The molecular picture of dynamics and structure offered by an atomic MD model for a plant secondary cell wall with varying degrees of acetylation can quantitatively test the hypotheses from the introduction, testing the mechanism of action for slower diffusion induced by increasing acetylation. We take advantage of the atomic resolution offered by MD to also quantify specific interactions and dynamical quantities such as ion-interaction times within the dense biopolymer mesh formed within a secondary cell wall, and tracking the time evolution of interactions broadly between biomass components. .