Tekin, E. DenizTekin, Emine Deniz2024-06-252024-06-2520152046-2069https://acikarsiv.thk.edu.tr/handle/123456789/1401We carried out united-atom molecular dynamics simulations to understand the structural properties of peptide amphiphile (PA)-based cylindrical nanofibers and the factors that play a role in the Self-Assembly process on some specific nanofibers. In our simulations, we start from various cylindrical nanofiber structures with a different number of layers and a different number of PAs in each layer, based on previous experimental and theoretical results. We find that the 19-layered nanofiber, with 12 PAs at each layer, distributed radially and uniformly with alkyl chains in the center, is the most stable configuration with a diameter of 8.4 nm which is consistent with experimental results. The most dominant secondary structures formed in the fibers are random coils and beta-sheets, respectively. We also find that hydrophobic interactions between the VVAG-VVAG moiety of the PA molecules and electrostatic interactions between D-Na+ and between E-R are responsible for the fiber's self-assembly properties. During the aggregation process, first dimers, then trimers are formed.EnglishSPINAL-CORD-INJURY; SECONDARY STRUCTURE; FIBERS; NANOSTRUCTURES; BIOMATERIALS; RECOGNITION; HYDRATION; SCAFFOLD; PACKINGArticle