An interesting idea was brought up in the Quantum Mechanics book, the concept that a particle such as an atom is not a solid object. If you've ever created a ball out of elastic bands, then if you imagine this hollowed out, then this is the wavefunction of the electron, an almost solid shell with a pretty much hollow centre. The 'nucleus' is really just three smaller balls of energy that make up the quarks. So the solid atom is a deception seen from the perspective that allows the balls of energy to act as solid objects. Since there are gaps in the elastic band sphere, this is where quantum tunnelling takes place, there is no solid wall, only very small gaps.
When seen from this perspective it is easier to imagine an electromagnetic disturbance coming across an electron, it then interacts via a small parcel of energy called a photon, which gives the electron a kick and allows it to jump to a larger orbit. We only see the photon emitted, so we see an object that has 'colour', a construct our brain creates to identify different levels of energy.