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Predicting the kinetics of RNA oligonucleotides using Markov state models
Giovanni Pinamonti, Jianbo Zhao, David E. Condon +4
Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obta…
Variational Koopman models: slow collective variables and molecular kinetics from short off-equilibrium simulations
Hao Wu, Feliks Nüske, Fabian Paul +3
Markov state models (MSMs) and Master equation models are popular approaches to approximate molecular kinetics, equilibria, metastable states, and reaction coordinates in terms of…
Spectral learning of dynamic systems from nonequilibrium data
Hao Wu, Frank Noé
Observable operator models (OOMs) and related models are one of the most important and powerful tools for modeling and analyzing stochastic systems. They exactly describe dynamics…
Reversible Markov chain estimation using convex-concave programming
Benjamin Trendelkamp-Schroer, Hao Wu, Frank Noe
We present a convex-concave reformulation of the reversible Markov chain estimation problem and outline an efficient numerical scheme for the solution of the resulting problem base…