1. Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann – All Atom Molecular Dynamics Coupling
- Author
-
Marco Lauricella, Letizia Chiodo, Fabio Bonaccorso, Mihir Durve, Andrea Montessori, Adriano Tiribocchi, Alessandro Loppini, Simonetta Filippi null, and Sauro Succi
- Subjects
Condensed Matter - Mesoscale and Nanoscale Physics ,Physics and Astronomy (miscellaneous) ,Mesoscale and Nanoscale Physics (cond-mat.mes-hall) ,FOS: Physical sciences ,Computational Physics (physics.comp-ph) ,Physics - Computational Physics - Abstract
Physiological solvent flows surround biological structures triggering therein collective motions. Notable examples are virus/host-cell interactions and solvent-mediated allosteric regulation. The present work describes a multiscale approach joining the Lattice Boltzmann fluid dynamics (for solvent flows) with the all-atom atomistic molecular dynamics (for proteins) to model functional interactions between flows and molecules. We present, as an applicative scenario, the study of the SARS-CoV-2 virus spike glycoprotein protein interacting with the surrounding solvent, modeled as a mesoscopic fluid. The equilibrium properties of the wild-type spike and of the Alpha variant in implicit solvent are described by suitable observables. The mesoscopic solvent description is critically compared to the all-atom solvent model, to quantify the advantages and limitations of the mesoscopic fluid description., Comment: 15 pages, 6 figures
- Published
- 2023