The accuracy of atomic clocks, in the microwave or in the optical domain, is now such that a new theoretical framework [1] is required, which includes: 1 -A fully quantum mechanical treatment of the atomic motion in free space and in the presence of a gravitational field (most cold atom interferometric devices use atoms in "free fall" in a fountain geometry), 2 -An account of simultaneous actions of gravitational and electromagnetic fields in the interaction zones, 3 -A second quantization of the matter fields to take into account their fermionic or bosonic character in order to discuss the role of coherent sources and their noise properties, 4 -A covariant treatment including spin to evaluate general relativistic effects. A theoretical description of atomic clocks revisited along these lines, is presented, using both an exact propagator of atom waves in gravito-inertial fields [2] and a covariant Dirac equation in the presence of weak gravitational fields [3]. Using this framework, recoil effects, spin-related effects, beam curvature effects, the sensitivity to gravito-inertial fields and the influence of the coherence of the atom source can be discussed in the context of present and future microwave and optical clocks.
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