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

Isochoric and Isobaric Processes01:21

Isochoric and Isobaric Processes

4.3K
A thermodynamic process that occurs at constant volume is called an isochoric process. According to the first law of thermodynamics, heat supplied or removed from the system is partially utilized to perform work and change the internal energy of the system. However, in an isochoric process, the volume remains constant. Hence, the work done by the system is zero. Therefore, the exchange of heat changes the internal energy of the system only. 
Suppose 1000 g of water is heated from 40...
4.3K
Generalized Hooke's Law01:22

Generalized Hooke's Law

2.7K
The generalized Hooke's Law is a broadened version of Hooke's Law, which extends to all types of stress and in every direction. Consider an isotropic material shaped into a cube subjected to multiaxial loading. In this scenario, normal stresses are exerted along the three coordinate axes. As a result of these stresses, the cubic shape deforms into a rectangular parallelepiped. Despite this deformation, the new shape maintains equal sides, and there is a normal strain in the direction of the...
2.7K
Generalized Anxiety Disorder01:30

Generalized Anxiety Disorder

669
Generalized Anxiety Disorder (GAD) is a chronic condition characterized by excessive and uncontrollable worry that persists for at least six months, significantly interfering with daily functioning. Unlike situational anxiety, which arises in response to specific stressors, GAD often occurs without a clear cause. Individuals may experience disproportionate worry about work, health, or relationships. For instance, a person might continuously fear poor health despite normal medical evaluations or...
669
Social Foundations of Self II: The Generalized Other01:20

Social Foundations of Self II: The Generalized Other

245
According to George Herbert Mead, as children progress beyond the game stage, they develop a more comprehensive understanding of societal rules and norms. This cognitive and social development enables them to internalize the expectations of the broader community, refining their ability to regulate behavior.Consistent participation in organized activities is crucial in helping children recognize that their actions are not isolated but contribute to a more significant, interconnected group...
245
Generalization, Discrimination, and Extinction01:24

Generalization, Discrimination, and Extinction

1.4K
Generalization, discrimination, and extinction are key concepts in operant conditioning that influence how behaviors are learned and maintained.
Generalization occurs when a behavior reinforced in one context is performed in similar situations. For instance, a student who studies diligently for calculus and receives excellent grades might apply the same study habits to psychology and history, expecting similar results. Generalization shows how learning in one setting can influence behavior in...
1.4K
Isothermal Processes01:21

Isothermal Processes

4.9K
A thermodynamic process that occurs at constant temperature is called an isothermal process. Heat slowly flows into the system or out of the system to maintain thermal equilibrium. Processes involving phase changes like water evaporation into steam or freezing water into ice at a constant temperature are examples of Isothermal Processes.
An ideal gas can also undergo isothermal expansion or compression.
For example, consider 1 mole of an ideal gas inside an isolated cylinder at initial volume V...
4.9K

You might also read

Related Articles

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

Sort by
Same author

OpenCafeMol With 3SPN.2 DNA Model: GPU Acceleration for Long-Time Coarse-Grained Chromatin Simulations.

Journal of computational chemistry·2026
Same author

Statistical Protein-Protein Interaction Analysis of HER2-Pertuzumab Complex by the Fragment Molecular Orbital Method.

Journal of computational chemistry·2026
Same author

SMC complex unidirectionally translocates DNA by coupling segment capture with an asymmetric kleisin path.

eLife·2026
Same author

Mechanistic models of asymmetric hand-over-hand translocation and nucleosome navigation by CMG helicase.

Nature communications·2025
Same author

A Structure-Based Approach for Predicting Odor Similarity of Molecules via Docking Simulations with Human Olfactory Receptors.

ACS omega·2025
Same author

Oligomerization Mechanism of Amyloid-<b>β</b> Peptides at Hydrophobic Interfaces Revealed by Molecular Dynamics Simulations.

The journal of physical chemistry. B·2025

Related Experiment Video

Updated: Jan 24, 2026

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
15:05

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

9.2K

Molecular simulations by generalized-ensemble algorithms in isothermal-isobaric ensemble.

Masataka Yamauchi1,2,3, Yoshiharu Mori4, Hisashi Okumura5,6,7

  • 1Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444-8585, Japan.

Biophysical Reviews
|May 23, 2019
PubMed
Summary

Generalized-ensemble algorithms enhance biomolecular simulations in the isothermal-isobaric ensemble. These advanced methods improve conformational sampling across temperature and pressure for more accurate physical quantity estimation.

Keywords:
Generalized-ensemble algorithmHigh pressureMolecular simulationProtein folding

More Related Videos

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

1.2K
Ensemble Force Spectroscopy by Shear Forces
07:30

Ensemble Force Spectroscopy by Shear Forces

Published on: July 26, 2022

1.9K

Related Experiment Videos

Last Updated: Jan 24, 2026

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
15:05

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

9.2K
Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

1.2K
Ensemble Force Spectroscopy by Shear Forces
07:30

Ensemble Force Spectroscopy by Shear Forces

Published on: July 26, 2022

1.9K

Area of Science:

  • Computational chemistry
  • Biophysics
  • Molecular dynamics

Background:

  • Generalized-ensemble algorithms are vital for studying biomolecules like proteins and DNA.
  • Traditional methods often focus on canonical ensembles, limiting experimental relevance.
  • Experimental conditions frequently involve controlling both temperature and pressure.

Purpose of the Study:

  • To review generalized-ensemble algorithms adapted for the isothermal-isobaric ensemble.
  • To highlight their advantages over conventional isothermal-isobaric simulations.
  • To demonstrate their utility in enhanced conformational sampling for biomolecules.

Main Methods:

  • Review of multibaric-multithermal algorithms.
  • Discussion of pressure- and temperature-simulated tempering.
  • Overview of replica-exchange and replica-permutation methods in the isothermal-isobaric ensemble.

Main Results:

  • Generalized-ensemble algorithms provide more efficient simulations than conventional methods.
  • These algorithms enable broader sampling of biomolecular conformations across temperature and pressure.
  • Improved accuracy in estimating physical quantities at various thermodynamic conditions.

Conclusions:

  • Isothermal-isobaric generalized-ensemble simulations offer superior efficiency and sampling range.
  • These methods are crucial for accurate biomolecular modeling under experimental conditions.
  • Applications demonstrate the practical utility of these advanced simulation techniques.