- Author:
- shawnm <shawnm@rocko.local>
- Date:
- 2025-06-03 15:47:26+12:00
- Desc:
- updated readme.rst
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/d28/rawfile/ee7c1be211c09cb9b1639edfc10505b89eae3510/Higgins_SERCA_to_PMCA_wVm_v1.cellml
<?xml version='1.0' encoding='UTF-8'?>
<!-- PMCA model from the Higgins, 2006 version here - https://www.cell.com/biophysj/fulltext/S0006-3495(06)71715-5
we abuse the BG_PMCA cellML code for building this mess, including the 'units' and 'constants' external files (make sure they in paths etc)-->
<model name="Higgins_PMCA" 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_Higgins.cellml">
<units name="mM" units_ref="mM"/>
<units name="uM" units_ref="uM"/>
<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="J_per_K_per_mol" units_ref="J_per_K_per_mol"/>
<units name="fmol_per_sec" units_ref="fmol_per_sec"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
<units name="pL" units_ref="pL"/>
<units name="fF" units_ref="fF"/>
<units name="fC" units_ref="fC"/>
<units name="fA" units_ref="fA"/>
</import>
<import xlink:href="units_and_constants/constants_BG.cellml">
<component component_ref="constants" name="constants"/>
</import>
<component name="environment">
<variable name="t" public_interface="out" units="second"/>
<!-- init-->
<!--this corresponds to 0.1162 uM from Tong, 2011 using 38 pL for cyt vol-->
<variable initial_value="0.0044156" name="q_Ca_i" public_interface="out" units="fmol"/>
<!--var q_Ca_i: fmol {init: 0.00001, pub: out};-->
<!--this corresponds to ca_ext from Tong, 2011 of 2500 mM-->
<variable initial_value="9500" name="q_Ca_ext" public_interface="out" units="fmol"/>
<!--var q_Ca_ext: fmol {init: 0.038, pub: out};-->
<!--this corresponds to ~200 uM given er_vol of 0.1*34pL -- roughly comparable to Higgins value(s)
Higgins uses fixed amounts of ADP, ATP, P set those below
var q_ADP: fmol {init: 1.3794, pub: out};
var q_ATP: fmol {init: 3.8, pub: out};-->
<!--altered to 1/4th each state
below state levels - note, if these are simply 1/4 may not work
instead use the Higgins constraint of P1 + P2 + (1/gamma)*(P3 + P4)
the external states are scaled by the volume ratio; if we set the total amount of pump protein to same value as Higgins:
Pt = 15 uM -> Pt = 15*uM_to_mM*1e-3*W_i*1e-12*1e15 = 0.57 fmol
then using gamma = 0.01 and setting P1 + P2 = 0.1, we get P3 & P4 = 0.00235
0.1 + (1/0.01)*(0.0047) = 0.57 fmol...-->
<variable initial_value="0.05" name="q_P1_PMCA" public_interface="out" units="fmol"/>
<variable initial_value="0.05" name="q_P2_PMCA" public_interface="out" units="fmol"/>
<variable initial_value="0.0024" name="q_P3_PMCA" public_interface="out" units="fmol"/>
<variable initial_value="0.0024" name="q_P4_PMCA" public_interface="out" units="fmol"/>
<!--var q_P_tot: amol {init: 1.0, pub: out};-->
</component>
<component name="PMCA_parameters">
<!--affinities
below with setting Kc=[K_MgATP 1]; and Nc with two rows, one for phosphates and one for Ca
Nc' = 0 0 0 0 0 0 -1 1 1 <-- phosphates
0 0 0 0 -1 1 0 0 0 <-- Ca2+-->
<variable initial_value="5.430482453404587e+05" name="K_P1_PMCA" public_interface="out" units="per_fmol"/>
<variable initial_value="1.941577749543757e+03" name="K_P2_PMCA" public_interface="out" units="per_fmol"/>
<variable initial_value="55.705521655592314" name="K_P3_PMCA" public_interface="out" units="per_fmol"/>
<variable initial_value="0.128936490014084" name="K_P4_PMCA" public_interface="out" units="per_fmol"/>
<variable initial_value="7.423867035246714" name="K_Ca_i" public_interface="out" units="per_fmol"/>
<variable initial_value="0.074238670352467" name="K_Ca_ext" public_interface="out" units="per_fmol"/>
<!--need K's for phosphates-->
<variable initial_value="3.293062720373533e+02" name="K_ATP" public_interface="out" units="per_fmol"/>
