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A generalization of the set of completely positive matrices called pairwise completely positive (PCP) matrices is introduced. These are pairs of matrices that share a joint decomposition so that one of them is necessarily positive semidefinite while the other one is necessarily entrywise non-negative. Basic properties of these matrix pairs are explored and several testable necessary and sufficient conditions are developed to help determine whether or not a pair is PCP. A connection with quantum entanglement is established by showing that determining whether or not a pair of matrices is pairwise completely positive is equivalent to determining whether or not a certain type of quantum state, called a conjugate local diagonal unitary invariant state, is separable. Many of the most important quantum states in entanglement theory are of this type, including isotropic states, mixed Dicke states (up to partial transposition), and maximally correlated states. As a specific application of these results, a wide family of states that have absolutely positive partial transpose are shown to in fact be separable.