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

Gibbs Free Energy02:39

Gibbs Free Energy

40.0K
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...
40.0K
Energy Diagrams - I01:14

Energy Diagrams - I

5.8K
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,...
5.8K
Energy Diagrams - II01:10

Energy Diagrams - II

14.1K
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...
14.1K
Force and Potential Energy in One Dimension01:13

Force and Potential Energy in One Dimension

6.6K
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...
6.6K
Free Energy and Equilibrium02:56

Free Energy and Equilibrium

27.6K
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...
27.6K
Free Energy and Equilibrium00:55

Free Energy and Equilibrium

9.5K
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...
9.5K

You might also read

Related Articles

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

Sort by
Same author

Ion transport in water film on silica and mica surfaces: Insights from microsecond molecular dynamics and logarithmic mean-force dynamics.

The Journal of chemical physics·2025
Same author

Nonsubstrate PI(4,5)P<sub>2</sub> interacts with the interdomain linker to control electrochemical coupling in voltage-sensing phosphatase (VSP).

Proceedings of the National Academy of Sciences of the United States of America·2025
Same author

Can intramolecular rotors govern the thermal conductivity of molecular materials?

The Journal of chemical physics·2025
Same author

Cell position-based evaluation of mechanical features of cells in multicellular systems.

Journal of theoretical biology·2025
Same author

Effective mechanical potential of cell-cell interaction in tissues harboring cavity and in cell sheet toward morphogenesis.

Frontiers in cell and developmental biology·2024
Same author

Ab Initio Characterization of the CO<sub>2</sub>-Water Interface Using Unsupervised Machine Learning for Dimensionality Reduction.

The journal of physical chemistry. B·2024

Related Experiment Video

Updated: Feb 28, 2026

Investigating Receptor-ligand Systems of the Cellulosome with AFM-based Single-molecule Force Spectroscopy
11:34

Investigating Receptor-ligand Systems of the Cellulosome with AFM-based Single-molecule Force Spectroscopy

Published on: December 20, 2013

7.8K

Free Energy Reconstruction from Logarithmic Mean-Force Dynamics Using Multiple Nonequilibrium Trajectories.

Tetsuya Morishita1,2, Yasushige Yonezawa3, Atsushi M Ito4,5

  • 1Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST) , 1-1-1 Umezono, Tsukuba 305-8568, Japan.

Journal of Chemical Theory and Computation
|June 13, 2017
PubMed
Summary
This summary is machine-generated.

Parallel dynamics enhances mean force estimation for free energy calculations by using multiple system replicas. This method, integrated into logarithmic mean-force dynamics (LogMFD), improves accuracy and efficiency in complex biosystems.

More Related Videos

Age-dependent Dynamics of Locomotion in Caenorhabditis elegans: A Lyapunov Exponent Analysis
06:44

Age-dependent Dynamics of Locomotion in Caenorhabditis elegans: A Lyapunov Exponent Analysis

Published on: September 23, 2025

637
An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids
11:03

An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids

Published on: December 4, 2017

9.1K

Related Experiment Videos

Last Updated: Feb 28, 2026

Investigating Receptor-ligand Systems of the Cellulosome with AFM-based Single-molecule Force Spectroscopy
11:34

Investigating Receptor-ligand Systems of the Cellulosome with AFM-based Single-molecule Force Spectroscopy

Published on: December 20, 2013

7.8K
Age-dependent Dynamics of Locomotion in Caenorhabditis elegans: A Lyapunov Exponent Analysis
06:44

Age-dependent Dynamics of Locomotion in Caenorhabditis elegans: A Lyapunov Exponent Analysis

Published on: September 23, 2025

637
An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids
11:03

An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids

Published on: December 4, 2017

9.1K

Area of Science:

  • Computational Chemistry and Physics
  • Molecular Dynamics Simulations
  • Biophysics

Background:

  • Estimating mean force (MF), the derivative of free energy with respect to collective variables (CVs), is crucial for calculating free energy differences.
  • Traditional methods often require integrating MF, posing computational challenges.
  • Logarithmic mean-force dynamics (LogMFD) offers on-the-fly free energy profile estimation by leveraging classical mechanics conservation laws.

Purpose of the Study:

  • To introduce parallel dynamics, a novel method for improving the accuracy and efficiency of mean force estimation.
  • To integrate parallel dynamics with LogMFD, creating logarithmic parallel dynamics (LogPD).
  • To demonstrate the effectiveness of LogPD using benchmark biosystems.

Main Methods:

  • Developed parallel dynamics employing multiple system replicas to evaluate the mean force.
  • Utilized a nonequilibrium path-ensemble and the Crooks-Jarzynski nonequilibrium work relation for MF evaluation.
  • Combined parallel dynamics with LogMFD to form logarithmic parallel dynamics (LogPD).

Main Results:

  • Parallel dynamics significantly improves mean force estimation by using multiple replicas.
  • The Crooks relation obviates the need for full-equilibrium states in MF estimation.
  • LogPD enhances sampling in hidden subspaces and improves accuracy and efficiency for free energy profiles in alanine dipeptide and adenylate kinase systems.

Conclusions:

  • Parallel dynamics offers a robust enhancement for mean force estimation in free energy calculations.
  • Logarithmic parallel dynamics (LogPD) provides a more accurate and efficient approach for computing free energy profiles.
  • The method shows promise for studying complex molecular systems.