Molecular dynamics study of tethered polymers in shear flow

Area of Science:

• Polymer Physics
• Computational Biophysics
• Fluid Dynamics

Background:

• Single-molecule experiments enable detailed characterization of macromolecular dynamics.
• Previous studies observed surprising recirculating motion in DNA chains under shear flow.
• Understanding polymer behavior in flow is crucial for various scientific and industrial applications.

Purpose of the Study:

• To investigate the dynamics of a polymer chain tethered to a surface under shear flow using molecular dynamics simulations.
• To replicate and explain the experimentally observed cyclic motion of polymer chains.
• To develop a new empirical relationship between shear flow and polymer chain deformation.

Main Methods:

• Molecular dynamics simulations with explicit hydrodynamic interactions.
• Utilizing a Freely Jointed Chain (FJC) model with Finitely Extensible Nonlinear Elastic (FENE) links.
• Analyzing polymer dynamics under confinement between two surfaces with a Poiseuille flow.

Main Results:

• Successfully reproduced the cyclic polymer motion observed in experimental studies.
• Demonstrated the utility of cross-correlation functions for measuring the period of this motion.
• Proposed a novel empirical equation correlating shear flow magnitude with polymer chain deformation, valid for both weak and strong flows.
• Observed packing effects near walls, chain-sticking phenomena, and the influence of hydrodynamic drag on fluid flow.

Conclusions:

• Molecular dynamics simulations accurately capture the complex cyclic motion of tethered polymer chains in shear flow.
• The proposed empirical equation provides a valuable tool for predicting polymer deformation under varying flow conditions.
• The study offers insights into wall effects and hydrodynamic interactions in confined polymer systems.