Diatoms secrete extracellular polymeric substances (EPS), or mucilage, around the cell wall that may serve to aid in motility and form a discrete layer that may help maintain thicker layers of EPS that have a greater role in adhesion. Mucilage molecules adhere to the diatom frustules, which are biosilica skeletons that develop from the diatom cell walls. Here, molecular dynamics methods were used to determine the characteristics of mucilage molecules as a function of pore size; notably 1,4-α-D-galacturonic acid, 1,4-β-glucuronic acid and 1,4-β-D-mannuronic acid. These uronic acids differ from each other in structure and extensibility as a function of their folding characteristics. Here, we find that when overlain upon a pore, mucilage molecules try to return to their native folded states but are restrained by their interactions with the silica surfaces. Furthermore, the extensibility of mucilage molecules over pore spaces affects the extent of mechanical energy required to straighten them. As such, different EPS molecules will affect sliding, friction and adhesion to subsequent layers of EPS in different ways. We conclude that higher EPS extensibility is homonymous with higher adhesive or frictive resistance since the molecules will be able to strain more before they reach the most extended (and thus rigid) conformation. The research herein is applicable to modern engineering as it yields insight into the biomimetic design of molecules and surfaces for improved adhesion or motility.