title: Properties of ideal composite knots.
abstract: The shortest tube of constant diameter that can form a given knot represents the 'ideal' form of the knot. Ideal knots provide an irreducible representation of the knot, and they have some intriguing mathematical and physical features, including a direct correspondence with the time-averaged shapes of knotted DNA molecules in solution. Here we describe the properties of ideal forms of composite knots-knots obtained by the sequential tying of two or more independent knots (called factor knots) on the same string. We find that the writhe (related to the handedness of crossing points) of composite knots is the sum of that of the ideal forms of the factor knots. By comparing ideal composite knots with simulated configurations of knotted, thermally fluctuating DNA, we conclude that the additivity of writhe applies also to randomly distorted configurations of composite knots and their corresponding factor knots. We show that composite knots with several factor knots may possess distinct structural isomers that can be interconverted only by loosening the knot.
authors.affiliation: Department of Chemistry, Rutgers the State University of New Jersey, New Brunswick 08903, USA.
authors.forename: V
authors.initials: V
authors.lastname: Katritch
authors.forename: W K
authors.initials: WK
authors.lastname: Olson
authors.forename: P
authors.initials: P
authors.lastname: Pieranski
authors.forename: J
authors.initials: J
authors.lastname: Dubochet
authors.forename: A
authors.initials: A
authors.lastname: Stasiak
mesh_terms: D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation