The effect of hydrodynamic interactions on the dynamics of DNA translocation through pores
The effect of hydrodynamic interactions on the dynamics of DNA translocation through pores
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DOI：
10.1063/1.2831777
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发表时间：
2008-02-28
影响因子：
4.4
通讯作者：
de Pablo, Juan J.
中科院分区：
文献类型：
--
作者：
Izmitli, Aslin;Schwartz, David. C.;de Pablo, Juan J.
在这项工作中，我们调查的DNA易位通过微孔的动力学的流体动力学相互作用的效果。我们模拟DNA作为一个珠弹簧链，并使用格子玻尔兹曼方法来模拟流场所产生的运动的分子。我们调查的自由排水入口的DNA的孔扩散，并发现，与实验一致，分子有更高的概率从一端进入孔。然后，我们考虑，电场驱动易位的21-210 μ m的DNA与和没有水动力相互作用。与实验相一致，我们研究易位事件比DNA的弛豫时间短得多。我们发现，在这个过程中的流体动力学相互作用的影响是导致不同的区域的分子，而不是由电压或链连接拉到孔，向孔移动。我们量化这种效果，并表明，它是小于不同的初始配置的分子所产生的链的易位动力学的差异。观察到易位时间与链长的幂律标度，在有和没有流体动力学相互作用的模拟中，指数分别为1.28 +/- 0.03和1.31 +/- 0.03。我们的研究结果是在最近的易位实验中进行的小孔，并表明，在这项工作中考虑的制度，流体动力学相互作用的易位时间链长的关系中起着次要的作用。对于快速易位过程，流体动力学相互作用的影响是局部的，决定DNA动力学的主要因素是分子的初始构型。(C)2008年美国物理学会。
In this work, we investigate the effect of hydrodynamic interactions on the dynamics of DNA translocation through micropores. We simulate DNA as a bead-spring chain and use a lattice Boltzmann method to simulate the flow field that arises from the motion of the molecule. We investigate the free-draining entrance of DNA to the pore by diffusion and find that, consistent with experiments, molecules have a higher probability of entering the pore from one end. We then consider the,electric-field driven translocation of 21-210 mu m DNA with and without hydrodynamic interactions. Consistent with experiments, we study translocation events that are much shorter than the relaxation time of DNA. We find that the effect of hydrodynamic interactions on this process is to cause different regions of a molecule, other than the ones pulled by voltage or chain connectivity into the pore, to move toward the pore. We quantify this effect and show that it is smaller than the difference in the translocation dynamics of chains that arises from different initial configurations of the molecules. A power-law scaling of translocation time with chain length is observed, with exponents of 1.28 +/- 0.03 and 1.31 +/- 0.03 in simulations with and without hydrodynamic interactions, respectively. Our results are in good agreement with recent translocation experiments conducted in small pores and show that, for the regime considered in this work, hydrodynamic interactions play a minor role in the relation of the translocation time to chain length. For fast translocation processes, the effect of hydrodynamic interactions is local and the main factor determining the dynamics of DNA is the initial configuration of the molecules. (C) 2008 American Institute of Physics.