ArticleJournal of chemical theory and computation2011
Beyond microscopic reversibility: Are observable non-equilibrium processes precisely reversible?
Article in Journal of chemical theory and computation, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- ModBindProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Symmetric Ligand Binding Pathways and Dual-State Bottleneck in [NiFe] Hydrogenases from Unbiased Molecular Dynamics.The journal of physical chemistry letters · 2025Article
- Rare-Event Sampling using a Reinforcement Learning-Based Weighted Ensemble Method.bioRxiv : the preprint server for biology · 2024Article
- WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data.Journal of chemical information and modeling · 2024Article
- Weighted ensemble: Recent mathematical developments.The Journal of chemical physics · 2023Article
- Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution.Journal of chemical theory and computation · 2022Article
- A gentle introduction to the non-equilibrium physics of trajectories: Theory, algorithms, and biomolecular applications.American journal of physics · 2021Article
- What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models.Journal of chemical theory and computation · 2021Article
- Transient probability currents provide upper and lower bounds on non-equilibrium steady-state currents in the Smoluchowski picture.The Journal of chemical physics · 2019Article
- Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant.Biophysical journal · 2019Article
- Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways.Biophysical journal · 2018Article
- Path-sampling strategies for simulating rare events in biomolecular systems.Current opinion in structural biology · 2017Review
- Article
- Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein-Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide.The journal of physical chemistry letters · 2016Article
- Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.PLoS computational biology · 2016Review
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses.Protein science : a publication of the Protein Society · 2016Article
- Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories.Journal of chemical theory and computation · 2014Article
- Using simulations to provide the framework for experimental protein folding studies.Archives of biochemistry and biophysics · 2013Review
- Peptide backbone sampling convergence with the adaptive biasing force algorithm.The journal of physical chemistry. B · 2013Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Although the principle of microscopic reversibility has been studied for many decades, there remain ambiguities in its application to non-equilibrium processes of importance to chemistry, physics and biology. Examples include whether protein unfolding should follow the same pathways and in the same proportions as folding, and whether unbinding should likewise mirror binding. Using continuum-space calculations which extend previous kinetic analyses, we demonstrate formally that the precise symmetry of forward and reverse processes is expected only under certain special conditions. Approximate symmetry will be exhibited under a separate set of conditions. Exact, approximate, and broken symmetry scenarios are verified in several ways: using numerical calculations on toy and molecular systems; using exact calculations on kinetic models of induced fit in protein-ligand binding; and based on reported experimental results. The analysis highlights intrinsic challenges and ambiguities in the design and analysis of both experiments and simulations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.