Multi-core CPU or GPU-accelerated multiscale modeling for biomolecular complexes

DOI10.2478/MLBMB-2013-0009MaRDI QIDQ2863940zbMATH OpenOpenAlexWikidataFDO

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

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-2013-0009

zbMATH Keywords

efficient computationGPUmesh generationmulti-scale modelingbiomolecular complexmulti-core CPU

Mathematics Subject Classification ID

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

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Cites work

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

Cited in

(4)

• Atom simplification and quality T-mesh generation for multi-resolution biomolecular surfaces
• A fast band-Krylov eigensolver for macromolecular functional motion simulation on multicore architectures and graphics processors
• Modelling of protein surface using parallel heterogeneous architectures
• Efficient and qualified mesh generation for Gaussian molecular surface using adaptive partition and piecewise polynomial approximation

Describes a project that uses

Uses Software

• tabipb
• QTFier
• TABI
• LBIE

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