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In this paper, we prove a general existence theorem for properly embedded minimal surfaces with free boundary in any compact Riemannian 3‐manifold M with boundary ∂M. These minimal surfaces are either disjoint from ∂M or meet ∂M orthogonally. The main feature of our result is that there is no assumptions on the curvature of M or convexity of ∂M. We prove the boundary regularity of the minimal surfaces at their free boundaries. Furthermore, we define a topological invariant, the filling genus, for compact 3‐manifolds with boundary and show that we can bound the genus of the minimal surface constructed above in terms of the filling genus of the ambient manifold M. Our proof employs a variant of the min‐max construction used by Colding and De Lellis on closed embedded minimal surfaces, which were first developed by Almgren and Pitts.

In this paper, we prove uniform curvature estimates for immersed stable free boundary minimal hypersurfaces satisfying a uniform area bound, which generalize the celebrated Schoen–Simon–Yau interior curvature estimates up to the free boundary. Our curvature estimates imply a smooth compactness theorem which is an essential ingredient in the min-max theory of free boundary minimal hypersurfaces developed by the last two authors. We also prove a monotonicity formula for free boundary minimal submanifolds in Riemannian manifolds for any dimension and codimension. For 3-manifolds with boundary, we prove a stronger curvature estimate for properly embedded stable free boundary minimal surfaces without a-priori area bound. This generalizes Schoen’s interior curvature estimates to the free boundary setting. Our proof uses the theory of minimal laminations developed by Colding and Minicozzi.

We introduce an Alexander polynomial for MOY graphs. For a framed trivalent MOY graph G, we refine the construction and obtain a framed ambient isotopy invariant \Delta(G,c)(t). The invariant \Delta(G,c)(t) satisfies a series of relations, which we call MOY type relations, and conversely these relations determine \Delta(G,c)(t). Using them we provide a graphical definition of the Alexander polynomial of a link. Finally, we discuss some properties and applications of our invariants.

We study Thurston’s Lipschitz and curve metrics, as well as the arc metric on the Teichmüller space of one-hold tori equipped with complete hyperbolic metrics with boundary holonomy of fixed length. We construct natural Lipschitz maps between two surfaces equipped with such hyperbolic metrics that generalize Thurston’s stretch maps and prove the following: (1) On the Teichmüller space of the torus with one boundary component, the Lipschitz and the curve metrics coincide and define a geodesic metric on this space. (2) On the same space, the arc and the curve metrics coincide when the length of the boundary component is ≤4arcsinh(1), but differ when the boundary length is large. We further apply our stretch map generalization to construct novel Thurston geodesics on the Teichmüller spaces of closed hyperbolic surfaces, and use these geodesics to show that the sum-symmetrization of the Thurston metric fails to exhibit Gromov hyperbolicity.