Model Mathematics

Component: environment

Component: cell

electric_potential=-protonmotive_force-delta_pH in_membrane_potential=0.65electric_potential ex_membrane_potential=-0.35electric_potential u=electric_potentialprotonmotive_force C0_i=10.0-pH_i-10.0-pH_i-dpHdpH r_buffi=c_buffiC0_i C0_e=10.0-pH_e-10.0-pH_e-dpHdpH r_buffe=c_buffeC0_e S=2.303RT Z=2.303RTF pH_e=-log10He1000000.0 pH_i=-log10Hi1000000.0 delta_pH=ZpH_i-pH_e

Component: redox_potentials

EmN=EmN0+Z2.0log10NADNADH EmU=EmU0+Z2.0log10UQUQH2 Emc=Emc0+Zlog10c_3c_2 Ema=Emc+protonmotive_force2.0+2.0u2.0

Component: NAD

NAD=Nt-NADH

Component: NADH

ddtimeNADH=vDH-vC1R_cmBN

Component: O2

ddtimeO2=-vC4

Component: Hi

ddtimeHi=4.0-2.0uvC3+4.0vC1-2.02.0+2.0uvC4+nAvSN+uvEX+1.0-uvPI+vLKR_cmr_buffi

Component: He

ddtimeHe=2.02.0+2.0uvC4+4.0-2.0uvC3+4.0vC1-nAvSN+uvEX+1.0-uvPI+vLK+vCK+vEFFr_buffe

Component: ADP_mi

ADP_mi=ADP_ti-ADP_fi

Component: ADP_fi

ADP_fi=ADP_ti1.0+Mg_fikDDi

Component: ADP_ti

ADP_ti=Ai_SUM-ATP_ti

Component: ATP_mi

ATP_mi=ATP_ti-ATP_fi

Component: ATP_fi

ATP_fi=ATP_ti1.0+Mg_fikDTi

Component: ATP_ti

ddtimeATP_ti=vSN-vEXR_cm

Component: ADP_me

ADP_me=ADP_te-ADP_fe

Component: ADP_fe

ADP_fe=ADP_te1.0+Mg_fekDDe

Component: ADP_te

ddtimeADP_te=vUT-vEX+2.0vAK+vCK

Component: ATP_me

ATP_me=ATP_te-ATP_fe

Component: ATP_fe

ATP_fe=ATP_te1.0+Mg_fekDTe

Component: ATP_te

ddtimeATP_te=vEX+vAK+vCK-vUT

Component: AMP_e

AMP_e=Ae_SUM-ATP_te+ADP_te

Component: Cr

Cr=C_SUM-PCr

Component: PCr

ddtimePCr=-vCK

Component: Pi_ji

Pi_ji=Pi_ti1.0+10.0pH_i-pKa

Component: Pi_je

Pi_je=Pi_te1.0+10.0pH_e-pKa

Component: Pi_ti

ddtimePi_ti=vPI-vSNR_cm

Component: Pi_te

ddtimePi_te=vUT-vPI

Component: Mg_fe

Component: Mg_fi

Component: P_SUM

P_SUM=PCr+ATP_te3.0+ADP_te2.0+AMP_e+Pi_te+ATP_ti3.0+ADP_ti2.0+Pi_tiR_cm

Component: c_2

ddtimec_2=vC3+vC42.0R_cm2.0

Component: c_3

c_3=ct-c_2

Component: UQ

UQ=Ut-UQH2

Component: UQH2

ddtimeUQH2=R_cmvC1-vC3

Component: a_2

ddtimea_2=at1.0+A3_2 A3_2=10.0Ema-Ema0Z

Component: a_3

a_3=at-a_2

Component: vDH

vDH = kDH 1.01.0+ KmN NAD NADH pD

Component: vC1

vC1 = kC1 delta_GC1 delta_GC1= EmU - EmN +protonmotive_force4.02.0

Component: vC3

vC3 = kC3 delta_GC3 delta_GC3= Emc - EmU +protonmotive_force4.0-2.0 u 2.0

Component: vC4

vC4 = kC4 a_2 c_2 1.01.0+ KmO O2

Component: vSN

vSN = kSN gamma -1.0 gamma +1.0 gamma =10.0 delta_GSN Z delta_GSN= nA protonmotive_force-delta_Gp delta_Gp= delta_Gp0 F + Z log101000000.0 ATP_ti ADP_ti Pi_ti

Component: vEX

vEX=kEXADP_feADP_fe+ATP_fe10.0-in_membrane_potentialZ-ADP_fiADP_fi+ATP_fi10.0-in_membrane_potentialZ1.01.0+km_ADPADP_fe

Component: vUT

vUT=kUT1.01.0+km_AATP_te

Component: vAK

vAK=kf_AKADP_meADP_fe-kb_AKATP_meAMP_e

Component: vLK

vLK=kL1kL2protonmotive_force-1.0

Component: vPI

vPI=kPIHePi_je-HiPi_ji

Component: vCK

vCK=kf_CKADP_tePCrHe-kb_CKATP_teCr

Component: vEFF

vEFF=k_EFFpH_o-pH_e