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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
  1. Agent-agent represents unbound neighboring agents, while agent + agent represents bound agents moving together.