Silence comes from strength and muscle control. The stronger, and more muscle control you have, the easier it will be to silence your movements. When landing you obviously don't slam your feet into the ground, but you do allow your legs' muscles to cushion your fall, absorbing most of the impact as the knees/ankles/waist bend through your muscles, and can further be dispersed with your hands.
From a scientific point of view, you're trying to disperse sound to low decibal ratings. You can achieve this with more (muscle) mass, and again, better muscular control. Sound and impact are directly proportionate, and the softer you land, the quieter the sound.
There's no such thing as complete silence, as this arises from vibrations, but it is possible to be extra quiet even with shoes. It's a conscious effort you have to make and will take some experimentation, but it is achievable. Isometrics would be a good place to start, to make yourself more bodily aware.
