//Created by libAntimony v2.4 model korzeniewski_zoladz_2001__environment(time_) // Variable initializations: time_ = ; end model korzeniewski_zoladz_2001__cell(R_cm, R, T, F, S, Z, electric_potential, protonmotive_force, ex_membrane_potential, in_membrane_potential, pH_e, pH_i, pKa, He, Hi, r_buffi, r_buffe, BN, u) // Assignment Rules: S := 2.303 * R * T; Z := 2.303 * R * (T / F); electric_potential := -(protonmotive_force - delta_pH); ex_membrane_potential := -0.35 * electric_potential; in_membrane_potential := 0.65 * electric_potential; pH_e := -log(He / 1000000.0); pH_i := -log(Hi / 1000000.0); delta_pH := Z * (pH_i - pH_e); C0_i := (power(10.0, - pH_i) - power(10.0, - pH_i - dpH)) / dpH; C0_e := (power(10.0, - pH_e) - power(10.0, - pH_e - dpH)) / dpH; r_buffi := c_buffi / C0_i; r_buffe := c_buffe / C0_e; u := electric_potential / protonmotive_force; // Variable initializations: R_cm = 15.0; R = 0.0083; T = 289.0; F = 0.0965; protonmotive_force = 190.0; c_buffi = 0.022; c_buffe = 0.025; pKa = 6.8; He = ; Hi = ; dpH = 0.001; BN = 5.0; end model korzeniewski_zoladz_2001__redox_potentials(EmN, EmU, Emc, Ema, Z, NAD, NADH, UQ, UQH2, c_2, c_3, protonmotive_force, u) // Assignment Rules: EmN := EmN0 + (Z / 2.0) * log(NAD / NADH); EmU := EmU0 + (Z / 2.0) * log(UQ / UQH2); Emc := Emc0 + Z * log(c_3 / c_2); Ema := Emc + protonmotive_force * ((2.0 + 2.0 * u) / 2.0); // Variable initializations: EmN0 = -320.0; EmU0 = 85.0; Emc0 = 250.0; Z = ; NAD = ; NADH = ; UQ = ; UQH2 = ; c_2 = ; c_3 = ; protonmotive_force = ; u = ; end model korzeniewski_zoladz_2001__NAD(NAD, NADH) // Assignment Rules: NAD := Nt - NADH; // Variable initializations: Nt = 2970.0; NADH = ; end model korzeniewski_zoladz_2001__NADH(NADH, BN, R_cm, vDH, vC1, time_) // Rate Rules: NADH' = (vDH - vC1) * (R_cm / BN); // Variable initializations: NADH = 500.0; BN = ; R_cm = ; vDH = ; vC1 = ; time_ = ; end model korzeniewski_zoladz_2001__O2(O2, vC4, time_) // Rate Rules: O2' = - vC4; // Variable initializations: O2 = 1.00; vC4 = ; time_ = ; end model korzeniewski_zoladz_2001__Hi(Hi, r_buffi, u, nA, vC4, vC1, vC3, vSN, vEX, vPI, vLK, R_cm, time_) // Rate Rules: Hi' = ((((4.0 - 2.0 * u) * vC3 + 4.0 * vC1) - (2.0 * (2.0 + 2.0 * u) * vC4 + nA * vSN + u * vEX + (1.0 - u) * vPI + vLK)) * R_cm) / r_buffi; // Variable initializations: Hi = 1.00; r_buffi = ; u = ; nA = ; vC4 = ; vC1 = ; vC3 = ; vSN = ; vEX = ; vPI = ; vLK = ; R_cm = ; time_ = ; end model korzeniewski_zoladz_2001__He(He, r_buffe, u, nA, vC4, vC1, vC3, vCK, vEFF, vSN, vEX, vPI, vLK, time_) // Rate Rules: He' = ((2.0 * (2.0 + 2.0 * u) * vC4 + (4.0 - 2.0 * u) * vC3 + 4.0 * vC1) - (nA * vSN + u * vEX + (1.0 - u) * vPI + vLK + vCK + vEFF)) / r_buffe; // Variable initializations: He = 1.00; r_buffe = ; u = ; nA = ; vC4 = ; vC1 = ; vC3 = ; vCK = ; vEFF = ; vSN = ; vEX = ; vPI = ; vLK = ; time_ = ; end model korzeniewski_zoladz_2001__ADP_mi(ADP_mi, ADP_ti, ADP_fi) // Assignment Rules: ADP_mi := ADP_ti - ADP_fi; // Variable