An associative memory Hamiltonian model for DNA and nucleosomes
Fig 2
DNA Persistence Length and Parametrization.
(a)(b) These figures show how persistence lengths depend on the strength of the energy interactions, λ, and the scale of structural fluctuations, σ. The bending persistence length is shown in panel (a), while the twisting persistence length is shown in panel (b). The σ is in reduced units (r.u.) which is 0.241 nm as explained in the Appendix A in S1 Document. Dots indicate the data points obtained by simulation; colored surfaces indicate their linear interpolation. The horizontal gray plane in (a) shows the experimentally determined bending persistence length of DNA, 150bp. This persistence length is set as the target for the optimization of the parameters. The red line indicates the intersection of the two surfaces, where our model meets the target persistence length value. Similarly, the gray box in (b) is the experimentally determined twisting persistence length, 75-360bp, our target in this case. (c) The figure shows the temperature dependence of bending persistence length. The four colored lines show results obtained using the WEChroM model. Black lines show experimental results published by Gray et al. [61] and Geggier et al. [62], respectively. As shown, the proposed model agrees well with the experimental observations for several couples of parameters (λ, σ).