An extended autoencoder model for reaction coordinate discovery in rare event molecular dynamics datasets

Transition path sampling for non-equilibrium dynamics without predefined reaction coordinates

(2020) P. Buijsman et al.   JOURNAL OF CHEMICAL PHYSICS

Machine learning approaches for analyzing and enhancing molecular dynamics simulations

(2020) Yihang Wang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Kinetic energy flows in activated dynamics of biomolecules

(2020) Huiyu Li et al.   JOURNAL OF CHEMICAL PHYSICS

Rate Prediction for Homogeneous Nucleation of Methane Hydrate at Moderate Supersaturation Using Transition Interface Sampling

(2020) A. Arjun et al.   JOURNAL OF PHYSICAL CHEMISTRY B

EncoderMap: Dimensionality Reduction and Generation of Molecule Conformations

(2019) Tobias Lemke et al.   Journal of Chemical Theory and Computation

Capabilities and limitations of time-lagged autoencoders for slow mode discovery in dynamical systems

(2019) Wei Chen et al.   JOURNAL OF CHEMICAL PHYSICS

Unbiased atomistic insight in the competing nucleation mechanisms of methane hydrates

(2019) Arjun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Past–future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics

(2019) Yihang Wang et al.   Nature Communications

Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design

(2018) Wei Chen et al.   JOURNAL OF CHEMICAL PHYSICS

OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics

(2018) David W. H. Swenson et al.   Journal of Chemical Theory and Computation

OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes

(2018) David W. H. Swenson et al.   Journal of Chemical Theory and Computation

Reaction mechanism and reaction coordinates from the viewpoint of energy flow

(2016) Wenjin Li et al.   JOURNAL OF CHEMICAL PHYSICS

Reducing the cost of evaluating the committor by a fitting procedure

(2015) Wenjin Li et al.   JOURNAL OF CHEMICAL PHYSICS

Umbrella sampling

(2011) Johannes Kästner   Wiley Interdisciplinary Reviews-Computational Molecular Science

The reweighted path ensemble

(2010) Jutta Rogal et al.   JOURNAL OF CHEMICAL PHYSICS

Amorphous Precursors in the Nucleation of Clathrate Hydrates

(2010) Liam C. Jacobson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events

(2008) Weinan E et al.   Annual Review of Physical Chemistry

An integrate-over-temperature approach for enhanced sampling

(2008) Yi Qin Gao   JOURNAL OF CHEMICAL PHYSICS