Sierzega, Z and Wereszczynski, J and Prior, C (2021) 'WASP: a software package for correctly characterizing the topological development of ribbon structures.', Scientific reports., 11 . p. 1527.
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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|Publisher Web site:||https://doi.org/10.1038/s41598-020-80851-8|
|Publisher statement:||This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.|
|Date accepted:||17 December 2020|
|Date deposited:||14 June 2021|
|Date of first online publication:||15 January 2021|
|Date first made open access:||14 June 2021|
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