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This article is from the Star Trek Tech FAQ, by Joshua Bell inexorabletash@hotmail.com with numerous contributions by others.

68 "How does the transporter work?" (Transporters - Star Trek)

While there is no absolute canonical answer, we can piece one together
from various clues, that fits nearly everything seen on-screen, and in
the TNG Tech Manual.

We have some evidence of the inner workings of transporters, but not
much. They employ Heisenberg compensators, pattern buffers, phase
transition coils, Biofilters, matter streams, confinement beams, and
matter-energy converters, and phased matter. As for what they do, we
know that you are conscious during transport (Star Trek II: The Wrath
of Khan, "Realm of Fear" [TNG]), but can also be held in stasis ("Day
of the Dove" [TOS], "Relics" [TNG]). Further, while in transport, you
appear whole to yourself.

I hypothesize that the Annular Confinement Beam first locks onto, then
disassembles the subject into phased matter, via the phase transition
coils, causing it to take on a very energy-like state somewhat akin to
plasma, called phased matter. The matter stream is then fed into the
pattern buffer, piped through wave-guide conduits to one of the beam
emitters on the hull of the starship, and then relayed to a point on
the ground where the ACB reconstructs the subject.

 

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