Bayesian Estimates of Free Energies from Nonequilibrium Work Data in the Presence of Instrument Noise

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The Jarzynski equality and the fluctuation theorem relate equilibrium free energy differences to nonequilibrium measurements of the work. These relations extend to single-molecule experiments that have probed the finite-time thermodynamics of proteins and nucleic acids. The effects of experimental error and instrument noise have not been considered previously. Here, we present a Bayesian formalism for estimating free energy changes from nonequilibrium work measurements that compensates for instrument noise and combines data from multiple driving protocols. We reanalyze a recent set of experiments in which a single RNA hairpin is unfolded and refolded using optical tweezers at three different rates. Interestingly, ... continued below

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Maragakis, Paul; Ritort, Felix; Bustamante, Carlos; Karplus, Martin & Crooks, Gavin E. July 8, 2008.

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The Jarzynski equality and the fluctuation theorem relate equilibrium free energy differences to nonequilibrium measurements of the work. These relations extend to single-molecule experiments that have probed the finite-time thermodynamics of proteins and nucleic acids. The effects of experimental error and instrument noise have not been considered previously. Here, we present a Bayesian formalism for estimating free energy changes from nonequilibrium work measurements that compensates for instrument noise and combines data from multiple driving protocols. We reanalyze a recent set of experiments in which a single RNA hairpin is unfolded and refolded using optical tweezers at three different rates. Interestingly, the fastest and farthest-from-equilibrium measurements contain the least instrumental noise and, therefore, provide a more accurate estimate of the free energies than a few slow, more noisy, near-equilibrium measurements. The methods we propose here will extend the scope of single-molecule experiments; they can be used in the analysis of data from measurements with atomic force microscopy, optical, and magnetic tweezers

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  • Journal Name: Journal of Chemical Physics; Journal Volume: 129; Related Information: Journal Publication Date: 2008

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  • Report No.: LBNL-62739
  • Grant Number: DE-AC02-05CH11231
  • Grant Number: GM 32543
  • Office of Scientific & Technical Information Report Number: 953227
  • Archival Resource Key: ark:/67531/metadc926773

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  • July 8, 2008

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  • Nov. 13, 2016, 7:26 p.m.

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  • Nov. 18, 2016, 2:19 p.m.

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Maragakis, Paul; Ritort, Felix; Bustamante, Carlos; Karplus, Martin & Crooks, Gavin E. Bayesian Estimates of Free Energies from Nonequilibrium Work Data in the Presence of Instrument Noise, article, July 8, 2008; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc926773/: accessed September 20, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.