TABLE 3.
Variables used in GranSim-CBMa
| Variable | Unit | Description |
|---|---|---|
| νb | h−1 | Growth rate |
| νL | h−1 | Net lipid inclusion generation rate |
| νpL | h−1 | Lipid inclusion production rate predicted by CBM |
| νcL | h−1 | Lipid inclusion consumption rate predicted by CBM |
| d | timestep−1 | Biomass degradation rate |
| η | Switching parameter to calculate objective function and biomass degradation rate | |
| MtbXList | List of M. tuberculosis agents in location X (E, extracellular; I, intracellular) | |
| Mtb(t) | No. of bacteria as continuous variables or individual agents in MtbList at timestep t | |
| Bi(t) | BU | Biomass of M. tuberculosis agent i at timestep t |
| Li(t) | fmol | Lipid inclusions of M. tuberculosis agent i at timestep t |
| Xi(t) | Location of M. tuberculosis agent i at timestep t (E, extracellular; I, intracellular) | |
| NM | No. of grid compartments in Moore neighborhood (adjacent grid compartments in a 2-dimensional grid) | |
| vilow | fmol/h · BU | Lower limit on import flux for nutrient i (set to zero) |
| viup | fmol/h · BU | Upper limit on import flux for nutrient i (dependent on Vmax,i and Ki) |
| Z | Objective function to be optimized by the CBM (a linear combination of νb and νL) |
a
Conversion factor, 10 min/timestep. 1 BU = 196 fg dry weight.