Literature DB >> 16711876

Rare events and the convergence of exponentially averaged work values.

Christopher Jarzynski1.   

Abstract

Equilibrium free energy differences are given by exponential averages of nonequilibrium work values; such averages, however, often converge poorly, as they are dominated by rare realizations. I show that there is a simple and intuitively appealing description of these rare but dominant realizations. This description is expressed as a duality between "forward" and "reverse" processes, and provides both heuristic insights and quantitative estimates regarding the number of realizations needed for convergence of the exponential average. Analogous results apply to the equilibrium perturbation method of estimating free energy differences. The pedagogical example of a piston and gas [R.C. Lua and A.Y. Grosberg, J. Phys. Chem. B 109, 6805 (2005)] is used to illustrate the general discussion.

Year:  2006        PMID: 16711876     DOI: 10.1103/PhysRevE.73.046105

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  24 in total

1.  Information Thermodynamics for Time Series of Signal-Response Models.

Authors:  Andrea Auconi; Andrea Giansanti; Edda Klipp
Journal:  Entropy (Basel)       Date:  2019-02-14       Impact factor: 2.524

2.  Density-dependent analysis of nonequilibrium paths improves free energy estimates.

Authors:  David D L Minh
Journal:  J Chem Phys       Date:  2009-05-28       Impact factor: 3.488

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.  Path integral analysis of Jarzynski's equality: analytical results.

Authors:  David D L Minh; Artur B Adib
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-02-18

5.  Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise.

Authors:  Paul Maragakis; Felix Ritort; Carlos Bustamante; Martin Karplus; Gavin E Crooks
Journal:  J Chem Phys       Date:  2008-07-14       Impact factor: 3.488

6.  Protein-protein interaction investigated by steered molecular dynamics: the TCR-pMHC complex.

Authors:  Michel A Cuendet; Olivier Michielin
Journal:  Biophys J       Date:  2008-07-11       Impact factor: 4.033

7.  Lead optimization mapper: automating free energy calculations for lead optimization.

Authors:  Shuai Liu; Yujie Wu; Teng Lin; Robert Abel; Jonathan P Redmann; Christopher M Summa; Vivian R Jaber; Nathan M Lim; David L Mobley
Journal:  J Comput Aided Mol Des       Date:  2013-09-26       Impact factor: 3.686

8.  Comparative energy measurements in single molecule interactions.

Authors:  W Liu; Vedrana Montana; Vladimir Parpura; U Mohideen
Journal:  Biophys J       Date:  2008-03-28       Impact factor: 4.033

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

Review 10.  Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding.

Authors:  Hagai Meirovitch; Srinath Cheluvaraja; Ronald P White
Journal:  Curr Protein Pept Sci       Date:  2009-06       Impact factor: 3.272

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