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
In this paper we introduce a new mathematical model for the active contraction of cardiac muscle,featuring different thermo-electric and nonlinear conductivity properties.The passive hyperelastic response of the tissu...In this paper we introduce a new mathematical model for the active contraction of cardiac muscle,featuring different thermo-electric and nonlinear conductivity properties.The passive hyperelastic response of the tissue is described by an orthotropic exponential model,whereas the ionic activity dictates active contraction in-corporated through the concept of orthotropic active strain.We use a fully incompressible formulation,and the generated strain modifies directly the conductivity mechanisms in the medium through the pull-back transformation.We also investigate the influence of thermo-electric effects in the onset of multiphysics emergent spatiotem-poral dynamics,using nonlinear diffusion.It turns out that these ingredients have a key role in reproducing pathological chaotic dynamics such as ventricular fibrillation during inflammatory events,for instance.The specific structure of the governing equations suggests to cast the problem in mixed-primal form and we write it in terms of Kirchhoff stress,displacements,solid pressure,dimensionless electric potential,activation generation,and ionic variables.We also advance a new mixed-primal finite element method for its numerical approximation,and we use it to explore the properties of the model and to assess the importance of coupling terms,by means of a few computational experiments in 3D.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.
基金supported by the Engineering and Physical Sciences Research Council(EPSRC)through the research grant EP/R00207X。
文摘In this paper we introduce a new mathematical model for the active contraction of cardiac muscle,featuring different thermo-electric and nonlinear conductivity properties.The passive hyperelastic response of the tissue is described by an orthotropic exponential model,whereas the ionic activity dictates active contraction in-corporated through the concept of orthotropic active strain.We use a fully incompressible formulation,and the generated strain modifies directly the conductivity mechanisms in the medium through the pull-back transformation.We also investigate the influence of thermo-electric effects in the onset of multiphysics emergent spatiotem-poral dynamics,using nonlinear diffusion.It turns out that these ingredients have a key role in reproducing pathological chaotic dynamics such as ventricular fibrillation during inflammatory events,for instance.The specific structure of the governing equations suggests to cast the problem in mixed-primal form and we write it in terms of Kirchhoff stress,displacements,solid pressure,dimensionless electric potential,activation generation,and ionic variables.We also advance a new mixed-primal finite element method for its numerical approximation,and we use it to explore the properties of the model and to assess the importance of coupling terms,by means of a few computational experiments in 3D.
