HI Ann,
You have a very interesting question...and I'll try and help you here :)
Looking at this, I would say....you can't have an atom of a plural....think about it....doesn't make sense. An atom could only come from one thing since it's soooo small!
I would say this may be the best thing you could say:
"...an atom of stone/an atom of a stone"
"...an atom of one gadget / an atom of a gadget"
Funny expression, but I hope this helps you some. Actually, when we were kids, we used to use this expressions quite extensively and had great fun creating insults for our friends! :)
Keep learning English!
David