Dissipative particle dynamics simulation of field-dependent DNA mobility in nanoslits |
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Authors: | Kun Yan Yu-Zong Chen Jongyoon Han Gui-Rong Liu Jian-Sheng Wang Nicolas G. Hadjiconstantinou |
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Affiliation: | 1. Computational Engineering Programme, Singapore-MIT Alliance, 4 Engineering Drive 3, Singapore, 117576, Singapore 2. Department of Pharmacy, National University of Singapore, 8 Science Drive 4, Singapore, 117543, Singapore 3. Department of Electrical Engineering and Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA 4. Department of Mechanical Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore, 117576, Singapore 5. Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore, 117542, Singapore 6. Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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Abstract: | The dynamics of DNA molecules in highly confined nanoslits under varying electric fields are studied using dissipative particle dynamics method, and our results show that manipulation of the electrical field can strongly influence DNA mobility. The mobility of DNA μ scales with electric field E as $ mu = mu^{text{H}} - k_{1} e^{{ - E/E_{c} }} . $ And the data points for different DNA lengths finally approach each other in strong fields, which suggest that the sensitivity to chain length is almost lost. To explain the unusual field-dependent phenomena, we analyze the time evolution of DNA configurations under different fields. For strong driving potentials when the system is dominated by the electric driving force, the DNA chains are more likely to hold coiled configurations. For weak driving potential when the random diffusion forces dominate, we see frequent dynamic transitions between stretched and coiled configuration, which may increase the drag resistance, therefore reduce the mobility. |
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