Fast analytical methods for macroscopic electrostatic models in biomolecular simulations

DOI10.1137/090774288MaRDI QIDQ3105796zbMATH OpenOpenAlexWikidataFDO

Authors Zhenli Xu, Wei Cai

Publication date 9 January 2012

Published in SIAM Review (Search for Journal in Brave)

Full work available at URL http://europepmc.org/articles/pmc3671632

zbMATH Keywords

electrostatic free energyelectrostatic interactionsfast algorithmgeneralized Born theoryhybrid explicit/implicit solvation modelsimage charge approximationmacroscopic solvent modelsmultipole expansionPoisson-Boltzmann equationreaction field

Mathematics Subject Classification ID

Second-order elliptic equations (35J15) PDEs in connection with biology, chemistry and other natural sciences (35Q92) Complexity and performance of numerical algorithms (65Y20) Motion of charged particles (78A35) Biological applications of optics and electromagnetic theory (78A70) Biophysics (92C05) Biochemistry, molecular biology (92C40)

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Cited in

(19)

• Dielectric properties of proteins from simulations: Tools and techniques
• ``New-version-fast-multipole-method accelerated electrostatic calculations in biomolecular sys\-tems
• A nonlinear elasticity model of macromolecular conformational change induced by electrostatic forces
• Many-body effects and electrostatics in biomolecules
• A hybrid method for systems of closely spaced dielectric spheres and ions
• Progress in developing Poisson-Boltzmann equation solvers
• Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding
• Computational electrostatics for biological applications. Geometric and numerical approaches to the description of electrostatic interaction between macromolecules. Proceedings of the CEBA international meeting, Genova, Italy, July 1--3, 2013
• Accuracy and efficiency in computing electrostatic potential for an ion channel model in layered dielectric/electrolyte media
• Comparison of efficient techniques for the simulation of dielectric objects in electrolytes
• Image approximations to electrostatic potentials in layered electrolytes/dielectrics and an ion-channel model
• Between Algorithm and Model: Different Molecular Surface Definitions for the Poisson-Boltzmann Based Electrostatic Characterization of Biomolecules in Solution
• Efficient implementation of the Barnes-Hut octree algorithm for Monte Carlo simulations of charged systems
• A fast method for evaluating Green's function in irregular domains with application to charge interaction in a nanopore
• Harmonic Surface Mapping Algorithm for Electrostatic Potentials in an Atomistic/Continuum Hybrid Model for Electrolyte Solutions
• Image charge methods for a three-dielectric-layer hybrid solvation model of biomolecules
• Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity
• AFMPB: an adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems
• A new numerical method for nonlocal electrostatics in biomolecular simulations

Describes a project that uses

Uses Software

• Gromacs
• APBS

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