// Created by libAntimony v2.8.0 // Warnings from automatic translation: // Unable to set the stoichiometry math for the reactant time in reaction re45 because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the reactant frq_gene in reaction frq_transcription because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the reactant wc1_gene in reaction wc1_transcription because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the reactant wc2_gene in reaction wc2_transcription because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the reactant vvd_gene in reaction vvd_transcription because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the reactant frq_mRNA in reaction frq_translation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the reactant wc1_mRNA in reaction wc1_translation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the reactant wc2_mRNA in reaction wc2_translation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the reactant vvd_mRNA in reaction vvd_translation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the product degraded_frq_mRNA in reaction frq_mRNA_degradation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the product degraded_wc1_mRNA in reaction wc1_mRNA_degradation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the product degraded_wc2_mRNA in reaction wc2_mRNA_degradation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the product degraded_vvd_mRNA in reaction vvd_mRNA_degradation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the product degraded_hyperFRQc in reaction hyperFRQc_degradation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the product degraded_hyperFFCn in reaction hyperFFCn_degradation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the product degraded_WC1c in reaction WC1c_degradation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the product degraded_WC2c in reaction WC2c_degradation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the product degraded_hyperWCCc in reaction hyperWCCc_degradation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the product degraded_hyperWCCn in reaction hyperWCCn_degradation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the product degraded_active_hypoWCCn in reaction active_hypoWCCn_degradation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the product degraded_L_WCCCVVDn in reaction L_WCC_degradation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the product degraded_VVDc in reaction VVDc_degradation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the product degraded_VVDn in reaction VVDn_degradation because stoichiometry math is not a defined concept in Antimony. // Unable to set the stoichiometry math for the product degraded_L_WCCCVVDn in reaction L_WCCVVD_degradation because stoichiometry math is not a defined concept in Antimony. model *MODEL1212150000() // Compartments and Species: compartment default, c1, c2; species L_WCC in c2, L_WCCVVDn in c2, $Period in default, Y in default; species X in default, T in default, VVDc in c1, VVDn in c2, WC1c in c1; species WC2c in c1, active_hypoWCCn in c2, $c_hypoFRQ_to_hyperFRQ in default; species hypoFRQc