存在两个纳米流体熵陷阱时聚合物的自由能景观

James M. Polson, Matthew Kozma
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引用次数: 0

摘要

最近,纳米流体力学实验被用来描述单个 DNA 分子在蚀刻有纳米孔阵列的窄缝中的行为特征。对实验数据的分析依赖于对基本自由能谱的分析估计。在本研究中,我们利用计算机模拟来明确计算自由能,并测试分析模型所采用的近似值。具体来说,蒙特卡罗模拟用于研究一种局限于复杂几何形状的聚合物,该几何形状由一个表面嵌入两个正方形纳米凹坑的纳米发光体组成。使用二维加权组图分析法(WHAM2D)计算自由能 $F$,它是两个纳米孔中包含的聚合物轮廓长度之和($\lambda_1$)和之差($\lambda_2$)的函数。我们发现自由能函数在约束尺寸方面的变化与采用简单理论模型的分析预测相当。然而,存在一些值得注意的定量差异,特别是 $F$ 相对于 $\lambda_1$ 的预测变化与观测变化之间的差异。我们的研究提供了一个有益的教训,即使用聚合物自由能景观的简单分析表达式来解释局限于复杂几何形状的 DNA 实验结果是有局限性的,并指出了对自由能进行精确数值计算的价值。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Free-energy landscape of a polymer in the presence of two nanofluidic entropic traps
Recently, nanofluidics experiments have been used to characterize the behavior of single DNA molecules confined to narrow slits etched with arrays of nanopits. Analysis of the experimental data relies on analytical estimates of the underlying free-energy landscape. In this study we use computer simulations to explicitly calculate the free energy and test the approximations employed in such analytical models. Specifically, Monte Carlo simulations were used to study a polymer confined to complex geometry consisting of a nanoslit with two square nanopits embedded in one of the surfaces. The two-dimensional Weighted Histogram Analysis Method (WHAM2D) is used to calculate the free energy, $F$, as a function of the sum ($\lambda_1$) and the difference ($\lambda_2$) of the length of the polymer contour contained in the two nanopits. We find the variation of the free-energy function with respect to confinement dimensions to be comparable to the analytical predictions that employ a simplistic theoretical model. However, there are some noteworthy quantitative discrepancies, particularly between the predicted and observed variation of $F$ with respect to $\lambda_1$. Our study provides a useful lesson on the limitations of using simplistic analytical expressions for polymer free-energy landscapes to interpret results for experiments of DNA confined to a complex geometry and points to the value of carrying out accurate numerical calculations of the free energy instead.
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