Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
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...
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 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:
Gibbs Free Energy and Thermodynamic Favorability02:23

Gibbs Free Energy and Thermodynamic Favorability

The spontaneity of a process depends upon the temperature of the system. Phase transitions, for example, will proceed spontaneously in one direction or the other depending upon the temperature of the substance in question. Likewise, some chemical reactions can also exhibit temperature-dependent spontaneities. To illustrate this concept, the equation relating free energy change to the enthalpy and entropy changes for the process is considered:
Gibbs Free Energy02:39

Gibbs 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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Primary age-related tauopathy in a Chinese cohort.

Journal of Zhejiang University. Science. B·2020
Same author

The metabolic effect of gut microbiota on drugs.

Drug metabolism reviews·2020
Same author

Population-based preference weights for the Adult Social Care Outcomes Toolkit (ASCOT) for service users for Austria: Findings from a best-worst experiment.

Social science & medicine (1982)·2020
Same author

Dissymmetric On-Surface Dehalogenation Reaction Steered by Preformed Self-Assembled Structure.

The journal of physical chemistry letters·2020
Same author

Exosomes mediate intercellular transfer of non-autonomous tolerance to proteasome inhibitors in mixed-lineage leukemia.

Cancer science·2020
Same author

Neuroprotective Effects of Selective Inhibition of Histone Deacetylase 3 in Experimental Stroke.

Translational stroke research·2020

Related Experiment Video

Updated: May 26, 2026

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

Efficient free-energy-profile reconstruction using adaptive stochastic perturbation protocols.

Ognjen Perišić1, Hui Lu

  • 1Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60607, USA.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|December 21, 2011
PubMed
Summary
This summary is machine-generated.

High dissipation limits free-energy calculations. Novel perturbation protocols improve potential of mean force (PMF) estimates by widening external work distribution, achieving high accuracy with fewer samples in simulations and experiments.

More Related Videos

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
05:57

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations

Published on: April 26, 2024

Related Experiment Videos

Last Updated: May 26, 2026

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
05:57

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations

Published on: April 26, 2024

Area of Science:

  • Statistical mechanics
  • Computational chemistry
  • Biophysics

Background:

  • Jarzynski-relation-based free-energy calculations face slow convergence with high dissipation.
  • Accurate potential of mean force (PMF) estimation is crucial in various scientific domains.

Purpose of the Study:

  • To introduce novel perturbation protocols for enhanced PMF calculation.
  • To reduce bias and improve convergence in free-energy estimates without increasing sample size.

Main Methods:

  • Developed two novel perturbation protocols.
  • Controlled widening of the external work distribution during system perturbation.
  • Applied protocols to numerical simulations and experimental setups.

Main Results:

  • Significantly improved the quality of PMF calculations.
  • Reduced estimate bias without additional sampling.
  • Achieved comparable accuracy to constant velocity pulling with <10% of samples.

Conclusions:

  • The novel protocols offer a more efficient method for PMF estimation.
  • Applicability to both simulations and real-world experiments broadens their utility.
  • Reduced computational cost and time for free-energy calculations.