A fast variational method for the construction of resolution adaptive C^2-smooth molecular surfaces

DOI10.1016/J.CMA.2008.12.042MaRDI QIDQ649401zbMATH OpenOpenAlexWikidataFDO

Authors Qin Zhang, Chandrajit L. Bajaj, Guo-Liang Xu

Publication date 30 November 2011

Published in Computer Methods in Applied Mechanics and Engineering (Search for Journal in Brave)

Full work available at URL http://europepmc.org/articles/pmc2755577

zbMATH Keywords

variational methodsmolecular surfacegeometric partial differential equationhigh-order level-set

Mathematics Subject Classification ID

Molecular, statistical, and kinetic theories in solid mechanics (74A25) Energy minimization in equilibrium problems in solid mechanics (74G65)

Recommendations

• Multiscale geometric modeling of macromolecules. I: Cartesian representation
• Dynamic maintenance and visualization of molecular surfaces.
• Model the solvent-excluded surface of 3D protein molecular structures using geometric PDE-based level-set method
• Accelerating smooth molecular surface calculation
• Efficient and qualified mesh generation for Gaussian molecular surface using adaptive partition and piecewise polynomial approximation

Cites work

• A PDE-based fast local level set method
• Construction of geometric partial differential equations in computational geometry
• Deformable smooth surface design
• Dynamic maintenance and visualization of molecular surfaces.
• Dynamic skin triangulation
• Fast molecular solvation energetics and forces computation
• Quality meshing of implicit solvation models of biomolecular structures
• Topology Based Selection and Curation of Level Sets
• Triangulating the surface of a molecule
• Variational principles, surface evolution, PDEs, level set methods, and the stereo problem

Cited in

(7)

• Wavelet BEM on molecular surfaces: solvent excluded surfaces
• Model the solvent-excluded surface of 3D protein molecular structures using geometric PDE-based level-set method
• Biomolecular surface construction by PDE transform
• Accelerating smooth molecular surface calculation
• Fast and scalable algorithms for constructing solvent-excluded surfaces of large biomolecules
• B-spline tight frame based force matching method
• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules

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Uses Software

• TexMol
• APBS

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