The secondary cell wall model used here contains the three major polymers, cellulose, hemicellulose, and lignin, in approximately the ratio found in hardwood (Table ). The cellulose model contains four 18-chain cellulose Iβ bundles with DP (degree of polymerization) of 40 in the 234432 motif (Figure ). Decorated xylan molecule with DP of 40 was used to represent hemicellulose. Experimental studies suggest that ~40-70% of the xylose residues are acetylated on C2 or C3 positions and D-glucuronic acid groups are also linked to C2 or C3 in ~10% of the xylose residues . In our xylan model, the D-glucuronic acid groups are linked to C2 in every one of eight xylose residues, whereas the acetyl groups are linked to C2 in every other xylose residue. In models where the C2 has been occupied by a D-glucuronic acid group, the acetyl group is linked to C3. All the substitution groups are located on the even-numbered xylose residues, leading to a xylan molecule with all decorations on the same side (Figure ). A schematic lignin 20-mer model proposed by for hardwood was used to construct the structure of the lignin polymer model, which contains 13 syringol units and 7 guaiacol units (S:G = 65:35) (Figure ). While the individual polymers were repeated to fill the simulation volume (Table ), and therefore the polymer distribution is not polydisperse like it would be in intact biomass, the system approximately represents intact biomass to within the limitations of current modeling approaches. The individual components were assembled using PACKMOL into a rectangular simulation volume. The generated PCW model was compressed slowly by decreasing the simulation box dimensions until a desired density of 1.5 g/cm 3 determined experimentally from dried wood was achieved at a box size of 78.8 Å x 78.8 Å x 210.6 Å. Sodium ions were added to maintain the total charge of the system to be neutral.