Modeling the dynamics of a confined, semiflexible polymer is a challenging problem, owing to the complicated interplay between the configurations of the chain, which are strongly affected by the length scale for the confinement relative to the persistence length of the chain, and the polymer-wall hydrodynamic interactions. At the same time, understanding these dynamics are crucial to the advancement of emerging genomic technologies that use confinement to stretch out DNA and “read” a genomic signature. In this mini-review, we begin by considering what is known experimentally and theoretically about the friction of a wormlike chain such as DNA confined in a slit or a channel. We then discuss how to estimate the friction coefficient of such a chain, either with dynamic simulations or via Monte Carlo sampling and the Kirkwood pre-averaging approximation. We then review our recent work on computing the diffusivity of DNA in nanoslits and nanochannels, and conclude with some promising avenues for future work and caveats about our approach.

中文翻译：

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限制在纳米狭缝和纳米通道中的 DNA 的流体动力学。

模拟受限的半柔性聚合物的动力学是一个具有挑战性的问题，因为链的构型之间存在复杂的相互作用，而链的构型受到相对于链的持久长度的限制长度尺度的强烈影响，并且聚合物-壁流体动力相互作用。与此同时，了解这些动态对于新兴基因组技术的进步至关重要，这些技术利用限制来延伸 DNA 并“读取”基因组特征。在这篇小评论中，我们首先考虑实验和理论上已知的关于蠕虫链（例如限制在狭缝或通道中的 DNA）的摩擦力。然后，我们讨论如何通过动态模拟或通过蒙特卡洛采样和柯克伍德预平均近似来估计此类链条的摩擦系数。然后，我们回顾了我们最近在计算纳米狭缝和纳米通道中 DNA 扩散率方面的工作，并总结了未来工作的一些有希望的途径以及对我们的方法的注意事项。