// Created by libAntimony v2.8.0
model *Leloup1999_CircClock_periodic()
// Compartments and Species:
compartment Cell, compartment_0000002;
species P0 in Cell, T0 in Cell, P1 in Cell, T1 in Cell, P2 in Cell, T2 in Cell;
species CC in Cell, Cn in compartment_0000002, Mp in Cell, Mt in Cell;
// Assignment Rules:
Pt := CC + Cn + P0 + P1 + P2;
Tt := CC + Cn + T0 + T1 + T2;
// Reactions:
P0_to_P1: P0 => P1; (Cell*P0_to_P1_V_1P*P0)/(P0_to_P1_K1_P + P0);
T0_to_T1: T0 => T1; (Cell*T0_to_T1_V_1T*T0)/(T0_to_T1_K_1T + T0);
P1_to_P0: P1 => P0; (Cell*P1_to_P0_V_2P*P1)/(P1_to_P0_K_2P + P1);
T1_to_T0: T1 => T0; (Cell*T1_to_T0_V_2T*T1)/(T1_to_T0_K_2T + T1);
P1_to_P2: P1 => P2; (Cell*P1_to_P2_V_3P*P1)/(P1_to_P2_K_3P + P1);
T1_to_T2: T1 => T2; (Cell*T1_to_T2_V_3T*T1)/(T1_to_T2_K_3T + T1);
P2_to_P1: P2 => P1; (Cell*P2_to_P1_V_4P*P2)/(P2_to_P1_K_4P + P2);
T2_to_T1: T2 => T1; (Cell*T2_to_T1_V_4T*T2)/(T2_to_T1_K_4T + T2);
P0_degradation: P0 => ; Cell*P0_degradation_k_d*P0;
T0_degradation: T0 => ; Cell*T0_degradation_k_d*T0;
P1_degradation: P1 => ; Cell*P1_degradation_k_d*P1;
T1_degradation: T1 => ; Cell*T1_degradation_k_d*T1;
P2_degradation: P2 => ; Cell*P2_degradation_k_d*P2 + (Cell*P2_degradation_V_dP*P2)/(P2_degradation_K_dP + P2);
T2_degradation: T2 => ; Cell*T2_degradation_k_d*T2 + (Cell*V_dT*T2)/(T2_degradation_K_dT + T2);
PT_complex_formation: P2 + T2 -> CC; Cell*PT_complex_formation_k3*P2*T2 - Cell*PT_complex_formation_k4*CC;
PT_complex_nucleation: CC -> Cn; Cell*PT_complex_nucleation_k1*CC - compartment_0000002*PT_complex_nucleation_k2*Cn;
PT_complex_degradation: CC => ; Cell*PT_complex_degradation_k_dC*CC;
PTnucl_complex_degradation: Cn => ; compartment_0000002*PTnucl_complex_degradation_k_dN*Cn;
Mp_production: => Mp; (Cell*Mp_production_v_sP*Mp_production_K_IP^Mp_production_n)/(Mp_production_K_IP^Mp_production_n + Cn^Mp_production_n);
Mt_production: => Mt; (Cell*Mt_production_V_sT*Mt_production_K_IT^Mt_production_n)/(Mt_production_K_IT^Mt_production_n + Cn^Mt_production_n);
P0_production: => P0; Cell*P0_production_k_sP*Mp;
T0_production: => T0; Cell*T0_production_k_sT*Mt;
Mp_degradation: Mp => ; Cell*Mp_degradation_k_d*Mp + (Cell*Mp_degradation_V_mP*Mp)/(Mp_degradation_K_mP + Mp);
Mt_degradation: Mt => ; Cell*Mt_degradation_k_d*Mt + (Cell*V_mT*Mt)/(Mt_degradation_K_mT + Mt);
// Species initializations:
P0 = 0;
T0 = 0;
P1 = 0;
T1 = 0;
P2 = 0;
T2 = 0;
CC = 0;
Cn = 0;
Mp = 0;
Mt = 0;
// Compartment initializations:
Cell = 1;
compartment_0000002 = 1;
// Variable initializations:
V_mT = 0.7;
V_dT = 2;
P0_to_P1_K1_P = 2;
P0_to_P1_V_1P = 8;
T0_to_T1_K_1T = 2;
T0_to_T1_V_1T = 8;
P1_to_P0_K_2P = 2;
P1_to_P0_V_2P = 1;
T1_to_T0_K_2T = 2;
T1_to_T0_V_2T = 1;
