DNA and its conformational transition can be used to design nanometer-scale structures,nano-tweezers and nanomechanical devices.Experiments and molecular simulations have been used to study the concentration effect on the A-DNA→B-DNA conformational transition,but a systematical investigation on counterion effect on the dynamics of this transition has not been reported up to now.In present work,restrained and unrestrained molecular dynamics(MD)simulations have been performed to characterize the stability of DNA conformations and the dynamics of A-DNA→B-DNA transitions in aqueous solutions with different alkali metal counterions.The DNA duplex d(CGCGAATTCGCG)2,coion Cl and counterions Li+,Na+,K+,Rb+and Cs+as well as water molecule were considered using the PARM99 force field in the AMBER8 package.It was found that B-form DNA is more stable than A-form DNA in aqueous electrolyte solutions with different alkali metal counterions.Increasing KCl concentration in solution hinders the A-DNA→B-DNA transition and the transition times for different alkali metal counterions conform to neither the simple sequence related to naked ion size nor to hydrated diameter,but an apparently abnormal sequence of K+
The effects of solid-fluid interactions on the vapor-liquid phase diagram,coexistence density,relative volatility and vaporization enthalpy have been investigated for confined binary systems of CO 2-CH 4,CO 2-N 2 and CH 4-N 2.The Gibbs ensemble Monte Carlo(GEMC) simulation results indicate that the confinement and the solid-fluid interaction have significant influences on the vapor-liquid equilibrium properties.The confinement and the strength of the solid-fluid interaction make the p-x i phase diagram move to higher pressure regions.They also make the two-phase region become narrower for each binary mixture.The strength of the solid-fluid interactions can cause increases in the coexistence liquid and vapor densities,and cause the decrease of the relative volatility and the vaporization enthalpy for the systems studied.As the pore width is decreased,the two-phase region of the binary mixture becomes narrower.
