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Topic: Jarzynski equality

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	The Nonequilibrium Thermodynamics of Small Systems - Physics Today July 2005
		Jarzynski's result—and Crooks's generalization as well—applies to systems that start at equilibrium and are then driven out of equilibrium by some external influence.
		As described in the text, the Jarzynski equality (JE) relates the change ΔG in free energy of two equilibrium states to an appropriate work average calculated with an irreversible path.
		In the Jarzynski scenario, and also in Crooks's generalized FT, the system is initially in thermal equilibrium but then driven out of equilibrium by the action of an external agent.
	www.physicstoday.org /vol-58/iss-7/p43.html (3668 words)

	Jarzynski equality - Wikipedia, the free encyclopedia
		The Jarzynski equality (JE) is an equation in statistical mechanics that relates free energy differences between two equilibrium states and non-equilibrium processes.
		Here k is the Boltzmann constant and T is the temperature of the system in the equilibrium state A (or, equivalently, the temperature of the heat reservoir with which the system was thermalized before the process took place).
		The Jarzynski equality actually encompasses more general scenarios where the final state of the system is out of equilibrium.
	en.wikipedia.org /wiki/Jarzynski_equality (529 words)

	Fluctuation theorem - Wikipedia, the free encyclopedia
		For rather obvious reasons this equality is called the Second Law Inequality [Searles and Evans, Aust J Chem, 57, 1119 (2004)].
		When this is done the so-called Jarzynski equality or nonequilibrium work relation, can be derived.
		Jarzynski equality - another nonequilibrium equality closely related to the fluctuation theorem and to the second law of thermodynamics
	en.wikipedia.org /wiki/Fluctuation_Theorem (1425 words)

	Citebase - A Quantum Analogue of the Jarzynski Equality (Site not responding. Last check: 2007-10-16)
		A quantum analogue of the Jarzynski equality is constructed.
		This equality connects an ensemble average of exponentiated work with the Helmholtz free-energy difference in a nonequilibrium switching process subject to a thermal heat bath.
		We derive quantum analogues of Jarzynski's relations, and discuss two applications, namely, a derivation of the law of entropy increase for general compound systems, and a preliminary analysis of heat transfer between two quantum systems at different temperatures.
	www.citebase.org /cgi-bin/citations?id=oai:arXiv.org:cond-mat/0007456 (957 words)

	ScienceWeek
		The path integral proof of this identity found in Jarzynski's Physical Review E paper (2) is accessible and clear, and a broader setting and more general proof were subsequently published by Crooks (3).
		If the experiment is done at constant temperature and pressure, then the free energy obtained from the generalized Jarzynski equality is the Gibbs free energy rather than the Helmholtz free energy in the original identity (4).
		Jarzynski points out that Hummer and Szabo have translated this abstract notion into a concrete proposal for an experimental method of measuring the properties of molecules.
	www.scienceweek.com /2003/sc031205-5.htm (1296 words)

	The OpenScience Project » The Jarzynski equality
		Jarzynski has a brief commentary in PNAS that describes it, but the major result is this equation:
		The conventional wisdom is that the equality is reserved for a special kind of driving that is done infinitely slowly (i.e.
		The best basic description of Jarzynski’s Equality we’ve found is in a wonderful article by Gerhard Hummer and Attila Szabo that relates the Equality to concepts like atomic force microscopy and steered molecular dynamics.
	www.openscience.org /blog/?p=103 (565 words)

	Biophysics seminar - 10/05/2005 - Nanoscale Biological Physics: From DNA Nanoparticle Assemblies to Protein ... (Site not responding. Last check: 2007-10-16)
		We have also explored the application of Jarzynski's equality to determining protein unfolding energies using single-molecule atomic force microscopy.
		Jarzynski's equality allows the determination of equilibrium properties from nonequilibrium measurements such as forced unfolding of single-molecules.
		Dynamic force spectroscopy of the I27 domain of human cardiac titin, a giant muscle protein responsible for the elasticity of the human heart, was performed, and the free energy curves of unfolding of titin were obtained using Jarzynski's estimator.
	www.physics.ohio-state.edu /~bio/ab10052005.html (200 words)

	ScienceWeek
		The path integral proof of this identity found in Jarzynski's Physical Review E paper (2) is accessible and clear, and a broader setting and more general proof were subsequently published by Crooks (3).
		If the experiment is done at constant temperature and pressure, then the free energy obtained from the generalized Jarzynski equality is the Gibbs free energy rather than the Helmholtz free energy in the original identity (4).
		Jarzynski points out that Hummer and Szabo have translated this abstract notion into a concrete proposal for an experimental method of measuring the properties of molecules.
	scienceweek.com /2003/sc031205-5.htm (1296 words)

