atomo

The etymology is the whole lesson, so take it first. Greek atomos means uncuttable: a-, not, plus temnein, to cut. Democritus argued that if you keep halving a thing you must eventually reach a piece that cannot be halved, and he named it after that property. Chemistry adopted the word in the nineteenth century, and then twentieth-century physics split it, so the standard term for the smallest unit of matter is a Greek word meaning "the thing that cannot be split". Nobody has ever bothered to fix it, in any language.

The same temnein is inside anatomio, cutting-up, and epitomo, a cutting short. Tomo, a volume of a book, is a cut-off portion of a larger work.

Not a seam in Esperanto. Atom- is one root of five letters. The a- that means "not" is Greek and does not exist as an Esperanto prefix - the language builds negation with ne- and mal-, so an uncuttable thing would be netranĉebla, which is exactly the sort of long honest word Esperanto prefers and exactly the sort of word nobody would call a particle. Compare atmosfero at rank 2,002, whose page makes the same point about atmo: the Greek is genuinely in there, and history is not morphology.

In use. Atoma is atomic, so atoma energio is nuclear power and atombombo the bomb. Atomo also survives in the older rhetorical sense of the smallest imaginable amount: ne atomo da vero, not an atom of truth. Atomkerno is the nucleus and elektrono the electron; the standard vocabulary of chemistry and physics is set out in Scienca Esperanto, which is also the page that explains why Esperanto imports terms like this whole rather than building them.