Part of it is getting hung up on the "single photon" terminology, which makes you think of light as existing solely as a particle. First of all, photons aren't atoms (!= proton), they're subatomic. More importantly for this application, light has this really weird physics property of existing as (or exhibiting properties of) both a particle and a wave. So perhaps a better analogy/simplification than "imprinting data onto an atom" would be something like "storing information in the diffraction patterns of a wave." By knowing how waves act, you can analyze such patterns and movements and "play the wave backwards" to determine the original shape (stencil) that formed it.
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Part of it is getting hung up on the "single photon" terminology, which makes you think of light as existing solely as a particle. First of all, photons aren't atoms (!= proton), they're subatomic. More importantly for this application, light has this really weird physics property of existing as (or exhibiting properties of) both a particle and a wave. So perhaps a better analogy/simplification than "imprinting data onto an atom" would be something like "storing information in the diffraction patterns of a wave." By knowing how waves act, you can analyze such patterns and movements and "play the wave backwards" to determine the original shape (stencil) that formed it.
particle/wave duality is a property of all fundamental particles, not just photons. Matter particles (electrons and quarks) also have this property.