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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…
Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states
Hao Wu, Antonia S. J. S. Mey, Edina Rosta +1
We propose a discrete transition-based reweighting analysis method (dTRAM) for analyzing configuration-space-discretized simulation trajectories produced at different thermodynamic…
Optimal estimation of free energies and stationary densities from multiple biased simulations
Hao Wu, Frank Noé
When studying high-dimensional dynamical systems such as macromolecules, quantum systems and polymers, a prime concern is the identification of the most probable states and their s…
Spectral rate theory for projected two-state kinetics
Jan-Hendrik Prinz, John D. Chodera, Frank Noe
Classical rate theories often fail in cases where the observable(s) or order parameter(s) used are poor reaction coordinates or the observed signal is deteriorated by noise, such t…