Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities

Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates

(2014) Mahmoud Moradi et al.   JOURNAL OF CHEMICAL PHYSICS

Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations

(2013) Mahmoud Moradi et al.   Journal of Physical Chemistry Letters

Using Nonequilibrium Fluctuation Theorems to Understand and Correct Errors in Equilibrium and Nonequilibrium Simulations of Discrete Langevin Dynamics

(2013) David A. Sivak et al.   Physical Review X

Langevin dynamics with constraints and computation of free energy differences

(2012) Tony Lelièvre et al.   MATHEMATICS OF COMPUTATION

Calculating relative transition rates with driven nonequilibrium simulations

(2011) Mahmoud Moradi et al.   CHEMICAL PHYSICS LETTERS

Estimating equilibrium ensemble averages using multiple time slices from driven nonequilibrium processes: Theory and application to free energies, moments, and thermodynamic length in single-molecule pulling experiments

(2011) David D. L. Minh et al.   JOURNAL OF CHEMICAL PHYSICS

Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation

(2010) Mahmoud Moradi et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers

(2010) Mahmoud Moradi et al.   JOURNAL OF CHEMICAL PHYSICS

Hummer and Szabo-like Potential of Mean Force Estimator for Bidirectional Nonequilibrium Pulling Experiments/Simulations

(2010) Paolo Nicolini et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Three Detailed Fluctuation Theorems

(2010) Massimiliano Esposito et al.   PHYSICAL REVIEW LETTERS

Replica exchange with nonequilibrium switches

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

Conformations and free energy landscapes of polyproline peptides

(2009) M. Moradi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Nonequilibrium work relations: foundations and applications

(2008) C. Jarzynskia   EUROPEAN PHYSICAL JOURNAL B

Adaptively biased molecular dynamics for free energy calculations

(2008) Volodymyr Babin et al.   JOURNAL OF CHEMICAL PHYSICS

A Differential Fluctuation Theorem†

(2008) Paul Maragakis et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Finding Transition Pathways Using the String Method with Swarms of Trajectories

(2008) Albert C. Pan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Optimized Free Energies from Bidirectional Single-Molecule Force Spectroscopy

(2008) David D. L. Minh et al.   PHYSICAL REVIEW LETTERS