in c1, hyperFRQc in c1, cycle in default, degraded_L_WCCCVVDn in c2; species degraded_VVDc in c1, degraded_VVDn in c2, degraded_WC1c in c1, degraded_WC2c in c1; species degraded_active_hypoWCCn in c2, degraded_frq_mRNA in c1, degraded_hyperFFCn in c2; species degraded_hyperFRQc in c1, degraded_hyperWCCc in c1, degraded_hyperWCCn in c2; species degraded_vvd_mRNA in c1, degraded_wc1_mRNA in c1, degraded_wc2_mRNA in c1; species frq_level_A in default, frq_mRNA in c1, hyperFRQn in c2, hyperWCCc in c1; species hyperWCCn in c2, hypoFRQn in c2, hypoWCCc in c1, hypoWCCn in c2; species $n_hypoFRQ_to_hyperFRQ in default, time_ in default, $total_FRQ in default; species $total_FRQc in default, $total_FRQn in default, $total_VVD in default; species $total_WC1 in default, $total_WC2 in default, $total_WCCn in default; species $total_hyper_FRQ in default, $total_hypoWCC in default, $total_hypo_FRQ in default; species vvd_gene in c2, vvd_mRNA in c1, wc1_mRNA in c1, wc2_mRNA in c1; species $total_hyperWCC in default, $s61 in default; substanceOnly species $frq_gene in c2, $wc1_gene in c2, $wc2_gene in c2; substanceOnly species line in default, line2 in default, line3 in default; // Assignment Rules: Period := Y - X; c_hypoFRQ_to_hyperFRQ := hypoFRQc/hyperFRQc; n_hypoFRQ_to_hyperFRQ := hypoFRQn/hyperFRQn; total_FRQ := hypoFRQc + hyperFRQc + hypoFRQn + hyperFRQn; total_FRQc := hypoFRQc + hyperFRQc; total_FRQn := hypoFRQn + hyperFRQn; total_VVD := VVDn + VVDc + L_WCCVVDn; total_WC1 := WC1c + hypoWCCc + hyperWCCc + hypoWCCn + hyperWCCn + active_hypoWCCn + L_WCC + L_WCCVVDn; total_WC2 := WC2c + hypoWCCc + hypoWCCn + hyperWCCn + hyperWCCc + active_hypoWCCn + L_WCC; total_WCCn := hypoWCCn + hyperWCCn + active_hypoWCCn + L_WCC; total_hyper_FRQ := hyperFRQn + hyperFRQc; total_hypoWCC := hypoWCCc + hypoWCCn; total_hypo_FRQ := hypoFRQn + hypoFRQc; total_hyperWCC := hyperWCCn + hyperWCCc; s61 := total_hyperWCC/total_hypoWCC; // Reactions: re45: time_ => T; 1; frq_transcription: $frq_gene => frq_mRNA; kmax_frq*(active_hypoWCCn^A_active_hypoWCCn_frq/(Km_frq^A_active_hypoWCCn_frq + active_hypoWCCn^A_active_hypoWCCn_frq)) + kadd_light_frq*L_WCC; wc1_transcription: $wc1_gene => wc1_mRNA; k_min_wc1 + kadd_wc1*active_hypoWCCn + kadd_L_wc1*L_WCC; wc2_transcription: $wc2_gene => wc2_mRNA; kmax_wc2*(1/(1 + hypoWCCn*ki_wc2_transcription)) + hypoFRQn*kadd_wc2_transcription_hypoFRQn; vvd_transcription: vvd_gene => vvd_mRNA; kadd_vvd_light_mRNA*L_WCC; frq_translation: frq_mRNA => hypoFRQc; frq_mRNA*k_hypoFRQc; wc1_translation: wc1_mRNA => WC1c; k_WC1c*wc1_mRNA; wc2_translation: wc2_mRNA => WC2c; wc2_mRNA*k_WC2c; vvd_translation: vvd_mRNA => VVDc; k_VVDc*vvd_mRNA; frq_mRNA_degradation: frq_mRNA => degraded_frq_mRNA; frq_mRNA*(kd_frq + hypoFRQc*kdfrq_hypoFRQc); wc1_mRNA_degradation: wc1_mRNA => degraded_wc1_mRNA; wc1_mRNA*kd_wc1; wc2_mRNA_degradation: wc2_mRNA => degraded_wc2_mRNA; wc2_mRNA*kd_wc2; vvd_mRNA_degradation: vvd_mRNA => degraded_vvd_mRNA; kd_vvd_mRNA*vvd_mRNA; hypoWCCc_formation: WC1c + WC2c => hypoWCCc; WC1c*WC2c*k_hypoWCCc; hypoFRQc_translocation_in_nucleus: hypoFRQc => hypoFRQn; kin_hypoFRQc*hypoFRQc; hypoWCCc_translocation_in_nucleus: hypoWCCc => hypoWCCn; hypoWCCc*kin_hypoWCCc; VVD_nuclear_localisation: VVDc => VVDn; kin_VVDc*VVDc; hypoFRQn_translocation_out_nucleus: hypoFRQn => hypoFRQc; hypoFRQn*kout_hypoFRQn; hyperFRQn_translocation_out_nucleus: hyperFRQn => hyperFRQc; hyperFRQn*kout_hyperFRQn; hyperWCCn_translocation_out_nucleus: hyperWCCn => hyperWCCc; hyperWCCn*kout_hyperWCCn; hypoFRQc_phosphorylation: hypoFRQc => hyperFRQc; hypoFRQc*kp_hypoFRQc; hypoFRQn_phosphorylation: hypoFRQn => hyperFRQn; hypoFRQn*kp_hypoFRQn; hypoWCCc_phosphorylation: hypoWCCc => hyperWCCc; hypoWCCc*kp_hypoWCCc; hypoWCCn_phosphorylation: hypoWCCn => hyperWCCn; kmaxp_hypoWCCn*hypoWCCn*(hypoFRQn^I_hypoFRQn_hyperWCCn/(Kmp_hypoFRQn_hyperWCCn^I_hypoFRQn_hyperWCCn + hypoFRQn^I_hypoFRQn_hyperWCCn)); hyperWCCc_dephosphorylation: hyperWCCc => hypoWCCc; hyperWCCc*kdp_hyperWCCc; hypoWCCn_activation: hypoWCCn => active_hypoWCCn; hypoWCCn*kact_hypoWCCn; L_WCC_formation: hypoWCCn => L_WCC; kact_L_WCC*hypoWCCn; WCCVVD_complex_formation: VVDn + L_WCC => L_WCCVVDn; VVDn*L_WCC*k_WCCVVD; WCCVVD_complex_disassociation: L_WCCVVDn => hypoWCCn + VVDn; L_WCCVVDn*k_dis_WCCVVD; hyperFRQc_degradation: hyperFRQc => degraded_hyperFRQc; hyperFRQc*kd_hyperFRQc; hyperFFCn_degradation: hyperFRQn => degraded_hyperFFCn; hyperFRQn*kd_hyperFRQn; WC1c_degradation: WC1c => degraded_WC1c; WC1c*kd_WC1c; WC2c_degradation: WC2c => degraded_WC2c; WC2c*kd_WC2c; hyperWCCc_degradation: hyperWCCc => degraded_hyperWCCc; hyperWCCc*kd_hyperWCCc; hyperWCCn_degradation: hyperWCCn => degraded_hyperWCCn; hyperWCCn*kd_hyperWCCn; active_hypoWCCn_degradation: active_hypoWCCn => degraded_active_hypoWCCn; active_hypoWCCn*kd_active_hypoWCCn; L_WCC_degradation: L_WCC => degraded_L_WCCCVVDn; L_WCC*kd_L_WCC; VVDc_degradation: VVDc => degraded_VVDc; VVDc*kd_VVDc; VVDn_degradation: VVDn => degraded_VVDn; VVDn*kd_VVDn; L_WCCVVD_degradation: L_WCCVVDn => degraded_L_WCCCVVDn; L_WCCVVDn*kd_WCCVVD; // Events: n_CYCLE: at 0 after time_ > 125 && frq_mRNA > frq_level_A: cycle = cycle + 1; light_on: at 0 after time_ > T_light_on: kact_L_WCC = kact_L_WCC_light; light_off: at 0 after time_ > T_light_on + LP: kact_L_WCC = 0; calculate_period_find_frq_level_A: at 0 after time_ > 125: frq_level_A = frq_mRNA; calculate_period_find_Y: at 0 after time_ > 125 && frq_mRNA > frq_level_A && cycle < 3: Y = time_; calculate_period_find_X: at 0 after time_ > 125 && frq_mRNA > frq_level_A && cycle < 2: X = time_; // Species initializations: L_WCC = 0; L_WCCVVDn = 0; Y = 0; X = 0; T = 0; VVDc = 0; VVDn = 0; WC1c = 0.039; WC2c = 6.11815; active_hypoWCCn = 0.05281/c2; hypoFRQc = 0.619449/c1; hyperFRQc = 0.368117/c1; cycle = 0; degraded_L_WCCCVVDn = 0; degraded_VVDc = 0; degraded_VVDn = 0; degraded_WC1c = 0; degraded_WC2c = 0; degraded_active_hypoWCCn = 0; degraded_frq_mRNA = 0; degraded_hyperFFCn = 0; degraded_hyperFRQc = 0; degraded_hyperWCCc = 0; degraded_hyperWCCn = 0; degraded_vvd_mRNA = 0; degraded_wc1_mRNA = 0; degraded_wc2_mRNA = 0; frq_gene = 1; frq_level_A = 0; frq_mRNA = 0.22321; hyperFRQn = 0.07298/c2; hyperWCCc = 0.496374/c1; hyperWCCn = 0.1573204/c2; hypoFRQn = 0.394774/c2; hypoWCCc = 0.4285/c1; hypoWCCn = 0.47086/c2; time_ = 0; vvd_gene = 1/c2; vvd_mRNA = 0; wc1_gene = 1; wc1_mRNA = 0.5218; wc2_gene = 1; wc2_mRNA = 0.636098; line = 1.8728/default; line2 = 0.985/default; line3 = 1.67/default; // Compartment initializations: default = 1; default has volume; c1 = 1; c1 has volume; c2 = 1; c2 has volume; // Variable initializations: T_light_on = 10000000; T_light_on has substance; kact_L_WCC = 0; kact_L_WCC has substance; kact_L_WCC_light = 5; kact_L_WCC_light has substance; LP = 60; LP has substance; kmax_frq = 7.3; kmax_frq has substance; Km_frq = 0.1; Km_frq has substance; A_active_hypoWCCn_frq = 4; A_active_hypoWCCn_frq has substance; k_hypoFRQc = 0.19; k_hypoFRQc has substance; kin_hypoFRQc = 0.1; kin_hypoFRQc has substance; k_WC1c = 0.226; k_WC1c has substance; k_WC2c = 1; k_WC2c has substance; k_hypoWCCc = 0.472; k_hypoWCCc has substance; kmaxp_hypoWCCn = 0.6; kmaxp_hypoWCCn has substance; Kmp_hypoFRQn_hyperWCCn = 0.475; Kmp_hypoFRQn_hyperWCCn has substance; I_hypoFRQn_hyperWCCn = 12; I_hypoFRQn_hyperWCCn has substance; kd_active_hypoWCCn = 1.29; kd_active_hypoWCCn has substance; kd_hyperFRQn = 0.27; kd_hyperFRQn has substance; kd_WC1c = 0.135; kd_WC1c has substance; kd_WC2c = 0.085; kd_WC2c has substance; kadd_wc1 = 1.2; kadd_wc1 has substance; kmax_wc2 = 1.6; kmax_wc2 has substance; kd_frq = 2; kd_frq has substance; kd_wc1 = 2.4; kd_wc1 has substance; kd_wc2 = 2.5; kd_wc2 has substance; kp_hypoFRQn = 0.1; kp_hypoFRQn has substance; kout_hyperFRQn = 0.3; kout_hyperFRQn has substance; kd_hyperFRQc = 0.27; kd_hyperFRQc has substance; kout_hyperWCCn = 0.29; kout_hyperWCCn has substance; kdp_hyperWCCc = 0.3; kdp_hyperWCCc has substance; kin_hypoWCCc = 0.3; kin_hypoWCCc has substance; kp_hypoFRQc = 0.1; kp_hypoFRQc has substance; kout_hypoFRQn = 0.1; kout_hypoFRQn has substance; kd_hyperWCCn = 0.05; kd_hyperWCCn has substance; kd_hyperWCCc = 0.05; kd_hyperWCCc has substance; kact_hypoWCCn = 0.15; kact_hypoWCCn has substance; kp_hypoWCCc = 0.3; kp_hypoWCCc has substance; on = 96; off = 120; k_VVDc = 0.68; k_VVDc has substance; kd_vvd_mRNA = 6.2; kd_vvd_mRNA has substance; kd_VVDc = 0.24; kd_VVDc has substance; kin_VVDc = 0.3; kin_VVDc has substance; kd_VVDn = 0.24; kd_VVDn has substance; kadd_light_frq = 320; kadd_light_frq has substance; kadd_L_wc1 = 90; kadd_L_wc1 has substance; kd_L_WCC = 6; kd_L_WCC has substance; kadd_vvd_light_mRNA = 800; kadd_vvd_light_mRNA has substance; kdfrq_hypoFRQc = 0.356; kdfrq_hypoFRQc has substance; ki_wc2_transcription = 0.03; ki_wc2_transcription has substance; kadd_wc2_transcription_hypoFRQn = 0.03; kadd_wc2_transcription_hypoFRQn has substance; k_min_wc1 = 1.19; k_min_wc1 has substance; k_WCCVVD = 20; k_WCCVVD has substance; k_dis_WCCVVD = 1.8; k_dis_WCCVVD has substance; kd_WCCVVD = 0.75; kd_WCCVVD has substance; LP2 = 0; LP2 has substance; LP3 = 0; LP3 has substance; // Other declarations: var kact_L_WCC, k_hypoFRQc; const default, c1, c2, T_light_on, kact_L_WCC_light, LP, kmax_frq, Km_frq; const A_active_hypoWCCn_frq, kin_hypoFRQc, k_WC1c, k_WC2c, k_hypoWCCc, kmaxp_hypoWCCn; const Kmp_hypoFRQn_hyperWCCn, I_hypoFRQn_hyperWCCn, kd_active_hypoWCCn; const kd_hyperFRQn, kd_WC1c, kd_WC2c, kadd_wc1, kmax_wc2, kd_frq, kd_wc1; const