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The green and red colors are emitted by atoms of oxygen after they are hit by fast electrons. Each element emits its characteristic colors, and for rarefied oxygen, these appear to us green or red. Typically, a delay of 0.5-1 second exists between collision and the emission (in this case--not in denser surroundings!), and that is why the rays of the aurora brighten and fade so slowly. The beam of electrons which "excites" the oxygen atoms may only last a small fraction of a second, but the afterglow persists 0.5-1 seconds or more.