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.

Can I simulate moving meshes in MCell?

There is experimental support for dynamic meshes. Please see the Dynamic Geometry tutorial for more information.

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.