Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann – All Atom Molecular Dynamics Coupling

DOI10.4208/CICP.OA-2022-0046MaRDI QIDQ5887618zbMATH OpenFDO

Authors Fabio Bonaccorso, Mihir Durve, Adriano Tiribocchi, Alessandro Loppini, Simonetta Filippi, Sauro Succi, Marco Lauricella, Andrea Montessori

Publication date 13 April 2023

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

Full work available at URL https://doi.org/10.4208/CICP.OA-2022-0046

zbMATH Keywords

biophysicslattice Boltzmannmolecular dynamicsSARS-CoV-2

Mathematics Subject Classification ID

Boltzmann equations (35Q20) Computational molecular dynamics in statistical mechanics (82M37) Biophysics (92C05) Physiological flow (92C35) Biochemistry, molecular biology (92C40)

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Cites work

• Coupling MD particles to a lattice-Boltzmann fluid through the use of conservative forces
• Fast parallel algorithms for short-range molecular dynamics
• Hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid
• Multiscale Coupling of Molecular Dynamics and Hydrodynamics: Application to DNA Translocation through a Nanopore
• The lattice Boltzmann equation. For complex states of flowing matter

Cited in

(3)

• Computational modeling of protein conformational changes -- application to the opening SARS-CoV-2 spike
• scientific article; zbMATH DE number 7674045 (Why is no real title available?)
• Dimension-free ergodicity of path integral molecular dynamics

Describes a project that uses

Uses Software

• PDB2PQR
• Gromacs
• I-TASSER
• VMD

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