A Statistical Approach to Knot Confinement Via Persistent Homology
Overview
Authors
Affiliations
In this paper, we study how randomly generated knots occupy a volume of space using topological methods. To this end, we consider the evolution of the first homology of an immersed metric neighbourhood of a knot's embedding for growing radii. Specifically, we extract features from the persistent homology (PH) of the Vietoris-Rips complexes built from point clouds associated with knots. Statistical analysis of our data shows the existence of increasing correlations between geometric quantities associated with the embedding and PH-based features, as a function of the knots' lengths. We further study the variation of these correlations for different knot types. Finally, this framework also allows us to define a simple notion of deviation from ideal configurations of knots.
Homology of homologous knotted proteins.
Benjamin K, Mukta L, Moryoussef G, Uren C, Harrington H, Tillmann U J R Soc Interface. 2023; 20(201):20220727.
PMID: 37122282 PMC: 10130707. DOI: 10.1098/rsif.2022.0727.