Optical clock-transitions such as the ones in Ytterbium are prime candidates for encoding qubits for quantum
information processing applications due to very low decoherence rates. In this work, we investigate the challenges
involved in using these prime candidates for fundamental tests of quantum mechanics. We design entangling
operations for pairs of indistinguishable atoms trapped in optical tweezers, as well as determine the feasibility
of rapid qubit rotation and measurement of qubits encoded in these desirable low-decoherence clock transitions.
In particular, we propose multi-photon transitions for fast rotation of qubits, followed by ultrafast readout via
resonant multiphoton ionization. The rapid measurement of atomic qubits is crucial for high-speed synchronization
of quantum information processors, but is also of interest for tests of Bell inequalities. We investigate a Bell
inequality test that avoids the detection loophole in entangled qubits, which are spacelike separated over only a
few meters.