Ever pause to consider that this may have been done intentionally as an example to demonstrate how bad grammar and punctuation can really fsck up the comprehension of a story?
Please learn the correct, use of the comma. This sentence does not make any sense as it is written...
"When strained in a particular manner, nanobubbles formed on a sheet of graphene, within which electrons came to occupy particular, quantum energy levels rather than the usual, continuous range of energies in unstrained graphene."
The explanation requiring the fewest assumptions is the most likely to be correct. -- William of Occam