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The lowest energy ion binding mode for BWYV RNA in 0.02 M Mg2+ and 0.054 M Na+ at T = 25 °C. The half-transparent spheres denote the (hydrated) Mg2+ ions. (a) and (c) The predicted ion distribution from the current modified TBI model with the many-body effect for (a) the native pseudoknot and (c) the hairpin structure. For comparison, (b) and (d) show the (lowest energy) ion binding mode for the pseudoknot and hairpin structures with the original TBI model without the many-body effect.
