FIGURE 3.
As a function of Gsim, for N ≤ 20 and M ≤ 6, we plot: (A) the Mfold initial run (Equation 5); (B) the re-evaluated free energies of Mfold's efn2 (Equation 6); (C) our GFJC2 formula (Equation 2); and (D) the best linear fit to simulation data Glinear = (4.3 + 0.07N + 0.2M)kcal/mol. It is clear that GFJC2 best approximates Gsim, demonstrating that FJC2 captures the correct polymer physics lacking in the Mfold formulas. The quality of the agreement allows us to incorporate hairpin loops on the same footing as multibranch loops and to consider coaxial stacking as a change in the effective M.