Biological Background
The bacterial flagellum is assembled from ~30 different proteins through seven
sequential complexation reactions. Multi-subunit assembly (up to 120 copies of
FlgE for the hook) is modeled using a scaffold-with-counters strategy
that generates 237 reaction rules from 7 biological reactions.
| # | Product | Subunits | Total |
|---|
| 1 | flhDC | 4× flhD + 2× flhC | 6 |
| 2 | flagellar motor switch | 26× fliG + 34× fliM + fliN | 61 |
| 3 | flagellar export apparatus subunit | flhA + flhB + fliO + fliP + fliQ + fliR + fliJ + 6× fliI | 13 |
| 4 | flagellar export apparatus | flagellar export apparatus subunit + 12× fliH | 13 |
| 5 | flagellar motor | flagellar motor switch + 2× fliL + flgH + motA + motB + flgB + flgC + flgF + flgG + flgI + fliF + fliE | 13 |
| 6 | flagellar hook | 120× flgE | 120 |
| 7 | flagella | flagellar export apparatus + flagellar motor + fliC + flgL + flgK + 5× fliD + flagellar hook | 11 |
NFSim simulates these rules efficiently without enumerating the species space,
using a network-free stochastic approach that scales well for large rule sets.
Modeling Approach
- Nucleation — two monomers react to create a Growing scaffold with internal counters
- Sequential growth — monomers bind one at a time, incrementing counters
- Completion — when all counters reach targets, the scaffold converts to the finished complex
Starting with enough monomers for 5 flagella (N=5), NFSim simulates 500 seconds of stochastic rule-based assembly. Complexes form hierarchically: FlhDC first (smallest, 6 subunits), then motor switch (61 subunits), export apparatus, motor, the 120-subunit hook, and finally complete flagella. This demonstrates the NFSimProcess bridge pattern running standalone.
ModeStandalone NFSim
Flagella3
Total Complexes14
Time Points501
Sim Duration500s
Runtime1.0s
Assembly Dynamics
Two processes composed via process-bigraph wired to shared state: MonomerProduction adds monomers every 1s at gene-expression rates (~1 flagellum worth per 100s), while NFSimProcess runs NFSim every 50s to assemble accumulated monomers. Monomer pools show sawtooth dynamics as production accumulates them between complexation steps. This is the core workflow demonstrating process composition.
ModeComposed Workflow
Flagella14
Total Complexes40
Time Points40
Sim Duration2000s
Runtime11.8s
Assembly Dynamics
Same composed workflow but with 3x monomer production rate, simulating overexpression of flagellar genes. The higher supply rate leads to faster assembly kinetics and larger monomer pools between complexation steps. Compare with the steady production configuration to see how production rate affects assembly yield.
ModeComposed Workflow
Flagella36
Total Complexes88
Time Points30
Sim Duration1500s
Runtime8.8s
Assembly Dynamics
