Table 1. Units used in MCell4 and suggested units for BioNetGen.
Unit N represents the number of molecules and M is molar concentration. BioNetGen interprets membranes (2D compartments) as thin volumes of thickness 10 nm. NFsim in BioNetGen does not fully support compartmental BNGL yet and the volume of the compartment must be incorporated into the rate units of the reactions occurring in that compartment, therefore NFsim’s bimolecular reaction rate unit does not contain a volumetric component. Additional units in MCell4 include: length in μm and diffusion constants in cm2 s−1.
| Simulation tool and mode of usage | Volume-volume or volume-surface bimolecular reaction rate | Surface-surface bimolecular reaction rate | Unimolecular reaction rate | Compartment volume | Seed species (initial molecule release) value |
|---|---|---|---|---|---|
| MCell4 with default units | M−1 s−1 | μm2 N−1s−1 | s−1 | μm3 | N |
| MCell4 with BNG units; BioNetGen ODE, SSA, PLA | μm3 N−1s−1 | μm3 N−1s−1 | s−1 | μm3 | N |
| BioNetGen NFsim | N−1s−1 | N−1s−1 | s−1 | ignored | N |