Actually ,there's an even bigger problem. In order to maintain the transfiguration, you'd have to touch that carbon atom again.
What does it mean, on a molecular level, to "touch" things? It's just repulsion of electrons. So if Harry has learnt to do partial transfiguration by considering things to be just piles of atoms, he might also be able to get around that restraint.
Of course, you are still completely right that transfiguring stuff into very small particles is quite dangerous: What if the atom sublimates? What if somebody somehow takes it up so it becomes part of that person's body? How to find it in case it gets lost in the atmosphere, in the sea, or anywhere else? Etcetera. All sorts of fatal mistakes can be done, and Harry will not want to risk dying, or making Hermione's recovery impossible.
This is a new thread to discuss Eliezer Yudkowsky’s Harry Potter and the Methods of Rationality and anything related to it. This thread is intended for discussing chapter 94. The previous thread has passed 200 comments.
There is now a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author’s Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: