Question

How are the helium atoms in this model different from real helium atoms?

Answer 1

Answer;

Real helium atoms are too small to see

Explanation;

-A helium atom is an atom of the chemical element helium.

-Helium is composed of two electrons bound by the electromagnetic force to a nucleus containing two protons along with either one or two neutrons, depending on the isotope, held together by the strong force.

Answer 2

With the information given in the question, we can only observe
that they are quite SIMILAR in at least one respect ... both the real
ones and those in 'this model' are quite invisible and intangible, and
we must take your word for it that they exist at all.

Like so many others in math and science, this question raises another
question:    "Which model are you talking about ?"