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

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...
Integration by Parts: Indefinite Integrals01:26

Integration by Parts: Indefinite Integrals

Integration by parts is a fundamental technique in calculus for evaluating integrals involving the product of two functions. It is particularly useful when direct integration is not feasible. The method is based on the product rule for differentiation, which states that the derivative of a product equals the derivative of the first function times the second, plus the first function times the derivative of the second. By integrating this identity and rearranging terms, the integration by parts...
Approximate Integration01:24

Approximate Integration

In many practical and theoretical contexts, the exact value of a definite integral may be inaccessible. This limitation typically arises when the antiderivative of a function is either unknown or cannot be expressed in a closed mathematical form. Alternatively, it can occur when a function is defined not by a formula but by a finite set of empirical data points, such as those collected during experiments. In these cases, approximate integration techniques provide a valuable solution.One of the...
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...
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...
Energy Diagrams - II01:10

Energy Diagrams - II

Energy diagrams are important to understand the dynamics of a system. The topology of an energy diagram helps illustrate the equilibrium points of the system.
The point in the energy diagram at which the system’s potential energy is the lowest is known as the local minima. The system tends to stay in this position indefinitely unless acted upon by a net force. The slope of the potential energy diagram at the local minima is zero, indicating that zero net force is acting on the system. The slope...

You might also read

Related Articles

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

Sort by
Same author

Effect of Salt Additives on Dinitrogen Activation Mediated by Boron-Based Compounds: Insights from Theory.

Inorganic chemistry·2026
Same author

Asymmetric α-Alkylation With Activated and Unactivated Electrophiles by a Highly Productive and Recyclable Lewis Acid/Imidazolium Catalyst.

Angewandte Chemie (International ed. in English)·2026
Same author

How to Train a Shallow Ensemble.

Journal of chemical theory and computation·2026
Same author

Fibroblast growth factor 23 is associated with cardiac disease severity in transthyretin amyloid cardiomyopathy.

Scientific reports·2026
Same author

Desorption dynamics of interstellar molecule on amorphous solid water investigated by machine learning potential-based PaCS-MD simulation.

The Journal of chemical physics·2026
Same author

Insights into the renin-angiotensin-aldosterone system in transthyretin amyloid cardiomyopathy.

European journal of heart failure·2026
Same journal

Revisiting crossed-correlated baths in open quantum systems simulated by HEOM or T-TEDOPA.

The Journal of chemical physics·2026
Same journal

Vesicle size and membrane composition control monomer transfer pathways in multicomponent lipid vesicles.

The Journal of chemical physics·2026
Same journal

Polaron-mediated exciton dynamics of P(NDI2OD-T2) unveiled by transient absorption spectroscopy under electrochemical conditions.

The Journal of chemical physics·2026
Same journal

Green-Kubo relation in a mesoscale odd fluid model.

The Journal of chemical physics·2026
Same journal

Nitrogenation of microscopic MoS2 surfaces by oxidation scanning probe lithography.

The Journal of chemical physics·2026
Same journal

Molecular structure, binding, and disorder in TDBC-Ag plexcitonic assemblies.

The Journal of chemical physics·2026
See all related articles

Related Experiment Video

Updated: May 20, 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

An algorithm to find minimum free-energy paths using umbrella integration.

Matthias U Bohner1, Johannes Kästner

  • 1Computational Biochemistry Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany.

The Journal of Chemical Physics
|July 27, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces a novel method for calculating free-energy barriers without needing a predefined reaction coordinate. It efficiently identifies transition states and pathways, simplifying complex molecular simulations.

Related Experiment Videos

Last Updated: May 20, 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

Area of Science:

  • Computational chemistry
  • Molecular dynamics
  • Statistical mechanics

Background:

  • Calculating free-energy barriers is crucial for understanding chemical reactions and molecular processes.
  • Traditional methods like umbrella sampling require a priori selection of reaction coordinates, limiting their applicability.
  • This limitation necessitates new approaches for accurate free-energy calculations.

Purpose of the Study:

  • To develop a method for calculating free-energy barriers that does not require a predefined reaction coordinate.
  • To enable the search for saddle points on free-energy surfaces in multiple dimensions.
  • To provide a robust approach for constructing minimum free-energy paths and calculating associated barriers.

Main Methods:

  • Multidimensional umbrella integration to obtain free-energy gradients and Hessians.
  • Gradient-following to identify saddle points and construct minimum free-energy paths.
  • Integration of orthogonal coordinates to determine free-energy changes along the path.

Main Results:

  • Successfully identified saddle points and minimum free-energy paths in a multidimensional space.
  • Calculated free-energy barriers for the alanine dipeptide in vacuum.
  • Demonstrated agreement with previously established methods for minima, transition states, and barriers.

Conclusions:

  • The developed method overcomes the limitation of a priori reaction coordinate selection in free-energy calculations.
  • This approach is applicable to complex systems and provides accurate results for free-energy barriers.
  • The method offers a significant advancement in computational chemistry for molecular simulations.