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Something I'm not sure I understand, though, is the difference between visible light with a wavelength of a certain colour and visible light with a wavelength stretched or compressed (that is, red-shifted or blue-shifted) to a certain colour. For example, what is the difference, physically, between light-waves that we see as "red" and light-waves that are Doppler-shifted into the red?
I think the first thing you need to realize is that visible light is no different than radio waves (except for the amount of energy in each wave). There is nothing "special" about the wavelengths that the human eye is able to detect. Non-visible light, such as infra-red or ultraviolet, can become visible light through the Doppler effect by changing the wavelength. Also, some organisms are able to detect infra-red wavelengths (eg rattlesnakes) and (IIRC) some are able to detect ultraviolet wavelengths (eg bees). Through instrumentation, humans are able to detect all of the EM wavelengths, from radio waves on up to x rays.
Another interesting problem caused by the Doppler effect concerns spaceflight. If we humans are ever able to build a craft that travels at high speeds, say 0.6 c, normal light will actually shift into the range of cosmic radiation (eg gamma rays, I think). In other words, humans would actually have to build shielding to protect themselves from normal visible light.
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However, if the nucleus doesn't interact with the light being received/released, just how does it contribute to the properties of visible colour in an atom?
The nucleus determines the ground and excited states that electrons are allowed to move between. That is, the nucleus determines the position of the electrons, and light is produced when electrons move between these positions. The nucleus "sets the table" as it were.
As to being able to "see" a single atom, this is a problem unto it's own. For a human to see something it has to be emmitting light. Therefore, without amplification or instrumentation, all we really see is the light produced by the atom, not the atom itself. Of course, this could be said of any object of any size so I don't know if this explanation helps or hurts.
This is the same problem that Maxwell ran into with his Demon. Maxwell came up with the idea that he could create "free" energy by separating low energy and high energy particles into separate containers. However, the problem he ran into was that it takes energy to measure the energy content of a particle. This is the same type of problem that we run into when trying to "look" at atoms.
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