I do classical molecular dynamics simulations for a living, and I feel the model using in this paper is pretty dramatically different than what would typically be described as classical dynamics. 2B atoms would be absolutely insane for any sort of simulation that resolves forces between atoms of even groups of atoms, especially in organic systems.

As far as I can tell from their model, molecules don't interact with each other ~at all~ through classical dynamics. Rather, they define concentrations of various molecules on a voxel grid, assign diffusion coffecients for molecules and define reaction rates between each pair of molecules. Within each voxel, concentrations are assumed constant and evolve through a stochastic Monte-Carlo type simulation. Diffusion is solved as a system of ODEs.

This is a cool large scale simulation using this method, but this is a far cry from an actual atomic-level simulation of a cell, even using the crude approximations of classical molecular dynamics. IMO it is kind of disingenuous for them to say 2B atoms simulation when atoms don't really exist in their model, but it's a press release so it should be expected.