We analyze the magnetic and transport properties of a double quantum dot coupled to superconducting leads. In addition to the possible phase transition to a $pi$ state, already present in the single dot case, this system exhibits a richer magnetic behavior due to the competition between Kondo and inter-dot antiferromagnetic coupling. We obtain results for the Josephson current which may help to understand recent experiments on superconductor-metallofullerene dimer junctions. We show that in such a system the Josephson effect can be used to control its magnetic configuration.
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