Literature DB >> 15268117

Single-ensemble nonequilibrium path-sampling estimates of free energy differences.

F Marty Ytreberg1, Daniel M Zuckerman.   

Abstract

We introduce a straightforward, single-ensemble, path sampling approach to calculate free energy differences based on Jarzynski's relation. For a two-dimensional "toy" test system, the new (minimally optimized) method performs roughly one hundred times faster than either optimized "traditional" Jarzynski calculations or conventional thermodynamic integration. The simplicity of the underlying formalism suggests the approach will find broad applicability in molecular systems.

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Year:  2004        PMID: 15268117     DOI: 10.1063/1.1760511

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  8 in total

1.  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

2.  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

3.  Optimized free energies from bidirectional single-molecule force spectroscopy.

Authors:  David D L Minh; Artur B Adib
Journal:  Phys Rev Lett       Date:  2008-05-06       Impact factor: 9.161

4.  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

5.  Enhanced Jarzynski free energy calculations using weighted ensemble.

Authors:  Nicole M Roussey; Alex Dickson
Journal:  J Chem Phys       Date:  2020-10-07       Impact factor: 3.488

6.  Transient probability currents provide upper and lower bounds on non-equilibrium steady-state currents in the Smoluchowski picture.

Authors:  Jeremy Copperman; David Aristoff; Dmitrii E Makarov; Gideon Simpson; Daniel M Zuckerman
Journal:  J Chem Phys       Date:  2019-11-07       Impact factor: 3.488

Review 7.  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

8.  An Information Theory Approach to Nonlinear, Nonequilibrium Thermodynamics.

Authors:  David M Rogers; Thomas L Beck; Susan B Rempe
Journal:  J Stat Phys       Date:  2011-10       Impact factor: 1.548

  8 in total

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