Equation 4.7 is useful to describe the average number of open base pairs. However, for each realization of the energies, , the function is a discontinuous function and has to be numerically calculated (see Fig. 4.10a black curve). Each discontinuity represents an opening of base pairs, i.e., a CUR. The size of a CUR is the difference of the number of open base pairs between two states. This way, we can calculate the size of the CUR from the function by extracting the step size of the discontinuities (Fig. 4.10a, red curve). A distribution of CUR sizes can be obtained for one realization (Fig. 4.10b, blue curve, inset).
The average distribution of CUR sizes can be obtained by simulating random realizations, calculating the CUR size distribution for each realization of the disorder and averaging over them. By varying the parameters of the model along a wide range we observe how the shape of the CUR size distribution depends on them. Generally speaking, we have observed that the shape of the CUR size distribution is independent of the mean NNBP energy (). It mostly depends on the standard deviation of the NNBP energies and on the trap stiffness . Figure 4.11 shows these dependencies for a model with the following parameters: nm, kcalmol simulated for a bp long sequence over realizations of the disorder.
JM Huguet 2014-02-12