ArticleThe journal of physical chemistry. B2009
Quantifying multiscale noise sources in single-molecule time series.
Article in The journal of physical chemistry. B, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Unraveling the Thousand Word Picture: An Introduction to Super-Resolution Data Analysis.Chemical reviews · 2017Article
- Article
- Data-driven techniques for detecting dynamical state changes in noisily measured 3D single-molecule trajectories.Molecules (Basel, Switzerland) · 2014Article
- Quantifying transient 3D dynamical phenomena of single mRNA particles in live yeast cell measurements.The journal of physical chemistry. B · 2013Article
- Multiscale mechanobiology: mechanics at the molecular, cellular, and tissue levels.Cell & bioscience · 2013Article
- Rate limit of protein elastic response is tether dependent.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- P-SPLINES USING DERIVATIVE INFORMATION.Multiscale modeling & simulation : a SIAM interdisciplinary journal · 2010Article
- Using stochastic models calibrated from nanosecond nonequilibrium simulations to approximate mesoscale information.The Journal of chemical physics · 2009Article
- Quantifying DNA melting transitions using single-molecule force spectroscopy.Journal of physics. Condensed matter : an Institute of Physics journal · 2009Article
- Extracting Kinetic and Stationary Distribution Information from Short MD Trajectories via a Collection of Surrogate Diffusion Models.Journal of chemical theory and computation · 2009Article
- Analyzing single-molecule manipulation experiments.Journal of molecular recognition : JMRArticle
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
When analyzing single-molecule data, a low-dimensional set of system observables typically serves as the observational data. We calibrate stochastic dynamical models from time series that record such observables. Numerical techniques for quantifying noise from multiple time scales in a single trajectory, including experimental instrument and inherent thermal noise, are demonstrated. The techniques are applied to study time series coming from both simulations and experiments associated with the nonequilibrium mechanical unfolding of titin's I27 domain. The estimated models can be used for several purposes, (1) detect dynamical signatures of "rare events" by analyzing the effective diffusion and force as a function of the monitored observable, (2) quantify the influence that conformational degrees of freedom, which are typically difficult to directly monitor experimentally, have on the dynamics of the monitored observable, (3) quantitatively compare the inherent thermal noise to other noise sources, for example, instrument noise, variation induced by conformational heterogeneity, and so forth, (4) simulate random quantities associated with repeated experiments, and (5) apply pathwise, that is, trajectory-wise, hypothesis tests to assess the goodness-of-fit of the models and even detect conformational transitions in noisy signals. These items are all illustrated with several examples.
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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.