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Items: 1 to 20 of 174

1.

The free energy of expansion and contraction: treatment of arbitrary systems using the Jarzynski equality.

Davie SJ, Reid JC, Searles DJ.

J Chem Phys. 2012 May 7;136(17):174111. doi: 10.1063/1.4707348.

PMID:
22583214
2.

Entropy-energy decomposition from nonequilibrium work trajectories.

Nummela J, Yassin F, Andricioaei I.

J Chem Phys. 2008 Jan 14;128(2):024104. doi: 10.1063/1.2817332.

PMID:
18205440
3.

On the estimation of the free energy, from a single equilibrium statistical ensemble, via particle reinsertion.

Boulougouris GC.

J Phys Chem B. 2012 Jan 26;116(3):997-1006. doi: 10.1021/jp2036185. Epub 2012 Jan 13.

PMID:
22168469
4.

Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality.

West DK, Olmsted PD, Paci E.

J Chem Phys. 2006 Nov 28;125(20):204910.

PMID:
17144743
5.

Application of computer simulation free-energy methods to compute the free energy of micellization as a function of micelle composition. 1. Theory.

Stephenson BC, Stafford KA, Beers KJ, Blankschtein D.

J Phys Chem B. 2008 Feb 14;112(6):1634-40. doi: 10.1021/jp0727603. Epub 2008 Jan 17.

PMID:
18198856
6.

Estimation of free-energy differences from computed work distributions: an application of Jarzynski's equality.

Echeverria I, Amzel LM.

J Phys Chem B. 2012 Sep 13;116(36):10986-95. doi: 10.1021/jp300527q. Epub 2012 Aug 30.

PMID:
22849340
7.

A generalized free energy perturbation theory accounting for end states with differing configuration space volume.

Ullmann RT, Ullmann GM.

J Phys Chem B. 2011 Jan 27;115(3):507-21. doi: 10.1021/jp1093838. Epub 2010 Dec 22.

PMID:
21175142
8.
9.

Straightforward quantum-mechanical derivation of the Crooks fluctuation theorem and the Jarzynski equality.

Cohen D, Imry Y.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jul;86(1 Pt 1):011111. Epub 2012 Jul 9.

PMID:
23005372
10.

Escorted free energy simulations.

Vaikuntanathan S, Jarzynski C.

J Chem Phys. 2011 Feb 7;134(5):054107. doi: 10.1063/1.3544679.

PMID:
21303092
11.

Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes.

Goette M, Grubm├╝ller H.

J Comput Chem. 2009 Feb;30(3):447-56. doi: 10.1002/jcc.21073.

PMID:
18677708
12.

Good practices in free-energy calculations.

Pohorille A, Jarzynski C, Chipot C.

J Phys Chem B. 2010 Aug 19;114(32):10235-53. doi: 10.1021/jp102971x.

PMID:
20701361
13.

Unified treatment of the quantum fluctuation theorem and the Jarzynski equality in terms of microscopic reversibility.

Monnai T.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Aug;72(2 Pt 2):027102. Epub 2005 Aug 9.

PMID:
16196752
14.

On the decomposition of free energies.

Brady GP, Szabo A, Sharp KA.

J Mol Biol. 1996 Oct 25;263(2):123-5.

PMID:
8913295
15.

Application of computer simulation free-energy methods to compute the free energy of micellization as a function of micelle composition. 2. Implementation.

Stephenson BC, Stafford KA, Beers KJ, Blankschtein D.

J Phys Chem B. 2008 Feb 14;112(6):1641-56. doi: 10.1021/jp072761v. Epub 2008 Jan 17.

PMID:
18198857
16.

Jarzynski equality: connections to thermodynamics and the second law.

Palmieri B, Ronis D.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Jan;75(1 Pt 1):011133. Epub 2007 Jan 31.

PMID:
17358136
17.

Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation.

Meirovitch H.

Curr Opin Struct Biol. 2007 Apr;17(2):181-6. Epub 2007 Mar 28. Review.

PMID:
17395451
18.
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20.

Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements.

Gore J, Ritort F, Bustamante C.

Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12564-9. Epub 2003 Oct 3.

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