Refined Chern-Simons Theory and Topological String

We show that refined Chern-Simons theory and large N duality can be used to study the refined topological string with and without branes. We derive the refined topological vertex of hep-th/0701156 and hep-th/0502061 from a link invariant of the refined SU(N) Chern-Simons theory on S^3, at infinite N. Quiver-like Chern-Simons theories, arising from Calabi-Yau manifolds with branes wrapped on several minimal S^3's, give a dual description of a large class of toric Calabi-Yau. We use this to derive the refined topological string amplitudes on a toric Calabi-Yau containing a shrinking P^2 surface. The result is suggestive of the refined topological vertex formalism for arbitrary toric Calabi-Yau manifolds in terms of a pair of vertices and a choice of a Morse flow on the toric graph, determining the vertex decomposition. The dependence on the flow is reminiscent of the approach to the refined topological string in upcoming work of Nekrasov and Okounkov. As a byproduct, we show that large N duality of the refined topological string explains the ``mirror symmetry`` of the refined colored HOMFLY invariants of knots.Comment: 58 pages, 18 figure

Knot Homology from Refined Chern-Simons Theory

We formulate a refinement of SU(N) Chern-Simons theory on a three-manifold via the refined topological string and the (2,0) theory on N M5 branes. The refined Chern-Simons theory is defined on any three-manifold with a semi-free circle action. We give an explicit solution of the theory, in terms of a one-parameter refinement of the S and T matrices of Chern-Simons theory, related to the theory of Macdonald polynomials. The ordinary and refined Chern-Simons theory are similar in many ways; for example, the Verlinde formula holds in both. We obtain new topological invariants of Seifert three-manifolds and torus knots inside them. We conjecture that the knot invariants we compute are the Poincare polynomials of the sl(n) knot homology theory. The latter includes the Khovanov-Rozansky knot homology, as a special case. The conjecture passes a number of nontrivial checks. We show that, for a large number of torus knots colored with the fundamental representation of SU(N), our knot invariants agree with the Poincare polynomials of Khovanov-Rozansky homology. As a byproduct, we show that our theory on S^3 has a large-N dual which is the refined topological string on X=O(-1)+O(-1)->P^1; this supports the conjecture by Gukov, Schwarz and Vafa relating the spectrum of BPS states on X to sl(n) knot homology. We also provide a matrix model description of some amplitudes of the refined Chern-Simons theory on S^3.Comment: 73 pages, 8 figures; minor corrections and improvements in presentatio