Theoretical probability distribution for finding a tagged bp at position x T open (solid line), compared with the result from the converged SA scheme (blue open squares). The underlying DNA sequence is given in Eq. (1).
Evolution of the free energy parameters of hydrogen bonding and base stacking as function of SA steps (full lines) from three separate SA runs. The black dashed horizontal lines represent the expected experimental values taken from Ref. 14, towards which convergence is expected to occur. Note the different scales on the vertical axes. The values for two pairs of bps, AT-AT and GA-TC, do not change in the SA procedure; these two pairs do not occur in the underlying sequence (1) and are thus not subject to the SA optimization criteria, i.e., they do not converge.
Evolution of ring factor ξ and critical exponent c from three different SA runs. The black dashed horizontal lines represent the expected literature value towards which convergence is expected to occur.
Plot of against x T at various SA steps. In each panel the red solid lines represents the original noisy data, and the blue dashed line is the output of SA runs. The blue open squares stand for the theoretical distribution P eq(x T ). The plot for 1500 SA steps already matches quite well the expected distribution P eq (x T ).
Magnitude of optimization parameters used in SA.
Comparison of experimental (Ref. 14) and simulated free energy data. Each simulation data is a mean of 1000 different SA outputs. The rightmost column shows the presence (√) or absence (×) of particular free energies in sequence (1). Units of free energies (ε st and ε hb ) reported here are kcal/mol. The last two rows of the table gives a comparison of the ring factor ξ and critical exponent c.
Article metrics loading...
Full text loading...