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

Electrostatic Boundary Conditions in Dielectrics01:27

Electrostatic Boundary Conditions in Dielectrics

2.1K
When an electric field passes from one homogeneous medium to another, crossing the boundary between the two mediums imparts a discontinuity in the electric field. This results in electrostatic boundary conditions that depend on the type of mediums the field propagates through.
Consider a case where both the mediums across a boundary are two different dielectric materials. Recall that the electric field and electric displacement are proportional and related through the material's permittivity....
2.1K
DNA as a Genetic Template02:05

DNA as a Genetic Template

28.8K
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
28.8K
Electronic Structure of Atoms02:28

Electronic Structure of Atoms

30.5K

An atom comprises protons and neutrons, which are contained inside the dense, central core called the nucleus, with electrons present around the nucleus. Taking into account the wave–particle duality of electrons and the uncertainty in position around the nucleus, quantum mechanics provides a more accurate model for the atomic structure. It describes atomic orbitals as the regions around the nucleus where electrons of discrete energy exist, characterized by four quantum...
30.5K
Molecular Models02:00

Molecular Models

45.5K
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.
45.5K
The Quantum-Mechanical Model of an Atom02:45

The Quantum-Mechanical Model of an Atom

61.6K
Shortly after de Broglie published his ideas that the electron in a hydrogen atom could be better thought of as being a circular standing wave instead of a particle moving in quantized circular orbits, Erwin Schrödinger extended de Broglie’s work by deriving what is now known as the Schrödinger equation. When Schrödinger applied his equation to hydrogen-like atoms, he was able to reproduce Bohr’s expression for the energy and, thus, the Rydberg formula governing hydrogen spectra.
61.6K
Electrostatic Boundary Conditions01:16

Electrostatic Boundary Conditions

1.1K
Consider an external electric field propagating through a homogeneous medium. When the electric field crosses the surface boundary of the medium, it undergoes a discontinuity. The electric field can be resolved into normal and tangential components. The amount by which the field changes at any boundary is given by the difference between the field components above and below the surface boundary.
The surface integral of an electric field is given by Gauss's law in integral form and is related to...
1.1K

You might also read

Related Articles

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

Sort by
Same author

hexABC seeking the physical code of DNA.

Nature communications·2026
Same author

Evolution of allostery without shape shifting: Internal dynamics drives functional diversification of a transcriptional repressor superfamily.

bioRxiv : the preprint server for biology·2026
Same author

Monoclonal antibodies against nitrated nerve growth factor reveal an oxidation-dependent pathogenic hallmark in ALS.

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

Unraveling the dual immunomodulatory and immunogenic roles of the central conserved cysteine-rich region in respiratory syncytial virus G protein.

Frontiers in microbiology·2026
Same author

Exploring elastin-like polypeptide tags and mini-intein for recombinant protein purification in Leishmaniatarentolae.

Protein expression and purification·2026
Same author

Announcement: Journal of Structural Biology: Paper of the year.

Journal of structural biology·2025

Related Experiment Video

Updated: Mar 29, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.6K

A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics.

Pablo D Dans1, Ari Zeida1, Matías R Machado1

  • 1Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay.

Journal of Chemical Theory and Computation
|December 1, 2015
PubMed
Summary

We developed a coarse-grain (CG) model for DNA molecular dynamics simulations. This model accurately reproduces DNA structures and dynamics, enabling multi-microsecond simulations with near-atomic detail.

More Related Videos

High-Speed Atomic Force Microscopy Imaging of DNA Three-Point-Star Motif Self Assembly Using Photothermal Off-Resonance Tapping
08:59

High-Speed Atomic Force Microscopy Imaging of DNA Three-Point-Star Motif Self Assembly Using Photothermal Off-Resonance Tapping

Published on: March 22, 2024

1.2K
Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
08:54

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

6.1K

Related Experiment Videos

Last Updated: Mar 29, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.6K
High-Speed Atomic Force Microscopy Imaging of DNA Three-Point-Star Motif Self Assembly Using Photothermal Off-Resonance Tapping
08:59

High-Speed Atomic Force Microscopy Imaging of DNA Three-Point-Star Motif Self Assembly Using Photothermal Off-Resonance Tapping

Published on: March 22, 2024

1.2K
Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
08:54

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

6.1K

Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Modeling

Background:

  • Coarse-grain (CG) techniques significantly extend simulation timescales for biological systems.
  • Limited CG models exist for nucleic acids, hindering large-scale DNA simulations.

Purpose of the Study:

  • To present a novel CG model for simulating DNA dynamics over multi-microsecond timescales.
  • To maintain the chemical specificity of DNA interactions within a simplified representation.

Main Methods:

  • Developed a CG model mapping nucleotides to six superatoms.
  • Employed a classical Hamiltonian with generalized Born electrostatics.
  • Validated against experimental structures, breathing dynamics, and A-to-B form transitions.

Main Results:

  • Accurately reproduced DNA structural and dynamic properties.
  • Qualitatively reproduced temperature-driven DNA melting, sensitive to ionic strength and sequence.
  • Reconstructed atomistic models from CG trajectories showed excellent agreement with all-atom simulations.

Conclusions:

  • The CG DNA model enables efficient, long-timescale molecular dynamics simulations.
  • The model preserves essential DNA recognition and conformational behavior.
  • Facilitates obtaining near-atomic detail from coarse-grained simulations.