Session: 14-10-01: Micro/Nanofluidics 2025 I

Paper Number: 167266

Comsol Simulation of Dna Capture Dynamics at Micro/nanochannel Interfaces 

Nanopore-based DNA analysis has emerged as a powerful and versatile technique for label-free, amplification-free, single-molecule detection, offering significant potential for high-throughput applications in genomics, diagnostics, and molecular biology. Despite substantial advancements in enhancing DNA capture rates through engineered micro/nanochannel interfaces, achieving efficient and reliable DNA capture remains a critical challenge. Our previous experimental studies have investigated how microchannel flow rates, inlet structure designs, and channel dimensions influence DNA capture within these interfaces. This study extends those efforts by incorporating computational simulations, aiming to deepen our understanding of the underlying mechanisms that govern DNA capture at the micro/nano interface.

 

In this study, we employed COMSOL Multiphysics to simulate the interactions between DNA molecules and the surrounding micro/nanochannel environment. The simulation model integrated several physical modules, including Electrostatics, Transport of Diluted Species, Creeping Flow, and Particle Tracing for Fluid Flow. These models enabled us to comprehensively assess the effects of key parameters, such as flow rate, DNA length, surface charge density of nanochannel walls, and the geometry of the channel on DNA capture efficiency. By replicating the experimental conditions, we examined how these factors influence convective transport, diffusion, and electrophoretic drift of DNA molecules within the channels.

 

Our simulations revealed a complex and nonlinear relationship between flow rate and capture efficiency at the micro/nano interface. Moderate flow rates were found to promote DNA transport to the sensing region, improving capture rates. However, increasing the flow rate beyond a certain threshold reduced the capture volume of the funnel-shaped inlet structure, thereby decreasing capture efficiency. This observation was consistent with our experimental results and highlighted the critical role of flow dynamics in optimizing capture rates. Additionally, larger DNA molecules were found to be more sensitive to convective flow due to their lower diffusion constants, which further influenced their capture efficiency. This detailed insight into the behavior of DNA molecules in these confined environments is invaluable for optimizing DNA capture mechanisms in nanopore-based systems.

 

This computational study offers important new insights into the dynamics of DNA capture in nanochannels, complementing and extending our experimental findings. By leveraging simulation-based approaches, we not only validate prior experimental results but also propose novel strategies for optimizing nanopore-based DNA analysis systems. These simulations provide a predictive framework for designing more efficient and scalable DNA capture mechanisms. The insights gained from this research hold significant promise for advancing the development of high-throughput DNA sensing technologies, making them more efficient, cost-effective, and applicable to a broader range of real-world applications.

Presenting Author: Junseo Choi Texas State University

Presenting Author Biography: Junseo Choi is an assistant professor in the Department of Engineering Technology at Texas State University. He earned his B.S. and M.S. in Chemical and Advanced Materials Engineering from Kyung Hee University in South Korea in 2004 and 2006, respectively, and completed his Ph.D. in Mechanical Engineering at Louisiana State University in 2013.

Authors:

Junseo Choi Texas State University
Devanda Lek Texas State University
In-Hyouk Song Texas State University
Byoung Hee You Texas State University