[dschuetz]

As far as I understand, dark matter is an educated guess (which was made upon the discovery that galaxies rotate differently than expected). Something out there must be causing gravity, but we cannot see it, which means that there is no observable EM interaction.

The next guess here is that dark energy has a much much higher rest energy so that no photon in this universe is able to interact with it via EM fields. The search for dark matter was unsuccessful so far, and the LHC is still trying to achieve higher energies to be able to detect dark matter. So, dark matter is just a guess.

The interactions inside atoms seem to have no known relations to EM, because, and this is my guess, there are much higher energies at work than we know. So, if dark matter is hiding behind high energies so that EM interaction seems impossible, why should it be different for EM interactions inside atoms. There still is a slim chance that it might be EM, just at much higher energies.

[danbruc]

The interactions inside atoms seem to have no known relations to EM [...]

The electromagnetic and the weak interaction are known to be different aspects of the unified electroweak interaction. There are several grand unified theories and a few hints that at even higher energies the electroweak and strong interaction also unifiy into the electronuclear interaction. Due to the high energies involved, only indirect experimental evidence seems accessable for the forseeable future but there are various groups looking for hints. I am not aware of any uncontroversial results but there are a few non-reproducable experiments, for example observations of magnetic monopoles, which might be due to experimental error but also due to the rarity of magnetic monopoles.