A penalty method to model particle interactions in DNA-laden flows.

Area of Science:

• Computational fluid dynamics
• Biophysics
• Microfluidics

Background:

• Microfluidic devices are crucial for biological analysis, requiring accurate simulation of fluid and DNA transport.
• Existing fluid-particle algorithms struggle with simulating long molecules like DNA due to unrealistic rod-crossing behaviors.
• Accurate modeling of DNA behavior at nanoscale within microchannels is essential for understanding biological processes.

Purpose of the Study:

• To develop and validate a novel hybrid fluid-particle algorithm for simulating DNA-laden fluid flow in microdevices.
• To address the physical limitations of previous algorithms, specifically the issue of rod crossing in polymer representations.
• To provide a more accurate computational tool for studying DNA transport and behavior in microfluidic systems.

Main Methods:

• A hybrid fluid-particle algorithm combining a finite difference method for fluid dynamics and a bead-rod model for DNA.
• Implementation of screened Coulombic forces using a Debye-Hückel potential to prevent unrealistic particle interactions.
• Coupling of the bead-rod polymer model to the fluid through hydrodynamic drag and stochastic thermal fluctuations.
• Utilized an embedded boundary volume-of-fluid formulation for accurate boundary condition handling.

Main Results:

• The developed algorithm successfully simulates the flow and transport of DNA through a post array microchannel in 2D.
• Demonstrated prevention of physically unrealistic rod crossing, leading to more accurate simulations compared to previous methods.
• Validated the algorithm's capability to simulate 3D flow in packed bed micro-columns, showcasing its versatility.

Conclusions:

• The hybrid fluid-particle algorithm offers a significant advancement in simulating DNA-laden microfluidic systems.
• The incorporation of screened Coulombic forces accurately models DNA interactions, enhancing simulation fidelity.
• This method provides a robust platform for investigating complex biological fluid dynamics in microdevices.