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. Author manuscript; available in PMC: 2022 Apr 19.
Published in final edited form as: J Phys Chem B. 2021 May 10;125(19):5035–5044. doi: 10.1021/acs.jpcb.1c02286

Table 2.

Important Simulation Variables and Order Parameters

notation (or
terminology)		 physical interpretation definition
ϕprotx volume fraction of proteins in the simulation box ϕprot = Ntot(4/3πR3)/L3, where R is the size of the protein monomer and L is the length of the cubic simulation box; this is a dimensionless quantity used to represent protein concentrations
L clus size of the single largest cluster
N tot total number of protein monomers in the system. Ntot = 1000 in our patchy-particle simulations
N RNA number of RNA chains in simulation parameter that is varied in our simulations to vary the protein/RNA ratio.
L RNA length of semiflexible RNA chains in LD simulations represented in terms of number of nucleotides
Rg radius of gyration of RNA