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They say that atoms are mostly 99.99999% empty space. But quantum physics says otherwise. The article claims the theory concluding atoms are mostly empty space  is outdated because it is based on Rutherford's experiment which looked at  collisions in high-energy scenarios where most atoms are colliding in low-energy conditions

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The claim that atoms are mostly empty space is a bit of an oversimplification of physics. If you divide of the volume of a whole atom with the volume of a nucleus, you do get something like that. The generally accepted quantum mechanical model of an atom means that electrons are not treated as particles, rather that they have wavelike behaviour and are usually depicted as fog or clouds of probability. This is sometimes described as electrons being everywhere in that fog all at once, which could be described as taking up the space. However, it is important to consider that models are just our best representations of reality, and models can have flaws too.

It is true that almost all of the mass in an atom is concentrated in a small amount of area, the nucleus, but this does not necessarily mean that the atom is mostly empty.

https://www.khanacademy.org/science/chemistry/atomic-structure-and-properties/orbitals-and-electrons/a/the-quantum-mechanical-model-of-the-atom

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by Novice (940 points)
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I like how in-depth you went with this fact-check, bringing in what seems to be some previous knowledge about this topic. Using Khan Academy as a source is smart because it is a trusted .org website and is used by many educators. I also like how you brought up how physicists don't have all the answers about atoms yet and we have to take our models with a grain of salt.

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