Nonequilibrium Molecular Dynamics Method to Generate Poiseuille-Like Flow between Lipid Bilayers.

Area of Science:

• Biophysics
• Computational Biology
• Soft Matter Physics

Background:

• Cellular processes involve complex fluid dynamics both inside and outside cells.
• Nonequilibrium molecular dynamics (NEMD) simulations are crucial for understanding biomolecular responses to these flows.

Purpose of the Study:

• To develop and validate a novel NEMD method for simulating Poiseuille-like flow between lipid bilayers.
• To investigate the influence of external forces and lipid-water interactions on flow dynamics.

Main Methods:

• Extended equilibrium molecular dynamics (MD) by applying constant external forces to water molecules.
• Utilized the Lagrange multiplier method to constrain the lipid bilayer's center of mass while allowing individual molecule fluctuation.
• Employed the Nosé-Hoover thermostat for precise temperature control in both the solution and membrane.

Main Results:

• Demonstrated a linear correlation between applied external force and generated flow velocity.
• Established a method to estimate necessary acceleration for achieving desired flow velocities.
• Observed that flow between lipid bilayers is slower than predicted by Navier-Stokes equations for rigid plates due to membrane-water interactions.

Conclusions:

• The proposed NEMD method effectively generates controlled fluid flow between lipid bilayers.
• This simulation technique provides insights into the dynamics of soft surfaces under flow conditions.
• The method is broadly applicable to various soft surface flow simulations beyond lipid membranes.