The role of spectator modes in the quantum-logic spectroscopy of single trapped molecular ions

Quantum-logic spectroscopy has become an increasingly important tool for the state detection and readout of trapped atomic and molecular ions which do not possess easily accessible closed-cycling optical transitions. In this approach, the internal state of the target ion is mapped onto a co-trapped auxiliary ion. This mapping is typically mediated by normal modes of motion of the two-ion Coulomb crystal in the trap. The present study investigates the role of spectator modes not directly involved in a measurement protocol relying on a state-dependent optical-dipole force. We identify a Debye-Waller-type effect that modifies the response of the two-ion string to the force. We show that cooling the spectator modes of the string allows for the detection of the rovibrational ground state of an $N_2^{+}$ molecular ion with a computed statistical fidelity exceeding 99.99%, improving on previous experiments by more than an order of magnitude while also halving the experimental time. This enhanced sensitivity enables the simultaneous identification of multiple rotational states with markedly weaker signals.