Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes

DOI10.2478/MLBMB-2013-0009zbMath1276.92030OpenAlexW2001962164WikidataQ37382382 ScholiaQ37382382MaRDI QIDQ2863940

Yuhui Cheng, J. Andrew McCammon, Tao Liao, Peter M. Kekenes-Huskey, Anushka Michailova, Yongjie Jessica Zhang, Michael Holst, Andrew D. McCulloch

Publication date: 5 December 2013

Published in: Computational and Mathematical Biophysics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.2478/mlbmb-2013-0009

zbMATH Keywords

mesh generationefficient computationGPUmulti-scale modelingbiomolecular complexmulti-core CPU

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) General theory of mathematical modeling (00A71)

Related Items (2)

Efficient and Qualified Mesh Generation for Gaussian Molecular Surface Using Adaptive Partition and Piecewise Polynomial Approximation ⋮ Atom Simplification and Quality T-mesh Generation for Multi-resolution Biomolecular Surfaces

Uses Software

• LBIE
• TABI
• QTFier
• tabipb

Cites Work

• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver
• Resolving topology ambiguity for multiple-material domains
• An efficient and scalable parallel algorithm for out-of-core isosurface extraction and rendering
• Relationship between tetrahedron shape measures
• Dynamic maintenance and visualization of molecular surfaces.
• ``New-version-fast-multipole-method accelerated electrostatic calculations in biomolecular sys\-tems
• 3D finite element meshing from imaging data
• Quality meshing of implicit solvation models of biomolecular structures
• High-order fractional partial differential equation transform for molecular surface construction
• Parallel Adaptive Finite Element Algorithms for Solving the Coupled Electro-diffusion Equations
• Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation
• Biomolecular surface construction by PDE transform
• A Fast and High Quality Multilevel Scheme for Partitioning Irregular Graphs
• Three-dimensional alpha shapes

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