Mazur Alexey K
CNRS UPR9080, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, Paris, 75005, France.
J Phys Chem B. 2008 Apr 24;112(16):4975-82. doi: 10.1021/jp711815x. Epub 2008 Mar 29.
The paper considers statistical properties of ensembles of chain conformations obtained by short-time Brownian dynamics (BD) of a coarse-grained DNA model in order to find out if the conditions necessary for accurate evaluation of the polymer elasticity are attainable in atom-level molecular dynamics (MD) simulations. To measure the bending persistence length (PL) with a 10% error using data accumulated in a single trajectory of a double helix of 15 base pairs, dynamics should be continued for a few microseconds. However, these estimates should be scaled down by about 2 orders of magnitude because the bending dynamics of short double helices in MD features much smaller relaxation times. As a result, good qualitative agreement with the worm-like chain (WLC) theory is reached in MD after tens of nanoseconds. The presently accessible durations of MD trajectories provide reasonably accurate evaluation of DNA elasticity and allow modeling of its mesoscopic properties. The surprisingly fast bending dynamics of short double helices in MD suggests that the microscopic mechanisms of DNA flexibility differ from a simple harmonic model.
本文研究了通过粗粒化DNA模型的短时间布朗动力学（BD）获得的链构象系综的统计特性，以确定在原子级分子动力学（MD）模拟中是否能够达到准确评估聚合物弹性所需的条件。为了使用在15个碱基对的双螺旋的单个轨迹中积累的数据以10%的误差测量弯曲持久长度（PL），动力学应持续几微秒。然而，这些估计值应缩小约2个数量级，因为MD中短双螺旋的弯曲动力学具有小得多的弛豫时间。结果，在几十纳秒后，MD与蠕虫状链（WLC）理论达成了良好的定性一致。目前可获得的MD轨迹持续时间能够对DNA弹性进行合理准确的评估，并允许对其介观性质进行建模。MD中短双螺旋惊人的快速弯曲动力学表明，DNA柔韧性的微观机制不同于简单的谐波模型。
