We introduce a novel spatio-temporal discretization for nonlinear Fokker-Planck equations on the multi-dimensional unit cube. This discretization is based on two structural properties of these equations: the first is the representation as a gradient flow of an entropy functional in the $L^2$-Wasserstein metric, the second is the Lagrangian nature, meaning that solutions can be written as the push forward transformation of the initial density under suitable flow maps. The resulting numerical scheme is entropy diminishing and mass conserving. Further, the scheme is weakly stable, which allows us to prove convergence under certain regularity assumptions. Finally, we present results from numerical experiments in space dimension $d=2$.
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