Efficient and Qualified Mesh Generation for Gaussian Molecular Surface Using Adaptive Partition and Piecewise Polynomial Approximation

DOI10.1137/16M1099704zbMath1393.65027arXiv1611.03474OpenAlexW2796274461MaRDI QIDQ4637667

Benzhuo Lu, Tiantian Liu, Minxin Chen

Publication date: 25 April 2018

Published in: SIAM Journal on Scientific Computing (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1611.03474

zbMATH Keywords

triangulationadaptive partitionsurface mesh generationGaussian surfacetrilinear polynomial

Mathematics Subject Classification ID

Mesh generation, refinement, and adaptive methods for the numerical solution of initial value and initial-boundary value problems involving PDEs (65M50) Computer-aided design (modeling of curves and surfaces) (65D17) General topics in the theory of software (68N01) Software, source code, etc. for problems pertaining to numerical analysis (65-04)

Related Items (10)

A new block preconditioner and improved finite element solver of Poisson-Nernst-Planck equation ⋮ SDPBS web server for calculation of electrostatics of ionic solvated biomolecules ⋮ Reliable computer simulation methods for electrostatic biomolecular models based on the Poisson-Boltzmann equation ⋮ A flux-jump preserved gradient recovery technique for accurately predicting the electrostatic field of an immersed biomolecule ⋮ Unnamed Item ⋮ An Effective Finite Element Iterative Solver for a Poisson--Nernst--Planck Ion Channel Model with Periodic Boundary Conditions ⋮ DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture ⋮ A stabilized finite element method for the Poisson-Nernst-Planck equations in three-dimensional ion channel simulations ⋮ TMSmesh ⋮ INN: interfaced neural networks as an accessible meshless approach for solving interface PDE problems

Uses Software

• TetGen
• PDB2PQR
• PAFMPB
• MetaMol
• SIMS
• GTEngine

Cites Work

• Unnamed Item
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• Tensor Decompositions and Applications
• Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy
• A simple and fast incremental randomized algorithm for computing trapezoidal decompositions and for triangulating polygons
• Quality mesh generation for molecular skin surfaces using restricted union of balls
• Triangulating a simple polygon in linear time
• Deformable smooth surface design
• Quality meshing of implicit solvation models of biomolecular structures
• Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes
• Morse Theory. (AM-51)
• Polygons Have Ears
• Three-dimensional alpha shapes
• TetGen, a Delaunay-Based Quality Tetrahedral Mesh Generator

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