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What does it mean the Van der Waals force comes from the fluctuating dipoles of the atoms? Why is the dipole moment fluctuating? Is it because the vacuum EM field is fluctuating then it stimulates the dipoles to fluctuate? Or do they not need to rely on the vacuum field to fluctuate?

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I think that you are more specifically referring to the London dispersion force. It is due to quantum fluctuations, unlike the Debeye force which is due to thermal fluctuations and the Keesom force which is due to electrostatics.

A simple derivation only takes into account the ground state fluctuation of the atoms and treating the electromagnetic field classically. Originally this was done by performing second order perturbation on the atoms. An alternative approach is to assimilate the atoms to independent harmonic oscillators with respective dipole moments proportional to the respective displacements. This is done for example in Kittel's Introduction to Solid State Physics. Adding the electrostatic dipole-dipole interaction couples linearly the oscillators (assuming they stay at a fixed distance), thereby shifting the ground state energy. This variation in ground state energy is then identified as the London dispersion force.

Including ground state fluctuations of the EM field using second quantisation is possible. However, since the electric potential is not dynamical, this will not change the force in the static limit. You can anticipate that it will rather modify the mass of the oscillators. A fully consistent treatment would be to include radiation effects.

Hope this helps.

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