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分形环聚合物中的随机缠结

Random Knotting in Fractal Ring Polymers.

作者信息

Rauscher Phillip M, de Pablo Juan J

机构信息

Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States.

Materials Science Division (MSD) and Center for Molecular Engineering (CME), Argonne National Laboratory, Lemont, Illinois 60439, United States.

出版信息

Macromolecules. 2022 Sep 27;55(18):8409-8417. doi: 10.1021/acs.macromol.2c01676. Epub 2022 Sep 8.

DOI:10.1021/acs.macromol.2c01676
PMID:36186575
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9520986/
Abstract

Many ring polymer systems of physical and biological interest exhibit both pronounced topological effects and nontrivial self-similarity, but the relationship between these two phenomena has not yet been clearly established. Here, we use theory and simulation to formulate such a connection by studying a fundamental topological property-the random knotting probability-for ring polymers with varying fractal dimension, . Using straightforward scaling arguments, we generalize a classic mathematical result, showing that the probability of a trivial knot decays exponentially with chain size, , for all fractal dimensions: () ∝ exp(-/ ). However, no such simple considerations can account for the dependence of the knotting length, , on , necessitating a more involved analytical calculation. This analysis reveals a complicated double-exponential dependence, which is well supported by numerical data. By contrast, functional forms typical of simple scaling theories fail to adequately describe the observations. These findings are equally valid for two-dimensional ring polymer systems, where "knotting" is defined as the intersection of any two segments.

摘要

许多具有物理和生物学意义的环状聚合物系统既表现出明显的拓扑效应,又具有非平凡的自相似性,但这两种现象之间的关系尚未明确确立。在此,我们通过研究具有不同分形维数(D)的环状聚合物的一种基本拓扑性质——随机打结概率,利用理论和模拟来建立这样一种联系。通过直接的标度论证,我们推广了一个经典数学结果,表明对于所有分形维数,平凡结的概率随链尺寸(N)呈指数衰减:(P(N) \propto \exp(-N / N_0))。然而,没有这样简单的考虑能够解释打结长度(N_k)对(D)的依赖性,这就需要进行更复杂的解析计算。该分析揭示了一种复杂的双指数依赖性,这得到了数值数据的有力支持。相比之下,简单标度理论的典型函数形式无法充分描述这些观测结果。这些发现对于二维环状聚合物系统同样有效,在二维系统中,“打结”被定义为任意两条链段的相交。

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Fractal and Knot-Free Chromosomes Facilitate Nucleoplasmic Transport.分形且无纽结的染色体有助于核质转运。
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Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function.纳米级染色质成像与分析平台将4D染色质组织与分子功能联系起来。
Sci Adv. 2021 Jan 1;7(1). doi: 10.1126/sciadv.abe4310. Print 2021 Jan.
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Hydrodynamic interactions in topologically linked ring polymers.拓扑连接环状聚合物中的流体动力学相互作用。
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Topoly: Python package to analyze topology of polymers.Topoly:用于分析聚合物拓扑结构的 Python 包。
Brief Bioinform. 2021 May 20;22(3). doi: 10.1093/bib/bbaa196.
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