Robert W. Ghrist & Philip J. Holmes 
Knots and Links in Three-Dimensional Flows [PDF ebook] 

The closed orbits of three-dimensional flows form knots and links. This book develops the tools – template theory and symbolic dynamics – needed for studying knotted orbits. This theory is applied to the problems of understanding local and global bifurcations, as well as the embedding data of orbits in Morse-smale, Smale, and integrable Hamiltonian flows. The necesssary background theory is sketched; however, some familiarity with low-dimensional topology and differential equations is assumed.