Simulations of DNA stretching by flow field in microchannels with complex geometry

Abstract

Recently, we have reported the experimental results of DNA stretching by flow field in three microchannels (C. H. Lee and C. C. Hsieh, Biomicrofluidics 7(1), 014109 (2013)) designed specifically for the purpose of preconditioning DNA conformation for easier stretching. The experimental results do not only demonstrate the superiority of the new devices but also provides detailed observation of DNA behavior in complex flow field that was not available before. In this study, we use Brownian dynamics-finite element method (BD-FEM) to simulate DNA behavior in these microchannels, and compare the results against the experiments. Although the hydrodynamic interaction (HI) between DNA segments and between DNA and the device boundaries was not included in the simulations, the simulation results are in fairly good agreement with the experimental data from either the aspect of the single molecule behavior or from the aspect of ensemble averaged properties. The discrepancy between the simulation and the experimental results can be explained by the neglect of HI effect in the simulations. Considering the huge savings on the computational cost from neglecting HI, we conclude that BD-FEM can be used as an efficient and economic designing tool for developing new microfluidic device for DNA manipulation.

Nonmonotonic DNA-length-dependent mobility in pluronic gels

“…Laachi et al [39] performed Brownian dynamics simulations on out-ofequilibrium transport of rigid DNA strands in a nanofilter, and predicted that longer DNA molecules traveled faster than shorter ones in periodic arrays of narrow slits and deep wells under strong electric fields, facilitated by the 'torque-assisted escape' during nonequilibrium transport processes. Considerable progress has been made in the understanding of DNA transport in electric fields [40][41][42][43] or flows [44,45] through microchannels, obstacle arrays, nanoslits, and other microfluidic devices using Brownian dynamics simulations.…”