Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2020.09.17.301309

WASP: A software package for correctly characterizing the topological development of ribbon structures

Sierzega, Z.·Wereszczynski, J.·Prior, C.
View original source ↗Export metadata ↓

Abstract

We introduce the Writhe Application Software Package (WASP) which can be used to characterise the topology of ribbon structures, the underlying mathematical model of DNA, Biopolymers, superfluid vorticies, elastic ropes and magnetic flux ropes. This characterisation 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 in local and non-local components distinctly characterizes local helical structure and knotting/linking of the ribbon. This decomposition provides additional information not given by alternative approaches. As an example application, the WASP routines are used to characterise the evolving topology (writhe) of DNA minicircle and open ended plectoneme formation magnetic/optical tweezer simulations. Finally it is demonstrated that a number of well known alternative writhe expressions are actually simplifications of the polar writhe measure.

Source connections

Explore related subjects

biophysicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Sierzega, Z., Wereszczynski, J., Prior, C.. 2020-09-18. WASP: A software package for correctly characterizing the topological development of ribbon structures. https://doi.org/10.1101/2020.09.17.301309

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Organised streaming of cerebrospinal fluid in the human third ventricle

Quasi-periodic pressure pulses associated with cardiac and respiratory activity generate reciprocating cerebrospinal fluid (CSF) motion in the human ventricles. Regular waves dominated by the cardiac cycle are overlaid with cycles of low-frequency respiratory waves, the latter to become stronger in forced breathing or even dominated by large successive flushes in NREM sleep. The present study investigates how such waves contribute to residual streaming within the human ventricles. Transient CFD simulations were performed in the third ventricle at varying parameters of frequency, stroke volume and wave-form asymmetry. Increasing the aqueduct peak Reynolds-number, either by small stroke volume and high frequency or large stroke volume at low frequency, transfers the flow from a reversible flow pattern to the formation of clear preferential pathways, alternating between the in- and outflow cycle. The resulting permanent streaming flux across the aqueduct relative to the mean oscillatory flow-rate, i.e. the dimensionless streaming ratio SR follows a rational saturation relation, SR [~] ReAq,peak/(C + ReAq,peak), demonstrating that increasing the peak aqueduct Reynolds number yields diminishing returns and bounds the relative contribution of residual inter-ventricular streaming. These findings demonstrate differences in hydrodynamic organisation in the third ventricle and highlight the importance of this organisation for intraventricular fluid exchange.

biophysics↗
bioRxiv2026

Amyloid stability and condensate material properties independently govern the hnRNPA2 condensate to fibril transition

hnRNPA2 is a component of cellular membraneless organelles many of which contain RNA and RNA-binding proteins (RBPs). RBPs frequently contain low-complexity domains (LCDs) that can also assemble into amyloid fibrils. Fibrils isolated from patients with frontotemporal lobar degeneration contain ordered segments of these LCDs and disease-associated mutations can enhance the homotypic interactions that promote aggregation. Although previous studies have largely examined the condensate-to-fibril transition by altering condensate stability, how amyloid structure governs this process remains poorly understood. Here, we show that the hnRNPA2 LCD forms a reproducible fibril fold and by combining structure-guided thermodynamic profiling, peptide design, mutagenesis and in vitro characterization under conditions with (two-phase) and without (one-phase) condensates, we define the molecular determinants of its assembly. We identify an aromatic triad within the fibril core that controls fibril formation kinetics and thermodynamic stability. Mutational analysis further reveals that condensate stability and fibril stability are largely independent. Finally, microrheology linked reduced condensate viscosity to faster fibril formation, supporting a role for condensate material properties in regulating aggregation kinetics. Together, these findings support a model in which the condensate-to-fibril transition is governed by the interplay between a disordered ''fuzzy coat'' and a fibril-forming aromatic triad within hnRNPA2. This work provides a structural framework for understanding how condensates can transition into amyloid assemblies.

biophysics↗
bioRxiv2026

hAM-pe soluble extract increases human keratinocyte HaCaT cell-line mobility in scratch assays

We have studied the impact of human amniotic membrane (hAM-pe) on wound closing speed in a scratch assay of human keratinocytes (HaCaT). Though not without limitations, scratch assays are useful for studying collective cellular displacement as a model of wound healing. We show that the treatment is effective in decreasing the average time that the cells need to completely close the wound, in agreement with previous \emph{in vivo} experiments. We developed an automated segmentation software, and verified that a linear fit, though not completely describing the wound edge dynamics, is a robust method for comparing treatments and control measurements. By tracking the individual motion of a subset of cells, we found that individual treatment does not cause an increase in individual speed enough to explain the effect of the treatment at the collective (wound edge) level. Instead, the mean squared displacement and numerical simulations of a simple model of interacting active Brownian particles support the view that the main effect of the treatment at the individual level is to increase the persistence of cellular motion.

biophysics↗