- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-06-17 11:26:02+12:00
- Desc:
- Init
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/8a9/rawfile/2ed0fcabd9b78ca5eaa4a4fd477aee7f02ba3c84/FCU_AP_and_FCU_EC_smalltest.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="FCU_AP_and_FCU_EC_small" 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_and_constants/units_BG.cellml">
<units name="mM" units_ref="mM"/>
<units name="fmol" units_ref="fmol"/>
<units name="per_fmol" units_ref="per_fmol"/>
<units name="J_per_mol" units_ref="J_per_mol"/>
<units name="fmol_per_sec" units_ref="fmol_per_sec"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
<units name="J_per_C" units_ref="J_per_C"/>
<units name="microm3" units_ref="microm3"/>
<units name="fF" units_ref="fF"/>
<units name="fC" units_ref="fC"/>
<units name="fA" units_ref="fA"/>
<units name="per_second" units_ref="per_second"/>
<units name="millivolt" units_ref="millivolt"/>
<units name="per_sec" units_ref="per_sec"/>
<units name="J_per_K_per_mol" units_ref="J_per_K_per_mol"/>
<units name="fmol_per_L" units_ref="fmol_per_L"/>
<units name="fmol_per_L_per_sec" units_ref="fmol_per_L_per_sec"/>
<units name="per_sec_per_fmol_per_L" units_ref="per_sec_per_fmol_per_L"/>
<units name="uM" units_ref="uM"/>
<units name="mM_per_sec" units_ref="mM_per_sec"/>
<units name="uM_per_sec" units_ref="uM_per_sec"/>
<units name="pL" units_ref="pL"/>
<units name="m_to_u" units_ref="m_to_u"/>
</import>
<import xlink:href="units_and_constants/constants_BG.cellml">
<component component_ref="constants" name="constants"/>
</import>
<import xlink:href="FCU_AP/CaB/BG_CaB.cellml">
<component component_ref="CaB" name="CaB"/>
</import>
<import xlink:href="FCU_EC/crossbridge_TRPN/BG_crossbridge_TRPN.cellml">
<component component_ref="crossbridge_TRPN" name="crossbridge_TRPN"/>
</import>
<units name="m_per_s">
<unit units="metre"/>
<unit exponent="-1" units="second"/>
</units>
<component name="BG_parameters">
<variable initial_value="0.000469987" name="kappa_CaB" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="82.4067" name="kappa_R_TRPNCa" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="8.82154" name="kappa_R_BU" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.283765" name="kappa_R_UW" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.00667683" name="kappa_R_WS" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="120183" name="kappa_R_SU" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.624848" name="K_Ca_i" public_interface="out" units="per_fmol"/>
<variable initial_value="3.1158" name="K_Ca_o" public_interface="out" units="per_fmol"/>
<variable initial_value="28.8225" name="K_TRPN" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0469618" name="K_Ca_TRPN" public_interface="out" units="per_fmol"/>
<variable initial_value="9.45563" name="K_B_XB" public_interface="out" units="per_fmol"/>
<variable initial_value="3.54586" name="K_U_XB" public_interface="out" units="per_fmol"/>
<variable initial_value="23.1845" name="K_W_XB" public_interface="out" units="per_fmol"/>
<variable initial_value="5.79612e-06" name="K_S_XB" public_interface="out" units="per_fmol"/>
<variable initial_value="2" name="zCa" public_interface="out" units="dimensionless"/>
<variable initial_value="1" name="zK" public_interface="out" units="dimensionless"/>
<variable initial_value="0.5" name="nK" public_interface="out" units="dimensionless"/>
<variable initial_value="0.51923" name="z_fX" public_interface="out" units="dimensionless"/>
<variable initial_value="0" name="z_fXi" public_interface="out" units="dimensionless"/>
<variable initial_value="-0.73169" name="z_rX" public_interface="out" units="dimensionless"/>
<variable initial_value="0.83216" name="z_rXi" public_interface="out" units="dimensionless"/>
<variable initial_value="1.1" name="n_Tm" public_interface="out" units="dimensionless"/>
<variable initial_value="2" name="n_CaTRPN" public_interface="out" units="dimensionless"/>
</component>
<component name="environment">
<variable name="time" public_interface="out" units="second"/>
<variable initial_value="34.4" name="vol_myo" public_interface="out" units="pL"/>
<variable initial_value="153400" name="C_m" public_interface="out" units="fF"/>
<variable initial_value="0.005663912" name="q_Ca_i" public_interface="out" units="fmol"/>
<variable initial_value="9.327272727" name="q_Ca_o" public_interface="out" units="fmol"/>
<variable initial_value="0.763997897" name="q_Ca_SR" public_interface="out" units="fmol"/>
<variable initial_value="1.8088" name="q_CMDN" public_interface="out" units="fmol"/>
<variable initial_value="0.0912" name="q_CMDN_Ca" public_interface="out" units="fmol"/>
<variable initial_value="481.46" name="q_Na_i" public_interface="out" units="fmol"/>
<variable initial_value="725.48" name="q_Na_o" public_interface="out" units="fmol"/>
<variable initial_value="3980.455327" name="q_K_i" public_interface="out" units="fmol"/>
<variable initial_value="27.98181818" name="q_K_o" public_interface="out" units="fmol"/>
