FIG. 2: (a) A snapshot of bp distance in a duplex of 300-bp ( ∼ 100 nm) long obtained from simulations of the Breathing DNA model. The shape of duplex thickness therefrom drawn manifests breathing, formation of bubble in the middle of the duplex and forks at the ends. (b) The simulation data on fraction of bound bp in the 300-bp long duplex vs. temperature. It shows a sharp transition into denaturation state at melting temperature ( ≈ 350 K). At physiological temperature ( ∼ 310 K), the fraction less than 1% is denatured (unbounded) either as bubbles or forks. bp long or about 100 nm, with free ends, and the fluctuating DNA thickness of about 2 nm therefrom constructed. The figure shows indeed the local denaturation exist in the forms of bubbles within the contour and fork at the ends. From the simulation we find the fraction of bound pairs undergoes a sharp transition from near unity to zero in agreement with experiment [13] at the melting temperature, which is about 350 K. It indicates that at the physiological temperature (310 K), the fraction of the bp that forms the local denaturation is less than 1%. Shown in the Fig. 3 are the size distributions of the bubbles ( P$_{b}$ ( n )) and forks ( P$_{f}$ ( n )) for the various contour lengths of the DNA fragments. The distribution of the bubble size with n bp open is remarkably independent of its position and the DNA length. For relatively large bubbles it follows the Poland-Sherega form [14] 5