molecular-dynamics simulations

Nedialkova, Lilia, Miguel Amat, Ioannis Kevrekidis, and Gerhard Hummer. (2014) 2014. “Diffusion Maps, Clustering and Fuzzy Markov Modeling in Peptide Folding Transitions”. Journal of Chemical Physics 141 (11): 114102.

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Coifman, Kevrekidis, Lafon, Maggioni, and Nadler. 2008. “DIFFUSION MAPS, REDUCTION COORDINATES, AND LOW DIMENSIONAL REPRESENTATION OF STOCHASTIC SYSTEMS”. Multiscale Modeling & Simulation 7 (2): 842-64.

Reference Link
Kim, Sang Beom, Carmeline Dsilva, Ioannis Kevrekidis, and Pablo Debenedetti. (2015) 2015. “Systematic Characterization of Protein Folding Pathways Using Diffusion Maps: Application to Trp-Cage Miniprotein”. Journal of Chemical Physics 142 (8): 085101.

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