<variable initial_value="0.005705386792576" name="K_ADP" public_interface="out" units="per_fmol"/>
<variable initial_value="0.005705386792576" name="K_Pi" public_interface="out" units="per_fmol"/>
<!--reaction rates-->
<variable initial_value="3.886341077574537e+05" name="kappa_PMCA_R1_2" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="2.868327520105214e-08" name="kappa_PMCA_R2_3" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="1.795154179118259e+10" name="kappa_PMCA_R3_4" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="37.843899707752300" name="kappa_PMCA_R4_1" public_interface="out" units="fmol_per_sec"/>
<!--set q's for phosphates-->
<!--var q_ATP: fmol {init: 114, pub: out};-->
<variable initial_value="0.38" name="q_ADP" public_interface="out" units="fmol"/>
<!--var q_Pi: fmol {init: 114, pub: out};-->
<!--below calculated via ss to get ca_cyt_i target of 0.1162 uM-->
<variable initial_value="194.6056" name="q_ATP" public_interface="out" units="fmol"/>
<variable initial_value="28.7888" name="q_Pi" public_interface="out" units="fmol"/>
<!--below number is from Luo and Rudy's value for 'capacitative membrane area, Vcap' of
1.534e-4 cm^2; that combined with the standard 1 uF/cm^2 gets you 1.534e5 fF below
none of this explained in Pan, 2018 other than citing the area number-->
<variable initial_value="153400" name="C_m" public_interface="out" units="fF"/>
<!--z for Ca2+ electrogenic transport-->
<variable initial_value="-2" name="z" public_interface="out" units="dimensionless"/>
<!--converted to C/mol
var zF: C_per_mol;-->
<!--zF = z*F;-->
<!--below corresponds to Vm = -85 mV
var q_mem: fC {init: -13039, pub: out};
below to -54 mV-->
<variable initial_value="-8.2836e+03" name="q_mem" public_interface="out" units="fC"/>
<!--below to 20 mV-->
<!--var q_mem: fC {init: 3068, pub: out};-->
<!--below to 0 mV
var q_mem: fC {init: 0, pub: out};-->
</component>
<component name="PMCA">
<!-- Physical parameters-->
<variable name="t" public_interface="in" units="second"/>
<variable name="R" public_interface="in" units="J_per_K_per_mol"/>
<variable name="T" public_interface="in" units="kelvin"/>
<variable name="F" public_interface="in" units="C_per_mol"/>
<!-- Bond graph parameters -->
<variable name="K_P1_PMCA" public_interface="in" units="per_fmol"/>
<variable name="K_P2_PMCA" public_interface="in" units="per_fmol"/>
<variable name="K_P3_PMCA" public_interface="in" units="per_fmol"/>
<variable name="K_P4_PMCA" public_interface="in" units="per_fmol"/>
<variable name="K_Ca_i" public_interface="in" units="per_fmol"/>
<variable name="K_Ca_ext" public_interface="in" units="per_fmol"/>
<!--need K's for phosphates-->
<variable name="K_ATP" public_interface="in" units="per_fmol"/>
<variable name="K_ADP" public_interface="in" units="per_fmol"/>
<variable name="K_Pi" public_interface="in" units="per_fmol"/>
<!--get q's for phosphates here since fixed-->
<variable name="q_ATP" public_interface="in" units="fmol"/>
<variable name="q_ADP" public_interface="in" units="fmol"/>
<variable name="q_Pi" public_interface="in" units="fmol"/>
<variable name="kappa_PMCA_R1_2" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_PMCA_R2_3" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_PMCA_R3_4" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_PMCA_R4_1" public_interface="in" units="fmol_per_sec"/>
<variable initial_value="1.5" name="n_Ca_i" units="dimensionless"/>
<variable initial_value="1.5" name="n_Ca_ext" units="dimensionless"/>
<!--below number is from Luo and Rudy's value for 'capacitative membrane area, Vcap' of
1.534e-4 cm^2; that combined with the standard 1 uF/cm^2 gets you 1.534e5 fF below
none of this explained in Pan, 2018 other than citing the area number-->
