Physiological solvent flows surround biological structures triggering therein collective motions.Notable examples are virus/host-cell interactions and solventmediated allosteric regulation.The present work describes a...Physiological solvent flows surround biological structures triggering therein collective motions.Notable examples are virus/host-cell interactions and solventmediated 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 equilibriumproperties 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.展开更多
基金funding from the European Research Council under the European Union’s Horizon 2020 Framework Programme(No.FP/2014-2020)ERC Grant Agreement No.739964(COPMAT)support on the HPC CRESCO facility used in the LB/MD simulations,under the initiative Associazione Big Data COVID-19 Fast Track.
文摘Physiological solvent flows surround biological structures triggering therein collective motions.Notable examples are virus/host-cell interactions and solventmediated 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 equilibriumproperties 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.
