Topology and Geometry of Biopolymers

ISBN-13: 9781470448400

Erica Flapan;Helen Wong

Opis

This book contains the proceedings of the AMS Special Session on Topology of Biopolymers, held from April 21-22, 2018, at Northeastern University, Boston, MA. The papers cover recent results on the topology and geometry of DNA and protein knotting using techniques from knot theory, spatial graph theory, differential geometry, molecular simulations, and laboratory experimentation. They include current work on the following topics: the density and supercoiling of DNA minicircles; the dependence of DNA geometry on its amino acid sequence; random models of DNA knotting; topological models of DNA replication and recombination; theories of how and why proteins knot; topological and geometric approaches to identifying entanglements in proteins; and topological and geometric techniques to predict protein folding rates. All of the articles are written as surveys intended for a broad interdisciplinary audience with a minimum of prerequisites. In addition to being a useful reference for experts, this book also provides an excellent introduction to the fast-moving field of topology and geometry of biopolymers.

Spis treści

• The topology and geometry of DNA: J. M. Fogg and L. Zechiedrich, Beyond the static DNA model of Watson and Crick
• P. Liu, R. Polischuk, Y. Diao, and J. Arsuaga, Characterizing the topology of kinetoplast DNA using random knotting
• A. Kasman and B. LeMesurier, Did sequence dependent geometry influence the evolution of the genetic code?
• T. Deguchi and E. Uehara, Topological sum rules in the knotting probabilities of DNA
• D. Buck and D. O'Donnol, Knotting of replication intermediates is narrowly restricted
• A. H. Moore and M. Vazquez, Recent advances on the non-coherent band surgery model for site-specific recombination
• The topology and geometry of proteins: S. E. Jackson, Why are there knots in proteins?
• A. Nunes and P. F. N. Faisca, Knotted proteins: Tie etiquette in structural biology
• D. Goundaroulis, J. Dorier, and A. Stasiak, Knotoids and protein structure
• K. C. Millett, Topological linking and entanglement in proteins
• E. Panagiotou and K. W. Plaxco, A topological study of protein folding kinetics.