Brownian Dynamics Simulation of Electrophoretic DNA Separation by the Normal Stress Effect

• Main Authors: Chao-Chen Kuo, 郭朝琛
• Other Authors: Chih-Chen Hsieh
• Format: Others
• Language: zh-TW
• Published: 2019
• Online Access: http://ndltd.ncl.edu.tw/handle/5k4a3c

碩士 === 國立臺灣大學 === 化學工程學研究所 === 107 === DNA separation and purification are widely used operations in biological and medical analyses. Compared with the traditional methods, DNA separation through microchannels by electrophoresis is more convenient and efficient. In the past experiments, we found that DNA migrated toward the convex wall as it passed through a converging-diverging microchannel. The migration was apparently driven by the normal stress, but it can only be observed when a post array was set at the inlet of the converging channel. In this study, Brownian Dynamics is used to simulate the behavior of DNA in microchannels to further understand the phenomenon. We also used the simulations to verify the design principles for improving the current device. We first investigated how the post array affects the normal stress induced DNA migration. We found that DNA hooked by a post will be stretched by the electric field. Since the normal stress is larger for more stretched DNA, the normal stress induced DNA migration is enhanced due to the presence of the post array. On the other hand, we have also replaced electric field with flow field. Although the normal stress induced migration is still observed, it is less prominent in flow field than in electric field due to the depletion of DNA at the channel walls caused by the hydrodynamic interactions. Second, we changed the shape of the converging and diverging channels to study the influence of the channel shape on the normal stress induced migration of DNA. We found that Deborah number (De) is a good indicator for the onset of the normal stress induced DNA migration. The migration only occurs for De>1 while DNA distributes evenly in the microchannel for De<1. We have applied this principle to design a pre-conditioning channel with higher De set in front of the separation channel. The separation efficiency of the device is clearly improved with the pre-conditioning channel. Third, we considered how to collect DNA samples at the end of the separation channel. In literatures, branched channel is usually employed for this purpose. However, the detailed design of the branched outlet channel could strongly affect the separation results. We found from our simulations that DNA usually moves along the electric field line, despite its molecular weight and the electric field strength. Therefore, we can use a fixed branched outlet channel with tunable applied electric potential in each outlet reservoir to control the electric field lines and therefore to optimize the collection of the separated samples. Although the normal stress induced DNA migration can be used to separate DNA with different sizes, the separation can never be complete. Thus, we simulated a special case that uses negative dielectophoresis (nDEP) to promote DNA moving away from the convex walls of the channel. Since the DEP force and the normal stress are competing, it is possible to find an optimal condition that could give a complete separation for a mixture of two different DNA samples. To conclude, we have successfully simulated the normal stress induced DNA migration in a converging-diverging channel by using Brownian dynamics. The simulations have helped us to understand the phenomenon more deeply. Moreover, we have developed several strategies to improve the separation efficiency of the device. We shall perform experiments to verify these strategies and hopefully invent a better DNA separation method in the future.