<variable name="C_m" public_interface="in" units="fF"/>
<variable name="z" public_interface="in" units="dimensionless"/>
<!--converted to C/mol-->
<variable name="zF" units="C_per_mol"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>zF</ci>
<apply>
<times/>
<ci>z</ci>
<ci>F</ci>
</apply>
</apply>
</math>
<!--qmem for Vmem tracking-->
<variable name="q_mem" public_interface="in" units="fC"/>
<variable name="V_mem" units="volt"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>V_mem</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="dimensionless">1</cn>
<ci>q_mem</ci>
</apply>
<ci>C_m</ci>
</apply>
</apply>
</math>
<!--var I_mem_NaK: fA {pub: out};-->
<!-- Input from global environment-->
<variable name="q_Ca_i" public_interface="in" units="fmol"/>
<variable name="q_Ca_ext" public_interface="in" units="fmol"/>
<!-- gate -->
<variable name="q_P1_PMCA" public_interface="in" units="fmol"/>
<variable name="q_P2_PMCA" public_interface="in" units="fmol"/>
<variable name="q_P3_PMCA" public_interface="in" units="fmol"/>
<variable name="q_P4_PMCA" public_interface="in" units="fmol"/>
<!--ratios q_Ca-->
<variable name="q_Ca_ratio" units="dimensionless"/>
<!-- Concentrations
note: Higgins gives umol / L; we likely need to check all dimensions in this thing...-->
<variable name="c_Ca_i" units="uM"/>
<variable name="c_Ca_ext" units="uM"/>
<variable initial_value="38.0" name="vol_i" units="pL"/>
<variable name="vol_ext" units="pL"/>
<!--steady-state ca ratio (as given by derivation in sage)
%from sagemath J_ss_pmca_from_serca_BG_wphosph_t3
cai_caext_ss_ratio_bg = (K_bg(6)/K_bg(5))*((K_bg(8)*K_bg(9)*q_adp*q_p)/(K_bg(7)*q_atp))^(2/3)-->
<variable name="q_Ca_ratio_analytic" units="dimensionless"/>
<!--q_Ca_ratio_analytic = K_Ca_ext/K_Ca_i*pow(K_ADP*K_Pi*q_ADP*q_Pi/(K_ATP*q_ATP), 0.6666666667{dimensionless});
below version with Vm term from sage notebokk pmca_from_higgins_Jss_BG_wVm-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>q_Ca_ratio_analytic</ci>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<times/>
<apply>
<divide/>
<cn cellml:units="dimensionless">2</cn>
<cn cellml:units="dimensionless">3</cn>
</apply>
<apply>
<divide/>
<ci>zF</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
<ci>q_mem</ci>
</apply>
<ci>C_m</ci>
</apply>
</apply>
<ci>K_Ca_ext</ci>
</apply>
<ci>K_Ca_i</ci>
</apply>
<apply>
<power/>
<apply>
<divide/>
<apply>
<times/>
<ci>K_ADP</ci>
<ci>K_Pi</ci>
<ci>q_ADP</ci>
<ci>q_Pi</ci>
</apply>
<apply>
<times/>
<ci>K_ATP</ci>
<ci>q_ATP</ci>
</apply>
</apply>
<cn cellml:units="dimensionless">0.6666666667</cn>
</apply>
</apply>
</apply>
<!--var vol_isr: pL;
just went with 100x cytosolic for now-->
<apply>
<eq/>
<ci>vol_ext</ci>
<apply>
<times/>
<ci>vol_i</ci>
<cn cellml:units="dimensionless">100</cn>
</apply>
</apply>
<!--vol_isr = vol_i+vol_ext;-->
<apply>
<eq/>
<ci>c_Ca_i</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="dimensionless">1000</cn>
<ci>q_Ca_i</ci>
</apply>
<ci>vol_i</ci>
</apply>
</apply>
<!--convert mM -> uM-->
<apply>
<eq/>
<ci>c_Ca_ext</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="dimensionless">1000</cn>
<ci>q_Ca_ext</ci>
</apply>
<ci>vol_ext</ci>
</apply>
</apply>
<!--ca ratio-->
<apply>
<eq/>
<ci>q_Ca_ratio</ci>
<apply>
<divide/>
<ci>q_Ca_i</ci>
<ci>q_Ca_ext</ci>
</apply>
</apply>
</math>
<!-- Constitutive equations-->
<variable name="mu_Ca_i" units="J_per_mol"/>
<variable name="v_Ca_i_PMCA" public_interface="out" units="fmol_per_sec"/>
<variable name="mu_Ca_SR" units="J_per_mol"/>
<variable name="V_Ca_Ext_PMCA" public_interface="out" units="fmol_per_sec"/>
<!--mu's for phosphates-->
<variable name="mu_ATP" units="J_per_mol"/>
<variable name="mu_ADP" units="J_per_mol"/>