<variable initial_value="264.1" name="q_MgATP" public_interface="out" units="fmol"/>
<variable initial_value="1.33" name="q_MgADP" public_interface="out" units="fmol"/>
<variable initial_value="570" name="q_Pi" public_interface="out" units="fmol"/>
<variable initial_value="0.0030534" name="q_H" public_interface="out" units="fmol"/>
<variable initial_value="0.0032" name="q_pCa" public_interface="out" units="fmol"/>
<variable initial_value="1e-9" name="q_pCa_Ca" public_interface="out" units="fmol"/>
<variable initial_value="2.57" name="q_TRPN" public_interface="out" units="fmol"/>
<variable initial_value="0.51484" name="q_TRPN_Ca" public_interface="out" units="fmol"/>
<variable initial_value="3.68876E-07" name="q_Ca_D" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_Ca_TRPN" public_interface="out" units="fmol"/>
<variable initial_value="1" name="q_B_XB" public_interface="out" units="fmol"/>
<variable initial_value="0" name="q_U_XB" public_interface="out" units="fmol"/>
<variable initial_value="0" name="q_W_XB" public_interface="out" units="fmol"/>
<variable initial_value="0" name="q_S_XB" public_interface="out" units="fmol"/>
<variable initial_value="4.028E+00" name="q_PLB" public_interface="out" units="fmol"/>
<variable initial_value="2.234E-03" name="q_PKACI" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_PLB_PKACI" public_interface="out" units="fmol"/>
<variable initial_value="3.382E-02" name="q_PP1" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_PLBp_PP1" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_PLBp" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_PLBp_baseline" public_interface="out" units="fmol"/>
<variable initial_value="1.999E-03" name="q_Ip" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_Ip_PP1" public_interface="out" units="fmol"/>
<variable name="n_CaTRPN" public_interface="in" units="dimensionless"/>
<variable initial_value="-13039" name="q_mem" public_interface="out" units="fC"/>
<variable name="V_mem" public_interface="out" units="J_per_C"/>
<!-- gate species-->
<!-- CaB imports-->
<variable name="v_CaB" public_interface="in" units="fmol_per_sec"/>
<variable name="I_mem_CaB" public_interface="in" units="fA"/>
<!-- crossbridge_TRPN imports-->
<variable name="v_R_TRPNCa" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R_BU" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R_UW" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R_WS" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R_SU" public_interface="in" units="fmol_per_sec"/>
<variable name="Tension" public_interface="in" units="kPa"/>
<variable name="SL" public_interface="in" units="metre"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>V_mem</ci>
<apply>
<divide/>
<ci>q_mem</ci>
<ci>C_m</ci>
</apply>
</apply>
</math>
<variable name="I_stim" units="fA"/>
<variable initial_value="1" name="stimPeriod" units="second"/>
<variable initial_value="0.0001" name="stimDuration" units="second"/>
<variable name="tPeriod" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>tPeriod</ci>
<apply>
<minus/>
<ci>time</ci>
<apply>
<times/>
<apply>
<floor/>
<apply>
<divide/>
<ci>time</ci>
<ci>stimPeriod</ci>
</apply>
</apply>
<ci>stimPeriod</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>I_stim</ci>
<piecewise>
<piece>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="dimensionless">1</cn>
<cn cellml:units="volt">0.075</cn>
<ci>C_m</ci>
</apply>
<ci>stimDuration</ci>
</apply>
<apply>
<and/>
<apply>
<geq/>
<ci>tPeriod</ci>
<cn cellml:units="second">0.3</cn>
</apply>
<apply>
<leq/>
<ci>tPeriod</ci>
<apply>
<plus/>
<cn cellml:units="second">0.3</cn>
<ci>stimDuration</ci>
</apply>
</apply>
</apply>
</piece>
<otherwise>
<cn cellml:units="fA">0.0</cn>
</otherwise>
</piecewise>
</apply>
</math>
<!-- changing sarcomere length-->
<variable name="dSL" public_interface="out" units="m_per_s"/>
<variable initial_value="19e-6" name="V_max" units="m_per_s"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>dSL</ci>
<piecewise>
<piece>
<apply>
<times/>
<cn cellml:units="dimensionless">1</cn>
<ci>V_max</ci>
</apply>
<apply>
<lt/>
<ci>time</ci>
<cn cellml:units="second">0.06</cn>
</apply>
</piece>
<piece>
<apply>
<times/>
<apply>
<minus/>
<cn cellml:units="dimensionless">0.1</cn>
</apply>
<ci>V_max</ci>
</apply>
<apply>
<and/>
<apply>
<gt/>
<ci>time</ci>
<cn cellml:units="second">0.5</cn>
</apply>
<apply>
<lt/>
<ci>time</ci>
<cn cellml:units="second">1.1</cn>
</apply>
</apply>
</piece>
<otherwise>
<apply>
<times/>
<cn cellml:units="dimensionless">0</cn>
<ci>V_max</ci>
