Identifying a Two-State Hamiltonian in the Presence of Decoherence

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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. For simple models of decoherence, this method can be applied even when the decoherence time is comparable to the oscillation period of the system.