Component: Environment

Component: Fixed_parameters

$H_e = 10 − pH_e$

$W_x = 0.9 W_m$

$W_i = 0.1 W_m$

$H_i = H_e$

$K_i = K_e$

Component: Adjustable_parameters

Component: Dehydrogenase_flux

$J_DH = x_DH (r NAD_x − NADH_x) (1 + Pi_x / k_Pi1) / (1 + Pi_x / k_Pi2)$

Component: dH_x_dt

$d H_x d t = x_buff H_x (J_DH − 5 J_C1 − 2 J_C3 − 4 J_C4 − n_A J_F1 + 2 J_Pi1 + J_Hle − J_KH) / W_x$

Component: dK_x_dt

$d K_x d t = (J_KH + J_K) / W_x$

Component: dMg_x_dt

$d Mg_x d t = (− J_MgATPx − J_MgADPx) / W_x$

Component: dNADH_x_dt

$d NADH_x d t = (J_DH − J_C1) / W_x$

Component: dQH2_dt

$d QH2 d t = (J_C1 − J_C3) / W_x$

Component: dCred_dt

$d Cred d t = (2 J_C3 − 2 J_C4) / W_i$

Component: dATP_x_dt

$d ATP_x d t = (J_F1 − J_ANT) / W_x$

Component: dADP_x_dt

$d ADP_x d t = (− J_F1 + J_ANT) / W_x$

Component: dATP_mx_dt

$d ATP_mx d t = J_MgATPx / W_x$

Component: dADP_mx_dt

$d ADP_mx d t = J_MgADPx / W_x$

Component: dPi_x_dt

$d Pi_x d t = (− J_F1 + J_Pi1) / W_x$

Component: dATP_i_dt

$d ATP_i d t = (J_ATP + J_ANT + J_AKi) / W_i$

Component: dADP_i_dt

$d ADP_i d t = (J_ADP − J_ANT − 2 J_AKi) / W_i$

Component: dAMP_i_dt

$d AMP_i d t = (J_AMP + J_AKi) / W_i$

Component: dATP_mi_dt

$d ATP_mi d t = J_MgATPi / W_i$

Component: dADP_mi_dt

$d ADP_mi d t = J_MgADPi / W_i$

Component: dPi_i_dt

$d Pi_i d t = (− J_Pi1 + J_Pi2) / W_i$

Component: dPsi_dt

$d dPsi d t = 1.48e5 (4 J_C1 + 2 J_C3 + 4 J_C4 − n_A J_F1 − J_ANT − J_Hle − J_K)$

Component: dO2_dt

$d O2 d t = 0$

Component: Electron_flux_complex_I

$dG_C1op = dG_C1o − 1 RT ln (H_x / 1e-7) − RT ln (Q / QH2)$

$J_C1 = x_C1 (e − ((dG_C1op + 4 dG_H) / RT) NADH_x − NAD_x)$

Component: Proton_motive_energy

$dG_H = F dPsi + RT ln (H_i / H_x)$

Component: Electron_flux_complex_III

$dG_C3op = dG_C3o + 2 RT ln (H_x / 1e-7) − RT ln (QH2 / Q)$

$J_C3 = x_C3 (1 + Pi_x / k_Pi3) / (1 + Pi_x / k_Pi4) (e − ((dG_C3op + 4 dG_H − 2 F dPsi) / 2 RT) Cox − Cred)$

Component: Electron_flux_complex_IV

$dG_C4op = dG_C4o − 2 RT ln (H_x / 1e-7) − RT / 2 ln O2$

$J_C4 = x_C4 1 / (1 + k_O2 / O2) Cred / Ctot (e − ((dG_C4op + 2 dG_H) / 2 RT) Cred − Cox e F dPsi / RT)$

Component: ATP_synthesis_flux

$J_F1 = x_F1 (e − ((dG_F1o − n_A dG_H) / RT) K_DD / K_DT ADP_mx Pi_x − ATP_mx)$

Component: MgATPx_binding_flux

$ATP_fx = ATP_x − ATP_mx$

$J_MgATPx = x_MgA (ATP_fx Mg_x − K_DT ATP_mx)$

Component: MgADPx_binding_flux

$ADP_fx = ADP_x − ADP_mx$

$J_MgADPx = x_MgA (ADP_fx Mg_x − K_DD ADP_mx)$

Component: MgATPi_binding_flux

$ATP_fi = ATP_i − ATP_mi$

$J_MgATPi = x_MgA (ATP_fi Mg_i − K_DT ATP_mi)$

Component: MgADPi_binding_flux

$ADP_fi = ADP_i − ADP_mi$

$J_MgADPi = x_MgA (ADP_fi Mg_i − K_DD ADP_mi)$

Component: ATP_substrate_flux

$J_ATP = gamma x_A (ATP_e − ATP_i)$

Component: ADP_substrate_flux

$J_ADP = gamma x_A (ADP_e − ADP_i)$

Component: AMP_substrate_flux

$J_AMP = gamma x_A (AMP_e − AMP_i)$

Component: Pi_substrate_flux

$J_Pi2 = gamma x_Pi2 (Pi_e − Pi_i)$

Component: ANT_flux

$Psi_x = − 0.65 dPsi$

$Psi_i = 0.35 dPsi$

$J_ANT = {x_ANT (ADP_fi / (ADP_fi + ATP_fi e − F Psi_i / RT) − ADP_fx / (ADP_fx + ATP_fx e − F Psi_x / RT)) ADP_fi / (ADP_fi + k_mADP) if (ADP_fi > 1E-12) ∨ (ATP_fi > 1E-12) 0 if$

Component: Phosphate_hydrogen_cotransporter_flux

$H2PIi = Pi_i H_i / (H_i + k_dHPi)$

$H2PIx = Pi_x H_x / (H_x + k_dHPi)$

$J_Pi1 = x_Pi1 (H_x H2PIi − H_i H2PIx) / (H2PIi + k_PiH)$

Component: Adenylate_kinase_flux

$J_AKi = x_AK (K_AK ADP_i ADP_i − AMP_i ATP_i)$

Component: Hydrogen_leak_flux

$J_Hle = x_Hle dPsi (H_i e F dPsi / RT − H_x) / (e F dPsi / RT − 1)$

Component: Passive_potassium_flux

$J_K = x_K dPsi (K_i e F dPsi / RT − K_x) / (e F dPsi / RT − 1)$

Component: Potassium_hydrogen_flux

$J_KH = x_KH (K_i H_x − K_x H_i)$

Component: NAD_x_concentration

$NAD_x = NADtot − NADH_x$

Component: Q_concentration

$Q = Qtot − QH2$

Component: Cox_concentration

$Cox = Ctot − Cred$

Component: ADP_binding

$ADP_fe = ADP_e − ADP_me$

$ADP_me = (K_DD + ADP_e + Mg_tot − ((K_DD + ADP_e + Mg_tot) 2 − 4 Mg_tot ADP_e) 0.5) / 2$

Component: Mg_binding

$Mg_e = Mg_tot − ADP_me$

$Mg_i = Mg_e$