initializations: ADP_ti = ; ADP_fi = ; end model korzeniewski_zoladz_2001__ADP_fi(ADP_fi, ADP_ti, Mg_fi, time_) // Assignment Rules: ADP_fi := ADP_ti / (1.0 + Mg_fi / kDDi); // Variable initializations: kDDi = 282; ADP_ti = ; Mg_fi = ; time_ = ; end model korzeniewski_zoladz_2001__ADP_ti(ADP_ti, ATP_ti) // Assignment Rules: ADP_ti := Ai_SUM - ATP_ti; // Variable initializations: Ai_SUM = 16260.0; ATP_ti = ; end model korzeniewski_zoladz_2001__ATP_mi(ATP_mi, ATP_ti, ATP_fi) // Assignment Rules: ATP_mi := ATP_ti - ATP_fi; // Variable initializations: ATP_ti = ; ATP_fi = ; end model korzeniewski_zoladz_2001__ATP_fi(ATP_fi, ATP_ti, Mg_fi) // Assignment Rules: ATP_fi := ATP_ti / (1.0 + Mg_fi / kDTi); // Variable initializations: kDTi = 17; ATP_ti = ; Mg_fi = ; end model korzeniewski_zoladz_2001__ATP_ti(ATP_ti, R_cm, vSN, vEX, time_) // Rate Rules: ATP_ti' = (vSN - vEX) * R_cm; // Variable initializations: ATP_ti = 1.00; R_cm = ; vSN = ; vEX = ; time_ = ; end model korzeniewski_zoladz_2001__ADP_me(ADP_me, ADP_te, ADP_fe) // Assignment Rules: ADP_me := ADP_te - ADP_fe; // Variable initializations: ADP_te = ; ADP_fe = ; end model korzeniewski_zoladz_2001__ADP_fe(ADP_fe, ADP_te, Mg_fe) // Assignment Rules: ADP_fe := ADP_te / (1.0 + Mg_fe / kDDe); // Variable initializations: kDDe = 347; ADP_te = ; Mg_fe = ; end model korzeniewski_zoladz_2001__ADP_te(ADP_te, vUT, vEX, vAK, vCK, time_) // Rate Rules: ADP_te' = vUT - (vEX + 2.0 * vAK + vCK); // Variable initializations: ADP_te = 1.00; vUT = ; vEX = ; vAK = ; vCK = ; time_ = ; end model korzeniewski_zoladz_2001__ATP_me(ATP_me, ATP_te, ATP_fe) // Assignment Rules: ATP_me := ATP_te - ATP_fe; // Variable initializations: ATP_te = ; ATP_fe = ; end model korzeniewski_zoladz_2001__ATP_fe(ATP_fe, ATP_te, Mg_fe) // Assignment Rules: ATP_fe := ATP_te / (1.0 + Mg_fe / kDTe); // Variable initializations: kDTe = 24; ATP_te = ; Mg_fe = ; end model korzeniewski_zoladz_2001__ATP_te(ATP_te, vUT, vEX, vAK, vCK, time_) // Rate Rules: ATP_te' = (vEX + vAK + vCK) - vUT; // Variable initializations: ATP_te = 1.00; vUT = ; vEX = ; vAK = ; vCK = ; time_ = ; end model korzeniewski_zoladz_2001__AMP_e(AMP_e, ATP_te, ADP_te) // Assignment Rules: AMP_e := Ae_SUM - (ATP_te + ADP_te); // Variable initializations: Ae_SUM = 1600.2; ATP_te = ; ADP_te = ; end model korzeniewski_zoladz_2001__Cr(Cr, PCr) // Assignment Rules: Cr := C_SUM - PCr; // Variable initializations: C_SUM = 35000.0; PCr = ; end model korzeniewski_zoladz_2001__PCr(PCr, vCK, time_) // Rate Rules: PCr' = - vCK; // Variable initializations: PCr = 1.00; vCK = ; time_ = ; end model korzeniewski_zoladz_2001__Pi_ji(Pi_ji, Pi_ti, pH_i, pKa, time_) // Assignment Rules: Pi_ji := Pi_ti / (1.0 + power(10.0, pH_i - pKa)); // Variable initializations: Pi_ti = ; pH_i = ; pKa = ; time_ = ; end model korzeniewski_zoladz_2001__Pi_je(Pi_je, Pi_te, pH_e, pKa, time_) // Assignment Rules: Pi_je := Pi_te / (1.0 + power(10.0, pH_e - pKa)); // Variable