	APS - 2005 APS March Meeting - Event - An Experimental Test of Jarzynski's Equality on Free Energy of Protein ... (Site not responding. Last check: 2007-10-16)
		We performed an experimental test of Jarzynski's equality on the mechanical unfolding of a giant protein, human cardiac titin.
		Jarzynski's estimator relates the free energy difference ($\Delta G$) between two equilibrium states and the work performed in switching between those states.
		We found that Jarzynski's equality results in a good estimate of protein unfolding free energy from non-equilibrium measurements.
	meetings.aps.org /Meeting/MAR05/Event/22169 (142 words)

	CHARMM Forums: How to calculate free energy of binding by Jarzynski's equality?
		I am interested in calculating the free energy of binding of a ligand by Jarzynski's equality, in which the complex is slowly pulled apart and the work done is taken as the free energy of binding, as Zhang et al.
		I see that the command PULL could be used to specify a pulling force, and the pulled distance could presumably be obtained by COOR DIFF for each trajectory, but I don't see how to compute the sum of the dot products between the two over all the atoms for each trajectory.
		After posing my question, it occured to me that the calculation might be done by writing the pulling distances (from COOR DIFF) to an external file and using the SYSTEM command to invoke a simple user program which would calculate the incremental work for each successive trajectory.
	www.charmm.org /ubbthreads/showflat.php?Cat=0&Number=9960&Main=9958 (333 words)

	Equilibrium Information from Nonequilibrium Measurements (Site not responding. Last check: 2007-10-16)
		Excerpt:andnbsp;Recent advances in statistical mechanical theory can be used to solve a fundamental problem in experimental thermodynamics.
		In 1997, Jarzynski proved an equality relating the irreversible work to the equilibrium free energy difference, G. This remarkable theoretical result states that it is possible to obtain equilibrium thermodynamic parameters from processes carried out arbitrarily far from equilibrium.
		We test Jarzynski's equality by mechanically stretching a single molecule of RNA reversibly and irreversibly between two conformations.
	www.comdig.org /print_article.php?id_article=6164 (104 words)

	GCC for Nanobiology
		He has studied the use of Jarzynski’s equality in his analysis as the theoretical tool that will provide the connection between the irreversible work performed in the non-equilibrium AFM pulling experiments and the thermodynamic free energies for protein unfolding.
		However, to apply Jarzynski’s equality to these experiments, we must first fully understand the equality’s behavior with respect to key experimental parameters.
		Specifically, at what pulling velocity free energy estimates using Jarzynski’s equality begin to diverge.
	cohesion.rice.edu /centersandinst/gcc/gccn_about.cfm?doc_id=9061 (271 words)

	2367-2370 (Site not responding. Last check: 2007-10-16)
		A quantum analogue of the Jarzynski equality is constructed.
		This equality connects an ensemble average of exponentiated work with the Helmholtz free-energy difference in a nonequilibrium switching process subject to a thermal heat bath.
		To confirm its validity in a practical situation, we also investigate an open quantum system that is a spin 1/2 system with a scanning magnetic field interacting with a thermal heat bath.
	jpsj.ipap.jp /link?JPSJ/69/2367 (171 words)

	Molecules off equilibrium : Jarzynski identity
		Flaw of Jarzynski's equality when applied to systems with several degrees of freedom
		Breakdown of the Jarzynski relation for an adiabatic stretching of an isotropic spring
		Unified treatment of the quantum fluctuation theorem and the Jarzynski equality in terms of microscopic reversibility
	www.fzu.cz /~slanina/bookmark_files/bkm1-2.html (691 words)

	Building Blocks for Biobots \| Science Beat
		Using optical tweezers, Bustamante, Liphardt, and their colleagues performed pioneering experiments on the mechanical unfolding of RNA molecules, which established that a mathematical relation known as the Jarzynski Equality is applicable in exploring how energy states govern the ways large biological molecules fold.
		A bead fluctuating in an optical trap balances the frictional force of the water through which it moves and the optical forces holding it in the trap; at different speeds, these fluctuations constitute different nonequilibrium steady states.
		The results of the study showed that the Jarzynski Equality can be used to recover thermodynamic information about nanoscale systems previously thought inaccessible, effectively extending thermodynamics into the realm of living things — including biobots.
	www.lbl.gov /Science-Articles/Archive/sb/Aug-2004/2_biobots.html (1359 words)

