Properties depending on the radial ionic concentration profiles are calculated by Monte Carlo simulation for several simple B-DNA models in the presence of added ͑monovalent͒ salt up to 2.5 M concentration. The models include both homogeneously and discretely charged polyions. Besides, the effect of hard and soft repulsive forces is considered. A novel model which represents the DNA grooved structure in a simplified manner is introduced. From a methodological point of view, special attention is paid to the treatment of long-range forces along the axial direction. Exact formulas for discretely charged polyelectrolytes are used. Regarding the density profile results, it is concluded that the main effect is not due to the discreteness of the positions of the charges, i.e., homogeneously charged models lead to properties not significantly different from discretely charged ones. A similar statement holds for the comparison between hard and soft models. Nevertheless, the inclusion of the grooved shape of DNA modifies this behavior. A double hump in the concentration profile function is brought about by the coupling between repulsive and coulombic forces in the grooved model. It is shown that not only this but also other properties of full atomic models of DNA are adequately predicted by our simplified grooved model. Finally, at high concentrations of added salt, it is seen that the condensed ionic cloud overneutralizes the polyelectrolyte charge. This charge reversal phenomenon, which is observed in all the models studied, has not been previously observed due to the high salt concentration required.

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The effect of the ionic charge on the ionic distribution around a simple B-DNA model at the continuum solvent level is investigated using Monte Carlo simulation. In the model, the DNA shape is approximated by a set of simple geometric elements with charges at the canonical phosphate positions. Three series of simulations for an infinitely diluted polyion with added salt have been carried out. In each of them the ionic strength is kept constant. At low ionic strength, the behavior of monovalent, divalent, and trivalent cations is studied. It is shown that the number of counterions within the grooves depend only weakly on its valence so the fraction of DNA charge canceled out at small distances increases with the charge of the cation. This results in a deeper penetration of the coions, which, for systems with highly charged counterions as a 3:1 salt, may even surpass the bulk concentration in the vicinity of the polyelectrolyte. Nevertheless, no overscreening of the DNA charge has been observed in this system. On the contrary, the charge reversal phenomenon appeared in the simulations at high ionic strength irrespective of the ionic valences. It seems that this feature occurs when the bulk concentration of the mobile ions is of the same order as the local concentration in the vicinity of DNA with no added salt. Finally, the competition between monovalent and divalent cations is studied at concentrations close to those of biological media. It is shown that the divalent cations push the monovalent ions out of the DNA surroundings even if their concentration is much lower.

The structure of the ions around two B-DNA models with added monovalent salt at the continuum solvent level is investigated by computer simulation. The salt concentrations cover a wide range, from 0.05 to 4.5 M. The simplicity of the so-called grooved primitive model ͑unit electron charges at the phosphate positions of canonical DNA and the grooves shape approximated by means of simple geometric elements͒ enables a detailed study of the counterion and coion distributions with a very small statistical noise. The inhomogeneity of the ionic distributions is noticeable along the axial direction up to distances of about 20 Å from the DNA axis. The counterions deeply penetrate into the DNA grooves even at very low added salt concentrations. In the minor groove, the counterions are preferentially located in its center whereas they lie at the sides of the major groove, close to the phosphate positions. The coions also enter within the major groove, especially in the systems at high added salt concentrations for which regions of absolute negative charge can be found within the groove. This can be explained in terms of an arrangement of ions with alternating charges. The grooved primitive model has also been solved in the context of the finite difference Poisson-Boltzmann theory. The theory accurately describes the ionic structure around DNA at low salt concentrations but the results deteriorate with increasing salt missing important qualitative features at or above molar concentrations. The other model investigated differs from the more detailed one in that the shape of DNA is not taken into account; a soft cylinder is used instead. The counterions accumulate in this model in front of the phosphates and the axial inhomogeneity of the distribution quickly vanishes. These results together with those of previous investigations lead to the conclusion that the coupling of the discrete description of the DNA charge with the steric effects due to the presence of the grooves is the primary determinant of the final ionic distribution, especially at high salt concentrations. This effect may play a decisive role in those DNA properties which are strongly dependent on the salt concentration, like the B-to Z-DNA conformational transition.

Voronoi polyhedra analysis of the local structure of water from ambient to supercritical conditions A Voronoi polyhedra analysis of structures of liquid water Voronoi polyhedra (VP) analysis of ionic solutions generated via Monte Carlo simulations for a wide range of concentrations and ionic charges are reported. The properties investigated are the VP volumes, VP surface shared with unlikellike-ions and VP nonsphericity configurational mean values distributions. The study shows that high concentrations favor a molten salt like structure while low concentrations tend to disrupt such ordering so small aggregates are more likely. The degree of separation between these forms is strongly determined by the charge of the ions. In the limit of low concentrationsihigh ionic charge, small clusters with some chainlike character are present which anticipates several features characteristic of the low density liquid-gas transition of the restricted primitive model.