// 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