Biased sampling of nonequilibrium trajectories: can fast switching simulations outperform conventional free energy calculation methods?

No abstract is available for this paper.

• Publication year

  2005

• Venue

  Journal of Physical Chemistry B

• Publication date

  2005-03-19

• Fields of study

  Medicine, Physics

• Identifiers
  DOI 10.1021/JP044556APMID 16851777
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Statistical Physics

  2007cited by this paper
• Single-ensemble nonequilibrium path-sampling estimates of free energy differences.

  2004cited by this paper
• Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements

  2003cited by this paper
• Theory of a systematic computational error in free energy differences.

  2002cited by this paper
• Transition path sampling: throwing ropes over rough mountain passes, in the dark.

  2002cited by this paper
• Understanding Molecular Simulation

  2001cited by this paper
• Efficient, multiple-range random walk algorithm to calculate the density of states.

  2000cited by this paper
• Direct dynamical calculation of entropy and free energy by adiabatic switching.

  1990cited by this paper
• Optimized Monte Carlo data analysis.

  1989cited by this paper
• Computer Simulation of Liquids

  1988cited by this paper
• Introduction To Modern Statistical Mechanics

  1987cited by this paper
• Regular and Stochastic Motion

  1982cited by this paper
• Mathematical Methods of Classical Mechanics

  1974cited by this paper
• An Introduction to Probability Theory and Its Applications

  1959cited by this paper

• Directional Curvature as a Design Lever for High-Efficiency CO 2 Electroreduction on NiN 4 -Doped Carbon Nanotubes

  2026cites this paper
• O2 Reduction Stimulates Adatom Generation on Cu(111) Catalyzing Hydrogen Evolution.

  2026cites this paper
• Ultrasmall Pr-doped InBi alloy nanospheres confined in carbon nanofibers enable high-efficiency CO2-to-formate conversion

  2026cites this paper
• One-pot co-upcycling of mixed polyolefin waste.

  2026cites this paper
• Reinforced Hydrogen-Bond Networks on Dehydrogenated Ni(OH) 2 Surfaces Boost HMF Electrooxidation via Mediated Adsorption Configuration and Bond Polarization

  2026cites this paper
• In Situ Reconstruction of a Cu(100) Surface for Promoted C–C Coupling in CO 2 Electroreduction from First-Principles Multiscale Modeling

  2026cites this paper
• Atomic-Level Insights into the Cation-Mediated Electrocatalytic C-N Coupling Mechanism over Cu Model Catalyst.

  2026cites this paper
• Stable Machine Learning Potentials for Liquid Metals via Dataset Engineering

  2026cites this paper
• Enhanced Regional Electric Potential Difference of Graphdiyne Through Asymmetric Substitution Strategy Boosts Li+ Migration in Composite Polymer Solid-State Electrolyte

  2025cites this paper
• Cyclobutane-linked nanothreads through thermal and photochemically mediated polymerization of cyclohexadiene

  2025cites this paper
• Kinetic cation effect in alkaline hydrogen electrocatalysis and double layer proton transfer

  2025cites this paper
• Quantum Annealing Algorithms for Estimating Ising Partition Functions

  2025cites this paper
• Atomic-Level Insights into Cation-Mediated Mechanism in Electrochemical Nitrogen Reduction.

  2025cites this paper
• Nonadiabatic Force Matching for Alchemical Free-Energy Estimation.

  2025cites this paper
• Shared Nitrogen in M-N-C Single-Atom Electrocatalysts Unlocks Langmuir-Hinshelwood Mechanism for CO-to-Formaldehyde Conversion.

  2025cites this paper
• Revealing the Fundamental Origin of the CO-Free Pathway Selectivity in Alkaline Methanol Electrooxidation on Bi-Modified Pt

  2025cites this paper
• Amorphous MoO2-wrapped Mo supported low-crystalline Co nanosheets for enhanced OH bond cleavage: synergistic effect of abundant active sites and robust interfaces.

  2025cites this paper
• Elucidating and contrasting the mechanisms for Mg and Ca sulfate ion-pair formation with multi-level embedded quantum mechanics/molecular dynamics simulations.

  2024cites this paper
• Towards superior CO2RR catalysts: Deciphering the selectivity puzzle over dual-atom catalyst.

  2024cites this paper
• Free energy calculations in biomolecule-nanomaterial interactions

  2024cites this paper
• Scaling relations and dynamical predictiveness of electric dipole strength on 2e- ORR catalytic property

  2024cites this paper
• cAIMD Simulations Guided Design of Atomic Praseodymium Doping In–Bi Nanofibers for High‐Energy‐Efficiency CO2 Electrolysis to Formate in Ultra‐Wide Potential Window

  2024cites this paper
• Sulfonic Acid Functionalized Ionic Liquids for Defect Passivation via Molecular Interactions for High-Quality Perovskite Films and Stable Solar Cells.

