After discussion with my colleagues what I understood is
If the material is cooled down (to nano kelvin) the wave function of the atom (mainly nuclei) is spread and it got overlapped with neighboring atoms.
If the number of atoms within this coherent volume is larger than one (and the atom is a boson i.e. total angular momentum of nuclei and electrons is an integer) then it will form a Bose-Einstein Condensate (BEC).
Due to the overlap of the nuclei wave functions the individuality of the
nuclei is lost and the surrounding electron cloud could not distinguish among the nuclei and all the electrons will make a common electron cloud among coherently connected nuclei. Hence the atoms as a whole act as single entity.
On the other hand in case of nanoparticles (NPs) the outer electron has sufficiently low energies such that their wave functions overlap and make a common electron cloud. However the inner electron cloud and nuclei remain separated from each other and maintain their individuality.
The two situations are quite different hence NPs possess coherency on the scale of low energy electrons but a NP is certainly not a BEC.