Evaluation of free energy landscapes from manipulation experiments

@article{Imparato2006EvaluationOF,
  title={Evaluation of free energy landscapes from manipulation experiments},
  author={Alberto Imparato and Luca Peliti},
  journal={Journal of Statistical Mechanics: Theory and Experiment},
  year={2006},
  volume={2006},
  pages={03005}
}
  • A. Imparato, L. Peliti
  • Published 24 January 2006
  • Computer Science
  • Journal of Statistical Mechanics: Theory and Experiment
A fluctuation relation, which is an extended form of the Jarzynski equality, is introduced and discussed. We show how to apply this relation in order to evaluate the free energy landscapes of simple systems. These systems are manipulated by varying the external field coupled with a systems' internal characteristic variable. Two different manipulation protocols are considered here: in the first case the external field is a linear function of time; in the second case it is a periodic function of… 
View PDF on arXiv
15 Citations

15 Citations

Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics
TLDR
The Jarzynski identity and the Crooks fluctuation theorem are reviewed and various algorithms building on these relations are surveyed, focusing on statistical efficiency and practical issues arising in their implementation and the analysis of the results.
Reconstruction of Energy Surfaces from Friction Force Microscopy Measurements with the Jarzynski Equality
Free energy is one of the most fundamental thermodynamic functions, determining relative phase stability and serving as a generating function for other thermodynamic quantities. The calculation of…
Analyzing friction forces with the Jarzynski equality
We investigate the applicability of the Jarzynski equality for reconstructing the energy landscape from force measurements obtained in single molecular unbinding and friction experiments. We…
Protein mechanical unfolding: a model with binary variables.
TLDR
The extended Jarzynski equality is exploited to investigate the possibility of reconstructing the free energy landscape of proteins with pulling experiments, and the kinetic parameters characterizing the protein unfolding agree nicely with experimental results, when these are available.
Heat flow in chains driven by thermal noise
We consider the large deviation function for a classical harmonic chain composed of N particles driven at the end points by heat reservoirs, first derived in the quantum regime by Saito and Dhar…
Measurement of work in single-molecule pulling experiments.
TLDR
This work quantifies the error that is made in a free energy estimate by means of the Jarzynski equality when the accumulated work expended on the whole system is erroneously replaced by the work transferred to the subsystem consisting of the sole molecular construct.
Fluctuation theorems for stochastic dynamics
Fluctuation theorems make use of time reversal to make predictions about entropy production in many-body systems far from thermal equilibrium. Here we review the wide variety of distinct, but…
Ising-like model for protein mechanical unfolding.
TLDR
The mechanical unfolding of proteins is studied by extending the Wako-Saitô-Muñoz-Eaton model, and the free energy landscape of the PIN1 as a function of the molecule length is computed.
The physics of pulling polyproteins: a review of single molecule force spectroscopy using the AFM to study protein unfolding.
TLDR
This review will introduce the technique of single molecule force spectroscopy using the atomic force microscope (AFM), with particular focus on its application to study proteins.
Sponsoring Organization.
TLDR
A computationally efficient all-atom model for proteins is presented, variants of which are used to perform Monte Carlo simulations in the other papers, and the effect of mutations on the folding properties of the peptide Aβ42 from Alzheimer’s disease is investigated.
...
...

References

SHOWING 1-10 OF 36 REFERENCES
Probing molecular free energy landscapes by periodic loading.
TLDR
A new method for obtaining the full profile of a molecule's free energy profile by introducing a periodic ramp and using Jarzynski's relation for obtaining equilibrium quantities from nonequilibrium data is proposed.
Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements
TLDR
The large N limit is derived for the Jarzynski estimator bias, variance, and mean square error that is correct for arbitrary perturbations and shows that, for near-equilibrium switching, the Jarzyk estimator is always superior to the mean work estimator and is even superior toThe fluctuation–dissipation estimator for small N.
A two-state kinetic model for the unfolding of single molecules by mechanical force
TLDR
The model yields estimates for parameters that characterize the unfolding kinetics under force in agreement with those obtained in recent experimental results, and a general equation for the minimum number of repeated experiments needed to obtain an equilibrium free energy, to within kBT, from nonequilibrium experiments is obtained.
Work-probability distribution in systems driven out of equilibrium.
  • A. Imparato, L. Peliti
  • Physics
    Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2005
TLDR
It is shown that the work probability distribution can be represented by a path integral, which is dominated by "classical" paths in the large system size limit, and compared with simulated manipulation of mean-field systems.
Path-ensemble averages in systems driven far from equilibrium
The Kawasaki nonlinear response relation, the transient fluctuation theorem, and the Jarzynski nonequilibrium work relation are all expressions that describe the behavior of a system that has been…
Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties.
Work and heat fluctuations in two-state systems: a trajectory thermodynamics formalism
Two-state models provide phenomenological descriptions of many different systems, ranging from physics to chemistry and biology. We investigate work fluctuations in an ensemble of two-state systems…
Work distribution and path integrals in general mean-field systems
We consider a mean-field system described by a general collective variable M, driven out of equilibrium by the manipulation of a parameter μ. Given a general dynamics compatible with its equilibrium…
Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach
It has recently been shown that the Helmholtz free energy difference between two equilibrium configurations of a system may be obtained from an ensemble of finite-time (nonequilibrium) measurements…
Distribution of work in isothermal nonequilibrium processes.
  • T. Speck, U. Seifert
  • Physics, Mathematics
    Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2004
TLDR
It is shown that the distribution of work required to drive the system from an initial equilibrium state to another is Gaussian for slow but finite driving by projection method techniques exploiting a small parameter defined as the switching rate between the two states of the system.
...
...