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

The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
Equilibrium Conditions for a Particle01:23

Equilibrium Conditions for a Particle

When an object is in equilibrium, it is either at rest or moving with a constant velocity. There are two types of equilibrium: static and dynamic. Static equilibrium occurs when an object is at rest, while dynamic equilibrium occurs when an object is moving with a constant velocity. In both cases, there must be a balance of forces acting on the object.
To understand the concept of equilibrium, let us first consider the forces acting on an object. When different forces act on an object, they can...
Dynamic Equilibrium02:20

Dynamic Equilibrium

A reversible chemical reaction represents a chemical process that proceeds in both forward (left to right) and reverse (right to left) directions. When the rates of the forward and reverse reactions are equal, the concentrations of the reactant and product species remain constant over time and the system is at equilibrium. A special double arrow is used to emphasize the reversible nature of the reaction. The relative concentrations of reactants and products in equilibrium systems vary greatly;...
Calculating Equilibrium Concentrations02:05

Calculating Equilibrium Concentrations

Being able to calculate equilibrium concentrations is essential to many areas of science and technology—for example, in the formulation and dosing of pharmaceutical products. After a drug is ingested or injected, it is typically involved in several chemical equilibria that affect its ultimate concentration in the body system of interest. Knowledge of the quantitative aspects of these equilibria is required to compute a dosage amount that will solicit the desired therapeutic effect.
A more...
Equilibrium and Balance01:15

Equilibrium and Balance

The inner ear assumes dual functionalities of auditory perception and equilibrium maintenance. The vestibule is the organ responsible for balance. This organ contains mechanoreceptors, specifically hair cells, endowed with stereocilia, which aid in deciphering information regarding the position and motion of our heads. Two intrinsic components, the utricle and saccule, help perceive head position, while the semicircular canals track head movement. Neurological messages initiated in the...

You might also read

Related Articles

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

Sort by
Same author

Walking the Tightrope: Balancing Opposing Cooperativities as an Operating Principle in Dynein Assembly.

bioRxiv : the preprint server for biology·2026
Same author

Randomized iterative trajectory reweighting for steady-state distributions without discretization error.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Rectifying AI-generated protein structure ensembles for equilibrium using physics-based computations.

bioRxiv : the preprint server for biology·2026
Same author

Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.

Cell systems·2026
Same author

Publisher's Note: "Reducing weighted ensemble variance with optimal trajectory management" [J. Chem. Phys. 164, 094110 (2026)].

The Journal of chemical physics·2026
Same author

Multiple data set Bayesian analysis synergistically boosts ITC parameter precision.

Biophysical journal·2026
Same journal

A Tubules-First Model for the Origin of Eukaryotic Membrane Traffic.

Annual review of biophysics·2026
Same journal

Seeking Biology's Physics Stories: Simplify, Simplify.

Annual review of biophysics·2026
Same journal

Pattern Formation Beyond Turing: Physical Principles of Mass-Conserving Reaction-Diffusion Systems.

Annual review of biophysics·2026
Same journal

Rigidity and Mechanical Response in Biological Structures.

Annual review of biophysics·2026
Same journal

Systems Biology of Aging, Metabolism, and Mitochondria.

Annual review of biophysics·2026
Same journal

Ligand Binding Dynamics of Ion Channels and GPCRs Using Single-Molecule Fluorescence.

Annual review of biophysics·2026
See all related articles

Related Experiment Video

Updated: Jun 4, 2026

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability
09:49

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Published on: April 2, 2015

Equilibrium sampling in biomolecular simulations.

Daniel M Zuckerman1

  • 1Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA. ddmmzz@pitt.edu

Annual Review of Biophysics
|March 5, 2011
PubMed
Summary
This summary is machine-generated.

Achieving equilibrium sampling for biomolecules in atomistic simulations is difficult. This review explores enhanced sampling methods, highlighting hardware advancements over algorithmic improvements for clearer progress.

More Related Videos

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates
06:48

Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates

Published on: January 5, 2024

Related Experiment Videos

Last Updated: Jun 4, 2026

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability
09:49

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Published on: April 2, 2015

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates
06:48

Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates

Published on: January 5, 2024

Area of Science:

  • Computational biology
  • Molecular dynamics simulations
  • Biophysics

Background:

  • Equilibrium sampling of biomolecules is a persistent challenge in atomistic simulations.
  • Over 30 years of research have focused on improving sampling capabilities.

Purpose of the Study:

  • To review and classify algorithms for enhanced sampling in biomolecular simulations.
  • To assess the impact of different approaches, including algorithms and hardware, on sampling efficiency.

Main Methods:

  • Classification of enhanced sampling algorithms based on underlying principles.
  • Review of strategies including new algorithms, parallelization, and novel hardware utilization.

Main Results:

  • Algorithms for enhanced sampling are diverse but often share core concepts.
  • Progress from novel hardware use is more evident than from algorithms alone.
  • Lack of standardized sampling measures hinders algorithm comparison.

Conclusions:

  • Novel hardware utilization offers a more discernible path to improved biomolecular simulation sampling.
  • Further development and standardization of sampling measures are crucial for algorithmic progress.