	MIT Chemistry: Robert J. Silbey
		Coherence in the B800 Ring of Purple Bacteria LH2, Y. Cheng and R. Silbey, Phys.
		Ordering of Limits in the Jarzynski Equality, S. Pressé and R. Silbey, J.
		Memory effects on the convergence properties of the Jarzynski equality, S.Pressé and R. Silbey, Phys.
	web.mit.edu /chemistry/www/faculty/silbey.html (367 words)

	Department of Bioengineering:
		The development of single-molecule techniques to study protein funciton at the molecular level has expanded our understanding on the details of how biology and medicine function at the macroscopic level.
		Her research focuses on the mechanical properties of titin, with an emphasis on applying Jarzynski's equality to determine the free energy of titin unfolding.
		"Protein Unfolding Energy Determined by Jarzynski's Equality." The 2006 APS March Meeting, Baltimore, MD. (13--17 March 2006) With N. Harris, L. Li, Y. Song, and W. Liao.
	bioe.rice.edu /FacultyDetail.cfm?RiceID=276 (1103 words)

	[No title]
		Recently, it has been shown that time-reversibility of deterministic or stochastic dynamics implies relations between fluctuation and dissipation in systems far from equilibrium, taking the form of intriguing equalities: the fluctuation theorem, the Jarzynski equality, and the Crooks relation.
		In this talk, I will attempt to explain these relations using simple kinetic models which can be solved analytically.
		71 (2005), 879, "Jarzynski equality for the Jepsen gas" -- 5_`‘’”•èéð ñ õìÝõËÝ¾Ýõ°¬°¡h-/h2QSh2QSCJaJh2QSh2QSCJOJQJ^JaJh2QSh2QS0JCJ aJ #jh2QSh2QSCJ UaJ jh2QSh2QSCJ UaJ h2QSh2QSaJh2QSh2QSCJ aJ 5_”•èéõz ì í ð ñ úúúñìúñúúúúúêgd2QS 7$8$H$gd2QSgd2QS ñ ý50P:p2QS°Ð/ °à=!°"°# $ %°°Ð°Ð Ð»DÐÉêyùºÎªK©kawai@uab.eduàÉêyùºÎªK©*mailto:kawai@uab.edu@@ñÿ@ NormalCJ_HaJmH sH tH V@V 2QS Heading 3$¤ð¤
	heisenberg.phy.uab.edu /News_Events/ColloquimHistory/Abstracts/kawai_9Jan06.doc (174 words)

	Software
		Data from umbrella sampling simulations can be combined by the weighted histogram analysis method (WHAM) [1-3].
		Nonequilibrium pulling experiments, including single-molecule force spectroscopy and steered molecular dynamics simulations, can be interpreted using Jarznyski's Equality [4-5].
		Hummer and Szabo's used Jarzynski's Equality to calculate potentials of mean force from such experiments [6-7].
	mccammon.ucsd.edu /~dminh/software/index.html (464 words)

	Department of Mathematics (Site not responding. Last check: 2007-10-16)
		LECTURE 2: Chaos, Lyapunov exponents and transport coefficients
		LECTURE 3: The Fluctuation Theorem, Jarzynski Equality and Crooks Relations - a dynamical resolution of the "Laws" of Thermodynamics
		Some excerpts from the popular press are available by clicking here.
	www.maths.mq.edu.au /talks/evans.html (106 words)

	Equilibrium Information from Nonequilibrium Measurements in an Experimental Test of Jarzynski's Equality -- Liphardt et ... (Site not responding. Last check: 2007-10-16)
		Recent advances in statistical mechanical theory can be used to solve a fundamental problem in experimental thermodynamics.
		In 1997, Jarzynski proved an equality relating the irreversible
		Trepagnier, C. Jarzynski, F. Ritort, G. Crooks, C. Bustamante, and J. Liphardt (2004)
	www.sciencemag.org /cgi/content/abstract/296/5574/1832 (631 words)

	CiteULike: ewalton's steered (Site not responding. Last check: 2007-10-16)
		Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality
		posted to bibtex-import dynamics jarzynski md molecular steered by ewalton as
		posted to bibtex-import dynamics jarzynski molecular steered by ewalton as
	www.citeulike.org /user/ewalton/tag/steered (158 words)

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