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We investigate the effect of anisotropic and long-range dipole-dipole interaction (DDI) on the center motions of nonoverlapping Bose-Einstein condensates (BEC) in bilayer and multilayer stacks. In the bilayer, it is shown analytically that while DDI plays no role in the in-phase modes of center motions of condensates, out-of-phase mode frequency () depends crucially on the strength of DDI (). At the small- limit, . In the multilayer stack, transverse modes associated with center motions of coupled condensates are found to be optical phonon like. At the long-wavelength limit, phonon velocity is proportional to .

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