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Related Concept Videos

Calculating Standard Free Energy Changes02:49

Calculating 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...
Free Energy01:21

Free 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...
Free Energy Changes for Nonstandard States03:25

Free Energy Changes for Nonstandard States

The free energy change for a process taking place with reactants and products present under nonstandard conditions (pressures other than 1 bar; concentrations other than 1 M) is related to the standard free energy change according to this equation:
Potential-Energy Criterion for Equilibrium01:16

Potential-Energy Criterion for Equilibrium

Potential energy or potential function plays an essential role in determining the stability of a mechanical system. If a system is subjected to both gravitational and elastic forces, the potential function of the system can be expressed as the algebraic sum of gravitational and elastic potential energy. If the system is in equilibrium and is displaced by a small amount, then the work done on the system equals the negative of the change in the system's potential energy from the initial to the...
Free Energy and Equilibrium00:55

Free Energy and Equilibrium

The free energy change for a process may be viewed as a measure of its driving force. A negative value for ΔG represents a driving force for the process in the forward direction, while a positive value represents a driving force for the process in the reverse direction. When ΔG is zero, the forward and reverse driving forces are equal, and the process occurs in both directions at the same rate (the system is at equilibrium).
The reaction quotient, Q, is a convenient measure of the status of an...
Free Energy and Equilibrium02:56

Free Energy and Equilibrium

The free energy change for a process may be viewed as a measure of its driving force. A negative value for ΔG represents a driving force for the process in the forward direction, while a positive value represents a driving force for the process in the reverse direction. When ΔGrxn is zero, the forward and reverse driving forces are equal, and the process occurs in both directions at the same rate (the system is at equilibrium).
Recall that Q is the numerical value of the mass action expression...

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Parallel-pulling protocol for free-energy evaluation.

Van A Ngo1

  • 1University of Southern California, Department of Physics and Astronomy, Los Angeles, California 90089-0242, USA. nvan@usc.edu

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|May 17, 2012
PubMed
Summary

This study introduces an efficient method for calculating free-energy differences using Jarzynski

Area of Science:

  • Computational physics
  • Statistical mechanics
  • Molecular dynamics simulations

Background:

  • Jarzynski's equality (JE) computes free-energy differences from work distributions.
  • Traditional methods require numerous simulations, posing computational challenges.
  • Existing methods like thermodynamic integration and umbrella sampling are computationally intensive.

Purpose of the Study:

  • To develop an efficient computational approach for free-energy calculations using Jarzynski's equality.
  • To propose novel stepwise pulling protocols for generating reliable work distributions.
  • To establish a method for assessing the accuracy of computed free-energy differences.

Main Methods:

  • A novel proof of Jarzynski's equality based on stepwise pulling procedures.

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  • Utilizing double Heaviside functions to describe potential activation/deactivation.
  • Developing sequential and parallel stepwise pulling protocols.
  • Analyzing reaction coordinate distributions for reliable work distributions.

    • Main Results:

    • Demonstrated an efficient method for free-energy calculations via Jarzynski's equality.
    • Proposed stepwise pulling protocols that require less relaxation time.
    • Introduced an alternative formula for free-energy differences, enabling accuracy assessment.
    • Achieved a 13% uncertainty in free-energy estimation for deca-alanine stretching with 0.4 ns relaxation time.

    Conclusions:

    • The proposed stepwise pulling protocols offer an efficient and accurate approach to free-energy calculations using Jarzynski's equality.
    • The combination of Jarzynski's equality and the alternative formula provides a robust way to validate computed free-energy differences.
    • This method significantly reduces computational cost and improves reliability in molecular dynamics simulations.