" public_interface="out" units="per_sec"/>
<variable initial_value="0.9190" name="k_19" public_interface="out" units="per_sec"/>
<variable initial_value="7.5887e7" name="k_20" public_interface="out" units="per_sec"/>
<variable initial_value="5.5066e6" name="km_1" public_interface="out" units="amount"/>
<variable initial_value="0.0433" name="km_2" public_interface="out" units="amount"/>
<variable initial_value="3.3823e7" name="Ca_Abas" public_interface="out" units="amount_per_sec"/>
<variable initial_value="1.3426" name="sink_A" public_interface="out" units="per_sec"/>
<variable initial_value="5.7961e7" name="sink_H" public_interface="out" units="per_sec"/>
<variable initial_value="0.9134" name="sink_P" public_interface="out" units="per_sec"/>
<variable initial_value="0.7554" name="sink_E" public_interface="out" units="per_sec"/>
<variable initial_value="945.52" name="PL" public_interface="out" units="amount"/>
<!-- calcium influx in the astrocyte-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>Glutamate_A</ci>
<apply>
<times/>
<ci>k_2</ci>
<ci>glu</ci>
</apply>
</apply>
<!-- calcium outflux in the astrocyte-->
<apply>
<eq/>
<ci>calcium_Astro1</ci>
<apply>
<times/>
<ci>Ca_Astro</ci>
<ci>sink_A</ci>
</apply>
</apply>
<!-- calcium induced AA-->
<apply>
<eq/>
<ci>calcium_Astro2</ci>
<apply>
<times/>
<ci>PL</ci>
<ci>Ca_Astro</ci>
<ci>k_4</ci>
</apply>
</apply>
<!-- AA turning into HETE-->
<apply>
<eq/>
<ci>AA_HETE</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>k_5</ci>
<ci>AA</ci>
</apply>
<apply>
<plus/>
<ci>km_1</ci>
<apply>
<times/>
<ci>k_8</ci>
<ci>NO</ci>
</apply>
</apply>
</apply>
</apply>
<!-- AA turning into PG-->
<apply>
<eq/>
<ci>AA_PG</ci>
<apply>
<times/>
<ci>k_6</ci>
<ci>AA</ci>
</apply>
</apply>
<!-- AA turning into EET-->
<apply>
<eq/>
<ci>AA_EET</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>k_7</ci>
<ci>AA</ci>
</apply>
<apply>
<plus/>
<ci>km_2</ci>
<apply>
<times/>
<ci>k_9</ci>
<ci>NO</ci>
</apply>
</apply>
</apply>
</apply>
<!-- delay state reactions-->
<apply>
<eq/>
<ci>v1_HETE</ci>
<apply>
<times/>
<ci>k_12</ci>
<ci>S1_HETE</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v2_HETE</ci>
<apply>
<times/>
<ci>k_13</ci>
<ci>S2_HETE</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v3_HETE</ci>
<apply>
<times/>
<ci>k_14</ci>
<ci>S3_HETE</ci>
</apply>
</apply>
<!-- HETE breakdown-->
<apply>
<eq/>
<ci>HETE_sink</ci>
<apply>
<times/>
<ci>HETE</ci>
<ci>sink_H</ci>
</apply>
</apply>
<!-- delay state reactions-->
<apply>
<eq/>
<ci>v1_PG</ci>
<apply>
<times/>
<ci>k_15</ci>
<ci>S1_PG</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v2_PG</ci>
<apply>
<times/>
<ci>k_16</ci>
<ci>S2_PG</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v3_PG</ci>
<apply>
<times/>
<ci>k_17</ci>
<ci>S3_PG</ci>
</apply>
</apply>
<!-- PG breakdown-->
<apply>
<eq/>
<ci>PG_sink</ci>
<apply>
<times/>
<ci>PG</ci>
<ci>sink_P</ci>
</apply>
</apply>
<!-- delay state reactions-->
<apply>
<eq/>
<ci>v1_EET</ci>
<apply>
<times/>
<ci>k_18</ci>
<ci>S1_EET</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v2_EET</ci>
<apply>
<times/>
<ci>k_19</ci>
<ci>S2_EET</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v3_EET</ci>
<apply>
<times/>
<ci>k_20</ci>
<ci>S3_EET</ci>
</apply>
</apply>
<!-- EET breakdown-->
<apply>
<eq/>
<ci>EET_sink</ci>
<apply>
<times/>
<ci>EET</ci>
<ci>sink_E</ci>
</apply>
</apply>
<!-- calcium influx in the astrocyte-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>Ca_Astro</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>Glutamate_A</ci>
<ci>calcium_Astro1</ci>
</apply>
<ci>Ca_Abas</ci>
</apply>
</apply>
<!-- change in AA level-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>AA</ci>
</apply>
<apply>
<minus/>
<ci>calcium_Astro2</ci>
<apply>
<plus/>
<ci>AA_HETE</ci>
<ci>AA_PG</ci>
<ci>AA_EET</ci>
</apply>
</apply>
</apply>
<!-- HETE effecting the blood vessels-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>HETE</ci>
</apply>
<apply>
<minus/>
<ci>v3_HETE</ci>
<ci>HETE_sink</ci>
</apply>
</apply>
<!-- delay states-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>S1_HETE</ci>
</apply>
<apply>
<minus/>
<ci>AA_HETE</ci>
<ci>v1_HETE</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>S2_HETE</ci>
</apply>
<apply>
<minus/>
<ci>v1_HETE</ci>
<ci>v2_HETE</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>S3_HETE</ci>
</apply>
<apply>
<minus/>
<ci>v2_HETE</ci>
<ci>v3_HETE</ci>
</apply>
</apply>
<!-- PG effecting blood vessels-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>PG</ci>
</apply>
<apply>
<minus/>
<ci>v3_PG</ci>
<ci>PG_sink</ci>
</apply>
</apply>
<!-- delay states-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>S1_PG</ci>
</apply>
<apply>
<minus/>
<ci>AA_PG</ci>
<ci>v1_PG</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>S2_PG</ci>
</apply>
<apply>
<minus/>
<ci>v1_PG</ci>
<ci>v2_PG</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>S3_PG</ci>
</apply>
<apply>
<minus/>
<ci>v2_PG</ci>
<ci>v3_PG</ci>
</apply>
</apply>
<!-- EET effeting the blood vessels-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>EET</ci>
</apply>
<apply>
<minus/>
<ci>v3_EET</ci>
<ci>EET_sink</ci>
</apply>
</apply>
<!-- delay states-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>S1_EET</ci>
</apply>
<apply>
<minus/>
<ci>AA_EET</ci>
<ci>v1_EET</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>S2_EET</ci>
</apply>
<apply>
<minus/>
<ci>v1_EET</ci>
<ci>v2_EET</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>S3_EET</ci>
</apply>
<apply>
<minus/>
<ci>v2_EET</ci>
<ci>v3_EET</ci>
</apply>
</apply>
</math>
</component>
</model>