  2024cites this paper
• Hydrogen Peroxide-Induced Overoxidation of Fe-N-C Catalysts: Implications for ORR Activity.

  2024cites this paper
• The Stability of Hydrogen-Bonded Ion-Pair Complex Unexpectedly Increases with Increasing Solvent Polarity.

  2024cites this paper
• Bubble-water/catalyst triphase interface microenvironment accelerates photocatalytic OER via optimizing semi-hydrophobic OH radical

  2024cites this paper
• Variational analysis of molecular free energy landscapes and AI implementations

  2024cites this paper
• Learned mappings for targeted free energy perturbation between peptide conformations.

  2023cites this paper
• Characterizing the Mechanisms of Ca and Mg Carbonate Ion-Pair Formation with Multi-Level Molecular Dynamics/Quantum Mechanics Simulations.

  2023cites this paper
• Revealing the role of double-layer microenvironments in pH-dependent oxygen reduction activity over metal-nitrogen-carbon catalysts

  2023cites this paper
• Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions

  2023cites this paper
• Probing pH-Dependent Dehydration Dynamics of Mg and Ca Cations in Aqueous Solutions with Multi-Level Quantum Mechanics/Molecular Dynamics Simulations.

  2023cites this paper
• Proton Shuttling by Polyaniline of High Brønsted Basicity for Improved Electrocatalytic Ethylene Production from CO2.

  2023cites this paper
• CO electroreduction on single-atom copper

  2023cites this paper
• Hydrogen bond network connectivity in the electric double layer dominates the kinetic pH effect in hydrogen electrocatalysis on Pt

  2022cites this paper
• Connectivity of Hydrogen Bond Networks in EDL Dominates the Kinetical pH Effect of Hydrogen Electrocatalysis on Pt

  2022cites this paper
• Mechanistic Exploration of Furfural Hydrogenation on Copper Surface in Aqueous Phase by DFT and AIMD simulations

  2022cites this paper
• Mpemba effect in crystallization of polybutene-1.

  2022cites this paper
• Nonuniform convergence in moment expansions of integral work relations.

  2022cites this paper
• Insights into ultrasound-promoted degradation of naphthenic acid compounds in oil sands process affected water. Part II: In silico quantum screening of hydroxyl radical initiated and propagated degradation of benzoic acid

  2022cites this paper
• Microscopic EDL structures and charge-potential relation on stepped platinum surface: Insights from the ab initio molecular dynamics simulations.

  2022cites this paper
• Revealing the Origin of Nitrogen Electroreduction Activity of Molybdenum Disulfide Supported Iron Atoms

  2022cites this paper
• Experimental methods in chemical engineering: Density functional theory

  2021cites this paper
• Computing Free Energies with Fluctuation Relations on Quantum Computers.

  2021cites this paper
• A multiscale modelling approach to elucidate the mechanism of the oxygen evolution reaction at the hematite-water interface.

  2021cites this paper
• Collective variable-based enhanced sampling and machine learning

  2021cites this paper
• Reweighted Jarzynski Sampling: Acceleration of Rare Events and Free Energy Calculation with a Bias Potential Learned from Nonequilibrium Work.

  2021cites this paper
• Best Practices for Alchemical Free Energy Calculations

  2020cites this paper
• Perspective on theoretical methods and modeling relating to electro-catalysis processes.

  2020cites this paper
• Critical Role of Surface Defects in the Controllable Deposition of Li2S on Graphene: From Molecule to Crystallite.

  2020cites this paper
• Best Practices for Alchemical Free Energy Calculations [Article v1.0].

  2020cites this paper
• Unveiling the Active Structure of Single Nickel Atom Catalysis: Critical Roles of Charge Capacity and Hydrogen Bonding.

  2020cites this paper
• Jarzynski’s Equality, Fluctuation Theorems, and Variance Reduction: Mathematical Analysis and Numerical Algorithms

  2019cites this paper
• Solvation free energies via alchemical simulations: let's get honest about sampling, once more.

  2019cites this paper
• Single molecule force spectroscopy of a streptomycin-binding RNA aptamer: An out-of-equilibrium molecular dynamics study.

  2019cites this paper
• Assessment of GAFF2 and OPLS-AA General Force Fields in Combination with the Water Models TIP3P, SPCE, and OPC3 for the Solvation Free Energy of Druglike Organic Molecules.

  2019cites this paper
• Precision and computational efficiency of nonequilibrium alchemical methods for computing free energies of solvation. II. Unidirectional estimates.