<variable name="mu_Pi" units="J_per_mol"/>
<variable name="mu_P1" units="J_per_mol"/>
<variable name="v_P1" units="fmol_per_sec"/>
<variable name="mu_P2" units="J_per_mol"/>
<variable name="v_P2" units="fmol_per_sec"/>
<variable name="mu_P3" units="J_per_mol"/>
<variable name="v_P3" units="fmol_per_sec"/>
<variable name="mu_P4" units="J_per_mol"/>
<variable name="v_P4" units="fmol_per_sec"/>
<variable name="Af_R1_2" units="J_per_mol"/>
<variable name="Ar_R1_2" units="J_per_mol"/>
<variable name="Af_R2_3" units="J_per_mol"/>
<variable name="Ar_R2_3" units="J_per_mol"/>
<variable name="Af_R3_4" units="J_per_mol"/>
<variable name="Ar_R3_4" units="J_per_mol"/>
<variable name="Af_R4_1" units="J_per_mol"/>
<variable name="Ar_R4_1" units="J_per_mol"/>
<variable name="v_PMCA_R1_2" units="fmol_per_sec"/>
<variable name="v_PMCA_R2_3" units="fmol_per_sec"/>
<variable name="v_PMCA_R3_4" units="fmol_per_sec"/>
<variable name="v_PMCA_R4_1" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_Ca_i</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Ca_i</ci>
<ci>q_Ca_i</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Ca_SR</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Ca_ext</ci>
<ci>q_Ca_ext</ci>
</apply>
</apply>
</apply>
</apply>
<!--define mu's for phosphates-->
<apply>
<eq/>
<ci>mu_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_ATP</ci>
<ci>q_ATP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_ADP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_ADP</ci>
<ci>q_ADP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Pi</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Pi</ci>
<ci>q_Pi</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_P1</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_P1_PMCA</ci>
<ci>q_P1_PMCA</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_P2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_P2_PMCA</ci>
<ci>q_P2_PMCA</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_P3</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_P3_PMCA</ci>
<ci>q_P3_PMCA</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_P4</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_P4_PMCA</ci>
<ci>q_P4_PMCA</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>Af_R1_2</ci>
<apply>
<plus/>
<ci>mu_P1</ci>
<apply>
<times/>
<ci>n_Ca_i</ci>
<ci>mu_Ca_i</ci>
</apply>
</apply>
</apply>
<!--add in Vmem term here-->
<apply>
<eq/>
<ci>Ar_R1_2</ci>
<apply>
<plus/>
<ci>mu_P2</ci>
<apply>
<times/>
<ci>zF</ci>
<ci>V_mem</ci>
</apply>
</apply>
</apply>
<!--Ar_R1_2 = mu_P2;-->
<!--Af_R2_3 = mu_P2;
Af for +ATP-->
<apply>
<eq/>
<ci>Af_R2_3</ci>
<apply>
<plus/>
<ci>mu_P2</ci>
<ci>mu_ATP</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>Ar_R2_3</ci>
<ci>mu_P3</ci>
</apply>
<apply>
<eq/>
<ci>Af_R3_4</ci>
<ci>mu_P3</ci>
</apply>
<apply>
<eq/>
<ci>Ar_R3_4</ci>
<apply>
<plus/>
<ci>mu_P4</ci>
<apply>
<times/>
<ci>n_Ca_ext</ci>
<ci>mu_Ca_SR</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>Af_R4_1</ci>
<ci>mu_P4</ci>
</apply>
<!--Ar_R4_1 = mu_P1;
Ar for +ADP + Pi-->
<apply>
<eq/>
<ci>Ar_R4_1</ci>
<apply>
<plus/>
<ci>mu_P1</ci>
<ci>mu_ADP</ci>
<ci>mu_Pi</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v_PMCA_R1_2</ci>
<apply>
<times/>
<cn cellml:units="dimensionless">1</cn>
<ci>kappa_PMCA_R1_2</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>Af_R1_2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>Ar_R1_2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_PMCA_R2_3</ci>
<apply>
<times/>
<cn cellml:units="dimensionless">1</cn>
<ci>kappa_PMCA_R2_3</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>Af_R2_3</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>Ar_R2_3</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_PMCA_R3_4</ci>
