Conformational entropy bottleneck in polymer nanopore interception driven by branching architecture and excluded volume

Abstract The transport of polymers through nanopores is fundamentally governed by the interplay between molecular topology and nanoconfinement. However, how branching architecture influences the critical interception size ( R h,c ) under weak compression—where diffusion dominates and chain deformation is negligible—remains poorly understood. Here, we address this challenge by integrating well-defined hyperbranched polystyrenes with tunable branch densities ( ρ = 1/25-1/650), monodisperse anodic aluminum oxide nanopores ( D = 28-96 nm), all-atom simulations, and theoretical modeling to uncover a conformational entropy bottleneck mechanism. We experimentally reveal a distinct power-law relationship R h,c ~ ρ −1/2 for hyperbranched polymers, in stark contrast to the classic behavior of linear chains. Moreover, hyperbranched architectures exhibit markedly weaker temperature dependence in interception behavior, attributed to enhanced intrachain excluded volume interactions. A combination of molecular dynamics simulation and theoretical analysis confirms that branching restricts conformational fluctuations, narrowing the distribution of accessible states and raising the free-energy barrier for pore entry. Our findings establish branching topology as a key regulator of polymer transport and interception in nanopores, offering new insights into the behavior of biopolymers like glycogen and starch in confined environments and guiding the design of advanced separation systems.