  2019cites this paper
• Nonequilibrium free-energy calculations of fluids using LAMMPS

  2019cites this paper
• Steering a solute between coexisting solvation states: Revisiting nonequilibrium work relations and the calculation of free energy differences.

  2019cites this paper
• Non-equilibrium Bio-Molecular Unfolding Under Tension

  2019cites this paper
• A generalized linear response framework for expanded ensemble and replica exchange simulations.

  2018cites this paper
• 0 A pr 2 01 1 Free Energy Changes , Fluctuations , and Path Probabilities

  2018cites this paper
• A pr 2 01 6 Non-equilibrium work energy relation for non-Hamiltonian dynamics

  2018cites this paper
• Melting Si: Beyond Density Functional Theory.

  2018cites this paper
• Jarzynski’s Equality, Fluctuation Theorems, and Variance Reduction: Mathematical Analysis and Numerical Algorithms

  2018cites this paper
• Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level

  2017cites this paper
• Comparison of Accuracy and Convergence Rate between Equilibrium and Nonequilibrium Alchemical Transformations for Calculation of Relative Binding Free Energy

  2017cites this paper
• A Lower Bound on Work Extraction Probability Prescribed by Nonequilibrium Work Relation

  2017cites this paper
• Landau free energies and restricted averages

  2017cites this paper
• Recovery of equilibrium free energy from non-equilibrium thermodynamics with mechanosensitive ion channels in E. coli

  2017cites this paper
• Estimation of Potentials of Mean Force from Nonequilibrium Pulling Simulations Using Both Minh-Adib Estimator and Weighted Histogram Analysis Method.

  2016cites this paper
• Trajectory Stratification of Stochastic Dynamics

  2016cites this paper
• Elastic Barrier Dynamical Freezing in Free Energy Calculations: A Way To Speed Up Nonequilibrium Molecular Dynamics Simulations by Orders of Magnitude.

  2016cites this paper
• I. Dissociation free energies of drug-receptor systems via non-equilibrium alchemical simulations: a theoretical framework.

  2016cites this paper
• Nonequilibrium free-energy calculation of solids using LAMMPS

  2016cites this paper
• Steered molecular dynamics study of inhibitor binding in the internal binding site in dehaloperoxidase-hemoglobin.

  2016cites this paper
• Alchemical Free Energy Calculations : Ready for Prime Time ?

  2016cites this paper
• Free Energy Calculations of Ligand–Protein Binding

  2015cites this paper
• Nonequilibrium work energy relation for non-Hamiltonian dynamics.

  2015cites this paper
• Common features of extraordinary rate theories.

  2015cites this paper
• Probing the conformational energetics of alkyl thiols on gold surfaces by means of a morphing/steering non-equilibrium tool.

  2015cites this paper
• Towards bulk thermodynamics via non-equilibrium methods: gaseous methane as a case study.

  2015cites this paper
• Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures.

  2015cites this paper
• Two Paths Diverged: Exploring Trajectories, Protocols, and Dynamic Phases

  2015cites this paper
• Markov Processes linking Thermodynamics and Turbulence

  2015cites this paper
• Preserving correlations between trajectories for efficient path sampling.

  2015cites this paper
• Notes on the Dynamics of Disorder On the Fluctuations of Dissipation : An Annotated Bibliography

  2015cites this paper
• Multidimensional integration through Markovian sampling under steered function morphing: A physical guise from statistical mechanics

  2014cites this paper
• High-precision work distributions for extreme nonequilibrium processes in large systems.

  2014cites this paper
• Looking for some free energy? Call JEFREE (…)

  2014cites this paper
• Impact of interfacial high-density water layer on accurate estimation of adsorption free energy by Jarzynski's equality.

  2014cites this paper
• One-Dimensional Steady Transport by Molecular Dynamics Simulation: Non-Boltzmann Position Distribution and Non-Arrhenius Dynamical Behavior

  2014cites this paper
• An introduction to best practices in free energy calculations.

  2013cites this paper
• Force-clamp experiments reveal the free-energy profile and diffusion coefficient of the collapse of protein molecules.

  2013cites this paper
• Structure-Based, Rational Design of T Cell Receptors

  2013cites this paper
• Stochastic thermodynamics of fluctuating density fields: non-equilibrium free energy differences under coarse-graining.

  2013cites this paper
• Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics

  2013influential citation
• Exploring Equilibrium Systems with Nonequilibrium Simulations

  2012cites this paper
• On the estimation of the free energy, from a single equilibrium statistical ensemble, via particle reinsertion.

  2012cites this paper
• Stochastic thermodynamics, fluctuation theorems and molecular machines

  2012cites this paper