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

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...
Energy Diagrams, Transition States, and Intermediates02:13

Energy Diagrams, Transition States, and Intermediates

Free-energy diagrams, or reaction coordinate diagrams, are graphs showing the energy changes that occur during a chemical reaction. The reaction coordinate represented on the horizontal axis shows how far the reaction has progressed structurally. Positions along the x-axis close to the reactants have structures resembling the reactants, while positions close to the products resemble the products.  Peaks on the energy diagram represent stable structures with measurable lifetimes, while other...
Thermodynamic Systems01:06

Thermodynamic Systems

A thermodynamic system is a set of objects whose thermodynamic properties are of interest. The system is considered to be embedded in its surroundings or the environment. The system and its environment can exchange heat and do work on each other through a boundary that separates them. However, the immediate surroundings of the system interact with it directly and therefore have a much stronger influence on its behavior and properties.
Consider an example of  tea boiling in a kettle. The tea and...
Thermodynamic Background01:18

Thermodynamic Background

The law of mass action states that "the rate of a chemical reaction is directly proportional to the product of the molar concentrations of the reactants." It means that the more 'active mass' or 'concentration' of the reactants present, the faster the reaction will proceed.In a chemical reaction, there are forward and reverse reactions. The forward reaction is the process where the reactants combine to form products. The reverse reaction is the process where the products break down to form the...
Energy Diagrams - I01:14

Energy Diagrams - I

The dynamics of a mechanical system can be easily understood by interpreting a potential energy diagram. Since energy is a scalar quantity, the interpretation of the dynamics of the system becomes even simpler.
Take the example of a skater on a parabolic ramp. The potential energy at different points along the ramp will be proportional to the height of the ramp, which varies quadratically with the horizontal position on the ramp. As the skater moves down the ramp from the highest position,...
The First Law of Thermodynamics01:13

The First Law of Thermodynamics

The first law of thermodynamics deals with the total amount of energy in the universe. It states that this total amount of energy is constant. In other words, there has always been, and always will be, exactly the same amount of energy in the universe. Energy exists in many different forms. According to the first law of thermodynamics, energy may transfer from place to place or transform into different forms, but it cannot be created or destroyed. The transfers and transformations of energy...

You might also read

Related Articles

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

Sort by
Same author

Accelerated Reaction Exploration across Scales: A Hybrid Operando and Modeling Study of Oxidation Kinetics in Monolayer Tungsten Disulfide.

Journal of the American Chemical Society·2026
Same author

Comparison of predictive approaches to the dynamics of activated catalytic processes.

Physical chemistry chemical physics : PCCP·2026
Same author

Comparison of Protein-Glycosaminoglycan Interactions in ff14sb/GLYCAM06j-1 and CHARMM36m Force Fields.

Journal of chemical information and modeling·2026
Same author

Energy Landscape Analysis of Membrane Proteins Using NMR-Based Hybrid Restraint Potentials.

Journal of chemical theory and computation·2026
Same author

Energy landscapes of the water hexamer and octamer for the MB-pol and TIP4P/2005 potentials.

The Journal of chemical physics·2026
Same author

Visualizing the energy landscape for a molecular dynamics trajectory.

The Journal of chemical physics·2026

Related Experiment Video

Updated: May 22, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Decoding the energy landscape: extracting structure, dynamics and thermodynamics.

David J Wales1

  • 1Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. dw34@cam.ac.uk

Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
|May 23, 2012
PubMed
Summary
This summary is machine-generated.

Understanding potential energy landscapes reveals connections between structure, dynamics, and thermodynamics across diverse systems. Visualizing these landscapes aids in predicting material properties and molecular behavior.

More Related Videos

Uncovering Hidden Dynamics of Natural Photonic Structures Using Holographic Imaging
05:45

Uncovering Hidden Dynamics of Natural Photonic Structures Using Holographic Imaging

Published on: March 31, 2022

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
09:42

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Published on: January 16, 2016

Related Experiment Videos

Last Updated: May 22, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Uncovering Hidden Dynamics of Natural Photonic Structures Using Holographic Imaging
05:45

Uncovering Hidden Dynamics of Natural Photonic Structures Using Holographic Imaging

Published on: March 31, 2022

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
09:42

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Published on: January 16, 2016

Area of Science:

  • Computational chemistry
  • Statistical mechanics
  • Materials science

Background:

  • Potential energy surfaces map molecular configurations and their energies.
  • Local minima and transition states define pathways for system evolution.
  • Disconnectivity graphs visualize complex energy landscapes.

Purpose of the Study:

  • To establish a framework for understanding observable properties from potential energy landscapes.
  • To explore the relationship between landscape organization and system dynamics/thermodynamics.
  • To connect energy landscape features to interparticle forces.

Main Methods:

  • Describing potential energy surfaces using local minima and transition states.
  • Visualizing energy landscapes with disconnectivity graphs.
  • Analyzing competing morphologies and multiple potential energy funnels.
  • Applying symmetry considerations and catastrophe theory.

Main Results:

  • A unified conceptual and computational framework for predicting properties.
  • Demonstrated commonalities in landscape-structure-dynamics-thermodynamics across atomic clusters, biomolecules, and condensed matter.
  • Identified characteristic heat capacity and relaxation time scales for competing morphologies.
  • Established connections between landscape motifs and interparticle forces.

Conclusions:

  • The organization of potential energy landscapes fundamentally governs system behavior.
  • Disconnectivity graphs provide valuable insights into structure-seeking systems.
  • Energy landscape analysis offers a powerful tool for diverse scientific fields.