Relaxation of a self-assembled structure of 144 peptide amphiphile (PA) molecules into cylindrical nanofibers is studied using atomistic molecular dynamics simulations including explicit water with physiological ion concentration. The PA for these studies includes a hydrophobic alkyl chain that is attached to the N-terminus of the sequence SLSLAAAEIKVAV. The self-assembly is initiated with PA molecules in a roughly cylindrical configuration, as suggested from previous experimental and theoretical investigations, and the cylindrical configuration that results is found to be stable during 40 ns simulations. In the converged structure of the resulting nanofiber, the cylinder radius is ∼44 Å, a result that is consistent with experimental results. Water and sodium ions can penetrate into the peptide portion of the fiber but not between the alkyl chains. Even though each PA has an identical sequence, a broad distribution of secondary structure is found in the converged structure of the nanofiber. The β-sheet population for the SLSL and IKV segments of the peptide is ∼25%, which is consistent with previous circular dichroism results. We also found that the epitope sequence IKVAV is located on the surface of the nanofiber, as designed for the promotion of the neurite growth. Our findings will be useful for designing new PA fibers that have improved bioactive properties.

Amphiphilic, linear conjugated poly[p-{2,5-bis(3-propoxysulfonicacidsodiumsalt)}phenylene]ethynylene (PPES) efficiently disperses single-walled carbon nanotubes (SWNTs) under ultrasonication conditions into the aqueous phase. Vis-NIR absorption spectroscopy, atomic force microscopy (AFM), and transmission electron microscopy (TEM) demonstrate that these solubilized SWNTs are highly individualized. AFM and TEM data reveal that the interaction of PPES with SWNTs gives rise to a self-assembled superstructure in which a polymer monolayer helically wraps the nanotube surface; the observed PPES pitch length (13 +/- 2 nm) confirms structural predictions made via molecular dynamics simulations. This work underscores design elements important for engineering well-defined nanotube-semiconducting polymer hybrid structures.

We have studied the self-assembly of peptide amphiphiles (PAs) into a cylindrical micelle fiber starting from a homogeneous mixture of PAs in water using coarse-grained molecular dynamics simulations. Nine independent 16 μs runs all show spontaneous fiber formation in which the PA molecules first form spherical micelles, and then micelles form a three-dimensional network via van der Waals interactions. As the hydrophobic core belonging to the different micelles merge, the three-dimensional network disappears and a fiber having a diameter of ∼80 Å appears. In agreement with atomistic simulation results, water molecules are excluded from the hydrophobic core and penetrate to ∼15 Å away from the axis of fiber. About 66% of the surface of fiber is covered with the IKVAV epitope, and ∼92% of the epitope is exposed to water molecules.