</apply>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Ca_i</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Ca_SR</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Ca_D</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Ca_o</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_CMDN</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_CMDN_Ca</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Na_i</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_K_i</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Na_o</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_K_o</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_MgATP</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_MgADP</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Pi</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_H</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_pCa</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_pCa_Ca</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_TRPN_Ca</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_TRPN</ci>
</apply>
<apply>
<minus/>
<ci>v_R_TRPNCa</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Ca_TRPN</ci>
</apply>
<ci>v_R_TRPNCa</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_B_XB</ci>
</apply>
<apply>
<minus/>
<ci>v_R_BU</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_U_XB</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>v_R_BU</ci>
<ci>v_R_UW</ci>
</apply>
<ci>v_R_SU</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_W_XB</ci>
</apply>
<apply>
<minus/>
<ci>v_R_UW</ci>
<ci>v_R_WS</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_S_XB</ci>
</apply>
<apply>
<minus/>
<ci>v_R_WS</ci>
<ci>v_R_SU</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_PLB</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_PKACI</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_PLB_PKACI</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_PP1</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_PLBp_PP1</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_PLBp</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Ip</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Ip_PP1</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_mem</ci>
</apply>
<ci>I_mem_CaB</ci>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="CaB"/>
<map_variables variable_1="time" variable_2="t"/>
<map_variables variable_1="q_Ca_i" variable_2="q_Ca_i"/>
<map_variables variable_1="q_Ca_o" variable_2="q_Ca_o"/>
<map_variables variable_1="v_CaB" variable_2="v_CaB"/>
<map_variables variable_1="q_mem" variable_2="q_mem"/>
<map_variables variable_1="V_mem" variable_2="V_mem"/>
<map_variables variable_1="I_mem_CaB" variable_2="I_mem_CaB"/>
</connection>
<connection>
<map_components component_1="environment" component_2="crossbridge_TRPN"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_TRPN" variable_2="q_TRPN"/>
<map_variables variable_1="q_Ca_i" variable_2="q_Ca_i"/>
<map_variables variable_1="q_Ca_TRPN" variable_2="q_Ca_TRPN"/>
<map_variables variable_1="q_B_XB" variable_2="q_B_XB"/>
<map_variables variable_1="q_U_XB" variable_2="q_U_XB"/>
<map_variables variable_1="q_W_XB" variable_2="q_W_XB"/>
<map_variables variable_1="q_S_XB" variable_2="q_S_XB"/>
<map_variables variable_1="v_R_TRPNCa" variable_2="v_R_TRPNCa"/>
<map_variables variable_1="v_R_BU" variable_2="v_R_BU"/>
<map_variables variable_1="v_R_UW" variable_2="v_R_UW"/>
<map_variables variable_1="v_R_WS" variable_2="v_R_WS"/>
<map_variables variable_1="v_R_SU" variable_2="v_R_SU"/>
<map_variables variable_1="Tension" variable_2="T_total"/>
<map_variables variable_1="SL" variable_2="SL"/>
<map_variables variable_1="dSL" variable_2="dSL"/>
</connection>
<connection>
<map_components component_1="environment" component_2="BG_parameters"/>
<map_variables variable_1="n_CaTRPN" variable_2="n_CaTRPN"/>
</connection>
<connection>
<map_components component_1="BG_parameters" component_2="CaB"/>
<map_variables variable_1="kappa_CaB" variable_2="kappa_CaB"/>
<map_variables variable_1="K_Ca_i" variable_2="K_Ca_i"/>
<map_variables variable_1="K_Ca_o" variable_2="K_Ca_o"/>
<map_variables variable_1="zCa" variable_2="zCa"/>
</connection>
<connection>
<map_components component_1="BG_parameters" component_2="crossbridge_TRPN"/>
<map_variables variable_1="kappa_R_TRPNCa" variable_2="kappa_R_TRPNCa"/>
<map_variables variable_1="kappa_R_BU" variable_2="kappa_R_BU"/>
<map_variables variable_1="kappa_R_UW" variable_2="kappa_R_UW"/>
<map_variables variable_1="kappa_R_WS" variable_2="kappa_R_WS"/>
<map_variables variable_1="kappa_R_SU" variable_2="kappa_R_SU"/>
<map_variables variable_1="K_TRPN" variable_2="K_TRPN"/>
<map_variables variable_1="K_Ca_i" variable_2="K_Ca_i"/>
<map_variables variable_1="K_Ca_TRPN" variable_2="K_Ca_TRPN"/>
<map_variables variable_1="K_B_XB" variable_2="K_B_XB"/>
<map_variables variable_1="K_U_XB" variable_2="K_U_XB"/>
<map_variables variable_1="K_W_XB" variable_2="K_W_XB"/>
<map_variables variable_1="K_S_XB" variable_2="K_S_XB"/>
<map_variables variable_1="n_Tm" variable_2="n_Tm"/>
<map_variables variable_1="n_CaTRPN" variable_2="n_CaTRPN"/>
</connection>
<connection>
<map_components component_1="constants" component_2="CaB"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
<map_variables variable_1="F" variable_2="F"/>
</connection>
<connection>
<map_components component_1="constants" component_2="crossbridge_TRPN"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>
