Related Experiment Video
Updated: Jul 4, 2026
06:45
Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope
Published on: February 28, 2019
Optimized free energies from bidirectional single-molecule force spectroscopy
1Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA. daveminh@gmail.com
Physical Review Letters
|June 4, 2008
Summary
This study introduces an optimized method for analyzing bidirectional experimental data to improve path-ensemble averages. The new bidirectional approach enhances the reconstruction of free energies and potentials of mean force, outperforming unidirectional methods.
Area of Science:
- Statistical Mechanics
- Physical Chemistry
- Computational Biophysics
Background:
- Estimating path-ensemble averages is crucial for understanding complex systems.
- Single-molecule force spectroscopy generates data from driven processes.
- Unidirectional methods for analyzing such data have limitations.
Purpose of the Study:
- To develop an optimized method for estimating path-ensemble averages using bidirectional data.
- To create bidirectional expressions for reconstructing free energies and potentials of mean force.
- To evaluate the performance of bidirectional methods against unidirectional strategies.
Main Methods:
- Development of an optimized estimator for path-ensemble averages.
- Formulation of bidirectional expressions for free energy and potential of mean force reconstruction.
- Application of methods to a model potential for numerical simulations.
Main Results:
- The proposed bidirectional method accurately estimates path-ensemble averages.
- Bidirectional expressions enable robust reconstruction of free energies and potentials of mean force.
- Numerical simulations demonstrate superior performance compared to unidirectional approaches.
Conclusions:
- The optimized bidirectional method offers a significant improvement for analyzing single-molecule force spectroscopy data.
- This approach provides a more accurate and reliable way to determine free energies and potentials of mean force.
- The developed techniques are applicable to biasing potentials of arbitrary stiffness.
More Related Videos
Related Concept Videos
02:49Calculating Standard Free Energy Changes
The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
01:13Force and Potential Energy in One Dimension
Force can be calculated from the expression for potential energy, which is a function of position. The component of a conservative force, in a particular direction, equals the negative of the derivative of the corresponding potential energy with respect to the displacement in that direction. For regions where potential energy changes rapidly with displacement, the work done and force is maximum. Also, when force is applied along the positive coordinate axis, the potential energy decreases with...
01:21Free Energy
Free energy—abbreviated as G for the scientist Gibbs who discovered it—is a measurement of useful energy that can be extracted from a reaction to do work. It is the energy in a chemical reaction that is available after entropy is accounted for. Reactions that take in energy are considered endergonic and reactions that release energy are exergonic. Plants carry out endergonic reactions by taking in sunlight and carbon dioxide to produce glucose and oxygen. Animals, in turn, break down the...
02:39Gibbs Free Energy
One of the challenges of using the second law of thermodynamics to determine if a process is spontaneous is that it requires measurements of the entropy change for the system and the entropy change for the surroundings. An alternative approach involving a new thermodynamic property defined in terms of system properties only was introduced in the late nineteenth century by American mathematician Josiah Willard Gibbs. This new property is called the Gibbs free energy (G) (or simply the free...