Hybrid multiscale simulation reveals focusing of a diffusing peptide molecule by parallel shear flow in water.

Abstract The hybrid Molecular Dynamics - Fluctuating Hydrodynamics model is extended for multi-resolution simulations of molecular diffusion in water under a steady shear flow. Cases of water self-diffusion and a small protein diffusion in water are considered. For the switched-off flow effect, the model is validated in comparison with the reference all-atom equilibrium molecular dynamics solution. With the flow effect included, the multiscale model correctly captures the mean flow velocity distribution as well as the difference between mean square deviations in different directions with respect to the flow in accordance with the diffusion theory. Results of the simulations are analysed in the context of using hydrodynamic flow gradients for molecular diffusion focusing. Highlights • A novel method is developed for multiscale simulations of liquids under Couette flow. • The model correctly captures structure and transport properties of a peptide in water. • The diffusion predictions for shear flow are in agreement with the previous results. • Application of a velocity strain to peptide diffusion in water has a focusing effect. • An analytical model is developed to explain the peptide diffusion simulation results. [ABSTRACT FROM AUTHOR]