kd_wc2, kp_hypoFRQn, kout_hyperFRQn, kd_hyperFRQc, kout_hyperWCCn; const kdp_hyperWCCc, kin_hypoWCCc, kp_hypoFRQc, kout_hypoFRQn, kd_hyperWCCn; const kd_hyperWCCc, kact_hypoWCCn, kp_hypoWCCc, on, off, k_VVDc, kd_vvd_mRNA; const kd_VVDc, kin_VVDc, kd_VVDn, kadd_light_frq, kadd_L_wc1, kd_L_WCC; const kadd_vvd_light_mRNA, kdfrq_hypoFRQc, ki_wc2_transcription, kadd_wc2_transcription_hypoFRQn; const k_min_wc1, k_WCCVVD, k_dis_WCCVVD, kd_WCCVVD, LP2, LP3; // Unit definitions: unit substance = mole; unit volume = litre; unit area = metre^2; unit length = metre; unit time_unit = second; // Display Names: time_unit is "time"; c1 is "Cytoplasm"; c2 is "Nucleus"; s61 is "hyper_hypo_WCC"; kact_L_WCC is "k_26"; kmax_frq is "k_01"; Km_frq is "K_01"; A_active_hypoWCCn_frq is "H_01"; k_hypoFRQc is "k_05"; kin_hypoFRQc is "k_14"; k_WC1c is "k_06"; k_WC2c is "k_07"; k_hypoWCCc is "k_13"; kmaxp_hypoWCCn is "k_23"; Kmp_hypoFRQn_hyperWCCn is "K_02"; I_hypoFRQn_hyperWCCn is "H_02"; kd_active_hypoWCCn is "k_35"; kd_hyperFRQn is "k_30"; kd_WC1c is "k_31"; kd_WC2c is "k_32"; kadd_wc1 is "k_02a01"; kmax_wc2 is "k_03"; kd_frq is "k_09"; kd_wc1 is "k_10"; kd_wc2 is "k_11"; kp_hypoFRQn is "k_21"; kout_hyperFRQn is "k_18"; kd_hyperFRQc is "k_29"; kout_hyperWCCn is "k_19"; kdp_hyperWCCc is "k_24"; kin_hypoWCCc is "k_15"; kp_hypoFRQc is "k_20"; kout_hypoFRQn is "k_17"; kd_hyperWCCn is "k_34"; kd_hyperWCCc is "k_33"; kact_hypoWCCn is "k_25"; kp_hypoWCCc is "k_22"; k_VVDc is "k_08"; kd_vvd_mRNA is "k_12"; kd_VVDc is "k_37"; kin_VVDc is "k_16"; kd_VVDn is "k_38"; kadd_light_frq is "k_01a"; kadd_L_wc1 is "k_02a02"; kd_L_WCC is "k_36"; kadd_vvd_light_mRNA is "k_04"; kdfrq_hypoFRQc is "k_09a"; ki_wc2_transcription is "k_03i"; kadd_wc2_transcription_hypoFRQn is "k_03a"; k_min_wc1 is "k_02"; k_WCCVVD is "k_27"; k_dis_WCCVVD is "k_28"; kd_WCCVVD is "k_39"; re45 is "Time"; frq_transcription is "re01"; wc1_transcription is "re02"; wc2_transcription is "re03"; vvd_transcription is "re04"; frq_translation is "re05"; wc1_translation is "re06"; wc2_translation is "re07"; vvd_translation is "re08"; frq_mRNA_degradation is "re09"; wc1_mRNA_degradation is "re10"; wc2_mRNA_degradation is "re11"; vvd_mRNA_degradation is "re12"; hypoWCCc_formation is "re13"; hypoFRQc_translocation_in_nucleus is "re14"; hypoWCCc_translocation_in_nucleus is "re15"; VVD_nuclear_localisation is "re16"; hypoFRQn_translocation_out_nucleus is "re17"; hyperFRQn_translocation_out_nucleus is "re18"; hyperWCCn_translocation_out_nucleus is "re19"; hypoFRQc_phosphorylation is "re20"; hypoFRQn_phosphorylation is "re21"; hypoWCCc_phosphorylation is "re22"; hypoWCCn_phosphorylation is "re23"; hyperWCCc_dephosphorylation is "re24"; hypoWCCn_activation is "re25"; L_WCC_formation is "re26"; WCCVVD_complex_formation is "re27"; WCCVVD_complex_disassociation is "re28"; hyperFRQc_degradation is "re29"; hyperFFCn_degradation is "re30"; WC1c_degradation is "re31"; WC2c_degradation is "re32"; hyperWCCc_degradation is "re33"; hyperWCCn_degradation is "re34"; active_hypoWCCn_degradation is "re35"; L_WCC_degradation is "re36"; VVDc_degradation is "re37"; VVDn_degradation is "re38"; L_WCCVVD_degradation is "re39"; end