A new numerical method for nonlocal electrostatics in biomolecular simulations

DOI10.1016/j.jcp.2010.01.040zbMath1193.92006OpenAlexW2011585371WikidataQ57011975 ScholiaQ57011975MaRDI QIDQ974285

B. E. Eshmatov

Publication date: 27 May 2010

Published in: Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jcp.2010.01.040

zbMATH Keywords

boundary element methodimmersed interface methodtransmission problembiomoleculesnonlocal electrostatics

Mathematics Subject Classification ID

Biological applications of optics and electromagnetic theory (78A70) Finite difference methods applied to problems in optics and electromagnetic theory (78M20) Biophysics (92C05)

Related Items (6)

EJIIM for the stationary Schrödinger equations with delta potential wells ⋮ Nonlocal electrostatics in spherical geometries using eigenfunction expansions of boundary-integral operators ⋮ Comparative assessment of nonlocal continuum solvent models exhibiting overscreening ⋮ An implicit boundary integral method for computing electric potential of macromolecules in solvent ⋮ A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules ⋮ A simple and efficient technique to accelerate the computation of a nonlocal dielectric model for electrostatics of biomolecule

Uses Software

• ATLAS
• AMBER
• KELLEY
• Netgen
• MeshLab
• BALL

Cites Work

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• Explicit jump immersed interface method for virtual material design of the effective elastic moduli of composite materials
• Quality mesh generation for molecular skin surfaces using restricted union of balls
• AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
• Structural boundary design via level set and immersed interface methods
• Optimal triangulation and quadric-based surface simplification
• A staggered grid‐based explicit jump immersed interface method for two‐dimensional Stokes flows
• The Immersed Interface Method for Nonlinear Differential Equations with Discontinuous Coefficients and Singular Sources
• The Explicit-Jump Immersed Interface Method: Finite Difference Methods for PDEs with Piecewise Smooth Solutions
• Rapid software prototyping in molecular modeling using the biochemical algorithms library (BALL)
• A Boundary Integral Formulation for Nonlocal Electrostatics
• Automated empirical optimizations of software and the ATLAS project

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