Distinguishing jammed monomer and polymer packings in three dimensions

Proteins are geometrically and physically complex structures made from combinations of amino acids. When a protein folds, stereochemical, steric, and other atomic interactions determine the possible conformations. A polymer chain of spherical monomers is an overly simplified approximation of a protein, but even at this coarse-grained level, the differences in the structural and mechanical properties of packings made from folding a polymer of spherical monomers and packings made from individual spherical monomers are not fully understood. In this work, we seek to discern the fundamental differences between packings of spherical monomers and packings of polymers with short-range attractive interactions. We start by modeling the polymer as a freely jointed chain of spherical monomers, and then consider freely rotating chains of spherical monomers with fixed bend angles. In future studies, we will consider non-spherical monomers that can mimic the backbone and side chains of individual amino acids. While still a coarse-grained approximation of a true protein core, the inclusion of bend angles and non-spherical monomers provides an in-depth investigation into the core packings of collapsed polymers that can begin to elucidate how the presence of a backbone can change the packing landscape in proteins.