//Created by libAntimony v2.4 model bakker_1997__environment(time_) // Variable initializations: time_ = ; end model bakker_1997__volume_ratio(Vc_Vg) // Variable initializations: Vc_Vg = 22.3; end model bakker_1997__Glc_o(Glc_o) // Variable initializations: Glc_o = 5.0; end model bakker_1997__Glc_i(Glc_i, V_HK, V_glucose_transport, time_) // Rate Rules: Glc_i' = V_glucose_transport - V_HK; // Variable initializations: Glc_i = 0.01; V_HK = ; V_glucose_transport = ; time_ = ; end model bakker_1997__Glc_6_P_g(Glc_6_P_g, Fru_6_P_g, hexose_P_g) // Assignment Rules: Glc_6_P_g := hexose_P_g / Keq_PGI; // Variable initializations: Keq_PGI = 0.29; Fru_6_P_g = ; hexose_P_g = ; end model bakker_1997__Fru_6_P_g(Fru_6_P_g, Glc_6_P_g, hexose_P_g) // Assignment Rules: Fru_6_P_g := hexose_P_g - Glc_6_P_g; // Variable initializations: Glc_6_P_g = ; hexose_P_g = ; end model bakker_1997__hexose_P_g(hexose_P_g, V_HK, V_PFK, time_) // Rate Rules: hexose_P_g' = V_HK - V_PFK; // Variable initializations: hexose_P_g = 0.01; V_HK = ; V_PFK = ; time_ = ; end model bakker_1997__Fru_1_6_BP_g(Fru_1_6_BP_g, V_PFK, V_ALD, time_) // Rate Rules: Fru_1_6_BP_g' = V_PFK - V_ALD; // Variable initializations: Fru_1_6_BP_g = 0.01; V_PFK = ; V_ALD = ; time_ = ; end model bakker_1997__GA_3_P_g(GA_3_P_g, Keq_TIM, DHAP_g) // Assignment Rules: GA_3_P_g := Keq_TIM * DHAP_g; // Variable initializations: Keq_TIM = ; DHAP_g = ; end model bakker_1997__triose_P(triose_P, V_ALD, V_GAPDH, V_GDH, V_GPO, time_) // Rate Rules: triose_P' = (2.0 * V_ALD + V_GPO) - (V_GAPDH + V_GDH); // Variable initializations: triose_P = 0.01; V_ALD = ; V_GAPDH = ; V_GDH = ; V_GPO = ; time_ = ; end model bakker_1997__one_three_BPGA_g(one_three_BPGA_g, V_GAPDH, V_PGK, time_) // Rate Rules: one_three_BPGA_g' = V_GAPDH - V_PGK; // Variable initializations: one_three_BPGA_g = 0.01; V_GAPDH = ; V_PGK = ; time_ = ; end model bakker_1997__three_PGA(three_PGA, N, Vc_Vg, Keq_PGM, Keq_ENO) // Assignment Rules: three_PGA := (N * (1.0 + Vc_Vg)) / (1.0 + (1.0 + Keq_PGM + Keq_PGM * Keq_ENO) * Vc_Vg); // Variable initializations: N = ; Vc_Vg = ; Keq_PGM = 0.187; Keq_ENO = 6.7; end model bakker_1997__two_PGA_c(two_PGA_c, three_PGA, Keq_PGM) // Assignment Rules: two_PGA_c := Keq_PGM * three_PGA; // Variable initializations: three_PGA = ; Keq_PGM = ; end model bakker_1997__N(N, V_PGK, V_PYK, time_) // Rate Rules: N' = V_PGK - V_PYK; // Variable