// Created by libAntimony v2.8.0
model *Smallbone2011_TrehaloseBiosynthesis()
// Compartments and Species:
compartment cell, medium;
species glc in cell, g1p in cell, g6p in cell, trh in cell, t6p in cell;
species udg in cell, $adp in cell, $atp in cell, $ppi in cell, $f6p in cell;
species $h in cell, $pho in cell, $udp in cell, $utp in cell, $h2o in cell;
species $glx in medium;
// Assignment Rules:
glc_change := log10(glc/glc_0);
g1p_change := log10(g1p/g1p_0);
g6p_change := log10(g6p/g6p_0);
trh_change := log10(trh/trh_0);
t6p_change := log10(t6p/t6p_0);
udg_change := log10(udg/udg_0);
// Reactions:
pgi: g6p -> $f6p; ((cell*pgi_shock^heat*pgi_Vmax)/pgi_Kg6p*(g6p - f6p/pgi_Keq))/(1 + g6p/pgi_Kg6p + f6p/pgi_Kf6p);
hxt: $glx -> glc; (cell*hxt_shock^heat*hxt_Vmax*(glx - glc))/hxt_Kglc/(1 + (glx + glc)/hxt_Kglc + (hxt_Ki*glx*glc)/hxt_Kglc^2);
hxk: glc + $atp => g6p + $adp + $h; ((cell*hxk_shock^heat*hxk_Vmax)/(hxk_Kglc*hxk_Katp)*(glc*atp - (g6p*adp)/hxk_Keq))/((1 + glc/hxk_Kglc + g6p/hxk_Kg6p + t6p/hxk_Kit6p)*(1 + atp/hxk_Katp + adp/hxk_Kadp));
pgm: g6p -> g1p; ((cell*pgm_shock^heat*pgm_Vmax)/pgm_Kg6p*(g6p - g1p/pgm_Keq))/(1 + g6p/pgm_Kg6p + g1p/pgm_Kg1p);
tpp: t6p + $h2o => trh + $pho; (cell*tpp_shock^heat*tpp_Vmax*t6p)/tpp_Kt6p/(1 + t6p/tpp_Kt6p);
tps: g6p + udg => t6p + $udp + $h; (cell*tps_activity*tps_shock^heat*tps_Vmax*g6p*udg)/(tps_Kg6p*tps_Kudg)/((1 + g6p/tps_Kg6p)*(1 + udg/tps_Kudg));
nth: trh + $h2o => 2glc; (cell*nth_shock^heat*nth_Vmax*trh)/nth_Ktrh/(1 + trh/nth_Ktrh);
ugp: g1p + $utp + $h => udg + $ppi; (cell*ugp_shock^heat*ugp_Vmax*utp*g1p)/(ugp_Kutp*ugp_Kg1p)/(ugp_Kiutp/ugp_Kutp + utp/ugp_Kutp + g1p/ugp_Kg1p + (utp*g1p)/(ugp_Kutp*ugp_Kg1p) + (ugp_Kiutp/ugp_Kutp*udg)/ugp_Kiudg + (g1p*udg)/(ugp_Kg1p*ugp_Kiudg));
// Species initializations:
glc = glc_0;
g1p = g1p_0;
g6p = g6p_0;
trh = trh_0;
t6p = t6p_0;
udg = udg_0;
adp = 1.282;
atp = 2.525;
ppi = ;
f6p = 0.625;
h = ;
pho = ;
udp = 0.2815;
utp = 0.6491;
h2o = ;
glx = 100;
// Compartment initializations:
cell = 1;
medium = 1;
// Variable initializations:
glc_0 = 0.09765;
glc_0 has mM;
g1p_0 = 0.1;
g1p_0 has mM;
g6p_0 = 2.675;
g6p_0 has mM;
trh_0 = 0.05;
trh_0 has mM;
t6p_0 = 0.02;
t6p_0 has mM;
udg_0 = 0.7;
udg_0 has mM;
heat = 0;
heat has dimensionless;
glc_change has dimensionless;
g1p_change has dimensionless;
g6p_change has dimensionless;
trh_change has dimensionless;
t6p_change has dimensionless;
udg_change has dimensionless;
pgi_Vmax = 1071;
pgi_Vmax has mM_per_min;
pgi_Kg6p = 1.4;
pgi_Kg6p has mM;
pgi_Kf6p = 0.29;
pgi_Kf6p has mM;
pgi_Keq = 0.3;
pgi_Keq has dimensionless;
pgi_shock = 1;
pgi_shock has dimensionless;
