Each of the orbs are the atoms. The brighter orbs that are nearest each other at the Praseodymium (Pr) atoms. The single orbs are the Scandium (Sc) atoms and the less prominent orbs are the Oxygen atoms. I believe based on the content of the article.The space between is just that, the space between the atoms. They are all in a lattice pattern due to how they are attracted to each other.