Table 1. Important simulation variables and order parameters.
Notation/Terminology | Physical Interpretation | Definition |
---|---|---|
Ntot | Total number of polymer chains in the system. Ntot = 400 in our simulations. | – |
Lclus | Size of the single largest cluster | represented as fraction of Ntot |
Sclus | Size of the cluster | represented as fraction of Ntot |
Cmono | Concentration of polymer chains in the simulation box | In units of μM |
φ | Bulk density of proteins (in their monomeric state) when the individual chains are randomly placed in the simulation box at the start of the simulation. |
is the the radius of gyration of proteins when they are randomly positioned in simulation box at the start of the simulation. |
φclus | Intra-cluster density of polymer chains. | is the radius of gyration of the system of proteins within the cluster. |
φclus /φ | Normalized intracluster density describing the degree of enrichment of polymer chains within the cluster. | For system-spanning networks, φclus /φ→1. For dense clusters, φclus /φ >> 1. |
εns | Interaction strength for isotropic, non-specific interactions between linker regions. εns in LD simulations is a pairwise interaction strength between individual beads In kMC simulations, εns is the net non-specific interaction strength between two lattice particles. | – . |
εsp | Strength of attractive interaction between functional domains (specific interactions). | – |
φlattice | Bulk density of monomers in the 2D-lattice in kMC simulations. This quantity is analogous to the concentration of monomers on the lattice. | φlattice = Ntot/L2, where L is the size of the 2D square-lattice. |
λ | Valency of the polymer chain, that is the number of adhesive functional domains per interacting polymer chain. | – |
Κ | Bending stiffness of the linker regions in LD simulations. A higher value of K is used to model stiffer linkers that prefer a more open configuration. | Κ = 2 kcal/mol, in LD simulations with flexible linkers. |
η | The viscosity of the medium in LD simulations | η = 10−3Pa.s in LD simulations, unless mentioned otherwise. |
kdiff | Diffusion rate of free monomers in the 2D-lattice kMC simulations. | – |
kbond | Rate of formation of specific interactions between neighboring particles in 2D-lattice kMC simulations. | – |