Skipping the Replica Exchange Ladder with Normalizing Flows

Exploration vs Convergence Speed in Adaptive-Bias Enhanced Sampling

(2022) Michele Invernizzi et al.   Journal of Chemical Theory and Computation

Adaptive Monte Carlo augmented with normalizing flows

(2022) Marylou Gabrié et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From data to noise to data for mixing physics across temperatures with generative artificial intelligence

(2022) Yihang Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neural mode jump Monte Carlo

(2021) Luigi Sbailò et al.   JOURNAL OF CHEMICAL PHYSICS

Targeted Free Energy Perturbation Revisited: Accurate Free Energies from Mapped Reference Potentials

(2021) Andrea Rizzi et al.   Journal of Physical Chemistry Letters

Rethinking Metadynamics: From Bias Potentials to Probability Distributions

(2020) Michele Invernizzi et al.   Journal of Physical Chemistry Letters

Targeted free energy estimation via learned mappings

(2020) Peter Wirnsberger et al.   JOURNAL OF CHEMICAL PHYSICS

Unified Approach to Enhanced Sampling

(2020) Michele Invernizzi et al.   Physical Review X

Making the Best of a Bad Situation: A Multiscale Approach to Free Energy Calculation

(2019) Michele Invernizzi et al.   Journal of Chemical Theory and Computation

Promoting transparency and reproducibility in enhanced molecular simulations

(2019)   NATURE METHODS

Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning

(2019) Frank Noé et al.   SCIENCE

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Density estimation by dual ascent of the log-likelihood

(2013) Esteban G. Tabak et al.   Communications in Mathematical Sciences

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

A Family of Nonparametric Density Estimation Algorithms

(2012) E. G. Tabak et al.   COMMUNICATIONS ON PURE AND APPLIED MATHEMATICS

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble

(2012) Michael Deighan et al.   Journal of Chemical Theory and Computation

Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)

(2011) Lingle Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation

(2011) J. P. Nilmeier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Replica exchange with nonequilibrium switches

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

Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations

(2008) Mark J. Abraham et al.   Journal of Chemical Theory and Computation