initializations: N = 0.01; V_PGK = ; V_PYK = ; time_ = ; end model bakker_1997__PEP_c(PEP_c, two_PGA_c, Keq_ENO) // Assignment Rules: PEP_c := Keq_ENO * two_PGA_c; // Variable initializations: two_PGA_c = ; Keq_ENO = ; end model bakker_1997__PYR_c(PYR_c, V_PYK, V_pyruvate_transport, time_) // Rate Rules: PYR_c' = V_PYK - V_pyruvate_transport; // Variable initializations: PYR_c = 0.01; V_PYK = ; V_pyruvate_transport = ; time_ = ; end model bakker_1997__glycerol_g(glycerol_g) // Variable initializations: glycerol_g = 0.00; end model bakker_1997__DHAP(DHAP, triose_P, Vc_Vg, Keq_TIM) // Assignment Rules: DHAP := (triose_P * (1.0 + Vc_Vg)) / (1.0 + Vc_Vg + Keq_TIM); // Variable initializations: triose_P = ; Vc_Vg = ; Keq_TIM = 0.045; end model bakker_1997__DHAP_c(DHAP_c, DHAP) // Assignment Rules: DHAP_c := DHAP; // Variable initializations: DHAP = ; end model bakker_1997__DHAP_g(DHAP_g, DHAP) // Assignment Rules: DHAP_g := DHAP; // Variable initializations: DHAP = ; end model bakker_1997__Gly_3_P(Gly_3_P, DHAP, Glc_6_P_g, Fru_6_P_g, Fru_1_6_BP_g, GA_3_P_g, one_three_BPGA_g, ATP_g, ADP_g, C4, Vc_Vg) // Assignment Rules: Gly_3_P := (C4 - (Glc_6_P_g + Fru_6_P_g + 2 * Fru_1_6_BP_g + GA_3_P_g + one_three_BPGA_g + 2 * ATP_g + ADP_g)) / (1 + Vc_Vg) - DHAP; // Variable initializations: DHAP = ; Glc_6_P_g = ; Fru_6_P_g = ; Fru_1_6_BP_g = ; GA_3_P_g = ; one_three_BPGA_g = ; ATP_g = ; ADP_g = ; C4 = ; Vc_Vg = ; end model bakker_1997__Gly_3_P_c(Gly_3_P_c, Gly_3_P) // Assignment Rules: Gly_3_P_c := Gly_3_P; // Variable initializations: Gly_3_P = ; end model bakker_1997__Gly_3_P_g(Gly_3_P_g, Gly_3_P) // Assignment Rules: Gly_3_P_g := Gly_3_P; // Variable initializations: Gly_3_P = ; end model bakker_1997__NAD_g(NAD_g, NADH_g, C3) // Assignment Rules: NAD_g := C3 - NADH_g; // Variable initializations: NADH_g = ; C3 = ; end model bakker_1997__NADH_g(NADH_g, V_GAPDH, V_GDH, time_) // Rate Rules: NADH_g' = V_GAPDH - V_GDH; // Variable initializations: NADH_g = 0.01; V_GAPDH = ; V_GDH = ; time_ = ; end model bakker_1997__P_g(P_g, V_HK, V_PGK, V_PFK, V_GK, time_) // Rate Rules: P_g' = (V_PGK + V_GK) - (V_HK + V_PFK); // Variable initializations: P_g = 0.01; V_HK = ; V_PGK = ; V_PFK = ; V_GK = ; time_ = ; end model bakker_1997__P_c(P_c, V_PYK, V_ATP_utilisation, time_) // Rate Rules: P_c' = V_PYK - V_ATP_utilisation; // Variable initializations: P_c = 0.01; V_PYK = ; V_ATP_utilisation = ; time_ = ; end model bakker_1997__ATP_g(ATP_g, P_g, C1) // Assignment Rules: ATP_g := ((C1 - -(P_g * (1.0 - 4.0 * Keq_AK))) + power(power(C1 - -(P_g * (1.0 - 4.0 * Keq_AK)), 2.0) - 4.0 * (1.0 - 4.0 * Keq_AK) * (- Keq_AK * power(P_g, 2.0)), 0.5)) / (2.0 * (1.0 - 4.0 * Keq_AK)); // Variable initializations: P_g = ; Keq_AK = 0.442; C1 = ; end model bakker_1997__ATP_c(ATP_c, P_c, C2) // Assignment Rules: ATP_c := ((C2 - -(P_c * (1.0 - 4.0 * Keq_AK))) + power(power(C2 - -(P_c * (1.0 - 4.0 * Keq_AK)), 2.0) - 4.0 * (1.0 - 4.0 * Keq_AK) * (- Keq_AK * power(P_c, 2.0)), 0.5)) / (2.0 * (1.0 - 4.0 * Keq_AK)); // Variable initializations: P_c = ; Keq_AK = 0.442; C2 = ; end model bakker_1997__ADP_g(ADP_g, ATP_g, P_g) // Assignment Rules: ADP_g := P_g - 2.0 * ATP_g; // Variable initializations: ATP_g = ; P_g = ; end model bakker_1997__ADP_c(ADP_c, ATP_c, P_c) // Assignment Rules: ADP_c := P_c - 2.0 * ATP_c; // Variable initializations: ATP_c = ; P_c = ; end model bakker_1997__AMP_g(AMP_g, ATP_g, ADP_g, C1) // Assignment Rules: AMP_g := C1 - (ATP_g + ADP_g); // Variable initializations: ATP_g = ; ADP_g = ; C1 = ; end model bakker_1997__AMP_c(AMP_c, ATP_c, ADP_c, C2) // Assignment Rules: AMP_c := C2 - (ATP_c + ADP_c); // Variable initializations: ATP_c = ; ADP_c = ; C2 = ; end model bakker_1997__C1(C1) // Variable initializations: C1 = 3.9; end model bakker_1997__C2(C2) // Variable initializations: C2 = 3.9; end model bakker_1997__C3(C3) // Variable initializations: C3 = 4.0; end model bakker_1997__C4(C4) // Variable initializations: C4 = 120.0; end model bakker_1997__V_glucose_transport(V_glucose_transport, Glc_o, Glc_i) // Assignment Rules: V_glucose_transport := V_glucose_transport_max * ((Glc_o - Glc_i) / (K_Glc + Glc_o + Glc_i + alpha * Glc_o * (Glc_i / K_Glc))); // Variable initializations: Glc_o = ; Glc_i = ; K_Glc = 2.0; alpha = 0.75; V_glucose_transport_max = 106.2; end model bakker_1997__V_pyruvate_transport(V_pyruvate_transport, PYR_c) // Assignment Rules: V_pyruvate_transport := V_pyruvate_transport_max * (PYR_c / K_pyruvate) * (1.0 + PYR_c / K_pyruvate); // Variable initializations: PYR_c = ; K_pyruvate = 1.96; V_pyruvate_transport_max = 160.0; end model bakker_1997__V_GPO(V_GPO, Gly_3_P_c) // Assignment Rules: V_GPO := V_GPO_max * (Gly_3_P_c / K_Gly_3_P) * (1.0 + Gly_3_P_c / K_Gly_3_P); // Variable initializations: Gly_3_P_c = ; K_Gly_3_P = 1.7; V_GPO_max = 200.0; end model bakker_1997__V_HK(V_HK, Glc_i, ATP_g, ADP_g) // Assignment Rules: V_HK := V_HK_max * (((ATP_g / K_ATP) * (Glc_i / K_Glc_i)) / ((1.0 + ATP_g / K_ATP + ADP_g / K_ADP) * (1.0 + Glc_i / K_Glc_i))); // Variable initializations: Glc_i = ; ATP_g = ; ADP_g = ; K_Glc_i = 0.1; K_ATP = 0.116; K_ADP = 0.126; V_HK_max = 625.0; end model bakker_1997__V_GAPDH(V_GAPDH, NAD_g, GA_3_P_g, one_three_BPGA_g, NADH_g) // Assignment Rules: V_GAPDH := V_GAPDH_max_plus * (((GA_3_P_g / K_GA_3_P) * (NAD_g / K_NAD - V_GAPDH_max_ratio) * (one_three_BPGA_g / K_1_3_BPGA) * (NADH_g / K_NADH)) / ((1.0 + GA_3_P_g / K_GA_3_P + one_three_BPGA_g / K_1_3_BPGA) * (1.0 + NAD_g / K_NAD + NADH_g / K_NADH))); // Variable initializations: NAD_g = ; GA_3_P_g = ; one_three_BPGA_g = ; NADH_g = ; K_NAD = 0.45; K_GA_3_P = 0.15; K_1_3_BPGA = 0.1; K_NADH = 0.02; V_GAPDH_max_plus = 1470.0; V_GAPDH_max_ratio = 0.67; end model bakker_1997__V_PGK(V_PGK, ADP_g, one_three_BPGA_g, three_PGA, ATP_g) // Assignment Rules: V_PGK := V_PGK_max_plus * (((one_three_BPGA_g / K_1_3_BPGA) * (ADP_g / K_ADP - V_PGK_max_ratio) * (three_PGA / K_3_PGA) * (ATP_g / K_ATP)) / ((1.0 + one_three_BPGA_g / K_1_3_BPGA + three_PGA / K_3_PGA) * (1.0 + ADP_g / K_ADP + ATP_g / K_ATP))); // Variable initializations: ADP_g = ; one_three_BPGA_g = ; three_PGA = ; ATP_g = ; K_ADP = 0.1; K_1_3_BPGA = 0.05; K_3_PGA = 1.62; K_ATP = 0.29; V_PGK_max_plus = 640.0; V_PGK_max_ratio = 0.029; end model bakker_1997__V_GK(V_GK, ADP_g, Gly_3_P_g, glycerol_g, ATP_g) // Assignment Rules: V_GK := V_GK_max_plus * (((Gly_3_P_g / K_Gly_3_P) * (ADP_g / K_ADP - V_GK_max_ratio) * (glycerol_g / K_glycerol) * (ATP_g / K_ATP)) / ((1.0 + Gly_3_P_g / K_Gly_3_P + glycerol_g / K_glycerol) * (1.0 + ADP_g / K_ADP + ATP_g / K_ATP))); // Variable initializations: ADP_g = ; Gly_3_P_g = ; glycerol_g = ; ATP_g = ; K_ADP = 0.12; K_Gly_3_P = 5.1; K_glycerol = 0.12; K_ATP = 0.19; V_GK_max_plus = 0.0; V_GK_max_ratio = 167.0; end model bakker_1997__V_GDH(V_GDH, NADH_g, Gly_3_P_g, DHAP_g, NAD_g) // Assignment Rules: V_GDH := V_GDH_max_plus * (((DHAP_g / K_DHAP) * (NADH_g / K_NADH - V_GDH_max_ratio) * (Gly_3_P_g / K_Gly_3_P) * (NAD_g / K_NAD)) / ((1.0 + DHAP_g / K_DHAP + Gly_3_P_g / K_Gly_3_P) * (1.0 + NADH_g / K_NADH + NAD_g / K_NAD))); // Variable initializations: NADH_g = ; Gly_3_P_g = ; DHAP_g = ; NAD_g = ; K_NADH = 0.01; K_Gly_3_P = 2.0; K_DHAP = 0.1; K_NAD = 