Literature DB >> 18518359

Optimized free energies from bidirectional single-molecule force spectroscopy.

David D L Minh1, Artur B Adib.   

Abstract

An optimized method for estimating path-ensemble averages using data from processes driven in opposite directions is presented. Based on this estimator, bidirectional expressions for reconstructing free energies and potentials of mean force from single-molecule force spectroscopy-valid for biasing potentials of arbitrary stiffness-are developed. Numerical simulations on a model potential indicate that these methods perform better than unidirectional strategies.

Mesh：

Year:  2008        PMID： 18518359      PMCID： PMC2504746          DOI： 10.1103/PhysRevLett.100.180602

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN： 0031-9007            Impact factor:   9.161


  15 in total

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4.  Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods.

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Journal:  Phys Rev Lett       Date:  2003-10-02       Impact factor: 9.161

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6.  Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies.

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8.  Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality.

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Journal:  J Chem Phys       Date:  2006-02-14       Impact factor: 3.488

9.  Entropy-energy decomposition from nonequilibrium work trajectories.

Authors:  Jeremiah Nummela; Faten Yassin; Ioan Andricioaei
Journal:  J Chem Phys       Date:  2008-01-14       Impact factor: 3.488

10.  Calculation of the potential of mean force from nonequilibrium measurements via maximum likelihood estimators.

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Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2008-03-04
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  18 in total

1.  Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation.

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Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-24       Impact factor: 11.205

2.  Free energy profiles from single-molecule pulling experiments.

Authors:  Gerhard Hummer; Attila Szabo
Journal:  Proc Natl Acad Sci U S A       Date:  2010-11-22       Impact factor: 11.205

3.  Using stochastic models calibrated from nanosecond nonequilibrium simulations to approximate mesoscale information.

Authors:  Christopher P Calderon; Lorant Janosi; Ioan Kosztin
Journal:  J Chem Phys       Date:  2009-04-14       Impact factor: 3.488

4.  Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations.

Authors:  F Marty Ytreberg
Journal:  J Chem Phys       Date:  2009-04-28       Impact factor: 3.488

5.  Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages.

Authors:  David D L Minh; John D Chodera
Journal:  J Chem Phys       Date:  2009-10-07       Impact factor: 3.488

6.  Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments.

Authors:  John D Chodera; Vijay S Pande
Journal:  Phys Rev Lett       Date:  2011-08-23       Impact factor: 9.161

7.  Mapping Ryanodine Binding Sites in the Pore Cavity of Ryanodine Receptors.

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Review 8.  RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

Authors:  Jiří Šponer; Giovanni Bussi; Miroslav Krepl; Pavel Banáš; Sandro Bottaro; Richard A Cunha; Alejandro Gil-Ley; Giovanni Pinamonti; Simón Poblete; Petr Jurečka; Nils G Walter; Michal Otyepka
Journal:  Chem Rev       Date:  2018-01-03       Impact factor: 60.622

9.  Quantifying multiscale noise sources in single-molecule time series.

Authors:  Christopher P Calderon; Nolan C Harris; Ching-Hwa Kiang; Dennis D Cox
Journal:  J Phys Chem B       Date:  2009-01-08       Impact factor: 2.991

10.  Gaussian-mixture umbrella sampling.

Authors:  Paul Maragakis; Arjan van der Vaart; Martin Karplus
Journal:  J Phys Chem B       Date:  2009-04-09       Impact factor: 2.991
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