ArticleThe journal of physical chemistry. B2012
Characterization of a dynamic string method for the construction of transition pathways in molecular reactions.
Article in The journal of physical chemistry. B, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- Thermodynamic and Kinetic Analysis of Molecular Conformational Dynamics in a Riemannian Framework.The journal of physical chemistry. A · 2026Article
- A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis.PLoS computational biology · 2024Article
- A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls.Journal of chemical theory and computation · 2022Article
- Computational methods and theory for ion channel research.Advances in physics: X · 2022Article
- String Method with Swarms-of-Trajectories, Mean Drifts, Lag Time, and Committor.The journal of physical chemistry. A · 2021Article
- Molecular Dynamics-Based Thermodynamic and Kinetic Characterization of Membrane Protein Conformational Transitions.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Predicting reaction coordinates in energy landscapes with diffusion anisotropy.The Journal of chemical physics · 2017Article
- A minimization principle for transition paths of maximum flux for collective variables.Theoretical chemistry accounts · 2017Article
- Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate:phosphate antiporter.Nature communications · 2015Article
- Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution.Journal of the American Chemical Society · 2015Article
- Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review.Frontiers in bioengineering and biotechnology · 2015Review
- Conformational Transition Pathways of Epidermal Growth Factor Receptor Kinase Domain from Multiple Molecular Dynamics Simulations and Bayesian Clustering.Journal of chemical theory and computation · 2014Article
- Comparison between Mean Forces and Swarms-of-Trajectories String Methods.Journal of chemical theory and computation · 2014Article
- Diffusion along the splitting/commitment probability reaction coordinate.The journal of physical chemistry. B · 2013Article
- Simulating rare events using a weighted ensemble-based string method.The Journal of chemical physics · 2013Article
- 15 Years of molecular simulation of drug-binding kinetics.Expert opinion on drug discoveryReview
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
We explore the theoretical foundation of different string methods used to find dominant reaction pathways in high-dimensional configuration spaces. Pathways are assessed by the amount of reactive flux they carry and by their orientation relative to the committor function. By examining the effects of transforming between different collective coordinates that span the same underlying space, we unmask artificial coordinate dependences in strings optimized to follow the free energy gradient. In contrast, strings optimized to follow the drift vector produce reaction pathways that are significantly less sensitive to reparameterizations of the collective coordinates. The differences in these paths arise because the drift vector depends on both the free energy gradient and the diffusion tensor of the coarse collective variables. Anisotropy and position dependence of diffusion tensors arise commonly in spaces of coarse variables, whose generally slow dynamics are obtained by nonlinear projections of the strongly coupled atomic motions. We show here that transition paths constructed to account for dynamics by following the drift vector will (to a close approximation) carry the maximum reactive flux both in systems with isotropic position dependent diffusion and in systems with constant but anisotropic diffusion. We derive a simple method for calculating the committor function along paths that follow the reactive flux. Lastly, we provide guidance for the practical implementation of the dynamic string method.
Indexed as
Identifiers
What OpenQuestion holds
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.