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We investigate theoretically how cold atoms, including Bose–Einstein condensates, are scattered from, or absorbed by, nanotubes with a view to analysing recent experiments. In particular, we consider the role of potential strength, quantum reflection, atomic interactions and tube vibrations on atom loss rates. Lifshitz theory calculations deliver a significantly stronger scattering potential than that found in experiment and we discuss possible reasons for this. We found that the scattering potential for dielectric tubes can be calculated to a good approximation using a modified pairwise summation approach, which is efficient and easily extendable to arbitrary geometries. Quantum reflection of atoms from a nanotube may become a significant factor at low temperatures, especially for non-metallic tubes. Interatomic interactions are shown to increase the rate at which atoms are lost to the nanotube and lead to non-trivial dynamics. Thermal nanotube vibrations do not significantly increase loss rates or reduce condensate fractions, but lower frequency oscillations can dramatically heat the cloud.