What defines the size of an atom

Every atom is different in its number of protons, its mass, and its size. The size of the atoms is determined by the size of their orbitals. The larger the quantum number "n" is, the larger the orbital is, which increases the size of the atom

explanation:

let the different atoms be x and y. each with four protons and same mass will be represented as follows.

mass number is number of protons + number of neutrons.

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since, it is given that one has a negative charge while the other is neutral. therefore, there will be increase in number of protons and the atom will be represented as follows.

according to periodic table, mass number of beryllium is 9 and it has atomic number 4 so, the atoms will be and .  

the protons and neutrons will be located inside the nucleus whereas the electrons will be revolving around the nucleus.