Mathematics of DNA Structure, Function and Interactions

Foreword.- Preface.- Nick Cozzarelli: A personal remembrance.- Mathematical methods in DNA topology: Applications to chromosome organization and site-specific recombination.- Conformational statistics of DNA and diffusion equations on the Euclidean group.- Perspectives on DNA looping.- Differences between positively and negatively supercoiled DNA that topoisomerases may distinguish.- Calibration of tethered particle motion experiments.- Difference topology: Analysis of high-order DNA-protein assemblies.- Useful intrusions of DNA topology into experiments on protein-DNA geometry.- Topological analysis of DNA-protein complexes.- Closing the loop on protein-DNA interactions: Interplay between shape and flexibility in nucleoprotein assemblies having implications for biological regulation.- Four-way helical junctions in DNA molecules.- Micromechanics of single supercoiled DNA molecules.- Flexibility of nucleosomes on topologically constrained DNA.- The mathematics of DNA structure, mechanics, and dynamics.- Paradox regained: a topological coupling of nucleosomal DNA wrapping and chromatin fibre coiling.- Statistical-mechanical analysis of enzymatic topological transformations in DNA molecules.- List of workshop participants.