Atoms go all the way back to Leucippus (perhaps further) in Western thought, at least. Lucretius' De rerum natura is all about atomism (and the Stallings translation is a true joy to read). I checked the OED to see about its usage in English, and it definitely originated before 1500.
Incidentally, I just read Leibniz's Monadology over the week, which is basically a trippy extension of atomism, and a quasi-precursor to theories of the God particle. Interesting stuff...
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