initializations: Pi_te = ; pH_e = ; pKa = ; time_ = ; end model korzeniewski_zoladz_2001__Pi_ti(Pi_ti, vPI, vSN, R_cm, time_) // Rate Rules: Pi_ti' = (vPI - vSN) * R_cm; // Variable initializations: Pi_ti = 1.00; vPI = ; vSN = ; R_cm = ; time_ = ; end model korzeniewski_zoladz_2001__Pi_te(Pi_te, vUT, vPI, time_) // Rate Rules: Pi_te' = vUT - vPI; // Variable initializations: Pi_te = 1.00; vUT = ; vPI = ; time_ = ; end model korzeniewski_zoladz_2001__Mg_fe(Mg_fe) // Variable initializations: Mg_fe = 4000.0; end model korzeniewski_zoladz_2001__Mg_fi(Mg_fi) // Variable initializations: Mg_fi = 380.0; end model korzeniewski_zoladz_2001__P_SUM(P_SUM, Pi_ti, Pi_te, PCr, ATP_te, ADP_te, AMP_e, ATP_ti, ADP_ti, R_cm, time_) // Assignment Rules: P_SUM := PCr + ATP_te * 3.0 + ADP_te * 2.0 + AMP_e + Pi_te + (ATP_ti * 3.0 + ADP_ti * 2.0 + Pi_ti) / R_cm; // Variable initializations: Pi_ti = ; Pi_te = ; PCr = ; ATP_te = ; ADP_te = ; AMP_e = ; ATP_ti = ; ADP_ti = ; R_cm = ; time_ = ; end model korzeniewski_zoladz_2001__c_2(c_2, R_cm, vC3, vC4, time_) // Rate Rules: c_2' = (vC3 + vC4 * 2.0) * R_cm * 2.0; // Variable initializations: c_2 = 1.00; R_cm = ; vC3 = ; vC4 = ; time_ = ; end model korzeniewski_zoladz_2001__c_3(c_3, c_2) // Assignment Rules: c_3 := ct - c_2; // Variable initializations: ct = 270.0; c_2 = ; end model korzeniewski_zoladz_2001__UQ(UQ, UQH2) // Assignment Rules: UQ := Ut - UQH2; // Variable initializations: Ut = 1350.0; UQH2 = ; end model korzeniewski_zoladz_2001__UQH2(UQH2, R_cm, vC1, vC3, time_) // Rate Rules: UQH2' = R_cm * (vC1 - vC3); // Variable initializations: UQH2 = 1.00; R_cm = ; vC1 = ; vC3 = ; time_ = ; end model korzeniewski_zoladz_2001__a_2(a_2, at_, Ema, Z, time_) // Assignment Rules: A3_2 := power(10.0, (Ema - Ema0) / Z); // Rate Rules: a_2' = at_ / (1.0 + A3_2); // Variable initializations: a_2 = 1.00; Ema0 = 540.0; at_ = 135.0; Ema = ; Z = ; time_ = ; end model korzeniewski_zoladz_2001__a_3(a_3, at_, a_2) // Assignment Rules: a_3 := at_ - a_2; // Variable initializations: at_ = ; a_2 = ; end model korzeniewski_zoladz_2001__vDH(vDH, NAD, NADH) // Assignment Rules: vDH := kDH * (1.0 / power(1.0 + KmN / (NAD / NADH), pD)); // Variable initializations: kDH = 28074; KmN = 100.0; pD = 0.8; NAD = ; NADH = ; end model korzeniewski_zoladz_2001__vC1(vC1, EmN, EmU, protonmotive_force) // Assignment Rules: vC1 := kC1 * delta_GC1; delta_GC1 := EmU - (EmN + protonmotive_force * (4.0 / 2.0)); // Variable initializations: kC1 = 238.95; EmN = ; EmU = ; protonmotive_force = ; end model korzeniewski_zoladz_2001__vC3(vC3, Emc, u, EmU, protonmotive_force) // Assignment Rules: vC3 := kC3 * delta_GC3; delta_GC3 := Emc - (EmU + protonmotive_force * ((4.0 - 2.0 * u) / 2.0)); // Variable initializations: kC3 = 136.41; Emc = ; u = ; EmU = ; protonmotive_force = ; end model korzeniewski_zoladz_2001__vC4(vC4, O2, c_2, a_2) // Assignment Rules: vC4 := kC4 * a_2 * c_2 * (1.0 / (1.0 + KmO / O2)); // Variable initializations: kC4 = 136.41; KmO = 120.0; O2 = ; c_2 = ; a_2 = ; end model korzeniewski_zoladz_2001__vSN(vSN, nA, Z, Emc, u, EmU, protonmotive_force, ATP_ti, ADP_ti, Pi_ti, F) // Assignment Rules: vSN := kSN * ((gamma - 1.0) / (gamma + 1.0)); delta_GSN := nA * protonmotive_force - delta_Gp; delta_Gp := delta_Gp0 / (F + Z * log(1000000.0 * (ATP_ti / (ADP_ti * Pi_ti)))); gamma := power(10.0, delta_GSN / Z); // Variable initializations: nA = 2.5; kSN = 34316.0; delta_Gp0 = 31.9; Z = ; Emc = ; u = ; EmU = ; protonmotive_force = ; ATP_ti = ; ADP_ti = ; Pi_ti = ; F = ; end model korzeniewski_zoladz_2001__vEX(vEX, Z, ATP_fi, ADP_fe, ADP_fi, ATP_fe, in_membrane_potential) // Assignment Rules: vEX := kEX * (ADP_fe / (ADP_fe + ATP_fe * power(10.0, - in_membrane_potential / Z)) - ADP_fi / (ADP_fi + ATP_fi * power(10.0, - in_membrane_potential / Z))) * (1.0 / (1.0 + km_ADP / ADP_fe)); // Variable initializations: Z = ; ATP_fi = ; ADP_fe = ; ADP_fi = ; ATP_fe = ; in_membrane_potential = ; kEX = 54572; km_ADP = 3.5; end model korzeniewski_zoladz_2001__vUT(vUT, ATP_te) // Assignment Rules: vUT := kUT * (1.0 / (1.0 + km_A / ATP_te)); // Variable initializations: ATP_te = ; km_A = 150.0; kUT = 686.5; end model korzeniewski_zoladz_2001__vAK(vAK, ADP_fe, ADP_me, ATP_me, AMP_e) // Assignment Rules: vAK := kf_AK * ADP_me * ADP_fe - kb_AK * ATP_me * AMP_e; // Variable initializations: ADP_fe = ; ADP_me = ; ATP_me = ; AMP_e = ; kf_AK = 862.10; kb_AK = 22.747; end model korzeniewski_zoladz_2001__vLK(vLK, protonmotive_force) // Assignment Rules: vLK := kL1 * (exp(kL2 * protonmotive_force) - 1.0); // Variable initializations: kL1 = 2.5; kL2 = 0.038; protonmotive_force = ; end model korzeniewski_zoladz_2001__vPI(vPI, Pi_je, He, Pi_ji, Hi) // Assignment Rules: vPI := kPI * (He * Pi_je - Hi * Pi_ji); // Variable initializations: Pi_je = ; He = ; Pi_ji = ; Hi = ; kPI = 69.421; end model korzeniewski_zoladz_2001__vCK(vCK, ATP_te, He, ADP_te, Cr, PCr) // Assignment Rules: vCK := kf_CK * ADP_te * PCr * He - kb_CK * ATP_te * Cr; // Variable initializations: ATP_te = ; He = ; ADP_te = ; Cr = ; PCr = ; kf_CK = 1.9258; kb_CK = 0.00087538; end model korzeniewski_zoladz_2001__vEFF(vEFF, pH_e) // Assignment Rules: vEFF := k_EFF * (pH_o - pH_e); // Variable initializations: pH_e = ; pH_o = 7.0; k_EFF = 1.9258; end model *korzeniewski_zoladz_2001____main() // Sub-modules, and any changes to those submodules: environment: korzeniewski_zoladz_2001__environment(time_); cell: korzeniewski_zoladz_2001__cell(R_cm, R, T, F, S, Z, electric_potential, protonmotive_force, ex_membrane_potential, in_membrane_potential, pH_e, pH_i, pKa, He0, Hi0, r_buffi, r_buffe, BN, u); redox_potentials: korzeniewski_zoladz_2001__redox_potentials(EmN, EmU, Emc, Ema, Z, NAD0, NADH0, UQ0, UQH20, c_20, c_30, protonmotive_force, u); NAD: korzeniewski_zoladz_2001__NAD(NAD0, NADH0); NADH: korzeniewski_zoladz_2001__NADH(NADH0, BN, R_cm, vDH0, vC10, time_); O2: korzeniewski_zoladz_2001__O2(O20, vC40, time_); Hi: