Kinetic diagram of the modules of the mitochondria model. (A–C) Kinetic diagram of the ATP synthase model (Pietrobon and Caplan, 1985). (A) The model consists of six states, representing different protein configurations. ATP molecules are represented as T, ADP molecules as D, phosphate as Pi, ATP synthase as E, and H⁺ as protons. The model considers the binding of ATP and ADP from the matrix and the IMS. (B) Each state is associated with a number from 1 to 6. A clockwise cycle, starting from state 6 corresponds to the binding of three protons from the IMS (6 → 5), followed by their transport to the matrix (5 → 4) and subsequent binding of ADP and Pi (4 → 3), to the synthesis of ATP (3 → 2), and unbinding of three protons in the matrix (2 → 1). Each transition has an associated rate constant k_ij. The list of all the reactions is in Table 1 and the list of parameters is in Table 2. (C) The cycles are considered positive in the counterclockwise direction and named a, b, and c. (D) Membrane potential considered in the ATP synthase model. ΔΨ = Ψ₄ − Ψ₁ is the electrical potential difference between the matrix and IMS (or cytosol), ΔΨ_m is the electrical potential difference across the membrane, $ΔΨbin$ and $ΔΨbex$ are the phase-boundary potentials. (E–G) Kinetic diagram of the ANT model. (E) The model consists of 11 states, L represents the free protein, and YLX is a triple molecular state with one X molecule bound from the matrix side and one Y molecule bound from the IMS. X and Y represent ATP or ADP molecules, respectively. The model has been adapted from previous work (Metelkin et al., 2006). (F) In this representation, the binding and unbinding of ATP and ADP are explicitly shown, molecules from the IMS side are in green, and those from the matrix side are in purple. (G) The cycles are considered positive going from the matrix to the IMS.