ATP calculation
In ceas: Cellular Energetics Analysis Software

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(ceas)

\usepackage[version=4,arrows=pgf]{mhchem} Proton production rate (PPR):

[\text{PPR} = \frac{\text{ECAR value}}{\text{buffer}}]

[\text{PPR}_{\text{mito}} = \frac{10^{\text{pH}-\text{pK}_a}}{1+10^{\text{pH}-\text{pK}_a}} \cdot \frac{\text{H}^+}{\text{O}_2} \cdot \text{OCR}]

Calculates the proton production from glucose during its conversion to bicarbonate and \ce{H+} assuming max (\frac{\ce{H}^+}{\ce{O2}}) of 1

[\text{PPR}\text{glyc} = \text{PPR} - \text{PPR}\text{resp}]

[ \ce{2H2 + O2 -> 2H2O} ]

Calculates the proton production from glucose during its conversion to (\ce{lactate + H+}).

Joules of ATP (JATP) production:

[ \text{ATP}{\text{glyc}} = \Bigl(\text{PPR}\text{glyc} \cdot \frac{\text{ATP}}{\text{lactate}}\Bigl) + \Bigl(\text{MITO}\text{resp} \cdot 2 \cdot \frac{\text{P}}{\text{O}\text{glyc}}\Bigl) ]

[ \frac{\text{ATP}}{\text{lactate}} = 1 ]

with (\frac{\text{P}}{{\text{O}_\text{glyc}}}) = 0.167 for glucose (0.242 for glycogen).

[ \text{ATP}\text{resp} = \Bigl(\text{coupled MITO}\text{resp} \cdot 2 \cdot \frac{\text{P}}{\text{O}\text{oxphos}}\Bigl) + \Bigl(\text{MITO}\text{resp} \cdot 2 \cdot \frac{\text{P}}{\text{O}_\text{TCA}}\Bigl) ]

with (\frac{\text{P}}{{\text{O}\text{oxphos}}}) = 2.486 and (\frac{\text{P}}{{\text{O}\text{TCA}}}) = 0.167.