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Poisson-Fermi Formulation of Nonlocal Electrostatics in Electrolyte Solutions

100%

Liu J.-L., Xie D., Eisenberg B.

Molecular Based Mathematical Biology

2017

tom 5

nr 1

116-124

We present a nonlocal electrostatic formulation of nonuniform ions and water molecules with interstitial voids that uses a Fermi-like distribution to account for steric and correlation efects in electrolyte solutions. The formulation is based on the volume exclusion of hard spheres leading to a steric potential and Maxwell’s displacement field with Yukawa-type interactions resulting in a nonlocal electric potential. The classical Poisson-Boltzmann model fails to describe steric and correlation effects important in a variety of chemical and biological systems, especially in high field or large concentration conditions found in and near binding sites, ion channels, and electrodes. Steric effects and correlations are apparent when we compare nonlocal Poisson-Fermi results to Poisson-Boltzmann calculations in electric double layer and to experimental measurements on the selectivity of potassium channels for K+ over Na+.

A Stochastic Solver of the Generalized Born Model

75%

Harris R. C., Mackoy T., Fenley M. O.

Molecular Based Mathematical Biology

2013

tom 1

63-74

A stochastic generalized Born (GB) solver is presented which can give predictions of energies arbitrarily close to those that would be given by exact effective GB radii, and, unlike analytical GB solvers, these errors are Gaussian with estimates that can be easily obtained from the algorithm. This method was tested by computing the electrostatic solvation energies (ΔGsolv) and the electrostatic binding energies (ΔGbind) of a set of DNA-drug complexes, a set of protein-drug complexes, a set of protein-protein complexes, and a set of RNA-peptide complexes. Its predictions of ΔGsolv agree with those of the linearized Poisson-Boltzmann equation, but it does not predict ΔGbind well, although these predictions of ΔGbind may be marginally better than those of traditional analytical GB solvers. Apparently, the GB model itself must be improved before accurate estimates of ΔGbind can be obtained.

Ograniczanie wyników

2 Molecular Based Mathematical Biology

1 Eisenberg B.

1 Fenley M. O.

1 Harris R. C.

1 Liu J.-L.

1 Mackoy T.

1 Xie D.

1 2017

1 2013

Wyniki wyszukiwania

Poisson-Fermi Formulation of Nonlocal Electrostatics in Electrolyte Solutions

A Stochastic Solver of the Generalized Born Model