TABLE 2.
GranSim rules for M. tuberculosis modeled as continuous variables or individual agentsa
| Bacterial event | Rule for continuous M. tuberculosis variables | Rule for individual M. tuberculosis agents |
|---|---|---|
| Growth (intracellular or extracellular) | νb = growth rate | νb = growth rate |
| Mtb(t + 1) = (1 + νb)Mtb(t) | Shuffle MtbList | |
| For i = 1 to Mtb(t) | ||
| Bi(t + 1) = (1 + νb)Bi(t) | ||
| If Bi > τdiv | ||
| Make new Mtb agent | ||
| Divide Bi and Li into fractions f and (1 − f) between two daughter agents | ||
| Else if Bi < τdeath | ||
| Mtb agent dies | ||
| Death (from host-mediated killing or lack of nutrients) | nrKill = nr of Mtb to kill | nrKill = nr of Mtb to kill |
| Mtb(t + 1) = Mtb(t)-nrKill | Shuffle MtbList | |
| Delete 1st “nrKill” Mtb agents on MtbList | ||
| Dispersion of a fraction of intracellular M. tuberculosis to Moore neighborhood (when a chronically infected macrophage bursts) | fd = fraction to disperse | fd = fraction to disperse |
| dispMtb = fdMtb(t) | dispMtb = fdMtb(t) | |
| dMtb = dispMtb/NM | dMtbBase = dispMtb/NM | |
| for m = 1 to NM | dMtbExtra = mod(dispMtb,NM) | |
| Mtbm(t + 1) = Mtbm(t) + dMtb | Shuffle MtbList | |
| For m = 1 to dMtbExtra | ||
| Move 1st “dMtbBase + 1” agents in MtbList to compartment m | ||
| For m = dMtbExtra + 1 to NM | ||
| Move 1st dMtbBase agents in MtbList to compartment m | ||
| Delete the rest of MtbList | ||
| Phagocytosis (move extracellular M. tuberculosis to intracellular location) | count = nr of Mtb to phagocytose | count = nr of Mtb to phagocytose |
| MtbE(t + 1) = MtbE(t) − count | Shuffle MtbEList | |
| MtbI(t + 1) = MtbI(t) + count | Move 1st “count” Mtb agents from MtbEList to MtbIList |