4.2.2 Height of the force rips

As seen in Eq. 4.9, there is a mean unzipping force defined by the mean value of the NNBP energies. However, a single realization of the model shows slopes and force rips around the mean average force (see Fig. 4.8d), which reflect the discontinuous opening of base pairs. The height of the force rips (i.e., the amplitudes of the sawtooth pattern) depend on the standard deviation $ \sigma _{\epsilon _i}$ of the energies and on the trap stiffness $ k$ (see Fig. 4.9). An interesting result is the fact that the stiffness of the trap directly affects the opening of base pairs. Therefore, the resolution in base pairs that can be observed during unzipping is partially determined by the stiffness. This feature of the model is quite relevant and it can be used to establish the experimental conditions that would allow to sequence the DNA through unzipping experiments.

Figure 4.9: FDC for different values of the experimental parameters. The heights of the force rips depend on the standard deviation $ \sigma _{\epsilon _i}$ and on the trap stiffness $ k$. Low $ \sigma _{\epsilon _i}=0.1$ kcal$ \cdot $mol$ ^{-1}$, high $ \sigma _{\epsilon _i}=1.0$ kcal$ \cdot $mol$ ^{-1}$, low $ k = 0.02$ pN$ \cdot $nm$ ^{-1}$ and high $ k = 0.5$ pN$ \cdot $nm$ ^{1}$. Note that the mean unzipping force is independent of $ \sigma _{\epsilon _i}$ and $ k$.

JM Huguet 2014-02-12