Density-functional theory and Monte Carlo simulation study on the electric double layer around DNA in mixed-size counterion systems.
A density-functional approach and canonical Monte Carlo simulations are presented for describing the ionic microscopic structure around the DNA molecule immersed in mixed-size counterion solutions. In the density-functional approach, the hard-sphere contribution to the Helmholtz energy functional is obtained from the modified fundamental measure theory [Y.-X. Yu and J. Z. Wu, J. Chem. Phys. 117, 10156 (2002)], and the electrostatic contribution is evaluated through a quadratic functional Taylor expansion. The new theory is suitable to the systems containing ions of arbitrary sizes and valences. In the established canonical Monte Carlo simulation, an iterative self-consistent method is used to evaluate the long-range energy, and another iterative algorithm is adopted to obtain desired bulk ionic concentrations. The ion distributions from the density-functional theory (DFT) are in good agreement with those from the corresponding Monte Carlo (MC) simulations. It is found that the ratio of the bulk concentrations of two species of counterions (cations) makes significant contribution to the ion distributions in the vicinity of DNA. Comparisons with the electrostatic potential profiles from the MC simulations show that the accuracy of the DFT becomes low when a small divalent cation exists. Both the DFT and MC simulation results illustrate that the electrostatic potential at the surface of DNA increases as the anion diameter or the total cation concentration is increased and decreases as the diameter of one cation species is increased. The calculation of electrostatic potential using real ion diameters shows that the accuracy of DFT predictions for divalent ions is also acceptable.
Wang
Ke
K
Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China.
Yu
Yang-Xin
YX
Gao
Guang-Hua
GH
Luo
Guang-Sheng
GS
D000465:Algorithms; D000838:Anions; D002412:Cations; D002413:Cations, Divalent; D004247:DNA / Q000737:chemistry*; D004563:Electrochemistry / Q000379:methods*; D007477:Ions; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D012107:Research Design; D055672:Static Electricity
D000838:Anions; D002412:Cations; D002413:Cations, Divalent; D007477:Ions; D004247:DNA