Subject: Re: CCL:Jarzynski's equality for free energy

From: Hans Martin Senn <senn.-at-.mpi-muelheim.mpg.de>
Date: Thu, 22 Apr 2004 17:45:54 +0200

Dear Masakatsu

This is a somewhat unstructered list of papers dealing with Jarzynski's  
equality. There are several articles dealing with its application to  
biomolecular systems.

[1]	G. E. Crooks,  Nonequilibrium Measurements of Free Energy  
Differences for Microscopically Reversible Markovian Systems , J. Stat.  
Phys. 1998, 90, 1481 1487.
[2]	G. E. Crooks,  Entropy production fluctuation theorem and the  
nonequilibrium work relation for free energy differences , Phys. Rev. E  
1999, 60, 2721 2726.
[3]	G. E. Crooks,  Path-ensemble averages in systems driven far from  
equilibrium , Phys. Rev. E 2000, 61, 2361 2366.
[4]	D. A. Hendrix, C. Jarzynski,  A  fast-growth  method of computing  
free energy differences , J. Chem. Phys 2001, 114, 5974 5981.
[5]	G. Hummer,  Fast-growth thermodynamic integration: Error and  
efficiency analysis , J. Chem. Phys 2001, 114, 7330 7337.
[6]	G. Hummer, A. Szabo,  Free energy reconstruction from  
nonequilibrium single-molecule pulling experiments , Proc. Natl. Acad.  
Sci. USA 2001, 98, 3658 3661.
[7]	C. Jarzynski,  Nonequilibrium Equality for Free Energy  
Differences , Phys. Rev. Lett. 1997, 78, 2690 2693.
[8]	C. Jarzynski,  Equilibrium free-energy differences from  
nonequilibrium measurements: A master-equation approach , Phys. Rev. E  
1997, 56, 5018 5035.
[9]	C. Jarzynski,  Equilibrium free energies from nonequilibrium  
processes , Acta Physica Polonica B 1998, 29, 1609 1622.
[10]	M. X. Jensen, S. Park, E. Tajkhorshid, K. Schulten,  Energetics of  
glycerol conduction through aquaglyceroporin GlpF , Proc. Natl. Acad.  
Sci. USA 2002, 99, 6731 6736.
[11]	S. Park, F. Khalili-Araghi, E. Tajkhorshid, K. Schulten,  Free  
energy calculation from steered molecular dynamics simulations using  
Jarzynski s equality , J. Chem. Phys 2003, 119, 3559 3566.
* Hu, Yun, Hermans, Mol. Simul 2002, 28, 67.
* Hummer, Mol. Simul 2002, 28, 81.
* Zuckerman, Woolf, PRL 2002, 89, 180602-1.
* Zuckerman, Woolf, CPL 2002, 351, 445.
* Gore, Ritort, Bustamante, PNAS 2003, 100, 12564.
* Fox, PNAS 2003, 100, 12537.
* Park, Schulten, JCP 2004, 120, 5946.

Best wishes

Hans Martin

On 22 Apr 2004, at 07:19, Masakatsu Ito wrote:
> Hi CCLers,
>
> I am looking for reviews and articles about the free energy
> calculation of biomolecules. I have been impressed by Jarzynski's
> equality (Phys.Rev.Lett. 78, 2690 (1997)) which enables one to
> estimate free energy difference from an ensemble of short MD
> simulations. This implies that the estimation can be drastically
> accelerated by distributed computing.  But those MD simulations should
> start from equilibrium, and I am wondering how such initial conditions
> can be prepared for biomolecules. Because it is notoriously difficult
> to get an equilibrium ensemble of biomolecular structures.
>
> Thus I am very interested in the application of Jarzynski's equality
> to biomolecular processes. Could someone please give me some advice or
> point me to articles?
>
> Thanks in advance for any help.
> Kind Regards,
>
> Masakatsu Ito , Ph.D
>
> Nanotechnology Research Center
> FUJITSU LABORATORIES LTD.
> 10-1 Morinosato-Wakamiya, Atsugi 243-0197 Japan
> Phone : +81-46-250-8234  Fax : +81-46-250-8844
> E-mail m-ito.-at-.jp.fujitsu.com
........................................................................ 
.
Dr. Hans Martin Senn
Max-Planck-Institut f|r Kohlenforschung
Kaiser-Wilhelm-Platz 1                          Phone +49 (0)208 306  
2163
D-45470 M|lheim an der Ruhr                       Fax +49 (0)208 306  
2996
Germany                                   E-mail  
senn.-at-.mpi-muelheim.mpg.de