Topology and Geometry of Biopolymers
About this Title
Erica Flapan, Pomona College, Claremont, CA and Helen Wong, Claremont McKenna College, Claremont, CA, Editors
Publication: Contemporary Mathematics
Publication Year: 2020; Volume 746
ISBNs: 978-1-4704-4840-0 (print); 978-1-4704-5456-2 (online)
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.
Graduate students and research mathematicians interested in applications of topology and DNA proteins.
Table of Contents
- Jonathan M. Fogg and Lynn 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
- Alex Kasman and Brenton LeMesurier – Did sequence dependent geometry influence the evolutionof the genetic code?
- Tetsuo Deguchi and Erica Uehara – Topological sum rules in the knotting probabilities of DNA
- Dorothy Buck and Danielle O’Donnol – Knotting of replication intermediates is narrowly restricted
- Allison H. Moore and Mariel Vazquez – Recent advances on the non-coherent band surgery model for site-specific recombination
- Sophie E. Jackson – Why are there knots in proteins?
- Ana Nunes and Patrícia F. N. Faísca – Knotted proteins: Tie etiquette in structural biology
- Dimos Goundaroulis, Julien Dorier and Andrzej Stasiak – Knotoids and protein structure
- Kenneth C. Millett – Topological linking and entanglement in proteins
- Eleni Panagiotou and Kevin W. Plaxco – A topological study of protein folding kinetics