ArticleMultiscale modeling & simulation : a SIAM interdisciplinary journal2020
OPTIMIZING WEIGHTED ENSEMBLE SAMPLING OF STEADY STATES.
Article in Multiscale modeling & simulation : a SIAM interdisciplinary journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Reducing weighted ensemble variance with optimal trajectory management.The Journal of chemical physics · 2026Article
- Weighted ensemble: Recent mathematical developments.The Journal of chemical physics · 2023Article
- A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0].Living journal of computational molecular science · 2023Article
- Application of Cement-Based Composite Nanomaterials in Prefabricated Thin-Wall Light Steel Structure Composite Wall.International journal of analytical chemistry · 2022Article
- Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling.Journal of chemical theory and computation · 2021Article
- A gentle introduction to the non-equilibrium physics of trajectories: Theory, algorithms, and biomolecular applications.American journal of physics · 2021Article
- A Minimal, Adaptive Binning Scheme for Weighted Ensemble Simulations.The journal of physical chemistry. A · 2021Article
- Accelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian "Microbin" Analysis.Journal of chemical theory and computation · 2020Article
- Enhanced Jarzynski free energy calculations using weighted ensemble.The Journal of chemical physics · 2020Article
- Transient probability currents provide upper and lower bounds on non-equilibrium steady-state currents in the Smoluchowski picture.The Journal of chemical physics · 2019Article
- Computational Estimation of Microsecond to Second Atomistic Folding Times.Journal of the American Chemical Society · 2019Article
- Weighted Ensemble Simulation: Advances in methods, software, and applications.Wiley interdisciplinary reviews. Computational molecular scienceArticle
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
We propose parameter optimization techniques for weighted ensemble sampling of Markov chains in the steady-state regime. Weighted ensemble consists of replicas of a Markov chain, each carrying a weight, that are periodically resampled according to their weights inside of each of a number of bins that partition state space. We derive, from first principles, strategies for optimizing the choices of weighted ensemble parameters, in particular the choice of bins and the number of replicas to maintain in each bin. In a simple numerical example, we compare our new strategies with more traditional ones and with direct Monte Carlo.
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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.