DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture

DOI10.4208/cicp.OA-2018-0098OpenAlexW2963589984WikidataQ128469522 ScholiaQ128469522MaRDI QIDQ5161413

Jackson Debuhr, Benzhuo Lu, Drake Niedzielski, T. Sterling, Silvio Mayolo, Bo Zhang

Publication date: 29 October 2021

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

Full work available at URL: https://arxiv.org/abs/1710.06316

zbMATH Keywords

boundary element methoddistributed computingPoisson-Boltzmann equationDASHMM

Mathematics Subject Classification ID

Other programming paradigms (object-oriented, sequential, concurrent, automatic, etc.) (68N19) Biophysics (92C05) Numerical analysis (65-XX) Computer science (68-XX)

Related Items

Distributed and Adaptive Fast Multipole Method in Three Dimensions, A High-Accurate Fast Poisson Solver Based on Harmonic Surface Mapping Algorithm, DAFMPB, INN: interfaced neural networks as an accessible meshless approach for solving interface PDE problems

Uses Software

• APBS
• UHBD
• MIBPB
• AFMPB
• TMSmesh
• PAFMPB
• PBEQ-Solver
• PyGBe
• TABI
• DASHMM
• tabipb
• VCMM

Cites Work

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• Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy
• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver
• A biomolecular electrostatics solver using python, GPUs and boundary elements that can handle solvent-filled cavities and stern layers
• Solution of acoustic scattering problems by means of second kind integral equations
• The electric potential of a macromolecule in a solvent: A fundamental approach
• Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
• ``New-version-fast-multipole-method accelerated electrostatic calculations in biomolecular sys\-tems
• A Fast Adaptive Multipole Algorithm for Particle Simulations
• Transmission problems for the Helmholtz equation
• Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver
• Efficient and Qualified Mesh Generation for Gaussian Molecular Surface Using Adaptive Partition and Piecewise Polynomial Approximation
• Hiding Global Communication Latency in the GMRES Algorithm on Massively Parallel Machines
• DASHMM: Dynamic Adaptive System for Hierarchical Multipole Methods
• AFMPB: an adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems