Identifying a two-state Hamiltonian in the presence of decoherence

Mapping the system evolution of a two-state system allows the determination of the effective system Hamiltonian directly. We show how this can be achieved even if the system is decohering appreciably over the observation time. A method to include various decoherence models is given and the limits of this technique are explored. This technique is applicable both to the problem of calibrating a control Hamiltonian for quantum computing applications and for precision experiments in two-state quantum systems. The accuracy of the results obtained with this technique are ultimately limited by the validity of the decoherence model used.