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Related Concept Videos

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;...
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...
Extraction: Partition and Distribution Coefficients01:14

Extraction: Partition and Distribution Coefficients

The distribution law or Nernst's distribution law is the law that governs the distribution of a solute between two immiscible solvents. This law, also known as the partition law, states that if a solute is added to the mixture of two immiscible solvents at a constant temperature, the solute is distributed between the two solvents in such a way that the ratio of solute concentrations in the solvents remains constant at equilibrium.
For extracting a solute from an aqueous phase into an organic...
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:
Free Energy and Equilibrium00:55

Free Energy and Equilibrium

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 status of an...

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Related Experiment Video

Updated: Jun 2, 2026

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

Equilibrium distribution from distributed computing (simulations of protein folding).

Riccardo Scalco1, Amedeo Caflisch

  • 1Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.

The Journal of Physical Chemistry. B
|April 27, 2011
PubMed
Summary

This study introduces a depth-first search algorithm to identify the largest ergodic component in molecular dynamics (MD) networks. This method improves the accuracy of free energy profiles and mean first passage times from simulations.

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Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates
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Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates

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Last Updated: Jun 2, 2026

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

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 chemistry
  • Biophysics
  • Statistical mechanics

Background:

  • Molecular dynamics (MD) simulations are crucial for studying protein dynamics.
  • Combining data from multiple short MD simulations can introduce statistical bias.
  • Markov state models (MSMs) built from combined simulations may not represent a true thermodynamic ensemble.

Purpose of the Study:

  • To develop a method for mitigating statistical bias in MSMs derived from multiple independent MD simulations.
  • To extract a statistically robust subset of the conformational space network.
  • To improve the accuracy of dynamic properties calculated from MD data.

Main Methods:

  • Introduction of a depth-first search (DFS) algorithm.
  • Identification of the largest ergodic component within the conformation space network.
  • Calculation of stationary distributions using the identified ergodic component.

Main Results:

  • The DFS algorithm successfully extracts the largest ergodic component from the network.
  • The steady state derived from the largest ergodic component provides more accurate free energy profiles.
  • Mean first passage times are also more accurately determined compared to original or symmetrized networks.

Conclusions:

  • The proposed DFS-based method effectively removes statistical bias in MSMs from multiple short MD simulations.
  • This approach leads to more reliable estimations of protein dynamics and thermodynamics.
  • The method offers a significant improvement for analyzing distributed computing MD data.