0.4; V_GDH_max_plus = 533.0; V_GDH_max_ratio = 0.28; end model bakker_1997__V_PFK(V_PFK, Fru_6_P_g, ATP_g) // Assignment Rules: V_PFK := V_PFK_max * ((power(Fru_6_P_g / Km_Fru_6_P, n) * (ATP_g / Km_ATP)) / ((1.0 + power(Fru_6_P_g / Km_Fru_6_P, n)) * (1.0 + ATP_g / Km_ATP))); // Variable initializations: Fru_6_P_g = ; ATP_g = ; n = 1.2; Km_Fru_6_P = 0.82; Km_ATP = 2.6E-2; V_PFK_max = 780.0; end model bakker_1997__V_PYK(V_PYK, PEP_c, ADP_c, ATP_c) // Assignment Rules: V_PYK := V_PYK_max * ((power(PEP_c / Km_PEP, n) * (ADP_c / Km_ADP)) / ((1.0 + power(PEP_c / Km_PEP, n)) * (1.0 + ADP_c / Km_ADP))); Km_PEP := 0.34 * (1.0 + ATP_c / 0.57 + ADP_c / 0.64); // Variable initializations: PEP_c = ; ADP_c = ; ATP_c = ; Km_ADP = 0.114; n = 2.5; V_PYK_max = 2.6E3; end model bakker_1997__V_ALD(V_ALD, Fru_1_6_BP_g, GA_3_P_g, DHAP_g, ATP_g, ADP_g, AMP_g) // Assignment Rules: V_ALD := V_ALD_max_plus * ((Fru_1_6_BP_g / Km_Fru_1_6_BP - V_ALD_max_ratio * ((GA_3_P_g * DHAP_g) / (Km_GA_3_P * Km_DHAP))) / (1.0 + Fru_1_6_BP_g / Km_Fru_1_6_BP + GA_3_P_g / Km_GA_3_P + DHAP_g / Km_DHAP + (Fru_1_6_BP_g * GA_3_P_g) / (Km_Fru_1_6_BP * Ki_GA_3_P) + (DHAP_g * GA_3_P_g) / (Km_DHAP * Km_GA_3_P))); Km_Fru_1_6_BP := 9E-3 * (1.0 + ATP_g / 0.68 + ADP_g / 1.51 + AMP_g / 3.65); // Variable initializations: Fru_1_6_BP_g = ; GA_3_P_g = ; DHAP_g = ; ATP_g = ; ADP_g = ; AMP_g = ; Km_GA_3_P = 6.7E-2; Ki_GA_3_P = 9.8E-2; Km_DHAP = 1.5E-2; V_ALD_max_plus = 780.0; V_ALD_max_ratio = 1.19; end model bakker_1997__V_ATP_utilisation(V_ATP_utilisation, ATP_c, ADP_c) // Assignment Rules: V_ATP_utilisation := k * (ATP_c / ADP_c); // Variable initializations: ATP_c = ; ADP_c = ; k = 50; end model *bakker_1997____main() // Sub-modules, and any changes to those submodules: environment: bakker_1997__environment(time_); volume_ratio: bakker_1997__volume_ratio(Vc_Vg); Glc_o: bakker_1997__Glc_o(Glc_o0); Glc_i: bakker_1997__Glc_i(Glc_i0, V_HK0, V_glucose_transport0, time_); Glc_6_P_g: bakker_1997__Glc_6_P_g(Glc_6_P_g0, Fru_6_P_g0, hexose_P_g0); Fru_6_P_g: bakker_1997__Fru_6_P_g(Fru_6_P_g0, Glc_6_P_g0, hexose_P_g0); hexose_P_g: bakker_1997__hexose_P_g(hexose_P_g0, V_HK0, V_PFK0, time_); Fru_1_6_BP_g: bakker_1997__Fru_1_6_BP_g(Fru_1_6_BP_g0, V_PFK0, V_ALD0, time_); GA_3_P_g: bakker_1997__GA_3_P_g(GA_3_P_g0, Keq_TIM, DHAP_g0); triose_P: bakker_1997__triose_P(triose_P0, V_ALD0, V_GAPDH0, V_GDH0, V_GPO0, time_); one_three_BPGA_g: bakker_1997__one_three_BPGA_g(one_three_BPGA_g0, V_GAPDH0, V_PGK0, time_); three_PGA: bakker_1997__three_PGA(three_PGA0, N0, Vc_Vg, Keq_PGM, Keq_ENO); two_PGA_c: bakker_1997__two_PGA_c(two_PGA_c0, three_PGA0, Keq_PGM); N: bakker_1997__N(N0, V_PGK0, V_PYK0, time_); PEP_c: bakker_1997__PEP_c(PEP_c0, two_PGA_c0, Keq_ENO); PYR_c: bakker_1997__PYR_c(PYR_c0, V_PYK0, V_pyruvate_transport0, time_); glycerol_g: bakker_1997__glycerol_g(glycerol_g0); DHAP: bakker_1997__DHAP(DHAP0, triose_P0, Vc_Vg, Keq_TIM); DHAP_c: bakker_1997__DHAP_c(DHAP_c0, DHAP0); DHAP_g: bakker_1997__DHAP_g(DHAP_g0, DHAP0); Gly_3_P: bakker_1997__Gly_3_P(Gly_3_P0, DHAP0, Glc_6_P_g0, Fru_6_P_g0, Fru_1_6_BP_g0, GA_3_P_g0, one_three_BPGA_g0, ATP_g0, ADP_g0, C40, Vc_Vg); Gly_3_P_c: bakker_1997__Gly_3_P_c(Gly_3_P_c0, Gly_3_P0); Gly_3_P_g: bakker_1997__Gly_3_P_g(Gly_3_P_g0, Gly_3_P0); NAD_g: bakker_1997__NAD_g(NAD_g0, NADH_g0, C30); NADH_g: bakker_1997__NADH_g(NADH_g0, V_GAPDH0, V_GDH0, time_); P_g: bakker_1997__P_g(P_g0, V_HK0, V_PGK0, V_PFK0, V_GK0, time_); P_c: bakker_1997__P_c(P_c0, V_PYK0, V_ATP_utilisation0, time_); ATP_g: bakker_1997__ATP_g(ATP_g0, P_g0, C10); ATP_c: bakker_1997__ATP_c(ATP_c0, P_c0, C20); ADP_g: bakker_1997__ADP_g(ADP_g0, ATP_g0, P_g0); ADP_c: bakker_1997__ADP_c(ADP_c0, ATP_c0, P_c0); AMP_g: bakker_1997__AMP_g(AMP_g0, ATP_g0, ADP_g0, C10); AMP_c: bakker_1997__AMP_c(AMP_c0, ATP_c0, ADP_c0, C20); C1: bakker_1997__C1(C10); C2: bakker_1997__C2(C20); C3: bakker_1997__C3(C30); C4: bakker_1997__C4(C40); V_glucose_transport: bakker_1997__V_glucose_transport(V_glucose_transport0, Glc_o0, Glc_i0); V_pyruvate_transport: bakker_1997__V_pyruvate_transport(V_pyruvate_transport0, PYR_c0); V_GPO: bakker_1997__V_GPO(V_GPO0, Gly_3_P_c0); V_HK: bakker_1997__V_HK(V_HK0, Glc_i0, ATP_g0, ADP_g0); V_GAPDH: bakker_1997__V_GAPDH(V_GAPDH0, NAD_g0, GA_3_P_g0, one_three_BPGA_g0, NADH_g0); V_PGK: bakker_1997__V_PGK(V_PGK0, ADP_g0, one_three_BPGA_g0, three_PGA0, ATP_g0); V_GK: bakker_1997__V_GK(V_GK0, ADP_g0, Gly_3_P_g0, glycerol_g0, ATP_g0); V_GDH: bakker_1997__V_GDH(V_GDH0, NADH_g0, Gly_3_P_g0, DHAP_g0, NAD_g0); V_PFK: bakker_1997__V_PFK(V_PFK0, Fru_6_P_g0, ATP_g0); V_PYK: bakker_1997__V_PYK(V_PYK0, PEP_c0, ADP_c0, ATP_c0); V_ALD: bakker_1997__V_ALD(V_ALD0, Fru_1_6_BP_g0, GA_3_P_g0, DHAP_g0, ATP_g0, ADP_g0, AMP_g0); V_ATP_utilisation: bakker_1997__V_ATP_utilisation(V_ATP_utilisation0, ATP_c0, ADP_c0); end