P1_to_P2_K_3P = 2;
P1_to_P2_V_3P = 8;
T1_to_T2_K_3T = 2;
T1_to_T2_V_3T = 8;
P2_to_P1_K_4P = 2;
P2_to_P1_V_4P = 1;
T2_to_T1_K_4T = 2;
T2_to_T1_V_4T = 1;
P0_degradation_k_d = 0.01;
T0_degradation_k_d = 0.01;
P1_degradation_k_d = 0.01;
T1_degradation_k_d = 0.01;
P2_degradation_k_d = 0.01;
P2_degradation_V_dP = 2;
P2_degradation_K_dP = 0.2;
T2_degradation_k_d = 0.01;
T2_degradation_K_dT = 0.2;
PT_complex_formation_k3 = 1.2;
PT_complex_formation_k4 = 0.6;
PT_complex_nucleation_k1 = 0.6;
PT_complex_nucleation_k2 = 0.2;
PT_complex_degradation_k_dC = 0.01;
PTnucl_complex_degradation_k_dN = 0.01;
Mp_production_v_sP = 1;
Mp_production_K_IP = 1;
Mp_production_n = 4;
Mt_production_V_sT = 1;
Mt_production_K_IT = 1;
Mt_production_n = 4;
P0_production_k_sP = 0.9;
T0_production_k_sT = 0.9;
Mp_degradation_k_d = 0.01;
Mp_degradation_V_mP = 0.7;
Mp_degradation_K_mP = 0.2;
Mt_degradation_k_d = 0.01;
Mt_degradation_K_mT = 0.2;
// Other declarations:
var Pt, Tt;
const Cell, compartment_0000002, V_mT, V_dT;
// Unit definitions:
unit substance = 1e-9 mole;
unit time_unit = 3600 second;
// Display Names:
substance is "nanomole (default)";
time_unit is "hour (default)";
Cell is "cytoplasm";
compartment_0000002 is "nucleus";
P0 is "PER Protein (unphosphorylated)";
T0 is "TIM Protein (unphosphorylated)";
P1 is "PER Protein (mono-phosphorylated)";
T1 is "TIM Protein (mono-phosphorylated)";
P2 is "PER Protein (bi-phosphorylated)";
T2 is "TIM Protein (bi-phosphorylated)";
CC is "Cytosolic PER-TIM Complex";
Cn is "Nuclear PER-TIM Complex";
Mp is "PER mRNA";
Mt is "TIM mRNA";
Pt is "Total Per";
Tt is "Total Tim";
P0_to_P1 is "First Phosphorylation of PER";
T0_to_T1 is "First Phosphorylation of TIM";
P1_to_P0 is "Dephosphorylation of PER (1st P)";
T1_to_T0 is "Dephosphorylation of TIM (1st P)";
P1_to_P2 is "Second Phosphorylation of PER";
T1_to_T2 is "Second Phosphorylation of TIM";
P2_to_P1 is "Dephosphorylation of PER (2nd P)";
T2_to_T1 is "Dephosphorylation of TIM (2nd P)";
P0_degradation is "PER degradation";
T0_degradation is "TIM degradation";
P1_degradation is "PER-1 degradation";
T1_degradation is "TIM-1 degradation";
P2_degradation is "PER-2 degradation";
T2_degradation is "TIM-2 degradation";
PT_complex_formation is "PER-TIM complex formation";
PT_complex_nucleation is "PER-TIM complex nucleation";
PT_complex_degradation is "PER-TIM complex degradation (cytosol)";
PTnucl_complex_degradation is "PER-TIM complex degradation (nuclear)";
Mp_production is "PER mRNA production";
Mt_production is "TIM mRNA production";
P0_production is "PER production";
T0_production is "TIM production";
Mp_degradation is "PER mRNA degradation";
Mt_degradation is "TIM mRNA degradation";
end