Motional Degrees of Freedom in Network Hamiltonian Models

Abstract

Network Hamiltonian Models (NHMs) provide an efficient framework for modeling the aggregation of interacting particles (e.g., the condensation of proteins into gel-like, oligomeric, or fibrillar states), representing the system as a network whose edges represent bound interactions. Terms within the network Hamiltonian represent multi-body interactions governing aggregation behavior, and are specified via topological degrees of freedom. Because motional degrees of freedom are not explicitly represented within the NHM, their influence must be indirectly accounted for by introduction of corresponding terms to the Hamiltonian. Here, we describe specifications for terms representing motional degrees of freedom of two, three, and four-body interactions. We also consider the impact of these terms on the aggregation states of a minimal system governed only by a pairwise edge potential, showing that three and four-body interactions favor condensation of the system into small droplet-like structures at low temperature.