Topology and geometry of biopolymers : AMS Special Session on Topology of Biopolymers, April 21-22, 2018, Northeastern University, Boston, Massachusetts

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. Contents Preface Part I. The Topology and Geometry of DNA Beyond the static DNA model of Watson and Crick • Jonathan M. Fogg and Lynn Zechiedrich Characterizing the topology of kinetoplast DNA using random knotting • P. Liu, R. Polischuk, Y. Diao, and J. Arsuaga Did sequence dependent geometry influence the evolution of the genetic code? • Alex Kasman and Brenton LeMesurier Topological sum rules in the knotting probabilities of DNA • Tetsuo Deguchi and Erica Uehara Knotting of replication intermediates is narrowly restricted • Dorothy Buck and Danielle O’Donnol Recent advances on the non-coherent band surgery model for site-specific recombination • Allison H. Moore and Mariel Vazquez Part II. The Topology and Geometry of Proteins Why are there knots in proteins? • Sophie E. Jackson Knotted proteins: Tie etiquette in structural biology • Ana Nunes and Patr ́ıcia F. N. Fa ́ısca Knotoids and protein structure • Dimos Goundaroulis, Julien Dorier, and Andrzej Stasiak Topological linking and entanglement in proteins • Kenneth C. Millett A topological study of protein folding kinetics • Eleni Panagiotou and Kevin W. Plaxco