WASP: a software package for correctly characterizing the topological development of ribbon structures.
WASP: a software package for correctly characterizing the topological development of ribbon structures.
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DOI：
10.1038/s41598-020-80851-8
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发表时间：
2021-01-15
影响因子：
4.6
通讯作者：
Prior C
中科院分区：
文献类型：
--
作者：
Sierzega Z;Wereszczynski J;Prior C
我们介绍了Writhe应用软件包（WASP），它可以用来表征带状结构的拓扑结构，DNA的底层数学模型，生物聚合物，超流体涡旋，弹性绳和磁通量绳。这种特性是通过开放带和封闭带的一般扭扭分解来实现的，特别是通过称为极性扭扭的量。我们展示了这种分解如何比DNA建模中常用的人工闭合方法更自然和直接。特别是，我们展示了如何将极性卷曲分解为局部和非局部成分，从而明显地表征了条带的局部螺旋结构和结/连接。这种分解提供了其他方法无法提供的额外信息。作为示例应用，WASP例程用于表征DNA微圆和开放式微粒粒子形成的演变拓扑结构（writhe），结果表明，局部和非局部成分的分解对于微粒粒子的检测特别重要。最后证明了一些众所周知的替代扭曲表达式实际上是极扭曲测度的简化。
We introduce the Writhe Application Software Package (WASP) which can be used to characterisze the topology of ribbon structures, the underlying mathematical model of DNA, Biopolymers, superfluid vorticies, elastic ropes and magnetic flux ropes. This characterization is achieved by the general twist–writhe decomposition of both open and closed ribbons, in particular through a quantity termed the polar writhe. We demonstrate how this decomposition is far more natural and straightforward than artificial closure methods commonly utilized in DNA modelling. In particular, we demonstrate how the decomposition of the polar writhe into local and non-local components distinctly characterizes the local helical structure and knotting/linking of the ribbon. This decomposition provides additional information not given by alternative approaches. As example applications, the WASP routines are used to characterise the evolving topology (writhe) of DNA minicircle and open ended plectoneme formation magnetic/optical tweezer simulations, and it is shown that the decomponsition into local and non-local components is particularly important for the detection of plectonemes. Finally it is demonstrated that a number of well known alternative writhe expressions are actually simplifications of the polar writhe measure.
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影响因子：
16.6
作者：
Irobalieva RN;Fogg JM;Catanese DJ Jr;Sutthibutpong T;Chen M;Barker AK;Ludtke SJ;Harris SA;Schmid MF;Chiu W;Zechiedrich L
通讯作者：
Zechiedrich L
影响因子：
4.9
作者：
Chintzoglou, Georgios;Patsourakos, Spiros;Vourlidas, Angelos
通讯作者：
Vourlidas, Angelos
影响因子：
2.4
作者：
Fain, B;Rudnick, J;Ostlund, S
通讯作者：
Ostlund, S
影响因子：
10.9
作者：
Lauric, Alexandra;Miller, Eric;Malek, Adel M.
通讯作者：
Malek, Adel M.
影响因子：
5.7
作者：
Lee, Franklin L.;Farimani, Amir Barati;Pande, Vijay S.
通讯作者：
Pande, Vijay S.