Translocation is a nonequilibrium process at all stages: Simulating the capture and translocation of a polymer by a nanopore,The Journal of Chemical Physics

当前位置： X-MOL 学术 › J. Chem. Phys. › 论文详情

Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)

Translocation is a nonequilibrium process at all stages: Simulating the capture and translocation of a polymer by a nanopore
The Journal of Chemical Physics ( IF 3.1 ) Pub Date : 2016-10-20 12:26:20 , DOI: 10.1063/1.4964630
Sarah C. Vollmer ₁ , Hendrick W. de Haan ₁

Affiliation

Langevin dynamics simulations of the capture of polymers by a nanopore and the subsequent translocation through the nanopore are performed. These simulations are conducted for several polymer lengths at two different values for the Péclet number, which quantifies the drift-diffusion balance of the system. The capture-translocation process is divided into several stages, and the dynamics of translocation are characterized by measuring the average time for each stage and also the average conformation of the polymer at each stage. Comparison to the standard simulation approach of simulating only the translocation process reveals several important differences. While in the standard protocol, the polymer is essentially equilibrated at the start of translocation, simulations of the capture process reveal a polymer that is elongated when it approaches the pore and either remains elongated or becomes compressed at the start of translocation depending on the drift-diffusion balance. These results demonstrate that translocation is a non-equilibrium process at all stages and that simulations assuming equilibration could yield improper results, even at a qualitative level. The scaling of the translocation time with polymer length is found to be significantly different between the two simulation protocols thus demonstrating that the capture step is an essential part of modeling the translocation process.

中文翻译：

易位在所有阶段都是非平衡过程：模拟纳米孔对聚合物的捕获和易位

进行了纳米孔捕获聚合物以及随后通过纳米孔的转移的朗格文动力学模拟。这些模拟是针对几个不同长度的聚合物的Péclet数进行的，这量化了系统的漂移-扩散平衡。捕获-转移过程分为几个阶段，通过测量每个阶段的平均时间以及每个阶段聚合物的平均构象来表征转移的动力学。与仅模拟易位过程的标准模拟方法相比，发现了一些重要的区别。在标准方案中，聚合物在转运开始时基本达到平衡，捕获过程的模拟表明，聚合物接近孔时会伸长，并在伸长开始时保持伸长或被压缩，具体取决于漂移-扩散平衡。这些结果表明，易位在所有阶段都是一个非平衡过程，并且假设平衡的模拟即使在定性水平上也会产生不正确的结果。发现在两种模拟方案之间，转移时间与聚合物长度的比例显着不同，因此表明捕获步骤是模拟转移过程的重要组成部分。这些结果表明，易位在所有阶段都是一个非平衡过程，并且假设平衡的模拟即使在定性水平上也会产生不正确的结果。发现在两种模拟方案之间，转移时间与聚合物长度的比例显着不同，因此表明捕获步骤是模拟转移过程的重要组成部分。这些结果表明，易位在所有阶段都是一个非平衡过程，并且假设平衡的模拟即使在定性水平上也会产生不正确的结果。发现在两种模拟方案之间，转移时间与聚合物长度的比例显着不同，因此表明捕获步骤是模拟转移过程的重要组成部分。

更新日期：2016-10-21

点击分享查看原文

点击收藏

阅读更多本刊新发论文