In this paper, decoherence in a system consisting of two Bose-Einstein condensates is investigated analytically. It is indicated that decoherence can be controlled through manipulating the interaction between the system and environment. The influence of the decoherence on quantum coherent atomic tunneling (AT) between two condensates with arbitrary initial states is studied in detail. Analytic expressions of the population difference (PD) and the AT current between two condensates are found. It is shown that the decoherence leads to the decay of the PD and the suppression of the AT current.
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