Ghobadpour Elham, Kolb Max, Ejtehadi Mohammad Reza, Everaers Ralf
Université Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS), TIMC, F-38000 Grenoble, France.
School of Nano Science, Institute for Research in Fundamental Sciences (IPM), 19395-5531, Tehran, Iran.
Phys Rev E. 2021 Jul;104(1-1):014501. doi: 10.1103/PhysRevE.104.014501.
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.
超螺旋DNA、皱缩的间期染色体和拓扑受限的环形聚合物通常呈现出树状、双折叠、随机分支的构型。在此，我们研究一种紧密双折叠环形聚合物的弹性晶格模型，该模型允许与扩散性质量传输相耦合的侧支的自发产生和删除，这种扩散性质量传输在空间和树的连通图上都是局部的。我们使用蒙特卡罗模拟来研究属于三种不同普适类别的系统：无排除体积相互作用的理想双折叠环、自回避双折叠环以及熔体状态下的双折叠环。观察到的静态性质与随机分支聚合物的弗洛里理论的精确结果、模拟和预测高度吻合。例如，在熔体状态下，环呈现出紧凑构型并表现出领地行为。特别地，我们表明出现的动力学与最近的标度理论高度一致，并阐明了与线性链熟悉的爬行动力学的定性差异。
