Modeling of particle interactions in DNA-laden flows at the microscale

Area of Science:

• Computational fluid dynamics
• Polymer physics
• Microfluidics

Background:

• Simulating DNA in microscale geometries requires accurate modeling of fluid-polymer interactions.
• Existing methods may not fully capture short-range forces crucial for polymer behavior.

Purpose of the Study:

• To develop and implement a simulation method for DNA-laden flows in complex microscale geometries.
• To incorporate short-range forces for precise modeling of polymer-polymer and polymer-surface interactions.

Main Methods:

• Utilized a finite difference method for fluid discretization and a Cartesian grid embedded boundary/volume-of-fluid method near boundaries.
• Represented DNA using a bead-rod polymer model, fully coupled with the fluid via hydrodynamic drag.
• Implemented two short-range interaction methods: a rigid constraint algorithm and a classical smooth potential.

Main Results:

• Successfully coupled fluid and polymer dynamics, incorporating short-range forces for interactions.
• Compared elastic collision models with smooth potentials for polymer-surface interactions.

Conclusions:

• The developed method provides a robust framework for simulating DNA in complex microfluidic systems.
• The implementation of short-range forces significantly improves the accuracy of polymer interaction modeling.