Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Distribution of Molecular Speeds

Distribution of Molecular Speeds

The motion of molecules in a gas is random in magnitude and direction for individual molecules, but a gas of many molecules has a predictable distribution of molecular speeds. This predictable distribution of molecular speeds is known as the Maxwell-Boltzmann distribution. The distribution of molecular speeds in liquids is comparable to that of gases but not identical and can help to understand the phenomenon of the boiling and vapor pressure of a liquid. Consider that a molecule requires a...

Molecular Kinetic Energy

Molecular Kinetic Energy

The word "gas" comes from the Flemish word meaning "chaos," first used to describe vapors by the chemist J. B. van Helmont. Consider a container filled with gas, with a continuous and random motion of molecules. During collisions, the velocity component parallel to the wall is unchanged, and the component perpendicular to the wall reverses direction but does not change in magnitude. If the molecule’s velocity changes in the x-direction, then its momentum is changed. During the short time of the...

Protein Dynamics in Living Cells

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...

Molecular Orbital Theory I

Molecular Orbital Theory I

Overview of Molecular Orbital Theory

Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

The Molecular Nature of Internal Energy

The Molecular Nature of Internal Energy

The internal energy of a molecule is determined by its degrees of freedom, including translational, rotational, and vibrational motions. In addition to these kinetic activities, the energy of molecules is also shaped by electronic energy, intermolecular forces, and the rest-mass energy of electrons and nuclei. These factors collectively influence the energy state of the molecules. The equipartition theorem of classical mechanics provides insight into this energy distribution. It posits that the...

You might also read

Related Articles

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

Sort by

Same author

GeoPep: A Geometry-Aware Masked Language Model for Protein-Peptide Binding Site Prediction.

Journal of chemical information and modeling·2026

Same author

The in vivo inhibitory function of the MHC-I α3 domain-CD8α interaction.

bioRxiv : the preprint server for biology·2026

Same author

Orchestrated metal ion repositioning defines the dynamic catalytic strategy of the essential DNA repair nuclease APE1.

bioRxiv : the preprint server for biology·2026

Same author

Subsets of adjacent nodes (SOAN): A fast method for computing suboptimal paths in protein dynamic networks.

Molecular physics·2026

Same author

Na<sup>+</sup>/K<sup>+</sup>-ATPase, cardiac glycosides, and tumor immunity.

Frontiers in chemistry·2026

Same author

Activation of mosquito and human transient receptor potential ankyrin 1 (TRPA1) channels by the natural drimane sesquiterpene cinnamodial.

Pesticide biochemistry and physiology·2026

Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 18, 2026

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

Molecular dynamics.

Xiaolin Cheng¹, Ivaylo Ivanov

¹Oak Ridge National Laboratory, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA. chengx@ornl.gov

Methods in Molecular Biology (Clifton, N.J.)

|September 26, 2012

Summary

This summary is machine-generated.

Molecular dynamics (MD) simulations offer detailed insights into biological mechanisms. This review explores using MD for computational toxicity, including enzyme flexibility and ion channel conduction barriers.

More Related Videos

New Features in Visual Dynamics 3.0

New Features in Visual Dynamics 3.0

Published on: August 9, 2024

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Published on: September 1, 2023

Related Experiment Videos

Last Updated: May 18, 2026

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

New Features in Visual Dynamics 3.0

New Features in Visual Dynamics 3.0

Published on: August 9, 2024

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Published on: September 1, 2023

Area of Science:

Computational biology
Biophysics
Toxicology

Background:

Molecular dynamics (MD) simulations are powerful tools for understanding biological processes at the atomic level.
MD involves calculating interatomic forces and integrating Newton's equations of motion to simulate atomic movement.
This technique has broad applications in various fields of biological and chemical research.

Purpose of the Study:

To provide an overview of applying MD simulations to computational toxicity assessments.
To illustrate the utility of MD in studying enzyme flexibility and ion channel function.

Main Methods:

Standard MD simulations to assess the flexibility of cytochrome P450 (CYP) enzymes.
Advanced MD simulations to investigate the ion conduction barrier in nicotinic acetylcholine receptors (nAChR).

Main Results:

MD simulations can reveal the dynamic behavior and flexibility of enzymes like CYP.
Advanced MD can quantify the energy barriers associated with ion transport through membrane proteins such as nAChR.

Conclusions:

MD simulations are valuable for detailed mechanistic studies in computational toxicology.
The presented case studies highlight the versatility of MD for investigating both enzyme dynamics and ion channel properties.