hxt_Vmax = 97.24;
hxt_Vmax has mM_per_min;
hxt_Kglc = 1.1918;
hxt_Kglc has mM;
hxt_Ki = 0.91;
hxt_Ki has dimensionless;
hxt_shock = 8;
hxt_shock has dimensionless;
hxk_Vmax = 289.6;
hxk_Vmax has mM_per_min;
hxk_Kglc = 0.08;
hxk_Kglc has mM;
hxk_Katp = 0.15;
hxk_Katp has mM;
hxk_Kg6p = 30;
hxk_Kg6p has mM;
hxk_Kadp = 0.23;
hxk_Kadp has mM;
hxk_Keq = 2000;
hxk_Keq has dimensionless;
hxk_Kit6p = 0.04;
hxk_Kit6p has mM;
hxk_shock = 8;
hxk_shock has dimensionless;
pgm_Vmax = 0.3545;
pgm_Vmax has mM_per_min;
pgm_Kg6p = 0.05;
pgm_Kg6p has mM;
pgm_Kg1p = 0.023;
pgm_Kg1p has mM;
pgm_Keq = 0.1667;
pgm_Keq has dimensionless;
pgm_shock = 16;
pgm_shock has dimensionless;
tpp_Vmax = 6.5;
tpp_Vmax has mM_per_min;
tpp_Kt6p = 0.5;
tpp_Kt6p has mM;
tpp_shock = 18;
tpp_shock has dimensionless;
tps_Vmax = 1.371;
tps_Vmax has mM_per_min;
tps_Kg6p = 3.8;
tps_Kg6p has mM;
tps_Kudg = 0.886;
tps_Kudg has mM;
tps_shock = 12;
tps_shock has dimensionless;
tps_activity = 1;
tps_activity has dimensionless;
nth_Vmax = 15.2;
nth_Vmax has mM_per_min;
nth_Ktrh = 2.99;
nth_Ktrh has mM;
nth_shock = 6;
nth_shock has dimensionless;
ugp_Vmax = 36.82;
ugp_Vmax has mM_per_min;
ugp_Kutp = 0.11;
ugp_Kutp has mM;
ugp_Kiutp = 0.11;
ugp_Kiutp has mM;
ugp_Kg1p = 0.32;
ugp_Kg1p has mM;
ugp_Kiudg = 0.0035;
ugp_Kiudg has mM;
ugp_shock = 16;
ugp_shock has dimensionless;
// Other declarations:
var glc_change, g1p_change, g6p_change, trh_change, t6p_change, udg_change;
const cell, medium, glc_0, g1p_0, g6p_0, trh_0, t6p_0, udg_0, heat;
// Unit definitions:
unit substance = 1e-3 mole;
unit time_unit = 60 second;
unit mM = 1e-3 mole / litre;
unit per_min = 1 / 60 second;
unit mM_per_min = 1e-3 mole / (litre * 60 second);
// Display Names:
substance is "mmol";
time_unit is "min";
per_min is "per min";
mM_per_min is "mM per min";
glc is "glucose";
g1p is "glucose 1-phosphate";
g6p is "glucose 6-phosphate";
trh is "trehalose";
t6p is "trehalose 6-phosphate";
udg is "UDP glucose";
adp is "ADP";
atp is "ATP";
ppi is "diphosphate";
f6p is "fructose 6-phosphate";
h is "H+";
pho is "phosphate";
udp is "UDP";
utp is "UTP";
h2o is "water";
glx is "glucose";
glc_change is "log10 change in glucose";
g1p_change is "log10 change in glucose 1-phosphate";
g6p_change is "log10 change in glucose 6-phosphate";
trh_change is "log10 change in trehalose";
t6p_change is "log10 change in trehalose 6-phosphate";
udg_change is "log10 change in UDP glucose";
pgi is "G6P isomerase";
hxt is "glucose transport";
hxk is "hexokinase";
pgm is "phosphoglucomutase";
tpp is "T6P phosphatase";
tps is "T6P synthase";
nth is "trehalase";
ugp is "UDP glucose phosphorylase";
end