A family of reduced-resolution simulation models that represent each RNA nucleotide by one to three interaction sites (rather than every atom) so that folding, cation binding, and phase separation can be studied at experimentally relevant length and time scales. Electrostatics are handled by combining implicit Debye-Huckel screening for monovalent ions with explicit treatment of divalent cations, and the models are calibrated against single-molecule and thermodynamic experiments on riboswitches and ribozymes.
Coarse-grained models replace each RNA nucleotide with one to three interaction sites so that folding, ion binding, and phase separation can be simulated at length and time scales beyond atomistic mo…