My question is specifically whether there exists a technique by which a single photon can be "tagged" or "encoded" in such a way that it can traverse our atmosphere and arrive at some sort of detector along with trillions of others and be singled out from the other photons. Would this be possible using quantum entanglement protocol? Or maybe precise timimg (knowing when the photon will arrive at the detctor based on knowing when it leaves and the distance between)? Thanks
Long distance quantum communication in Earth's atmosphere is possible. There are successful realizations of quantum key distribution and quantum teleportation, showing that it is possible to detect single photons and entangled pairs having traveled distances up to 300 km. Of course, the losses are huge and unavoidable, so the total attenuation for a link between two Canary islands in the mentioned experiments was around 30 dB for single photons and 70 dB for pairs. It means that the source of entangled photons has to be quite bright: the one used in Canary experiments produced $~10^6$ pairs/s. And only about 0.07 pairs/s were detected at the receiving side. Nevertheless, the noise, mostly coming from stray light and detector dark counts, can be made low enough (~200 Hz) to reach coincidence signal-to-noise ratio of 15:1. This is achieved by frequency filtering and timing - the coincidence window was limited to 3 ns, and that required corrections for time drift of GPS-based clock synchronization system. Active synchronization was done utilizing temporal correlations of entangled photons: the local time was adjusted to maximize the coincident events rate. Authors call it "entanglement-assisted clock synchronization".
There are several sources of losses in free space atmospheric links: scattering and absorption of ~0.07 dB/km, diffraction losses due to limited aperture on the receiving side which is unavoidable, as well as beam wandering and distortion due to atmospheric turbulence. Beam wandering may be to some extent fixed by active tracking systems. As for specific "shaping" of photons, there are some speculations on using the beams with orbital angular momentum to reduce the effects of turbulence, but these do not seem to be very realistic, and some authors tend to claim that to the contrary, higher-order Laguerre-Gaussian beams are more sensitive to turbulent distortions.
Satellite quantum communication is a feasible task, we will probably see it in the nearest future. In some aspects it is even simpler, since the path travelled in the dense layer of atmosphere is much shorter. Inter-planet optical communication at the single-photon level would have to deal with enormous losses just due to diffraction spreading of the beam, it does not seem to be possible with current technology.