  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.
