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Our results showed that the reduction in conformational entropy by inserting a cargo into the NPC increased the free energy by an amount substantially greater than the thermal energy (≫kBT), whereas the free energy change was negligible ( less then kBT) for small cargoes (less than ~6 nm in size), indicating the size-dependent selectivity emerges from the entropic effect. Our models suggested that the entropy-induced selectivity of the NPC depends sensitively upon the physical parameters such as the flexibility and the length of FG-Nups.