Seems unlikely that the researchers are really simulating this on a molecular level as claimed in that article. Perhaps they are using the neuron as the unit instead?
"At the push of a button, the model could reconstruct biologically accurate neurons based on detailed experimental data, and automatically connect them in a biological manner, a task that involves positioning around 30 million synapses in precise 3D locations." [1]
It doesn't necessarily mean they aren't modeling molecules, but the wording hints that they aren't.
