Fluctuating hydrodynamics methods for dynamic coarse-grained implicit-solvent simulations in LAMMPS

DOI10.1137/15M1026390MaRDI QIDQ2830581zbMATH OpenOpenAlexFDO

Authors Y. Wang, Jon Karl Sigurdsson, Paul J. Atzberger

Publication date 28 October 2016

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

Full work available at URL https://doi.org/10.1137/15m1026390

zbMATH Keywords

immersed boundary methodfluctuating hydrodynamicsimplicit solventcoarse-grainedsoft materialsstochastic eulerian Lagrangian method

Mathematics Subject Classification ID

Packaged methods for numerical algorithms (65Y15) Finite difference methods for initial value and initial-boundary value problems involving PDEs (65M06) Physiological flows (76Z05) Physiological flow (92C35)

Recommendations

• Hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid
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• Smoothed dissipative particle dynamics package for LAMMPS
• Algorithm Refinement for Fluctuating Hydrodynamics
• ESPResSo 3.1: Molecular Dynamics Software for Coarse-Grained Models

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Cited in

(5)

• Stochastic discontinuous Galerkin methods (SDGM) based on fluctuation-dissipation balance
• Hydrodynamic flows on curved surfaces: spectral numerical methods for radial manifold shapes
• LAMMPS lb/fluid fix version 2: improved hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid
• Hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid
• Coarse-grained methods for heterogeneous vesicles with phase-separated domains: elastic mechanics of shape fluctuations, plate compression, and channel insertion

Describes a project that uses

Uses Software

• SELM
• Jython
• LAMMPS

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