Literature DB >> 17930381

Measuring thermodynamic length.

Gavin E Crooks1.   

Abstract

Thermodynamic length is a metric distance between equilibrium thermodynamic states. Among other interesting properties, this metric asymptotically bounds the dissipation induced by a finite time transformation of a thermodynamic system. It is also connected to the Jensen-Shannon divergence, Fisher information, and Rao's entropy differential metric. Therefore, thermodynamic length is of central interest in understanding matter out of equilibrium. In this Letter, we will consider how to define thermodynamic length for a small system described by equilibrium statistical mechanics and how to measure thermodynamic length within a computer simulation. Surprisingly, Bennett's classic acceptance ratio method for measuring free energy differences also measures thermodynamic length.

Year:  2007        PMID: 17930381     DOI: 10.1103/PhysRevLett.99.100602

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  22 in total

1.  Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation.

Authors:  Jerome P Nilmeier; Gavin E Crooks; David D L Minh; John D Chodera
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-24       Impact factor: 11.205

2.  The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.

Authors:  Andrea Rizzi; Travis Jensen; David R Slochower; Matteo Aldeghi; Vytautas Gapsys; Dimitris Ntekoumes; Stefano Bosisio; Michail Papadourakis; Niel M Henriksen; Bert L de Groot; Zoe Cournia; Alex Dickson; Julien Michel; Michael K Gilson; Michael R Shirts; David L Mobley; John D Chodera
Journal:  J Comput Aided Mol Des       Date:  2020-01-27       Impact factor: 3.686

3.  Sloppiness in spontaneously active neuronal networks.

Authors:  Dagmara Panas; Hayder Amin; Alessandro Maccione; Oliver Muthmann; Mark van Rossum; Luca Berdondini; Matthias H Hennig
Journal:  J Neurosci       Date:  2015-06-03       Impact factor: 6.167

4.  Thermodynamic efficiency of contagions: a statistical mechanical analysis of the SIS epidemic model.

Authors:  Nathan Harding; Ramil Nigmatullin; Mikhail Prokopenko
Journal:  Interface Focus       Date:  2018-10-19       Impact factor: 3.906

5.  Phase Transitions in Spatial Connectivity during Influenza Pandemics.

Authors:  Nathan Harding; Richard Spinney; Mikhail Prokopenko
Journal:  Entropy (Basel)       Date:  2020-01-22       Impact factor: 2.524

6.  Energy dissipation bounds for autonomous thermodynamic cycles.

Authors:  Samuel J Bryant; Benjamin B Machta
Journal:  Proc Natl Acad Sci U S A       Date:  2020-02-04       Impact factor: 11.205

7.  Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors.

Authors:  David D L Minh
Journal:  J Comput Chem       Date:  2019-08-09       Impact factor: 3.376

8.  Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion.

Authors:  Christopher L McClendon; Lan Hua; Abriela Barreiro; Matthew P Jacobson
Journal:  J Chem Theory Comput       Date:  2012-04-13       Impact factor: 6.006

9.  Biomolecular Simulations under Realistic Macroscopic Salt Conditions.

Authors:  Gregory A Ross; Ariën S Rustenburg; Patrick B Grinaway; Josh Fass; John D Chodera
Journal:  J Phys Chem B       Date:  2018-05-31       Impact factor: 2.991

10.  Cancer biomarker discovery: the entropic hallmark.

Authors:  Regina Berretta; Pablo Moscato
Journal:  PLoS One       Date:  2010-08-18       Impact factor: 3.240

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.