Make sure you take a look at the lecture given by Sean Hanna at the Subtle Technologies event held at Toronto University.  While he readily admits that the manipulation of individual molecules for the production of nano-scale materials is still out of the realm of reality, his focus has been to study micro-structures (at the scale of the millimeter instead of the nanometer) and genetic algorithms in order to create learning materials.  His research is readily applicable at other scales as well.   Click here to go to the lecture.