Experimental free-energy measurements of kinetic molecular states using fluctuation theorems

@article{Alemany2012ExperimentalFM,
  title={Experimental free-energy measurements of kinetic molecular states using fluctuation theorems},
  author={Anna Alemany and Alessandro Mossa and Ivan Junier and Felix Ritort},
  journal={Nature Physics},
  year={2012},
  volume={8},
  pages={688-694}
}
Short-lived kinetic states between equilibria are difficult to access experimentally, despite being crucial in many dynamical processes. Single-molecule experiments demonstrate that an extended fluctuation relation allows extraction of the free energies of these metastable states under non-equilibrium conditions. 

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References

SHOWING 1-10 OF 32 REFERENCES

Recovery of free energy branches in single molecule experiments.

The approach is based on a fluctuation relation that is valid for dissipative transformations in partially equilibrated systems and uses optical tweezers to determine the free energy branches of the native and unfolded states of a two-state molecule as a function of the pulling control parameter.

Experimental validation of free-energy-landscape reconstruction from non-equilibrium single-molecule force spectroscopy measurements

The energy-landscape theory is an important tool for investigating how proteins fold. Hummer and Szabo conceived a simple method for constructing folding-energy landscapes from single-molecule

Free energy reconstruction from nonequilibrium single-molecule pulling experiments

  • G. HummerA. Szabó
  • Physics
    Proceedings of the National Academy of Sciences of the United States of America
  • 2001
It is shown how equilibrium free energy profiles can be extracted rigorously from repeated nonequilibrium force measurements on the basis of an extension of Jarzynski's remarkable identity between free energies and the irreversible work.

Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods.

It is demonstrated that the acceptance ratio method yields the lowest variance for any estimator of the free energy which is unbiased in the limit of large numbers of measurements.

Measurement of work in single-molecule pulling experiments.

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.

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

It is shown that the Crooks fluctuation theorem can be used to determine folding free energies for folding and unfolding processes occurring in weak as well as strong nonequilibrium regimes, thereby providing a test of its validity under such conditions.

Dynamic force spectroscopy of DNA hairpins: I. Force kinetics and free energy landscapes

This work designs a specific DNA hairpin sequence that shows two-state cooperative folding under mechanical tension and carried out pulling experiments using optical tweezers to test the theory and shows how to determine the parameters that characterize the molecular free energy landscape of such sequences from rupture force kinetic studies.

Experimental demonstration of information-to-energy conversion and validation of the generalized Jarzynski equality

Feedback mechanisms such as the ‘demon’ in Maxwell’s well-known thought experiment can, in principle, enable the transformation of information into energy, without violating the second law of

Folding and unfolding of a triple-branch DNA molecule with four conformational states

A useful method to identify permanently frayed molecules by estimating the number of opened base-pairs from the measured force jump values is found, due to the specific design of the molecule.

A differential fluctuation theorem.

An approach for measuring conformational free energy differences is devised, and its applicability to the analysis of molecular dynamics simulations is demonstrated by estimating the free energy difference between two conformers of the alanine dipeptide model system.