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

Area of Science:

• Biophysics
• Computational Biology
• Materials Science

Background:

• Characterizing the topology of ribbon structures is crucial for understanding DNA, biopolymers, and other complex systems.
• Existing methods for analyzing ribbon topology often rely on artificial closure, limiting their accuracy and applicability.

Purpose of the Study:

• To introduce the Writhe Application Software Package (WASP) for comprehensive ribbon topology characterization.
• To present a novel twist-writhe decomposition using polar writhe for analyzing both open and closed ribbons.
• To demonstrate the superiority of this method over artificial closure techniques in DNA modeling.

Main Methods:

• Developed the Writhe Application Software Package (WASP).
• Implemented a general twist-writhe decomposition based on polar writhe.
• Applied WASP to analyze DNA minicircles and plectoneme formation in simulations.

Main Results:

• The polar writhe decomposition naturally characterizes ribbon topology, distinguishing local helical structure from global knotting/linking.
• WASP provides insights not available with alternative methods.
• The decomposition into local and non-local components is vital for detecting plectonemes in DNA simulations.
• Established that common writhe expressions are simplifications of the polar writhe measure.

Conclusions:

• WASP offers a more natural and informative approach to ribbon topology analysis compared to existing methods.
• The polar writhe decomposition, particularly its local and non-local components, enhances the understanding of complex topological structures like DNA plectonemes.
• This method has broad applications in biophysics, polymer science, and beyond.