// Created by libAntimony v2.8.0 model *model_0000001() // Compartments and Species: compartment nucleus, cytoplasm; species M_T in cytoplasm, M_P in cytoplasm, T0 in cytoplasm, T1 in cytoplasm; species T2 in cytoplasm, P0 in cytoplasm, P1 in cytoplasm, P2 in cytoplasm; species C in cytoplasm, CN in nucleus, $Tt in cytoplasm, $Pt in cytoplasm; // Assignment Rules: Tt := T0 + T1 + T2 + C + (CN*nucleus)/cytoplasm; Pt := P0 + P1 + P2 + C + (CN*nucleus)/cytoplasm; v_dT := (1 + (v_dT_fac - 1)*ceil(sin(time/l_d*pi)*0.9))*v_dT_dark; // Reactions: per_trans: => M_P; (per_trans_v_sP*per_trans_Ki_P^n)/(per_trans_Ki_P^n + CN^n); tim_trans: => M_T; (tim_trans_v_sT*tim_trans_Ki_T^n)/(tim_trans_Ki_T^n + CN^n); M_T_decay: M_T => ; (M_T_decay_v_mT/(M_T_decay_K_mT + M_T) + kd)*M_T*cytoplasm; M_P_decay: M_P => ; (M_P_decay_v_mP/(M_P_decay_K_mP + M_P) + kd)*M_P*cytoplasm; PER_transl: => P0; PER_transl_k_sP*M_P*cytoplasm; TIM_transl: => T0; TIM_transl_k_sT*M_T*cytoplasm; PO_decay: P0 => ; kd*P0*cytoplasm; P1_decay: P1 => ; kd*P1*cytoplasm; P2_decay: P2 => ; kd*P2*cytoplasm; T0_decay: T0 => ; kd*T0*cytoplasm; T1_decay: T1 => ; kd*T1*cytoplasm; T2_decay: T2 => ; kd*T2*cytoplasm; C_form: P2 + T2 => C; (C_form_k3*T2*P2 - C_form_k4*C)*cytoplasm; C_decay: C => ; C_decay_kd_C*C*cytoplasm; CN_decay: CN => ; CN_decay_kd_CN*CN*nucleus; C_transp: C -> CN; C_transp_k1*C*cytoplasm - C_transp_k2*CN*nucleus; P_pho: P0 => P1; (P_pho_V_1P*P0)/(P_pho_K_1P + P0)*cytoplasm; P1_pho: P1 => P2; (P1_pho_V_3P*P1)/(P1_pho_K_3P + P1)*cytoplasm; P1_depho: P1 => P0; (P1_depho_V_2P*P1)/(P1_depho_K_2P + P1)*cytoplasm; P2_depho: P2 => P1; (P2_depho_V_4P*P2)/(P2_depho_K_4P + P2)*cytoplasm; T_pho: T0 => T1; (T_pho_V_1T*T0)/(T_pho_K_1T + T0)*cytoplasm; T1_pho: T1 => T2; (T1_pho_V_3T*T1)/(T1_pho_K_3T + T1)*cytoplasm; T1_depho: T1 => T0; (T1_depho_V_2T*T1)/(T1_depho_K_2T + T1)*cytoplasm; T2_depho: T2 => T1; (T2_depho_V_4T*T2)/(T2_depho_K_4T + T2)*cytoplasm; T2_light_deact: T2 => ; (v_dT*T2)/(T2_light_deact_K_dT + T2)*cytoplasm; P2_light_deact: P2 => ; (P2_light_deact_v_dP*P2)/(P2_light_deact_K_dP + P2)*cytoplasm; // Species initializations: M_T = 1.41; M_P = 0.09; T0 = 0.54; T1 = 0.79; T2 = 4.65; P0 = 0.02; P1 = 0.02; P2 = 0.01; C = 0.18; CN = 1.2; // Compartment initializations: nucleus = 1; nucleus has litre; cytoplasm = 1; cytoplasm has litre; // Variable initializations: n = 4; n has dimensionless; kd = 0.01; kd has perh; v_dT has nMph; v_dT_fac = 2; v_dT_fac has dimensionless; l_d = 12; l_d has time_unit; v_dT_dark = 2; v_dT_dark has nMph; per_trans_v_sP = 0.8; per_trans_v_sP has nmph; per_trans_Ki_P = 1; per_trans_Ki_P has nM; tim_trans_v_sT = 1; tim_trans_v_sT has nmph; tim_trans_Ki_T = 1; tim_trans_Ki_T has nM; M_T_decay_v_mT = 0.7; M_T_decay_v_mT has nMph; M_T_decay_K_mT = 0.2; M_T_decay_K_mT has nM; M_P_decay_v_mP = 0.8; M_P_decay_v_mP has nMph; M_P_decay_K_mP = 0.2; M_P_decay_K_mP has nM; PER_transl_k_sP = 0.9; PER_transl_k_sP has perh; TIM_transl_k_sT = 