Do you know how they deal with DNA? Does it fit in a single voxel? (Probably no). Are strands of DNA and RNA treated in chunks in a chain of voxels? Does the simulation perform transcription?
I don't believe there is any case where a molecule in one voxel knows about molecules in other voxels. DNA and RNA is coarse grained where a 'molecule' might represent a specific sequence of interest rather than a full chain. Transcription and translation are modeled, essentially by saying if the neccessary ingredients are present in a voxel (DNA/RNA sequences, enzymes, raw materials, etc) there is some chance of forming mRNA or a protein as a function of the molecular concentrations present in the voxel. DNA and RNA reactions are treated with somewhat different equations than the rest of the molecules, I think to handle the coarse graining.
Do you see a future for this simulation method with increased computing power, or do you think limitations of the method might still limit its applicability. Maybe this is naivete coming from atomistic perspective, but it seems to me that the inability to model reactions that aren't explicitly predefined would be a significant challenge.