论文标题

打结和连接的弧的几何预测指标

Geometric Predictors of Knotted and Linked Arcs

论文作者

Sleiman, Joseph L, Burton, Robin H, Caraglio, Michele, Fosado, Yair Augusto Gutierrez, Michieletto, Davide

论文摘要

受到某些蛋白质在DNA分子中的“有感觉”结和纠缠的启发,我们在这里询问是否存在局部几何特征,这些特征是否可以用作通用聚合物的基本拓扑结构的读出。我们对打结和连接的半快速聚合物进行分子模拟,并研究四个几何措施,以预测拓扑纠缠:局部曲率,局部密度,局部1D WRITHE和非本地3D Writhe。我们发现局部曲率是纠缠的不良预测指标。相比之下,具有最大局部密度或扭动的段与最短的打结和连接的弧相关的时间多达90%。我们发现,这种精度可在不同的结中保留,并且在明显的球形限制下也保留了这种精度,这是在打结的聚合物中的分离基本交叉点。我们进一步发现,非本地3D Writhe是结位置的最佳几何读数。最后,我们讨论这些几何特征如何用于计算一般聚合物熔体和凝胶中的纠缠。

Inspired by how certain proteins "sense" knots and entanglements in DNA molecules, here we ask if there exist local geometric features that may be used as a read-out of the underlying topology of generic polymers. We perform molecular simulations of knotted and linked semiflexbile polymers and study four geometric measures to predict topological entanglements: local curvature, local density, local 1D writhe and non-local 3D writhe. We discover that local curvature is a poor predictor of entanglements. In contrast, segments with maximum local density or writhe correlate as much as 90% of the time with the shortest knotted and linked arcs. We find that this accuracy is preserved across different knot types and also under significant spherical confinement, which is known to delocalise essential crossings in knotted polymers. We further discover that non-local 3D writhe is the best geometric read-out of knot location. Finally, we discuss how these geometric features may be used to computationally analyse entanglements in generic polymer melts and gels.

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