13. FAQ

What are the units in MCell and CellBlender?

In MCell, the units of space are microns, the units of time are seconds, diffusion constants are \(cm^2/s\), unimolecular reactions are \(s^{-1}\), volume-volume/volume-surface bimolecular reactions are \(M^{-1}s^{-1}\), and surface-surface bimolecular reactions are \({\mu}m^2N^{-1}s^{-1}\). M refers to molarity, and N is the number of reactants. One blender unit in CellBlender is equivalent to one micron.

MCell also provides option to use units compatible with BioNetGen ODE, SSA, and PLA solvers (not with NFSim that uses different units). This option can be enabled on the Settings & Preferences panel by selecting BioNetGen Units Mode or in Python by setting Model.config.use_bng_units to True. When enabled, unimolecular reactions use the same unit \(s^{-1}\), and all bimolecular reactions use \({\mu}m^3N^{-1}s^{-1}\). For surface-surface reactions, it is assumed that the thickness of the mmembrane is 10 \(nm\) and conversion from \({\mu}m^3N^{-1}s^{-1}\) to \({\mu}m^2N^{-1}s^{-1}\) is made by simply dividing the provided BioNetGen unit by 0.01 \({\mu}m\).

Can I simulate moving meshes in MCell?

To use dynamic geometry in MCell4, Python code needs to be written. For more details see Model.add_vertex_move and Model.apply_vertex_moves.

There was also an experimental support for dynamic meshes in MCell3 that is described here Dynamic Geometry.

Can I change the default molecule size?

Often, people mistakenly assume that the INTERACTION_RADIUS corresponds to a molecule’s true radius. In reality, molecules are points in MCell. As such, molecules can be infinitely close to each other. The interaction radius is only used for finding reaction partners. Reasonably small changes to the interaction radius won’t have any significant effect, and there is usually no reason to change the default value.

Why is MCell running so slow?

Your simulation could be running slow for any number of reasons. Check Optimizing Your Simulation for some possible solutions for speeding up your simulation.