Each of the inhabitants of this universe contain their own small assembly program, something like:

[ MoveRandom
, Rotate CCW 
, NOP
, ... 
]

Since this environment is dedicated to a narrow application, optimizations are possible. For example, since cells occupy a planar discrete space, cells may not overlap each other therefore the critters block each other's movement. This is true for all the inhabitants, so that constraint is handled by the universe runtime. The assembly interpreter doesn't have to spend time on collision detection. DNA doesn't encode Newton's laws.

Stage-1 of the project is complete - the thing works. Stage-2 will implement multicellular activity, where the single cells from stage-1 combine, connected by static or pivot joints that allow for more degrees of freedom, eventually with top down command. Maybe the cells will evolve ways to merge their programs effectively, or maybe they will need help.