Lateral migration of peptides in transversely sheared flows in water: An atomistic-scale-resolving simulation

Abstract

For atomistic scale-resolving simulations of peptide diffusion, which are representative of molecular sorting in micro-fluidic device, a hybrid Fluctuating Hydrodynamics - Molecular Dynamics (FH/MD) model is implemented based on the two-phase flow analogy framework. Thanks to the used framework, in comparison with existing simulations in the literature, the suggested model captures inter-atomic forces between the peptides and the surrounding shell of water atoms at atomistic resolution while concurrently taking into account the non-uniform flow effect. In comparison with previous applications of the hybrid two-phase flow analogy method, multiple moving atomic-resolution zones are implemented for the first time here. The moving zones comprise one and two peptides solvated in water with a Poiseuille flow applied, where each diffusing peptide and the surrounding water shell are dynamically resolved. The models are validated in comparison with the pure all-atom molecular dynamics simulations for the no flow case and then used to investigate how the flow rate and the starting location of peptides in the parabolic flow profile affect their lateral migration over a range of flow Reynolds numbers. It is estimated that for the Poiseuille flows considered, the FH/MD model is 2–20 times faster in comparison with the conventional all-atom non-equilibrium molecular dynamics simulations.