Location: SLC transporters @ a70688f8c9b0 / Facilitated transporter / CellMLV2 / params_BG_fit.cellml

Author:

Weiwei Ai <wai484@aucklanduni.ac.nz>

Date:

2024-04-03 14:25:12+13:00

Desc:

Add volume factor for full BG params and re-run the simulation

Permanent Source URI:

https://models.physiomeproject.org/workspace/b65/rawfile/a70688f8c9b0f3e6f14c008fb76adfbb445b095c/Facilitated transporter/CellMLV2/params_BG_fit.cellml

<?xml version="1.0" encoding="UTF-8"?>
<model xmlns="http://www.cellml.org/cellml/2.0#" name="params_BG">
  <import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="units.cellml">
    <units units_ref="fmol_per_s" name="fmol_per_s"/>
    <units units_ref="J_per_K_mol" name="J_per_K_mol"/>
    <units units_ref="per_fmol" name="per_fmol"/>
    <units units_ref="fmol" name="fmol"/>
    <units units_ref="per_s" name="per_s"/>
    <units units_ref="pL" name="pL"/>
    <units units_ref="uM" name="uM"/>
    <units units_ref="mM" name="mM"/>
  </import>
  <units name="per_fmol_s">
    <unit exponent="-1" units="fmol"/>
    <unit units="per_s"/>
  </units>
  <units name="amol">
    <unit prefix="atto" units="mole"/>
  </units>
  <component name="params_BG">
    <variable name="R" units="J_per_K_mol" initial_value="8.31" interface="public"/>
    <variable name="T" units="kelvin" initial_value="273.15" interface="public"/>
    <variable name="K_Ai" units="per_fmol" interface="public"/>
    <variable name="q_init_Ai" units="fmol" interface="public"/>
    <variable name="K_Ao" units="per_fmol" interface="public"/>
    <variable name="q_init_Ao" units="fmol" interface="public"/>
    <variable name="K_1" units="per_fmol" initial_value="1e-6" interface="public"/>
    <variable name="q_init_1" units="fmol" initial_value="0.1501" interface="public"/>
    <variable name="K_2" units="per_fmol" interface="public"/>
    <variable name="q_init_2" units="fmol" initial_value="0.1501" interface="public"/>
    <variable name="K_3" units="per_fmol" initial_value="1e-5" interface="public"/>
    <variable name="q_init_3" units="fmol" initial_value="0.1501" interface="public"/>
    <variable name="K_4" units="per_fmol" interface="public"/>
    <variable name="q_init_4" units="fmol" initial_value="0.1501" interface="public"/>
    <variable name="kappa_r1" units="fmol_per_s" interface="public"/>
    <variable name="kappa_r2" units="fmol_per_s" interface="public"/>
    <variable name="kappa_r3" units="fmol_per_s" interface="public"/>
    <variable name="kappa_r4" units="fmol_per_s" interface="public"/>
    <variable name="c" units="per_s" initial_value="1113"/>
    <variable name="d" units="per_s" initial_value="90.3"/>
    <variable name="g" units="per_s" initial_value="12.1"/>
    <variable name="h" units="per_s" initial_value="0.726"/>
    <variable name="a" units="per_fmol_s" initial_value="50"/>
    <variable name="b" units="per_s"/>
    <variable name="E" units="fmol" interface="public"/>
    <variable name="GC" units="uM" initial_value="6.67"/>
    <variable name="V_i" units="pL" initial_value="90"/>
    <variable name="g_i" units="mM" initial_value="10"/>
    <variable name="g_o" units="mM" initial_value="1e-8"/>
    <variable name="V_o" units="pL" initial_value="90" interface="public"/>
    <math xmlns="http://www.w3.org/1998/Math/MathML" xmlns:cellml="http://www.cellml.org/cellml/2.0#">
      <apply>
        <eq/>
        <ci>K_2</ci>
        <apply>
          <divide/>
          <apply>
            <times/>
            <ci>K_3</ci>
            <ci>c</ci>
          </apply>
          <ci>d</ci>
        </apply>
      </apply>
      <apply>
        <eq/>
        <ci>K_4</ci>
        <apply>
          <divide/>
          <apply>
            <times/>
            <ci>K_1</ci>
            <ci>h</ci>
          </apply>
          <ci>g</ci>
        </apply>
      </apply>
      <apply>
        <eq/>
        <ci>K_Ao</ci>
        <apply>
          <divide/>
          <apply>
            <times/>
            <apply>
              <divide/>
              <ci>K_2</ci>
              <ci>K_1</ci>
            </apply>
            <ci>a</ci>
          </apply>
          <ci>b</ci>
        </apply>
      </apply>
      <apply>
        <eq/>
        <ci>b</ci>
        <apply>
          <times/>
          <cn cellml:units="mM">9.5</cn>
          <ci>V_o</ci>
          <ci>a</ci>
        </apply>
      </apply>
      <apply>
        <eq/>
        <ci>K_Ai</ci>
        <ci>K_Ao</ci>
      </apply>
      <apply>
        <eq/>
        <ci>kappa_r1</ci>
        <apply>
          <divide/>
          <ci>h</ci>
          <ci>K_4</ci>
        </apply>
      </apply>
      <apply>
        <eq/>
        <ci>kappa_r2</ci>
        <apply>
          <divide/>
          <ci>c</ci>
          <ci>K_2</ci>
        </apply>
      </apply>
      <apply>
        <eq/>
        <ci>kappa_r3</ci>
        <apply>
          <divide/>
          <ci>b</ci>
          <ci>K_2</ci>
        </apply>
      </apply>
      <apply>
        <eq/>
        <ci>kappa_r4</ci>
        <apply>
          <times/>
          <cn cellml:units="dimensionless">1</cn>
          <ci>kappa_r3</ci>
        </apply>
      </apply>
      <apply>
        <eq/>
        <ci>E</ci>
        <apply>
          <divide/>
          <apply>
            <times/>
            <ci>GC</ci>
            <ci>V_i</ci>
            <cn cellml:units="fmol">1</cn>
          </apply>
          <cn cellml:units="amol">1000</cn>
        </apply>
      </apply>
      <apply>
        <eq/>
        <ci>q_init_Ao</ci>
        <apply>
          <times/>
          <ci>g_o</ci>
          <ci>V_o</ci>
        </apply>
      </apply>
      <apply>
        <eq/>
        <ci>q_init_Ai</ci>
        <apply>
          <times/>
          <ci>g_i</ci>
          <ci>V_i</ci>
        </apply>
      </apply>
    </math>
  </component>
</model>