Reaction coordinates in complex systems-a perspective

Discovering Collective Variables of Molecular Transitions via Genetic Algorithms and Neural Networks

(2021) Ferry Hooft et al.   Journal of Chemical Theory and Computation

Machine learning meets chemical physics

(2021) Michele Ceriotti et al.   JOURNAL OF CHEMICAL PHYSICS

Machine learning potentials for extended systems: a perspective

(2021) Jörg Behler et al.   EUROPEAN PHYSICAL JOURNAL B

Machine Learning for Molecular Simulation

(2020) Frank Noé et al.   Annual Review of Physical Chemistry

Performance and Cost Assessment of Machine Learning Interatomic Potentials

(2020) Yunxing Zuo et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Understanding the role of predictive time delay and biased propagator in RAVE

(2020) Yihang Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Data-Driven Collective Variables for Enhanced Sampling

(2020) Luigi Bonati et al.   Journal of Physical Chemistry Letters

Machine learning for collective variable discovery and enhanced sampling in biomolecular simulation

(2020) Hythem Sidky et al.   MOLECULAR PHYSICS

Identification of a multi-dimensional reaction coordinate for crystal nucleation in Ni3Al

(2020) Yanyan Liang et al.   JOURNAL OF CHEMICAL PHYSICS

New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems

(2020) Jaewoon Jung et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Unsupervised machine learning in atomistic simulations, between predictions and understanding

(2019) Michele Ceriotti   JOURNAL OF CHEMICAL PHYSICS

Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations

(2019) Jaewoon Jung et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Machine Learning Interatomic Potentials as Emerging Tools for Materials Science

(2019) Volker L. Deringer et al.   ADVANCED MATERIALS

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

(2019) Yihang Wang et al.   Nature Communications

Neural-Network-Based Path Collective Variables for Enhanced Sampling of Phase Transformations

(2019) Jutta Rogal et al.   PHYSICAL REVIEW LETTERS

Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)

(2018) João Marcelo Lamim Ribeiro et al.   JOURNAL OF CHEMICAL PHYSICS

Endpoint-restricted adiabatic free energy dynamics approach for the exploration of biomolecular conformational equilibria

(2018) Michel A. Cuendet et al.   JOURNAL OF CHEMICAL PHYSICS

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

Collective Variables from Local Fluctuations

(2018) Dan Mendels et al.   Journal of Physical Chemistry Letters

Automated design of collective variables using supervised machine learning

(2018) Mohammad M. Sultan et al.   JOURNAL OF CHEMICAL PHYSICS

Toward Achieving Efficient and Accurate Ligand-Protein Unbinding with Deep Learning and Molecular Dynamics through RAVE

(2018) João Marcelo Lamim Ribeiro et al.   Journal of Chemical Theory and Computation

Defining an Optimal Metric for the Path Collective Variables

(2018) Ladislav Hovan et al.   Journal of Chemical Theory and Computation

Maximum Likelihood Analysis of Reaction Coordinates during Solidification in Ni

(2018) Grisell Díaz Leines et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Transition path sampling of rare events by shooting from the top

(2017) Hendrik Jung et al.   JOURNAL OF CHEMICAL PHYSICS

Nonlinear machine learning in simulations of soft and biological materials

(2017) J. Wang et al.   MOLECULAR SIMULATION

Reaction Coordinates and Mechanistic Hypothesis Tests

(2016) Baron Peters   Annual Review of Physical Chemistry

Perspective: Machine learning potentials for atomistic simulations

(2016) Jörg Behler   JOURNAL OF CHEMICAL PHYSICS

Molecular mechanism for cavitation in water under tension

(2016) Georg Menzl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Easy Transition Path Sampling Methods: Flexible-Length Aimless Shooting and Permutation Shooting

(2015) Ryan Gotchy Mullen et al.   Journal of Chemical Theory and Computation

A string reaction coordinate for the folding of a polymer chain

(2015) Christian Leitold et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Transmission Coefficients, Committors, and Solvent Coordinates in Ion-Pair Dissociation

(2014) Ryan Gotchy Mullen et al.   Journal of Chemical Theory and Computation

Recent developments in methods for identifying reaction coordinates

(2014) Wenjin Li et al.   MOLECULAR SIMULATION

Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions

(2013) Mary A. Rohrdanz et al.   Annual Review of Physical Chemistry

Optimising reaction coordinates for crystallisation by tuning the crystallinity definition

(2013) Swetlana Jungblut et al.   MOLECULAR PHYSICS

Inertial likelihood maximization for reaction coordinates with high transmission coefficients

(2012) Baron Peters   CHEMICAL PHYSICS LETTERS

Toward the Mechanism of Ionic Dissociation in Water

(2012) Andrew J. Ballard et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

(2012) G. A. Tribello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reaction coordinates for the crystal nucleation of colloidal suspensions extracted from the reweighted path ensemble

(2011) Wolfgang Lechner et al.   JOURNAL OF CHEMICAL PHYSICS

Optimizing Nucleus Size Metrics for Liquid–Solid Nucleation from Transition Paths of Near-Nanosecond Duration

(2011) Gregg T. Beckham et al.   Journal of Physical Chemistry Letters

Splitting Probabilities as a Test of Reaction Coordinate Choice in Single-Molecule Experiments

(2011) John D. Chodera et al.   PHYSICAL REVIEW LETTERS

Role of the Prestructured Surface Cloud in Crystal Nucleation

(2011) Wolfgang Lechner et al.   PHYSICAL REVIEW LETTERS

The reweighted path ensemble

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

Nonlinear reaction coordinate analysis in the reweighted path ensemble

(2010) Wolfgang Lechner et al.   JOURNAL OF CHEMICAL PHYSICS

Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein

(2010) J. Vreede et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transition state analysis of solid-solid transformations in nanocrystals

(2009) Michael Grünwald et al.   JOURNAL OF CHEMICAL PHYSICS

Artificial reaction coordinate “tunneling” in free-energy calculations: The catalytic reaction of RNase H

(2009) Edina Rosta et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Forward flux sampling for rare event simulations

(2009) Rosalind J Allen et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Rare events via multiple reaction channels sampled by path replica exchange

(2008) Peter G. Bolhuis   JOURNAL OF CHEMICAL PHYSICS

Adaptive biasing force method for scalar and vector free energy calculations

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

Efficient and Direct Generation of Multidimensional Free Energy Surfaces via Adiabatic Dynamics without Coordinate Transformations

(2008) Jerry B. Abrams et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

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