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Xu, Zhenli

Publications and source records attributed to Xu, Zhenli.

Self-consistent field model for strong electrostatic correlations and inhomogeneous dielectric media

Electrostatic correlations and variable permittivity of electrolytes are essential for exploring many chemical and physical properties of interfaces in aqueous solutions. We propose a continuum electrostatic model for the treatment of these effects in the framework of the self-consistent field theory. The model incorporates a space- or field-dependent dielectric permittivity and an excluded ion-size effect for the correlation energy. This results in a self-energy modified Poisson-Nernst-Planck or Poisson-Boltzmann equation together with state equations for the self energy and the dielectric function. We show that the ionic size is of significant importance in predicting a finite self energy for an ion in an inhomogeneous medium. Asymptotic approximation is proposed for the solution of a generalized Debye-Hückel equation, which has been shown to capture the ionic correlation and dielectric self energy. Through simulating ionic distribution surrounding a macroion, the modified self-consistent field model is shown to agree with particle-based Monte Carlo simulations. Numerical results for symmetric and asymmetric electrolytes demonstrate that the model is able to predict the charge inversion at high correlation regime in the presence of multivalent interfacial ions which is beyond the mean-field theory and also show strong effect to double layer structure due to the space- or field-dependent dielectric permittivity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Treecode-based generalized Born method

We have developed a treecode-based O(N log N) algorithm for the generalized Born (GB) implicit solvation model. Our treecode-based GB (tGB) is based on the GBr6 [J. Phys. Chem. B 111, 3055 (2007)], an analytical GB method with a pairwise descreening approximation for the R6 volume integral expression. The algorithm is composed of a cutoff scheme for the effective Born radii calculation, and a treecode implementation of the GB charge–charge pair interactions. Test results demonstrate that the tGB algorithm can reproduce the vdW surface based Poisson solvation energy with an average relative error less than 0.6% while providing an almost linear-scaling calculation for a representative set of 25 proteins with different sizes (from 2815 atoms to 65456 atoms). For a typical system of 10k atoms, the tGB calculation is three times faster than the direct summation as implemented in the original GBr6 model. Thus, our tGB method provides an efficient way for performing implicit solvent GB simulations of larger biomolecular systems at longer time scales.

59 BASIC BIOLOGICAL SCIENCES↗

Image Charge Method for Reaction Fields in a Hybrid Ion-Channel Model

A multiple-image method is proposed to approximate the reaction-field potential of a source charge inside a finite length cylinder due to the electric polarization of the surrounding membrane and bulk water. When applied to a hybrid ion-channel model, this method allows a fast and accurate treatment of the electrostatic interactions of protein with membrane and solvent. To treat the channel/membrane interface boundary conditions of the electric potential, an optimization approach is used to derive image charges by fitting the reaction-field potential expressed in terms of cylindric harmonics. Meanwhile, additional image charges are introduced to satisfy the boundary conditions at the planar membrane interfaces. In the end, we convert the electrostatic interaction problem in a complex inhomogeneous system of ion channel/membrane/water into one in a homogeneous free space embedded with discrete charges (the source charge and image charges). The accuracy of this method is then validated numerically in calculating the solvation self-energy of a point charge.

59 BASIC BIOLOGICAL SCIENCES↗