Figure 2. Molecular dynamics simulations of monolayers of oligoalanine peptides attached covalently to a surface.

5 × 5 monolayer of 10-mer oligoalanine (Ala10), modeled as (c) an α-helical or (d) a linear conformation. Each model of the monolayer was simulated for 1 ns and further analysis was performed on the central peptide (red) relative to its eight neighbors (blue). Also shown is the distribution of the: (a) angle of the central peptide intra-peptide hydrogen bonds; (b) number of inter-peptide hydrogen bonds between the central peptide and neighboring ones.