CASPULE: A computational tool to study sticker spacer polymer condensates
Fig 2
Quantification of clustering dynamics.
(A) Illustration of the two-component sticker-spacer system. Each component consists of 10 stickers (red and cyan beads) and 40 spacers (yellow beads). We only allow heterotypic interactions, that is, red stickers interact with cyan stickers, but red-red or cyan-cyan are not allowed. (B) Stickers engage in specific interactions (Es). A complementary sticker (red and cyan) pair can form a reversible bond within a cutoff radius, Rcut. Once bonded, they cannot engage with another sticker that may be present within Rcut. In other words, each sticker has a valency of 1. (C) All beads (except bonded stickers) in the system experience non-specific interactions (Ens), modelled by Lennard-Jones (LJ) potential. One bead can interact with multiple beads, permitted by volume exclusions. A bead diameter (σ) is set by the minimum distance between two bead centers. (D) Snapshots of a multi-chain system undergoing clustering as a function of time. A total of 400 chains (200 chains each type) are placed uniformly inside a cubic box (length = 800Å). Sticker-sticker (Es = 6kT) interactions drive inter-chain crosslinking and weaker spacer-spacer (Ens = 0.3kT) interactions tune the cluster compaction. (E) Energy time course of the system. Ebond includes all the bonds (permanent and breakable) present in the system. Epair refers to the sum of contact energies coming from the pairwise Lennard-Jones interactions. Eangle is angular energy. Epotential = Ebond + Epair + Eangle. Energy unit is kcal/mol. (F) Time course of radius of gyration (Rgsystem) and sticker saturation. Inset shows the zoomed in version of the first half. The red dashed line indicates the time needed to equilibrate the system’s Rg, while the blue dashed line indicates the time needed by the stickers to reach to a steady saturation level. In (E,F), data is averaged over 5 stochastic runs. Solid line is mean, shaded area is standard deviation.