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

Force and Potential Energy in One Dimension01:13

Force and Potential Energy in One Dimension

6.6K
Force can be calculated from the expression for potential energy, which is a function of position. The component of a conservative force, in a particular direction, equals the negative of the derivative of the corresponding potential energy with respect to the displacement in that direction. For regions where potential energy changes rapidly with displacement, the work done and force is maximum. Also, when force is applied along the positive coordinate axis, the potential energy decreases with...
6.6K
Valence Bond Theory02:42

Valence Bond Theory

11.6K
Coordination compounds and complexes exhibit different colors, geometries, and magnetic behavior, depending on the metal atom/ion and ligands from which they are composed. In an attempt to explain the bonding and structure of coordination complexes, Linus Pauling proposed the valence bond theory, or VBT, using the concepts of hybridization and the overlapping of the atomic orbitals. According to VBT, the central metal atom or ion (Lewis acid) hybridizes to provide empty orbitals of suitable...
11.6K
Crystal Field Theory - Octahedral Complexes02:58

Crystal Field Theory - Octahedral Complexes

31.6K
Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
31.6K
Intermolecular Forces03:13

Intermolecular Forces

76.7K
Atoms and molecules interact through bonds (or forces): intramolecular and intermolecular. The forces are electrostatic as they arise from interactions (attractive or repulsive) between charged species (permanent, partial, or temporary charges) and exist with varying strengths between ions, polar, nonpolar, and neutral molecules. The different types of intermolecular forces are ion–dipole, dipole–dipole, hydrogen bonds, and dispersion; among these, dipole–dipole, hydrogen...
76.7K
Intermolecular Forces03:13

Intermolecular Forces

19.5K
19.5K
Polyprotic Acids03:38

Polyprotic Acids

34.1K
Acids are classified by the number of protons per molecule that they can give up in a reaction. Acids such as HCl, HNO3, and HCN that contain one ionizable hydrogen atom in each molecule are called monoprotic acids. Their reactions with water are:
34.1K

You might also read

Related Articles

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

Sort by
Same author

RNA fold prediction by Monte Carlo in graph space and the statistical mechanics of tertiary interactions.

RNA (New York, N.Y.)·2024
Same author

Hydration Waters Make Up for the Missing Third Hydrogen Bond in the A·T Base Pair.

ACS physical chemistry Au·2024
Same author

Experimenting with At-Home General Chemistry Laboratories During the COVID-19 Pandemic.

Journal of chemical education·2023
Same author

Host cell RecA activates a mobile element-encoded mutagenic DNA polymerase.

Nucleic acids research·2022
Same author

Nucleic acid folding simulations using a physics-based atomistic free energy model.

The Journal of chemical physics·2022
Same author

Diagrammatic approaches to RNA structures with trinucleotide repeats.

Biophysical journal·2021

Related Experiment Video

Updated: Mar 24, 2026

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

An implicit divalent counterion force field for RNA molecular dynamics.

Paul S Henke1, Chi H Mak1

  • 1Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.

The Journal of Chemical Physics
|March 17, 2016
PubMed
Summary

A new, efficient molecular dynamics model accurately simulates divalent counterions, crucial for understanding RNA structure and flexibility under varying salt conditions.

More Related Videos

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

3.4K
Nanomanipulation of Single RNA Molecules by Optical Tweezers
06:59

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

15.6K

Related Experiment Videos

Last Updated: Mar 24, 2026

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
Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

3.4K
Nanomanipulation of Single RNA Molecules by Optical Tweezers
06:59

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

15.6K

Area of Science:

  • Computational chemistry
  • Biophysics
  • Molecular modeling

Background:

  • Accurately simulating polyvalent counterions (e.g., Mg2+) in molecular dynamics is challenging for polyelectrolytes like nucleic acids.
  • These ions significantly influence electrostatic screening and intrachain interactions, impacting RNA secondary and tertiary structures.

Purpose of the Study:

  • To develop and validate a computationally efficient force field for divalent counterions in RNA molecular dynamics simulations.
  • To enable realistic reproduction of RNA structural details using both atomistic and coarse-grained models.

Main Methods:

  • Integration of a novel implicit counterion model into molecular dynamics simulations.
  • Development and parameterization of a coarse-grained RNA model compatible with the new counterion force field.
  • Analysis of RNA structural flexibility, particularly two-way junctions, under different salt concentrations.

Main Results:

  • The new model realistically reproduces key structural features of single-stranded and base-paired RNA constructs.
  • The divalent counterion model is computationally efficient and compatible with existing force fields.
  • Optimized parameters for a coarse-grained RNA model are provided.

Conclusions:

  • This new divalent counterion model offers a practical and efficient approach for simulating RNA structures.
  • The model accurately captures the influence of salt conditions on RNA structural flexibility, such as in two-way junctions.