korzeniewski_zoladz_2001__Hi(Hi0, r_buffi, u, nA, vC40, vC10, vC30, vSN0, vEX0, vPI0, vLK0, R_cm, time_); He: korzeniewski_zoladz_2001__He(He0, r_buffe, u, nA, vC40, vC10, vC30, vCK0, vEFF0, vSN0, vEX0, vPI0, vLK0, time_); ADP_mi: korzeniewski_zoladz_2001__ADP_mi(ADP_mi0, ADP_ti0, ADP_fi0); ADP_fi: korzeniewski_zoladz_2001__ADP_fi(ADP_fi0, ADP_ti0, Mg_fi0, time_); ADP_ti: korzeniewski_zoladz_2001__ADP_ti(ADP_ti0, ATP_ti0); ATP_mi: korzeniewski_zoladz_2001__ATP_mi(ATP_mi0, ATP_ti0, ATP_fi0); ATP_fi: korzeniewski_zoladz_2001__ATP_fi(ATP_fi0, ATP_ti0, Mg_fi0); ATP_ti: korzeniewski_zoladz_2001__ATP_ti(ATP_ti0, R_cm, vSN0, vEX0, time_); ADP_me: korzeniewski_zoladz_2001__ADP_me(ADP_me0, ADP_te0, ADP_fe0); ADP_fe: korzeniewski_zoladz_2001__ADP_fe(ADP_fe0, ADP_te0, Mg_fe0); ADP_te: korzeniewski_zoladz_2001__ADP_te(ADP_te0, vUT0, vEX0, vAK0, vCK0, time_); ATP_me: korzeniewski_zoladz_2001__ATP_me(ATP_me0, ATP_te0, ATP_fe0); ATP_fe: korzeniewski_zoladz_2001__ATP_fe(ATP_fe0, ATP_te0, Mg_fe0); ATP_te: korzeniewski_zoladz_2001__ATP_te(ATP_te0, vUT0, vEX0, vAK0, vCK0, time_); AMP_e: korzeniewski_zoladz_2001__AMP_e(AMP_e0, ATP_te0, ADP_te0); Cr: korzeniewski_zoladz_2001__Cr(Cr0, PCr0); PCr: korzeniewski_zoladz_2001__PCr(PCr0, vCK0, time_); Pi_ji: korzeniewski_zoladz_2001__Pi_ji(Pi_ji0, Pi_ti0, pH_i, pKa, time_); Pi_je: korzeniewski_zoladz_2001__Pi_je(Pi_je0, Pi_te0, pH_e, pKa, time_); Pi_ti: korzeniewski_zoladz_2001__Pi_ti(Pi_ti0, vPI0, vSN0, R_cm, time_); Pi_te: korzeniewski_zoladz_2001__Pi_te(Pi_te0, vUT0, vPI0, time_); Mg_fe: korzeniewski_zoladz_2001__Mg_fe(Mg_fe0); Mg_fi: korzeniewski_zoladz_2001__Mg_fi(Mg_fi0); P_SUM: korzeniewski_zoladz_2001__P_SUM(P_SUM0, Pi_ti0, Pi_te0, PCr0, ATP_te0, ADP_te0, AMP_e0, ATP_ti0, ADP_ti0, R_cm, time_); c_2: korzeniewski_zoladz_2001__c_2(c_20, R_cm, vC30, vC40, time_); c_3: korzeniewski_zoladz_2001__c_3(c_30, c_20); UQ: korzeniewski_zoladz_2001__UQ(UQ0, UQH20); UQH2: korzeniewski_zoladz_2001__UQH2(UQH20, R_cm, vC10, vC30, time_); a_2: korzeniewski_zoladz_2001__a_2(a_20, at_, Ema, Z, time_); a_3: korzeniewski_zoladz_2001__a_3(a_30, at_, a_20); vDH: korzeniewski_zoladz_2001__vDH(vDH0, NAD0, NADH0); vC1: korzeniewski_zoladz_2001__vC1(vC10, EmN, EmU, protonmotive_force); vC3: korzeniewski_zoladz_2001__vC3(vC30, Emc, u, EmU, protonmotive_force); vC4: korzeniewski_zoladz_2001__vC4(vC40, O20, c_20, a_20); vSN: korzeniewski_zoladz_2001__vSN(vSN0, nA, Z, Emc, u, EmU, protonmotive_force, ATP_ti0, ADP_ti0, Pi_ti0, F); vEX: korzeniewski_zoladz_2001__vEX(vEX0, Z, ATP_fi0, ADP_fe0, ADP_fi0, ATP_fe0, in_membrane_potential); vUT: korzeniewski_zoladz_2001__vUT(vUT0, ATP_te0); vAK: korzeniewski_zoladz_2001__vAK(vAK0, ADP_fe0, ADP_me0, ATP_me0, AMP_e0); vLK: korzeniewski_zoladz_2001__vLK(vLK0, protonmotive_force); vPI: korzeniewski_zoladz_2001__vPI(vPI0, Pi_je0, He0, Pi_ji0, Hi0); vCK: korzeniewski_zoladz_2001__vCK(vCK0, ATP_te0, He0, ADP_te0, Cr0, PCr0); vEFF: korzeniewski_zoladz_2001__vEFF(vEFF0, pH_e); end