0.9; TIM_transl_k_sT has perh; C_form_k3 = 1.2; C_form_k3 has pnMph; C_form_k4 = 0.6; C_form_k4 has perh; C_decay_kd_C = 0.01; C_decay_kd_C has perh; CN_decay_kd_CN = 0.01; CN_decay_kd_CN has perh; C_transp_k1 = 1.2; C_transp_k1 has perh; C_transp_k2 = 0.2; C_transp_k2 has perh; P_pho_V_1P = 8; P_pho_V_1P has nMph; P_pho_K_1P = 2; P_pho_K_1P has nM; P1_pho_V_3P = 8; P1_pho_V_3P has nMph; P1_pho_K_3P = 2; P1_pho_K_3P has nM; P1_depho_K_2P = 2; P1_depho_K_2P has nM; P1_depho_V_2P = 1; P1_depho_V_2P has nMph; P2_depho_V_4P = 1; P2_depho_V_4P has nMph; P2_depho_K_4P = 2; P2_depho_K_4P has nM; T_pho_V_1T = 8; T_pho_V_1T has nMph; T_pho_K_1T = 2; T_pho_K_1T has nM; T1_pho_V_3T = 8; T1_pho_V_3T has nMph; T1_pho_K_3T = 2; T1_pho_K_3T has nM; T1_depho_K_2T = 2; T1_depho_K_2T has nM; T1_depho_V_2T = 1; T1_depho_V_2T has nMph; T2_depho_V_4T = 1; T2_depho_V_4T has nMph; T2_depho_K_4T = 2; T2_depho_K_4T has nM; T2_light_deact_K_dT = 0.2; T2_light_deact_K_dT has nM; P2_light_deact_v_dP = 2; P2_light_deact_v_dP has nMph; P2_light_deact_K_dP = 0.2; P2_light_deact_K_dP has nM; // Other declarations: var v_dT; const nucleus, cytoplasm, n, kd, v_dT_fac, l_d, v_dT_dark; // Unit definitions: unit substance = 1e-9 mole; unit nM = 1e-9 mole / litre; unit time_unit = 3.6e3 second; unit nMph = 1e-9 mole / (3.6e3 second * litre); unit perh = 1 / 3.6e3 second; unit pnMph = litre / (3.6e3 second * 1e-9 mole); unit nmph = 1e-9 mole / 3.6e3 second; // Display Names: substance is "nanomolar"; nM is "nanomoleperlitre"; time_unit is "hours"; nMph is "nanoMperHour"; perh is "perhour"; pnMph is "pernMperHour"; nmph is "nanomolperhour"; M_T is "tim mRNA"; M_P is "per mRNA"; T0 is "TIM"; T1 is "TIM-p"; T2 is "TIM-pp"; P0 is "PER"; P1 is "PER-p"; P2 is "PER-pp"; C is "PER_TIM complex cytoplasm"; CN is "PER_TIM complex nuclear"; Tt is "total TIM"; Pt is "total PER"; n is "transkr_rep_hill_coefficient"; kd is "degradation_rate"; v_dT is "T2_lightdecay_rate"; v_dT_fac is "v_dT_fold_incr_during_light"; l_d is "light_dark_period"; v_dT_dark is "v_dT_value_darkness"; per_trans is "per transkription"; tim_trans is "tim transkription"; M_T_decay is "tim mRNA decay"; M_P_decay is "per mRNA decay"; PER_transl is "PER tranlation"; TIM_transl is "TIM translation"; PO_decay is "PER decay"; P1_decay is "PER-p decay"; P2_decay is "PER-pp decay"; T0_decay is "TIM decay"; T1_decay is "TIM-p decay"; T2_decay is "TIM-pp decay"; C_form is "Per_TIM complex formation"; C_decay is "cytopl. PER_TIM compl. decay"; CN_decay is "nuclear PER_TIM compl. decay"; C_transp is "PER_TIM complex shuttling"; P_pho is "PER phosphorylation"; P1_pho is "PER-p phosphorylation"; P1_depho is "PER-p dephosphorylation"; P2_depho is "PER-pp dephosphorylation"; T_pho is "TIM phosphorylation"; T1_pho is "TIM-p phosphorylation"; T1_depho is "TIM-p dephosphorylation"; T2_depho is "TIM-pp dephosphorylation"; T2_light_deact is "TIM-pp light deactivation"; P2_light_deact is "PER-pp light deactivation"; end