<apply>
<times/>
<cn cellml:units="dimensionless">1</cn>
<ci>kappa_PMCA_R3_4</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>Af_R3_4</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>Ar_R3_4</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_PMCA_R4_1</ci>
<apply>
<times/>
<cn cellml:units="dimensionless">1</cn>
<ci>kappa_PMCA_R4_1</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>Af_R4_1</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>Ar_R4_1</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_Ca_i_PMCA</ci>
<apply>
<times/>
<apply>
<minus/>
<ci>n_Ca_i</ci>
</apply>
<ci>v_PMCA_R1_2</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>V_Ca_Ext_PMCA</ci>
<apply>
<times/>
<ci>n_Ca_ext</ci>
<ci>v_PMCA_R3_4</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v_P1</ci>
<apply>
<minus/>
<ci>v_PMCA_R4_1</ci>
<ci>v_PMCA_R1_2</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v_P2</ci>
<apply>
<minus/>
<ci>v_PMCA_R1_2</ci>
<ci>v_PMCA_R2_3</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v_P3</ci>
<apply>
<minus/>
<ci>v_PMCA_R2_3</ci>
<ci>v_PMCA_R3_4</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v_P4</ci>
<apply>
<minus/>
<ci>v_PMCA_R3_4</ci>
<ci>v_PMCA_R4_1</ci>
</apply>
</apply>
<!--state odes defined here-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_P1_PMCA</ci>
</apply>
<ci>v_P1</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_P2_PMCA</ci>
</apply>
<ci>v_P2</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_P3_PMCA</ci>
</apply>
<ci>v_P3</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_P4_PMCA</ci>
</apply>
<ci>v_P4</ci>
</apply>
<!--calcium odes-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_Ca_i</ci>
</apply>
<ci>v_Ca_i_PMCA</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_Ca_ext</ci>
</apply>
<ci>V_Ca_Ext_PMCA</ci>
</apply>
</math>
</component>
<connection>
<map_components component_1="constants" component_2="PMCA"/>
<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="environment" component_2="PMCA"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="q_Ca_i" variable_2="q_Ca_i"/>
<map_variables variable_1="q_Ca_ext" variable_2="q_Ca_ext"/>
<map_variables variable_1="q_P1_PMCA" variable_2="q_P1_PMCA"/>
<map_variables variable_1="q_P2_PMCA" variable_2="q_P2_PMCA"/>
<map_variables variable_1="q_P3_PMCA" variable_2="q_P3_PMCA"/>
<map_variables variable_1="q_P4_PMCA" variable_2="q_P4_PMCA"/>
<!--vars q_mem and q_mem;-->
</connection>
<connection>
<map_components component_1="PMCA_parameters" component_2="PMCA"/>
<map_variables variable_1="kappa_PMCA_R1_2" variable_2="kappa_PMCA_R1_2"/>
<map_variables variable_1="kappa_PMCA_R2_3" variable_2="kappa_PMCA_R2_3"/>
<map_variables variable_1="kappa_PMCA_R3_4" variable_2="kappa_PMCA_R3_4"/>
<map_variables variable_1="kappa_PMCA_R4_1" variable_2="kappa_PMCA_R4_1"/>
<map_variables variable_1="K_P1_PMCA" variable_2="K_P1_PMCA"/>
<map_variables variable_1="K_P2_PMCA" variable_2="K_P2_PMCA"/>
<map_variables variable_1="K_P3_PMCA" variable_2="K_P3_PMCA"/>
<map_variables variable_1="K_P4_PMCA" variable_2="K_P4_PMCA"/>
<map_variables variable_1="K_Ca_i" variable_2="K_Ca_i"/>
<map_variables variable_1="K_Ca_ext" variable_2="K_Ca_ext"/>
<map_variables variable_1="C_m" variable_2="C_m"/>
<map_variables variable_1="z" variable_2="z"/>
<!--add K's and q's for phosph-->
<map_variables variable_1="K_ATP" variable_2="K_ATP"/>
<map_variables variable_1="K_ADP" variable_2="K_ADP"/>
<map_variables variable_1="K_Pi" variable_2="K_Pi"/>
<map_variables variable_1="q_ATP" variable_2="q_ATP"/>
<map_variables variable_1="q_ADP" variable_2="q_ADP"/>
<map_variables variable_1="q_Pi" variable_2="q_Pi"/>
<map_variables variable_1="q_mem" variable_2="q_mem"/>
</connection>
</model>
