Polymer collapse and jamming: The role of the backbone connectivity and adhesive interactions in determining the properties of the cores of collapsed polymers and folded proteins

Proteins are important biopolymers that not only reliably fold to stable conformations, but also possess collective dynamics and response that are essential for performing biological functions. Previous work has shown that the interiors of proteins are densely packed, i.e. similar to jammed packings of purely repulsive amino acid-shaped particles. Therefore, soft matter approaches are uniquely positioned to model the structural and mechanical properties of protein cores. While much work over the past two decades has explored the properties of jammed packings of disconnected repulsive particles, complexities emerge when applying these approaches to collapsed biopolymers due to open boundary conditions, polymer backbone connectivity, and attractions between monomers. Here, we generate jammed packings of repulsive monomers and of a repulsive polymer chain and thermally collapsed systems of sticky monomers and a sticky polymer chain. Two main questions arise: 1. How similar is the thermal collapse of sticky particles to jamming of repulsive particles under isotropic compression? and 2. How do connectivity and adhesive interactions impact the structural and mechanical properties? To this end, we analyze the interior packing fraction, number of contacts above isostaticity, and the emergence of excess low-frequency modes in the vibrational density of states.