// 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