Table 3 Interacting agents, rule execution probabilities, and behavior
From: Agent-based modeling of competence phenotype switching in Bacillus subtilis
Rules | Interacting agents | Probability | Resulting action |
|---|---|---|---|
bind | Repressor-Promoter | 0.5 | Repressor + Promoter |
DegU-Promoter | 0.5 | DegU + Promoter | |
ComX-Promoter | 0.5 | ComX + Promoter | |
ComK-Promoter | 0.5 | ComK + Promoter | |
ComK-Promoter-DegU | 0.8 | ComK + Promoter + DegU | |
ComK-ComK | 0.8 | ComK + ComK | |
Ribosome-mRNA | 0.9 | Ribosome + mRNA | |
ClpC/ClpP + MecA-ComK | 0.6 | ClpC/ClpP + MecA + ComK | |
ClpC/ClpP + MecA-ComS | 0.7 | ClpC/ClpP + MecA + ComS | |
ClpP/ClpC-MecA | 0.5 | ClpC/ClpP + MecA | |
consumePeptide | Cell | 0.8 | New ComX |
death | mRNA | 0.0001 | Remove mRNA |
ClpC/ClpP + MecA + ComK/ComS | 0.5 | Remove ComK or Remove ComS | |
Cell | 0.0001 | Remove Cell | |
dissociation | Repressor | 0.0001 | Repressor-Promoter |
DegU | 0.0001 | DegU-Promoter | |
generatePeptide | Cell | 0.8 | |
Life | Cell | 0.8 | New Cell if not starving |
Cell | 0.0001 | Remove Repressor if starving | |
Move | Cell | 0.5 | chemotaxis |
Move | ComK, ComS, ComX, DegU, MecA, ClpC/ClpP, mRNA, Ribosome, Repressor | Random walk, see text | |
Shove | Cell | - | |
transcription | Promoter | 0.0001 | New mRNA |
Promoter + ComK dimer | 0.001 | New mRNA | |
Promoter + ComK tertramer | 0.5 | New mRNA | |
Promoter + ComX | 0.5 | New mRNA | |
translation | Ribosome + mRNA | 0.5 | New ComK or New ComS |