Greg Dean asked:
When weíre looking at an image of an individual atom, as in when IBM posted that amazing picture in 1990 with IBM spelled out in xenon atoms on a surface what are we actually seeing? Protons, neutrons, electrons?
That kind of image was probably from a scanning-tunnelling electron microscope on which you get a very sharp point where itís so sharp itís probably only got one or two atoms on the end. They scan that very slowly across the surface of a material. With a scanning-tunnelling electron microscope you measure the amount of electric current going between that and the material. You apply a tiny voltage, measure the current between that tip and the surface. Youíre actually measuring the resistance of the surface.
There are other similar images where you can measure the force on that tip. Youíre basically measuring the force between the end of the tip and the surface at the bottom. If the atoms are higher up the force will go up and vice versa.