Without interaction, the two-qubit Hamiltonian operator is , so its evolution factors as . It maps each product state to another product state, and cannot implement an entangling two-qubit gate such as a CNOT gate.
In an ion trap, the Coulomb interaction couples the ions' displacements into collective vibrational normal modes. The qubit states are internal atomic states; lasers coupling internal excitation to creation or annihilation of a shared vibrational quantum allow that motion to carry conditional information between ions. Thus the physical mediator is a collective motional normal mode of the Coulomb-coupled chain, rather than a direct resonant exchange between isolated internal qubit transitions. Ground-state cooling and resolved motional sidebands support the ideal pulse model used here.
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