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In contrast to extensively studied defects in traditional materials, we report here a systematic investigation of the formation mechanism of intrinsic defects in self-assembled peptide nanostructures. The Monte Carlo simulations with our simplified dynamic hierarchical model revealed that the symmetry breaking of layer bending mode at the two ends during morphological transformation is responsible for intrinsic defect formation, whose microscopic origin is the mismatch between layer stacking along the side-chain direction and layer growth along the hydrogen bond direction. Moreover, defect formation does not affect the chirality of the self-assembled structure, which is determined by the initial steps of the peptide self-assembly process.


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