Caption: A Helium-4 (He-4) atom and nucleus as a representative atom and atomic nucleus.
The scaled-up region in the upper right corner shows atomic nucleus in an ABSTRACT way. It consists of two protons (RED colored) and two neutrons (VIOLET colored).
Features:
So nuclei are order of magnitude 10**5 times smaller than atoms.
But nuclei are typically ∼ 2000 to 5000 times more massive than the electrons that set the size scale of the atoms.
So overwhelmingly, the mass of atoms is in their nuclei.
The darker the shading the higher the density.
What is density of existence?
Quantum mechanics dictates that particles do NOT exist at one point, but are spread out in a continuum superposition of position.
The fractional amount of any particle at any point is the density of existence.
The density of existence itself is determined from wave function of the particle.
The spread out nature of particle existence is one of the things that makes quantum mechanics so tricky.
That atoms are tightly bound together is a sort of miracle of the quantum mechanics, arrangement, and the existence of nuclei.
Also the colors are just for visualization. The actual colors of protons and neutrons depend on the light they reflect in whatever context they are in. Yours truly guesses that isolated free protons probably reflect all visible light impinging on them, and so are shiny. For isolated free neutrons, yours truly has NO idea.
Isolated free electrons are also shiny. However, bound in atoms and molecules, electrons can scatter light only from the available transitions, and so would look "shiny" only in isolated spectral lines. Of course, atoms and molecules can also absorb electromagnetic radiation (EMR) and redistribute energy to spectral lines other than those of absorption.
The positively charged protons repel each other by the electric force, of course, but the strong nuclear force overcomes this.