TY - JOUR
T1 - Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann — All Atom Molecular Dynamics Coupling
AU - Lauricella , Marco
AU - Chiodo , Letizia
AU - Bonaccorso , Fabio
AU - Durve , Mihir
AU - Montessori , Andrea
AU - Tiribocchi , Adriano
AU - Loppini , Alessandro
AU - Filippi , Simonetta
AU - Succi , Sauro
JO - Communications in Computational Physics
VL - 1
SP - 57
EP - 76
PY - 2023
DA - 2023/02
SN - 33
DO - http://doi.org/10.4208/cicp.OA-2022-0046
UR - https://global-sci.org/intro/article_detail/cicp/21425.html
KW - SARS-CoV-2, biophysics, lattice Boltzmann, molecular dynamics.
AB - <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>