Department of Chemical Engineering, Stanford University, Stanford, California 94025, USA.
J Chem Phys. 2009 Dec 14;131(22):224905. doi: 10.1063/1.3251058.
In this work, we examine the conformational dynamics of long polymer molecules under confinement, as in the recently developed anti-Brownian electrokinetic (ABEL) trap [A. Cohen and W. Moerner, Proc. Natl. Acad. Sci. USA. 103, 4362 (2006)]. We analyze polymer motion using Brownian dynamics simulations (bead-spring and bead-rod models) and via Monte Carlo methods. We first verify Cohen and Moerner's (2007) single molecule observations regarding the existence of short time correlations [Phys. Rev. Lett. 98, 116001 (2007)] in the motion of a polymer's center of mass, which arise due to fluctuating hydrodynamic interactions. Thereafter, following Cohen and Moerner, we use principal component analysis to extract the principal modes governing polymer conformation and find that confinement and backbone bending only affect small polymers and should not play a significant role in the dynamics of long polymers such as lambda-DNA. We find excellent agreement between our principal component analysis modes and those measured by Cohen and Moerner [Proc. Natl. Acad. Sci. U.S.A. 104, 12622 (2007)]. Finally, to explore the effect of excluded volume, in particular, the effect of the excluded volume parameter (z), we use image-image correlations to examine its relation to polymer dynamics. Image-image correlation measurements performed on lambda-DNA in the ABEL trap did not display a simple exponential-type behavior and motivated the use of stretched exponential functions to determine the characteristic timescale (tau) governing conformational dynamics. We show that tau scales with polymer length as N(2) and decreases with increasing z. Furthermore, we can collapse a variety of data when tauN(-2) is plotted with respect to N/z(m) (m=0.14 for freespace and 0.366 for walls).
在这项工作中，我们研究了长聚合物分子在受限环境下的构象动力学，这种受限环境类似于最近开发的反布朗运动电动（ABEL）陷阱[Cohen 和 Moerner，Proc. Natl. Acad. Sci. USA. 103, 4362 (2006)]。我们使用布朗动力学模拟（珠-簧和珠-棒模型）和蒙特卡罗方法分析聚合物的运动。我们首先验证了 Cohen 和 Moerner（2007）关于聚合物质心运动中短时间相关性存在的单分子观察结果[Phys. Rev. Lett. 98, 116001 (2007)]，这种相关性是由波动的流体力学相互作用引起的。此后，我们遵循 Cohen 和 Moerner 的方法，使用主成分分析提取控制聚合物构象的主要模式，并发现受限和主链弯曲仅影响小聚合物，不应在长聚合物如 lambda-DNA 的动力学中发挥重要作用。我们发现，我们的主成分分析模式与 Cohen 和 Moerner 测量的模式之间存在极好的一致性[Proc. Natl. Acad. Sci. U.S.A. 104, 12622 (2007)]。最后，为了探索排除体积的影响，特别是排除体积参数（z）的影响，我们使用图像-图像相关来研究其与聚合物动力学的关系。在 ABEL 陷阱中对 lambda-DNA 进行的图像-图像相关测量未显示出简单的指数型行为，这促使我们使用扩展指数函数来确定控制构象动力学的特征时间尺度（tau）。我们表明，tau 与聚合物长度呈 N(2)比例缩放，并随 z 的增加而减小。此外，当将 tauN(-2)相对于 N/z(m)（在自由空间中为 m=0.14，在壁面处为 m=0.366）作图时，我们可以将各种数据合并。
