Galerkin approximation of dynamical quantities using trajectory data

A Minimum Variance Clustering Approach Produces Robust and Interpretable Coarse-Grained Models

(2018) Brooke E. Husic et al.   Journal of Chemical Theory and Computation

Data-Driven Model Reduction and Transfer Operator Approximation

(2018) Stefan Klus et al.   JOURNAL OF NONLINEAR SCIENCE

Markov State Models: From an Art to a Science

(2018) Brooke E. Husic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Point Cloud Discretization of Fokker--Planck Operators for Committor Functions

(2018) Rongjie Lai et al.   MULTISCALE MODELING & SIMULATION

VAMPnets for deep learning of molecular kinetics

(2018) Andreas Mardt et al.   Nature Communications

Recovery of Protein Folding Funnels from Single-Molecule Time Series by Delay Embeddings and Manifold Learning

(2018) Jiang Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Variational Koopman models: Slow collective variables and molecular kinetics from short off-equilibrium simulations

(2017) Hao Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Ward Clustering Improves Cross-Validated Markov State Models of Protein Folding

(2017) Brooke E. Husic et al.   Journal of Chemical Theory and Computation

Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes

(2017) An Ghysels et al.   Journal of Chemical Theory and Computation

Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules

(2017) Wei Wang et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Landmark diffusion maps (L-dMaps): Accelerated manifold learning out-of-sample extension

(2017) Andrew W. Long et al.   APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS

Data-driven spectral decomposition and forecasting of ergodic dynamical systems

(2017) Dimitrios Giannakis   APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS

Variable bandwidth diffusion kernels

(2016) Tyrus Berry et al.   APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS

Effect of Clustering Algorithm on Establishing Markov State Model for Molecular Dynamics Simulations

(2016) Yan Li et al.   Journal of Chemical Information and Modeling

Variational tensor approach for approximating the rare-event kinetics of macromolecular systems

(2016) Feliks Nüske et al.   JOURNAL OF CHEMICAL PHYSICS

Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models

(2016) Ernesto Suárez et al.   Journal of Chemical Theory and Computation

A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes

(2016) Victor Ovchinnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamics from noisy data with extreme timing uncertainty

(2016) R. Fung et al.   NATURE

Markov State Models Provide Insights into Dynamic Modulation of Protein Function

(2015) Diwakar Shukla et al.   ACCOUNTS OF CHEMICAL RESEARCH

A critical appraisal of Markov state models

(2015) Ch. Schütte et al.   European Physical Journal-Special Topics

Preserving correlations between trajectories for efficient path sampling

(2015) Todd R. Gingrich et al.   JOURNAL OF CHEMICAL PHYSICS

Exact milestoning

(2015) Juan M. Bello-Rivas et al.   JOURNAL OF CHEMICAL PHYSICS

Systematic characterization of protein folding pathways using diffusion maps: Application to Trp-cage miniprotein

(2015) Sang Beom Kim et al.   JOURNAL OF CHEMICAL PHYSICS

A Basis Set for Peptides for the Variational Approach to Conformational Kinetics

(2015) F. Vitalini et al.   Journal of Chemical Theory and Computation

Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps

(2015) Lorenzo Boninsegna et al.   Journal of Chemical Theory and Computation

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

(2015) Martin K. Scherer et al.   Journal of Chemical Theory and Computation

A Data–Driven Approximation of the Koopman Operator: Extending Dynamic Mode Decomposition

(2015) Matthew O. Williams et al.   JOURNAL OF NONLINEAR SCIENCE

Nonparametric forecasting of low-dimensional dynamical systems

(2015) Tyrus Berry et al.   PHYSICAL REVIEW E

Multidimensional reaction rate theory with anisotropic diffusion

(2014) Alexander M. Berezhkovskii et al.   JOURNAL OF CHEMICAL PHYSICS

Perspective: Markov models for long-timescale biomolecular dynamics

(2014) C. R. Schwantes et al.   JOURNAL OF CHEMICAL PHYSICS

Automatic State Partitioning for Multibody Systems (APM): An Efficient Algorithm for Constructing Markov State Models To Elucidate Conformational Dynamics of Multibody Systems

(2014) Fu Kit Sheong et al.   Journal of Chemical Theory and Computation

Variational Approach to Molecular Kinetics

(2014) Feliks Nüske et al.   Journal of Chemical Theory and Computation

Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories

(2014) Ernesto Suárez et al.   Journal of Chemical Theory and Computation

Nonlinear Machine Learning of Patchy Colloid Self-Assembly Pathways and Mechanisms

(2014) Andrew W. Long et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Spectral Rate Theory for Two-State Kinetics

(2014) Jan-Hendrik Prinz et al.   Physical Review X

Transition-path theory calculations on non-uniform meshes in two and three dimensions using finite elements

(2013) Mauro Lapelosa et al.   COMPUTER PHYSICS COMMUNICATIONS

Consensus for the Fip35 folding mechanism?

(2013) Ganna Berezovska et al.   JOURNAL OF CHEMICAL PHYSICS

Identification of slow molecular order parameters for Markov model construction

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

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

(2013) Christian R. Schwantes et al.   Journal of Chemical Theory and Computation

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

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

Time-Scale Separation from Diffusion-Mapped Delay Coordinates

(2013) T. Berry et al.   SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS

Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification

(2013) Susanna Röblitz et al.   Advances in Data Analysis and Classification

Steered transition path sampling

(2012) Nicholas Guttenberg et al.   JOURNAL OF CHEMICAL PHYSICS

Variants of Dynamic Mode Decomposition: Boundary Condition, Koopman, and Fourier Analyses

(2012) Kevin K. Chen et al.   JOURNAL OF NONLINEAR SCIENCE

Estimating the Eigenvalue Error of Markov State Models

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

Nonlinear dimensionality reduction in molecular simulation: The diffusion map approach

(2011) Andrew L. Ferguson et al.   CHEMICAL PHYSICS LETTERS

Determination of reaction coordinates via locally scaled diffusion map

(2011) Mary A. Rohrdanz et al.   JOURNAL OF CHEMICAL PHYSICS

Markov state models based on milestoning

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

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

(2011) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Delineation of Folding Pathways of a β-Sheet Miniprotein

(2011) Wenwei Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computational Design and Experimental Testing of the Fastest-Folding β-Sheet Protein

(2010) Stefano Piana et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Systematic determination of order parameters for chain dynamics using diffusion maps

(2010) A. L. Ferguson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Progress and challenges in the automated construction of Markov state models for full protein systems

(2009) Gregory R. Bowman et al.   JOURNAL OF CHEMICAL PHYSICS

Exact rate calculations by trajectory parallelization and tilting

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Separating forward and backward pathways in nonequilibrium umbrella sampling

(2009) Alex Dickson et al.   JOURNAL OF CHEMICAL PHYSICS

Transition Path Theory for Markov Jump Processes

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

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

Clustering high-dimensional data

(2009) Hans-Peter Kriegel et al.   ACM Transactions on Knowledge Discovery from Data

Transition networks for modeling the kinetics of conformational change in macromolecules

(2008) Frank Noé et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Precision shooting: Sampling long transition pathways

(2008) Michael Grünwald et al.   JOURNAL OF CHEMICAL PHYSICS

A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT

(2008) J. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA