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Bioaccumulation of perfluoroalkyl and polyfluoroalkyl substances (PFASs) is an important indicator of their hazard. Partitioning to membrane phospholipids is one of the pathways for their bioaccumulation. However, the molecular mechanism on PFASs uptake into membrane phospholipids is not yet to be fully understood. In this work, we used molecular dynamics (MD) simulations to study the uptake processes of PFOS and its alternatives (6:2 Cl-PFESA and OBS) into DPPC bilayers, and to evaluate their interaction with DPPC bilayers and their effect on properties of DPPC bilayers. The result of free energy changes shows that a barrier of 2–3 kcal mol−1 exists when these adsorbed PFASs on the surface are absorbed into DPPC bilayers. After incorporating into DPPC bilayers, three DPPC molecules interact with and thus stabilize a PFOS (or 6:2 Cl-PFESA or OBS) molecule. And another role of the three DPPC molecules is to shield these PFASs from exposure to water environment. These PFASs have the similar condensing effect on the model membrane. The molecular-level study is beneficial for understanding the bioaccumulation and toxicity of PFOS and its alternatives. [Display omitted] • The uptake of PFOS, 6:2 Cl-PFESA and OBS into DPPC bilayers is easy to happen. • A barrier of 2–3 kcal mol−1 needs to be overcome during the uptake processes. • Three DPPC molecules interact with a PFOS (or 6:2 Cl-PFESA or OBS) molecule. • A role of three DPPC molecules is to shield PFASs from exposure to water molecules. • PFOS, 6:2 Cl-PFESA and OBS have the similar condensing effect on DPPC bilayers. [ABSTRACT FROM AUTHOR]