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.
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机译：我们已经使用布朗动力学有限元方法（BD-FEM）来指导微流体设备的优化，该设备旨在拉伸DNA进行基因定位。原始设计是在我们先前的研究中提出的[C. C. Hsieh和T. H. Lin，《生物微流体学》（> 5 （4），044106（2011））]展示了一种新的预处理策略，可通过电泳利用微收缩促进DNA拉伸。在这项研究中，我们研究了原始设备用于拉伸大小从48.5 kbp（λ-DNA）到166 kbp（T4-DNA）的DNA的效率。发现该装置的效率随着DNA分子量的增加而降低。效率损失的原因由BD-FEM确定，并通过在电场和势流之间进行类比来提出改进的设计。改进后的设备不仅恢复了延伸大DNA的效率，而且也胜过了延伸小DNA的原始设备。
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