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Our word "atom" comes from the ancient Greek words "atomos"; "a" meaning "no" or "not", and "tomos" meaning "cut". Therefore, the word "atomos" translates to "no cut". It was named such because it was a theoretical form of base matter, which could not be reduced (Or, cut) any further. However, in modern terminology, atom is a misnomer, as we now know atoms may be broken down further in to protons, neutrons and electrons; and all of which, with the exception of electrons, may be broken down further in to quarks.
Atom means indivisible in Greek (atomos) so they named the atom atom because it is the smallest form of matter indivisible by chemical methods.

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