Nonlinear dimensionality reduction in molecular simulation: The diffusion map approach

►The diffusion map approach is a nonlinear dimensionality reduction technique. ► We review its applications in the field of molecular simulation. ► Diffusion maps can systematically extract the important underlying dynamical modes. ► Kinetically meaningful, low-dimensional embeddings may be constructed. ► We provide examples of applications to n-alkanes, peptides and driven interfaces.