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Phonon dynamics in Bi, Bi2Se2, and CuxBi2Se3 (x=0, 0.1, 0.125) single crystals was investigated using femtosecond pump-probe spectroscopy. Two damped oscillations in measured transient reflectivity changes were observed, respectively, attributed to coherent optical and acoustic phonons. The frequency shift of the phonon modes in Bi-rich Bi2Se2 crystals indicates the intercalation of the additional Bi atoms into the Bi2Se3 matrix and formation of the Bi-2 layer between the quintuple layers (QLs). The deformation of QLs in CuxBi2Se3 crystals was also found. These phonon dynamics results suggest that Cu atoms in CuxBi2Se3 crystals are predominantly intercalated between pair of QLs. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4754005]