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

Li, Fan; Korotkin, Ivan; Farafonov, Vladimir; Karabasov, Sergey A.

doi:10.1016/j.molliq.2021.116111

Cited by 2 publications

(1 citation statement)

References 54 publications

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“…Interfacial water properties are also pertinent for the restructuring processes of cellular membranes − and organismal signaling . The advent of advanced high-speed atomic force microscopy (H-S AFM) opens new opportunities for measuring the dynamic piconewton forces, which occur within microseconds and nanometer structural rearrangements with subsecond resolution. , AFM tools are used to detect the equilibrium structure of water layers, but the dynamic behavior is still beyond the experimental reach in the submicrosecond and nanosecond regions typical of structural rearrangements and biocatalytic molecular systems. − While the time step of molecular dynamic (MD) simulations is orders of magnitude too small and so are their system sizes to model such processes, which involve collective dynamics of many water molecules, the hybrid multiscale methods, which combine MD with continuum fluid dynamic simulations, − provide an attractive opportunity for the modeling of realistic-size systems while resolving details of the molecular ordering. Here, we report the detection of water structuring between a silica AFM colloidal tip and a cleaved mica surface.…”

Section: Introductionmentioning

confidence: 99%

Interfacial Layer Breaker: A Violation of Stokes’ Law in High-Speed Atomic Force Microscope Flows

Smoukov

Korotkin

et al. 2022

Langmuir

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Structured water near surfaces is important in nonclassical crystallization, biomineralization, and restructuring of cellular membranes. In addition to equilibrium structures, studied by atomic force microscopy (AFM), high-speed AFM (H-S AFM) can now detect piconewton forces in microseconds. With increasing speeds and decreasing tip diameters, there is a danger that continuum water models will not hold, and molecular dynamic (MD) simulations would be needed for accurate predictions. MD simulations, however, can only evolve over tens of nanoseconds due to memory and computational efficiency/speed limitations, so new methods are needed to bridge the gap. Here, we report a hybrid, multiscale simulation method, which can bridge the size and time scale gaps to existing experiments. Structured water is studied between a moving silica AFM colloidal tip and a cleaved mica surface. The computational domain includes 1,472,766 atoms. To mimic the effect of long-range hydrodynamic forces occurring in water, when moving the AFM tip at speeds from 5 × 10 −7 to 30 m/s, a hybrid multiscale method with local atomistic resolution is used, which serves as an effective open-domain boundary condition. The multiscale simulation is thus equivalent to using a macroscopically large computational domain with equilibrium boundary conditions. Quantification of the drag force shows the breaking of continuum behavior. Nonmonotonic dependence on both the tip speed and distance from the surface implies breaking of the hydration layer around the moving tip at time scales smaller than water cluster formation and strong water compressibility effects at the highest speeds.

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Section: Introductionmentioning

confidence: 99%

Interfacial Layer Breaker: A Violation of Stokes’ Law in High-Speed Atomic Force Microscope Flows

Smoukov

Korotkin

et al. 2022

Langmuir

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A Thermostat‐Consistent Fully Coupled Molecular Dynamics–Generalized Fluctuating Hydrodynamics Model for Non‐Equilibrium Flows

Liu

Korotkin

Rao

et al. 2021

Advcd Theory and Sims

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The thermostat-consistent fully coupled molecular dynamics-generalized fluctuating hydrodynamics method is developed for non-equilibrium water flow simulations. The model allows for strong coupling between the atomistic and the continuum hydrodynamics representations of water and shows an improved stability in comparison with the previous formulations of similar multiscale methods. Numerical results are demonstrated for a periodic nano-scale Poiseuille flow problem with SPC/E water. The computed time-averaged velocity profiles are compared with the analytical solution, and the thermal velocity fluctuations are well reproduced in comparison with the equilibrium molecular dynamics simulation. Several options to account for the long-range electrostatics interactions available in GROMACS are incorporated in the model and compared. It is demonstrated that the suggested non-equilibrium multiscale model is a factor of 4 to 18 faster in comparison with the standard all-atom equilibrium molecular dynamics model for the same computational domain size.

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

Cited by 2 publications

References 54 publications

Interfacial Layer Breaker: A Violation of Stokes’ Law in High-Speed Atomic Force Microscope Flows

Interfacial Layer Breaker: A Violation of Stokes’ Law in High-Speed Atomic Force Microscope Flows

A Thermostat‐Consistent Fully Coupled Molecular Dynamics–Generalized Fluctuating Hydrodynamics Model for Non‐Equilibrium Flows

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