Brownian Dynamics Simulation of DNA Separation in Microchannel with Sparse Post Arrays
| Autor: | Po-Hung Wu, 吳柏宏 |
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| Rok vydání: | 2017 |
| Druh dokumentu: | 學位論文 ; thesis |
| Popis: | 105 Microchannel with hexagonal post arrays is one of the novel devices designed for rapid separation of very long DNA by electrophoresis. However, its efficiency is poor at high Peclet number (or electric field) due to the channeling effect which reduces the probability of collision between DNA and posts. To overcome this drawback, we propose four different design of microchannels and test their ability for separating two model DNA, namely λ-DNA (48.5 kbp) and T4-DNA (165.6 kbp), by using Brownian Dynamics simulation in conjunction with finite element method. In the first design, we add a microexpansion in front of the post arrays so that the collision probability between DNA and posts increases due to the pre-stretching of DNA at the microexpansion. However, the separation power was found only increasing marginally due to the increasing variation of the available path for DNA electrophoresis. In the second and the third design, we replace electric field with flow field to reduce the variety of DNA path by a depletion layer caused by hydrodynamic interaction. However, in experiments DNA were found stuck easily at the narrow part of the channel. Moreover, the broad DNA injection band leads to a significant drop in separation resolution. In the last design, we connect the first design in parallel in order to reduce both the width of the injection band and the chance of channel clog. We also found DNA move toward convexed wall due to a normal force, and this phenomenon results in a reduction in DNA path. With this design, we obtain a good separation resolution in short time based on our simulation. We also investigated the factors that contribute to the standard deviation of DNA distribution. We found the variation of DNA path dominates at low Pe but the DNA unhooking time dominates at high Pe. Thus, it is important to control both factors for further improvement of the device. To conclude, we have used simulation to help improving the design of microchannel with post arrays for the purpose of DNA separation. |
| Databáze: | Networked Digital Library of Theses & Dissertations |
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