@Article{CiCP-33-57,
author = {Lauricella , MarcoChiodo , LetiziaBonaccorso , FabioDurve , MihirMontessori , AndreaTiribocchi , AdrianoLoppini , AlessandroFilippi , Simonetta and Succi , Sauro},
title = {Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann — All Atom Molecular Dynamics Coupling},
journal = {Communications in Computational Physics},
year = {2023},
volume = {33},
number = {1},
pages = {57--76},
abstract = {<p style="text-align: justify;">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.</p>},
issn = {1991-7120},
doi = {https://doi.org/10.4208/cicp.OA-2022-0046},
url = {http://global-sci.org/intro/article_detail/cicp/21425.html}
}