Figure 5.

Modeling of surface-localized ions and their effect on the diffuse ion atmosphere. (a) Ions were placed sequentially at sites near the surface of the DNA molecule with the greatest magnitude of the potential, and the NPBE was solved again after each ion addition (see text). DNA models with ions represented as r = 2 Å spheres are shown for $N_{\text{I}}^{\left(\text{S}\right)}=$ 0, 5, 10, 15, and 20 (rendered using Pymol version 1.2r1, DeLano Scientific, Portland, OR). (b) For each model, the total number of ions within a cylindrical volume, V_cyl, with radius R centered on the helical axis of the DNA (inset) was computed. The number of excess ions includes the explicit ions shown in (a) and the excess ion density from the NPBE solution (open circles). To see this figure in color, go online.