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I have found the following definition of the proton:

the subatomic particle found in the atom's dense central core that has a positive charge

Why is "the" used before "atom"? Would not it be better with an indefinite article?

the subatomic particle found in an atom's dense central core that has a positive charge

As it is found in any atom (an oxygen atom, a carbon atom etc.)

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This is the use of the for "the prototype", "the abstract", "X-s in general".

We see it also in the phrase that used to be common in the middle of the last century "splitting the atom".

It used to be more common that it is now - it has particularly gone out of fashion for talking about animals and people - The elephant is a quadruped with a long trunk would now much more commonly be plural - Elephants are quadrupeds ..

Similarly, I would find found in the dense central core of atoms more natural today than the example you give. But both your quoted example, and your suggestion with an are possible.

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