WASP

WASP computes polar writhe and performs twist–writhe decomposition to quantify the topology of open and closed ribbon structures, including DNA, biopolymers, superfluid vortices, elastic ropes, and magnetic flux ropes.

Key Features:

• Twist–Writhe Decomposition: Employs a general twist–writhe decomposition for both open and closed ribbon structures, avoiding artificial closure methods.
• Polar Writhe Quantification: Computes polar writhe and decomposes it into local and non-local components to distinguish local helical structure from knotting and linking.
• Versatility in Application: Applies to ribbon-like systems such as DNA, biopolymers, superfluid vortices, elastic ropes, and magnetic flux ropes and can be used with molecular dynamics (MD) trajectories.
• Enhanced Topological Insights: Retains topological contributions omitted or simplified by alternative writhe expressions, providing additional information on ribbon topology.

Scientific Applications:

• DNA topology: Characterizes evolving topology of DNA structures, including analysis of writhe dynamics in DNA minicircles.
• Plectoneme formation: Analyzes formation of open-ended plectonemes observed in magnetic and optical tweezer simulations.
• MD trajectory analysis: Quantifies topological changes in ribbon-like systems from molecular dynamics (MD) trajectories.

Methodology:

Computational methods explicitly include a general twist–writhe decomposition for open and closed ribbons and computation of polar writhe with decomposition into local and non-local components; the approach is applied to molecular dynamics (MD) trajectories.