Multiscale molecular dynamics using the matched interface and boundary method

DOI10.1016/J.JCP.2010.09.031zbMath1246.82028OpenAlexW1996033088WikidataQ42364131 ScholiaQ42364131MaRDI QIDQ621913

Sumit K. Garg

Publication date: 31 January 2011

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

Full work available at URL: http://europepmc.org/articles/pmc2981041

zbMATH Keywords

molecular dynamicsPoisson-Boltzmann equationimplicit solvent modelmatched interface and boundaryinterface methodbiomolecules

Mathematics Subject Classification ID

Biological applications of optics and electromagnetic theory (78A70) Biochemistry, molecular biology (92C40) Interface problems; diffusion-limited aggregation arising in equilibrium statistical mechanics (82B24)

Related Items (19)

Enriched gradient recovery for interface solutions of the Poisson-Boltzmann equation ⋮ Biomolecular surface construction by PDE transform ⋮ Quantum dynamics in continuum for proton transport II: Variational solvent-solute interface ⋮ Geometric and electrostatic modeling using molecular rigidity functions ⋮ Parallel higher-order boundary integral electrostatics computation on molecular surfaces with curved triangulation ⋮ A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules ⋮ Multiscale geometric modeling of macromolecules. I: Cartesian representation ⋮ Second order method for solving 3D elasticity equations with complex interfaces ⋮ A Galerkin formulation of the MIB method for three dimensional elliptic interface problems ⋮ Pseudo-transient ghost fluid methods for the Poisson-Boltzmann equation with a two-component regularization ⋮ A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation ⋮ Adaptively deformed mesh based interface method for elliptic equations with discontinuous coefficients ⋮ A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver ⋮ Accurate PKa Computation Using Matched Interface and Boundary (MIB) Method Based Poisson-Boltzmann Solver ⋮ MIB Galerkin method for elliptic interface problems ⋮ MIB method for elliptic equations with multi-material interfaces ⋮ Multiscale models of compact bone ⋮ High-order fractional partial differential equation transform for molecular surface construction ⋮ Matched interface and boundary method for elasticity interface problems

Uses Software

• Unnamed Item
• APBS
• CHARMM

Cites Work

• Unnamed Item
• Differential geometry based solvation model. I: Eulerian formulation
• A finite element method for interface problems in domains with smooth boundaries and interfaces
• Differential geometry based multiscale models
• Geometric and potential driving formation and evolution of biomolecular surfaces
• On the fictitious-domain and interpolation formulations of the matched interface and boundary (MIB) method
• Matched interface and boundary (MIB) method for elliptic problems with sharp-edged interfaces
• The electric potential of a macromolecule in a solvent: A fundamental approach
• Numerical analysis of blood flow in the heart
• Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
• A non-oscillatory Eulerian approach to interfaces in multimaterial flows (the ghost fluid method)
• High-order FDTD methods via derivative matching for Maxwell's equations with material interfaces
• A boundary condition capturing method for Poisson's equation on irregular domains
• Immersed finite element method and its applications to biological systems
• A coupling interface method for elliptic interface problems
• Three-dimensional matched interface and boundary (MIB) method for treating geometric singularities
• A new minimization protocol for solving nonlinear Poisson-Boltzmann mortar finite element equation
• High order matched interface and boundary method for elliptic equations with discontinuous coefficients and singular sources
• Quality meshing of implicit solvation models of biomolecular structures
• The finite element method for elliptic equations with discontinuous coefficients
• The numerical approximation of a delta function with application to level set methods
• The Immersed Interface Method for Elliptic Equations with Discontinuous Coefficients and Singular Sources
• The Fast Solution of Poisson’s and the Biharmonic Equations on Irregular Regions

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