Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding

DOI10.2478/MLBMB-2013-0007MaRDI QIDQ2863933zbMATH OpenOpenAlexWikidataFDO

Authors Amelia B. Kreienkamp, Lucy Y. Liu, Mona S. Minkara, Matthew G. Knepley, Jaydeep P. Bardhan, Mala L. Radhakrishnan

Publication date 5 December 2013

Published in Molecular Based Mathematical Biology (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://doi.org/10.2478/mlbmb-2013-0007

zbMATH Keywords

component analysismolecular electrostaticsimplicit solvent modelsboundary-element methodsBIBEEcontinuum solvation

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Fundamental solutions, Green's function methods, etc. for boundary value problems involving PDEs (65N80) Boundary element methods for boundary value problems involving PDEs (65N38) Biophysics (92C05)

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Cites work

• scientific article; zbMATH DE number 1138543 (Why is no real title available?)
• scientific article; zbMATH DE number 3004850 (Why is no real title available?)
• scientific article; zbMATH DE number 745249 (Why is no real title available?)
• An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics
• Certified reduced basis methods and output bounds for the harmonic Maxwell's equations
• Ellipsoidal harmonics. Theory and applications
• Error analysis in numerical solution of acoustic integral equations
• Fast analytical methods for macroscopic electrostatic models in biomolecular simulations
• Matched interface and boundary (MIB) method for elliptic problems with sharp-edged interfaces
• On the magnetostatic integral operator for ellipsoids
• The Numerical Solution of Integral Equations of the Second Kind
• The electric potential of a macromolecule in a solvent: A fundamental approach
• The reduced basis method for the electric field integral equation
• Theory of Solutions of Molecules Containing Widely Separated Charges with Special Application to Zwitterions

Cited in

(4)

• The Extent of Anisotropic Interactions Between Protein Molecules in Electrolyte Solutions
• A Fast Accurate Boundary Integral Method for Potentials on Closely Packed Cells
• A Boundary Integral Formulation for Nonlocal Electrostatics
• Multiscale models and approximation algorithms for protein electrostatics

Describes a project that uses

Uses Software

• MIBPB
• CHARMM
• Matlab

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