A computational package for measuring Topological Entanglement in Polymers, Proteins and Periodic systems (TEPPP)
A computational package for measuring Topological Entanglement in Polymers, Proteins and Periodic systems (TEPPP)
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DOI：
10.1016/j.cpc.2022.108639
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发表时间：
2023-01-24
影响因子：
6.3
通讯作者：
Panagiotou, Eleni
中科院分区：
文献类型：
--
作者：
Herschberg, Tom;Pifer, Kyle;Panagiotou, Eleni
许多材料，如聚合物熔体、溶液、生物聚合物和纺织品，都是由缠结的长丝组成的。这些系统中的纠缠显着影响其机械性能和功能。我们介绍了聚合物，蛋白质和周期系统（TEPPP）软件的拓扑纠缠，使在这样的系统中测量拓扑和几何复杂性。特别地，该软件使得能够计算系统中的每个细丝或细丝对的Writhe、高斯连接积分和琼斯多项式，无论它们是开放的还是闭合的。特别是，对于采用周期性边界条件（PBC）的系统，该软件还允许使用周期性链接数和周期性缠绕来计算PBC中的总成对纠缠。对于线性（开）链，TEPPP可以计算所有这些拓扑参数（包括琼斯多项式），而无需任何封闭方案。此外，TEPPP还能够测量沿着一条链或一对链在不同长度尺度下的自纠缠和成对纠缠。通过对输入文件进行适当的预处理，代码还可以用于星星或分支架构。我们提供了如何使用代码的例子，我们目前的纠缠效应在聚合物中使用这个包的结果。我们展示了如何TEPPP可以用来测量线性聚合物链在熔体中的拓扑纠缠，揭示了以前从未见过的微妙的纠缠转变。我们还使用TEPPP分析了两嵌段共聚物熔体中的打结效应及其位置，发现打结局域化转变与这些体系中的层状无序转变一致。最后，我们使用TEPPP来揭示SARS-CoV-2刺突蛋白的一些拓扑结构，该结构指出了包含S1/S2切割位点的区域中的有趣结构。程序摘要程序标题：聚合物、蛋白质和周期性系统中的拓扑缠结（TEPPP）软件CPC程序文件库链接：https：//doi.org/10.17632/ygdbpnhpzw.1开发人员的存储库链接：https：//github.com/TEPPP-software许可条款：BSD 3-clause编程语言：C++补充材料：问题的性质：测量线性或环形细丝系统中的单和成对缠结和打结（开放或封闭曲线）在3空间或系统中采用周期性边界条件（PBC）在不同的长度尺度。解决方法：TEPPP可用于测量三维空间中单链或多链细丝系统或采用PBC的系统中的拓扑纠缠复杂度。给定曲线的坐标作为输入，TEPPP可以计算高斯连接积分、Writhe、Jones多项式、周期多项式、
Many materials, like polymer melts, solutions, biopolymers and textiles, are composed of entangled filaments. The entanglement in these systems significantly affects their mechanical properties and their function. We introduce the Topological Entanglement in Polymers, Proteins and Periodic systems (TEPPP) software, that enables to measure the topological and geometrical complexity in such systems. In particular, this software enables the computation of the Writhe, the Gauss linking integral and the Jones polynomial of each filament or pair of filaments in the system, whether they are open or closed. In particular, for systems employing Periodic Boundary Conditions (PBC), the software also allows to compute the total pairwise entanglement in PBC, using the Periodic linking number and the Periodic Writhe. For linear (open) chains, TEPPP can calculate all these topological parameters (including the Jones polynomial) without any closure scheme. In addition, TEPPP also enables measuring self and pairwise entanglement at different length-scales along a chain or a pair of chains. With appropriate preprocessing of input files, the code can also be used for star or branched architectures. We provide examples of how the code is used and we present results on the entanglement effect in polymers obtained using this package. We show how TEPPP can be used to measure the topological entanglement of linear polymer chains in a melt, revealing subtle entanglement transitions never seen before. We also used TEPPP to analyze the effect of knotting and its location in diblock copolymer melts, which reveals that knotting localization transition coincides with lamellar-disorder transition in these systems. Finally, we use TEPPP to reveal some of the topological structure of the SARS-CoV-2 Spike protein, which points to interesting structure in a region that contains the S1/S2 cleavage site.Program summaryProgram Title: Topological Entanglement in Polymers, Proteins and Periodic systems (TEPPP) softwareCPC Library link to program files: https://doi .org /10 .17632 /ygdbpnhpzw.1Developer's repository link: https://github .com /TEPPP-softwareLicensing provisions: BSD 3-clauseProgramming language: C++ Supplementary material:Nature of problem: Measuring single and pairwise entanglement and knotting in systems of linear or ring filaments (open or closed curves) in 3-space or in systems employing Periodic Boundary Conditions (PBC) at different length scales.Solution method: TEPPP can be used to measure topological entanglement complexity in single or multi -chain filament systems in 3-space or in systems employing PBC. Given as input the coordinates of the curves, TEPPP can compute the Gauss linking integral, the Writhe, the Jones polynomial, the Periodic