Fig 1.
Bioenergetic components of the respiratory model.
The figure depicts the fluxes and variables of the oxidative phosphorylation model. The flux of the electron transport chain energizes the membrane which is used by the ATP synthase to create ATP. The potassium uniport creates a potassium gradient that can be used by the cell as a battery in darkness [3], while the sodium-proton antiport is used to regulate internal pH. X: unknown electron donor.
Table 1.
The model variables.
Table 2.
Parameter estimation results for the electroneutral model.
Fig 2.
Model output for intracellular ATP and ADP concentrations.
Lines labeled EN: electroneutral model using set EN5 in Table 2. Lines labeled EG: electrogenic model using parameter set EG1 in Table 3.
Fig 3.
Model output for intracellular potassium and sodium ions.
Triangles: experimental data from [3]. Lines labeled EN: electroneutral model using set EN5 in Table 2. Lines labeled EG: electrogenic model using parameter set EG1 in Table 3.
Fig 4.
Model output for the proton motive force (pmf), ΔΨ and ΔpH.
The dynamics of the variables are plotted for a short interval (A) and a long interval (B). Lines labeled EN: electroneutral model using set EN5 in Table 2. Lines labeled EG: electrogenic model using parameter set EG1 in Table 3. 58ΔpH: ΔpH converted to mV for comparison with ΔΨ and pmf. At the last time point in (A), the electroneutral model has reached the following percentage of the steady state values: 87% of the pmf, 89% of ΔΨ and 80% of 58ΔpH, while the electrogenic model has reached 92% of the pmf, 96% of ΔΨ and 86% of 58ΔpH. The short interval (A) was plotted in logarithmic scale in Fig A in S1 File to show when the jumps in values occurred.
Table 3.
Parameter estimation results for the electrogenic model.
Fig 5.
Model output for oxygen consumption.
Oxygen consumption of the electroneutral model using parameter set EN5 and electrogenic model using parameter set EG1. Data taken from [24].
Fig 6.
The building blocks of a cell obtained by harmonizing the different data gathered from literature [25, 26].
A 1 ml OD cell suspension contains 1.81 μL cell pellet and 1.36 × 109 halobacterial cells. (A) The 1.81 μL cell pellet consists of 0.47 μL cellular organic material, 0.45 μL cellular basal salt and 0.89 μL inter-cellular basal salt. The total cell volume (1.36 μL from the sum of organic material and cellular basal salt) contains 0.80 μL water. (B) Using a buoyant density of 1.2 mg/mL for the cells [25, 26], the 1.36 μL cell volume is 1.63 μg. This consists of 0.80 μg water and other components. (C) Assuming that a cell pellet contains 1.36 × 109 halobacterial cells, then an individual cell has a mass of 1.2 pg. (D) The components by volume of a cell is given. See S1 File for more details. Units: μL = micro liters, pg = pico grams, fL = femto liters.
Table 4.
Parameter sensitivities.
Table 5.
Initial values of the model variables and constant total concentrations.
Table 6.
Experimental data used in the cost function (Eq (25)).