Monte Carlo simulation of a lattice model for the dynamics of randomly branching double-folded ring polymers,Physical Review E

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Monte Carlo simulation of a lattice model for the dynamics of randomly branching double-folded ring polymers
Physical Review E ( IF 2.2 ) Pub Date : 2021-07-13 , DOI: 10.1103/physreve.104.014501
Elham Ghobadpour _{1,

2} , Max Kolb ₃ , Mohammad Reza Ejtehadi ₄ , Ralf Everaers ₃

Affiliation

Supercoiled DNA, crumpled interphase chromosomes, and topologically constrained ring polymers often adopt treelike, double-folded, randomly branching configurations. Here we study an elastic lattice model for tightly double-folded ring polymers, which allows for the spontaneous creation and deletion of side branches coupled to a diffusive mass transport, which is local both in space and on the connectivity graph of the tree. We use Monte Carlo simulations to study systems falling into three different universality classes: ideal double-folded rings without excluded volume interactions, self-avoiding double-folded rings, and double-folded rings in the melt state. The observed static properties are in good agreement with exact results, simulations, and predictions of Flory theory for randomly branching polymers. For example, in the melt state rings adopt compact configurations and exhibit territorial behavior. In particular, we show that the emergent dynamics is in excellent agreement with a recent scaling theory and illustrate the qualitative differences with the familiar reptation dynamics of linear chains.

中文翻译：

随机支化双折叠环聚合物动力学的晶格模型的蒙特卡罗模拟

超螺旋 DNA、皱巴巴的相间染色体和拓扑约束的环状聚合物通常采用树状、双折叠、随机分支的配置。在这里，我们研究了紧密双折叠环聚合物的弹性晶格模型，它允许与扩散质量传输耦合的侧枝的自发创建和删除，这在空间和树的连接图上都是局部的。我们使用蒙特卡罗模拟来研究分为三个不同通用性类别的系统：没有排除体积相互作用的理想双折叠环、自回避双折叠环和处于熔化状态的双折叠环。观察到的静态特性与 Flory 理论对随机支化聚合物的精确结果、模拟和预测非常一致。例如，在熔化状态下，环采用紧凑的配置并表现出领土行为。特别是，我们表明涌现动力学与最近的缩放理论非常一致，并说明了与熟悉的线性链的爬行动力学的定性差异。

更新日期：2021-07-13

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