ArticleThe Journal of chemical physics2009
Using stochastic models calibrated from nanosecond nonequilibrium simulations to approximate mesoscale information.
Article in The Journal of chemical physics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 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
6 citing papers in PubMed.
- The Importance of Molecular Size, Concentration, and Thermal Conditions in Enhancing Lignin Derivatives' Interactions with Skin-like Membranes: Implications for Cosmetic and Therapeutic Applications.International journal of molecular sciences · 2025Article
- Quantifying transient 3D dynamical phenomena of single mRNA particles in live yeast cell measurements.The journal of physical chemistry. B · 2013Article
- Multiscale modeling of biological functions.Physical chemistry chemical physics : PCCP · 2011Review
- Renormalizing SMD: the renormalization approach and its use in long time simulations and accelerated PMF calculations of macromolecules.The journal of physical chemistry. B · 2010Article
- P-SPLINES USING DERIVATIVE INFORMATION.Multiscale modeling & simulation : a SIAM interdisciplinary journal · 2010Article
- Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages.The Journal of chemical physics · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
We demonstrate how the surrogate process approximation (SPA) method can be used to compute both the potential of mean force along a reaction coordinate and the associated diffusion coefficient using a relatively small number (10-20) of bidirectional nonequilibrium trajectories coming from a complex system. Our method provides confidence bands which take the variability of the initial configuration of the high-dimensional system, continuous nature of the work paths, and thermal fluctuations into account. Maximum-likelihood-type methods are used to estimate a stochastic differential equation (SDE) approximating the dynamics. For each observed time series, we estimate a new SDE resulting in a collection of SPA models. The physical significance of the collection of SPA models is discussed and methods for exploiting information in the population of estimated SPA models are demonstrated and suggested. Molecular dynamics simulations of potassium ion dynamics inside a gramicidin A channel are used to demonstrate the methodology, although SPA-type modeling has also proven useful in analyzing single-molecule experimental time series [J. Phys. Chem. B 113, 118 (2009)].
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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.