Literature DB >> 19045140

Nonequilibrium fluctuation-dissipation theorem of Brownian dynamics.

L Y Chen1.   

Abstract

Studying the Brownian motion of a system driven by an external control from one macroscopic state to another macroscopic state, this paper presents the derivation of a nonlinear fluctuation-dissipation theorem (FDT). The new FDT relates the nonequilibrium work to the equilibrium free-energy difference in a very simple manner. It is valid wherever the Brownian dynamics is applicable. It recovers the well-known Crooks fluctuation theorem (CFT) within the quasiequilibrium regime where the dissipative work is nearly zero. It will also be shown that the CFT's fundamental assumption of microscopic reversibility is not obeyed in experiments such as mechanically unfolding biological molecules, in which the external driving forces depend on the system's coordinates.

Mesh:

Year:  2008        PMID: 19045140      PMCID: PMC2671654          DOI: 10.1063/1.2992153

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


  9 in total

1.  Free energy reconstruction from nonequilibrium single-molecule pulling experiments.

Authors:  G Hummer; A Szabo
Journal:  Proc Natl Acad Sci U S A       Date:  2001-03-27       Impact factor: 11.205

2.  Reversible unfolding of single RNA molecules by mechanical force.

Authors:  J Liphardt; B Onoa; S B Smith; I Tinoco; C Bustamante
Journal:  Science       Date:  2001-04-27       Impact factor: 47.728

3.  Scalable molecular dynamics with NAMD.

Authors:  James C Phillips; Rosemary Braun; Wei Wang; James Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D Skeel; Laxmikant Kalé; Klaus Schulten
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

4.  Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies.

Authors:  D Collin; F Ritort; C Jarzynski; S B Smith; I Tinoco; C Bustamante
Journal:  Nature       Date:  2005-09-08       Impact factor: 49.962

5.  Work-probability distribution in systems driven out of equilibrium.

Authors:  A Imparato; L Peliti
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-10-14

Review 6.  Comparison of free energy methods for molecular systems.

Authors:  F Marty Ytreberg; Robert H Swendsen; Daniel M Zuckerman
Journal:  J Chem Phys       Date:  2006-11-14       Impact factor: 3.488

7.  Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality.

Authors:  Ioan Kosztin; Bogdan Barz; Lorant Janosi
Journal:  J Chem Phys       Date:  2006-02-14       Impact factor: 3.488

8.  Failure of the work-Hamiltonian connection for free-energy calculations.

Authors:  Jose M G Vilar; J Miguel Rubi
Journal:  Phys Rev Lett       Date:  2008-01-16       Impact factor: 9.161

9.  On the Crooks fluctuation theorem and the Jarzynski equality.

Authors:  L Y Chen
Journal:  J Chem Phys       Date:  2008-09-07       Impact factor: 3.488

  9 in total
  19 in total

1.  Erythritol predicted to inhibit permeation of water and solutes through the conducting pore of P. falciparum aquaporin.

Authors:  Liao Y Chen
Journal:  Biophys Chem       Date:  2015-01-14       Impact factor: 2.352

2.  In silico experiments of single-chain antibody fragment against drugs of abuse.

Authors:  Guodong Hu; L Y Chen
Journal:  Biophys Chem       Date:  2010-10-18       Impact factor: 2.352

3.  Interaction between functionalized gold nanoparticles in physiological saline.

Authors:  Shada A Alsharif; Liao Y Chen; Alfredo Tlahuice-Flores; Robert L Whetten; Miguel Jose Yacaman
Journal:  Phys Chem Chem Phys       Date:  2014-03-07       Impact factor: 3.676

4.  Free-energy landscape of glycerol permeation through aquaglyceroporin GlpF determined from steered molecular dynamics simulations.

Authors:  L Y Chen
Journal:  Biophys Chem       Date:  2010-06-11       Impact factor: 2.352

5.  Insights into the mechanisms of the selectivity filter of Escherichia coli aquaporin Z.

Authors:  Guodong Hu; Liao Y Chen; Jihua Wang
Journal:  J Mol Model       Date:  2012-03-06       Impact factor: 1.810

6.  Exploring the free-energy landscapes of biological systems with steered molecular dynamics.

Authors:  L Y Chen
Journal:  Phys Chem Chem Phys       Date:  2011-02-25       Impact factor: 3.676

7.  Molecular dynamics study of human carbonic anhydrase II in complex with Zn(2+) and acetazolamide on the basis of all-atom force field simulations.

Authors:  Thierry O Wambo; Liao Y Chen; Stanton F McHardy; Andrew T Tsin
Journal:  Biophys Chem       Date:  2016-05-18       Impact factor: 2.352

8.  Application of the Brown dynamics fluctuation-dissipation theorem to the study of Plasmodium berghei transporter protein PbAQP.

Authors:  Liao Y Chen
Journal:  Front Phys       Date:  2020-04-17

9.  Insights into scFv:drug binding using the molecular dynamics simulation and free energy calculation.

Authors:  Guodong Hu; Qinggang Zhang; L Y Chen
Journal:  J Mol Model       Date:  2010-11-26       Impact factor: 1.810

10.  Computing Protein-Protein Association Affinity with Hybrid Steered Molecular Dynamics.

Authors:  Roberto A Rodriguez; Lili Yu; Liao Y Chen
Journal:  J Chem Theory Comput       Date:  2015-09-08       Impact factor: 6.006

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