title: Simulation guided design of a microfluidic device for electrophoretic stretching of DNA.
abstract: We have used Brownian dynamics-finite element method (BD-FEM) to guide the optimization of a microfluidic device designed to stretch DNA for gene mapping. The original design was proposed in our previous study [C. C. Hsieh and T. H. Lin, Biomicrofluidics 5(4), 044106 (2011)] for demonstrating a new pre-conditioning strategy to facilitate DNA stretching through a microcontraction using electrophoresis. In this study, we examine the efficiency of the original device for stretching DNA with different sizes ranging from 48.5 kbp (λ-DNA) to 166 kbp (T4-DNA). The efficiency of the device is found to deteriorate with increasing DNA molecular weight. The cause of the efficiency loss is determined by BD-FEM, and a modified design is proposed by drawing an analogy between an electric field and a potential flow. The modified device does not only regain the efficiency for stretching large DNA but also outperforms the original device for stretching small DNA.
authors.affiliation: Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan.
authors.forename: Chih-Chen
authors.initials: CC
authors.lastname: Hsieh
authors.forename: Tsung-Hsien
authors.initials: TH
authors.lastname: Lin
authors.forename: Chiou-De
authors.initials: CD
authors.lastname: Huang