Fig. 5: Flowchart describing the graph-theoretic analysis of simulations of dense phases of N130 and rpL5.
From: Biomolecular condensates form spatially inhomogeneous network fluids
We start by selecting a set of residues of interest. As an illustrative example, we pick the acidic residues in N130 and the basic residues in rpL5. To determine an edge, we compute the g(r) between sets of beads where the first minimum serves as the distance cutoff for bead adjacency. Given this cutoff, we construct the bead-to-bead adjacency matrices. The system includes the N130 PD. Performing appropriate block summations of the bead-to-bead adjacency matrix generates the molecular adjacency matrix. The latter is analyzed using standard graph-theoretic analyses. As an example, a random embedding is shown where the size of a node corresponds to the degree of centrality of that node.
