Transition Manifolds of Complex Metastable Systems

Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics

(2017) Wei Zhang et al.   Entropy

Identification of simple reaction coordinates from complex dynamics

(2017) Robert T. McGibbon et al.   JOURNAL OF CHEMICAL PHYSICS

Set-free Markov state model building

(2017) Marcus Weber et al.   JOURNAL OF CHEMICAL PHYSICS

ATLAS: A Geometric Approach to Learning High-Dimensional Stochastic Systems Near Manifolds

(2017) Miles Crosskey et al.   MULTISCALE MODELING & SIMULATION

Effective dynamics along given reaction coordinates, and reaction rate theory

(2016) Wei Zhang et al.   FARADAY DISCUSSIONS

A trajectory-free framework for analysing multiscale systems

(2016) Gary Froyland et al.   PHYSICA D-NONLINEAR PHENOMENA

Data-Driven Reduction for a Class of Multiscale Fast-Slow Stochastic Dynamical Systems

(2016) Carmeline J. Dsilva et al.   SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS

Effective dynamics along given reaction coordinates, and reaction rate theory

(2016) Wei Zhang et al.   FARADAY DISCUSSIONS

Pseudogenerators of Spatial Transfer Operators

(2015) Andreas Bittracher et al.   SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Recent developments in methods for identifying reaction coordinates

(2014) Wenjin Li et al.   MOLECULAR SIMULATION

A Computational Method to Extract Macroscopic Variables and Their Dynamics in Multiscale Systems

(2014) Gary Froyland et al.   SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

(2013) Frank Noé et al.   MULTISCALE MODELING & SIMULATION

Non-stationary forward flux sampling

(2012) Nils B. Becker et al.   JOURNAL OF CHEMICAL PHYSICS

Optimizing transition states via kernel-based machine learning

(2012) Zachary D. Pozun et al.   JOURNAL OF CHEMICAL PHYSICS

Estimating the Eigenvalue Error of Markov State Models

(2012) Natasa Djurdjevac et al.   MULTISCALE MODELING & SIMULATION

Markov state models based on milestoning

(2011) Christof Schütte et al.   JOURNAL OF CHEMICAL PHYSICS

Everything you wanted to know about Markov State Models but were afraid to ask

(2010) Vijay S. Pande et al.   METHODS

On the Approximation Quality of Markov State Models

(2010) Marco Sarich et al.   MULTISCALE MODELING & SIMULATION

Effective dynamics using conditional expectations

(2010) Frédéric Legoll et al.   NONLINEARITY

Transition Path Theory for Markov Jump Processes

(2009) Philipp Metzner et al.   MULTISCALE MODELING & SIMULATION

Detecting intrinsic slow variables in stochastic dynamical systems by anisotropic diffusion maps

(2009) A. Singer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coordinate-dependent diffusion in protein folding

(2009) R. B. Best et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discretization of the Frobenius–Perron Operator Using a Sparse Haar Tensor Basis: The Sparse Ulam Method

(2009) Oliver Junge et al.   SIAM JOURNAL ON NUMERICAL ANALYSIS

Equation-Free Multiscale Computation: Algorithms and Applications

(2008) Ioannis G. Kevrekidis et al.   Annual Review of Physical Chemistry

Adaptive biasing force method for scalar and vector free energy calculations

(2008) Eric Darve et al.   JOURNAL OF CHEMICAL PHYSICS

Diffusion Maps, Reduction Coordinates, and Low Dimensional Representation of Stochastic Systems

(2008) R. R. Coifman et al.   MULTISCALE MODELING & SIMULATION

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS