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

Electrostatic Boundary Conditions

Electrostatic Boundary Conditions

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...

Electrostatic Boundary Conditions in Dielectrics

Electrostatic Boundary Conditions in Dielectrics

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.

Chemical Shift: Internal References and Solvent Effects

Chemical Shift: Internal References and Solvent Effects

In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
The internal reference compound generally used in NMR spectroscopy is tetramethylsilane (TMS). TMS is preferred because it is chemically inert, soluble in NMR solvents, and easily removable. Also, the highly shielded methyl protons in TMS yield an intense...

Interfacial Electrochemical Methods: Overview

Interfacial Electrochemical Methods: Overview

Interfacial electrochemical methods focus on the phenomena occurring at the boundary between an electrode and a solution, as opposed to bulk methods that concentrate on the solution's overall properties. These interfacial methods are classified as either static or dynamic based on the presence of a nonzero current in the electrochemical cell and the consistency of analyte concentrations. Static methods, such as potentiometry, measure the cell's potential without any significant current passing...

Potential Due to a Polarized Object

Potential Due to a Polarized Object

A neutral atom consists of a positively charged nucleus surrounded by a negatively charged electron cloud. When placed in an external electric field, the external electric force pulls the electrons and nucleus apart, opposite to the intrinsic attraction between the nucleus and the electrons. The opposing forces balance each other with a slight shift between the center of masses of the nucleus and the electron cloud, resulting in a polarized atom. On the other hand, a few molecules, like water,...

Intermolecular Forces

Intermolecular Forces

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 bonds, and dispersion...

You might also read

Related Articles

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

Sort by

Same author

High-Q two-dimensional perovskite topological laser.

Optics express·2024

Same author

Enzymatic Degradation of Deoxynivalenol with the Engineered Detoxification Enzyme Fhb7.

JACS Au·2024

Same author

Increased panicle nitrogen application improves rice yield by alleviating high-temperature damage during panicle initiation to anther development.

Physiologia plantarum·2024

Same author

Pneumocephalus and empyema in the subarachnoid space: An unusual imaging feature secondary to spinal-epidural anesthesia.

Heliyon·2024

Same author

WITHDRAWN: Chloroplast genome evolution of Berberis (Berberidaceae): Implications for phylogeny and metabarcoding.

Genomics·2024

Same author

A multi-factor combination prediction model of carbon emissions based on improved CEEMDAN.

Environmental science and pollution research international·2024

Search research articles

Related Experiment Video

Updated: May 28, 2026

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent.

Johnny Wu¹, Xia Zhen, Hujun Shen

¹Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712-1062, USA.

The Journal of Chemical Physics

|October 28, 2011

Summary

A new coarse-grain (CG) model accurately simulates polypeptide behavior, capturing essential forces like electrostatics and solvation. This efficient framework aids biomolecular modeling by reproducing atomic-level accuracy in simulations.

More Related Videos

Spatial Separation of Molecular Conformers and Clusters

Spatial Separation of Molecular Conformers and Clusters

Published on: January 9, 2014

Interactive Molecular Model Assembly with 3D Printing

Interactive Molecular Model Assembly with 3D Printing

Published on: August 13, 2020

Related Experiment Videos

Last Updated: May 28, 2026

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

Spatial Separation of Molecular Conformers and Clusters

Spatial Separation of Molecular Conformers and Clusters

Published on: January 9, 2014

Interactive Molecular Model Assembly with 3D Printing

Interactive Molecular Model Assembly with 3D Printing

Published on: August 13, 2020

Area of Science:

Computational chemistry
Biophysics
Molecular modeling

Background:

Accurate polypeptide simulation is crucial for understanding biomolecular processes.
Existing coarse-grain (CG) models often sacrifice accuracy for efficiency.
Developing transferable CG models that retain fundamental force representations is a key challenge.

Purpose of the Study:

To present a general, transferable CG framework for polypeptide simulations.
To explicitly represent fundamental intermolecular forces (electrostatic, repulsion-dispersion, solvation) at a CG level.
To validate the CG model against all-atom simulations and experimental data.

Main Methods:

Development of a CG framework using the Gay-Berne potential and electrostatic point multipole expansion.
Incorporation of solvent effects via Generalized Kirkwood theory.
Calibration against all-atom simulations of model compounds.
Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanines (5 and 12 residues).

Main Results:

The CG alanine dipeptide model quantitatively reproduces conformational energy, including electrostatic and solvation components, compared to all-atom force fields.
Simulations show CG polyalanines fold into alpha helix and beta sheet structures.
A higher "beta strand" fraction was observed in 5-residue polyalanine compared to 12-residue polyalanine.
Conformational distributions align with recent all-atom simulations and experimental findings.

Conclusions:

The presented CG framework offers a balance of accuracy and efficiency for biomolecular modeling.
The explicit representation of intermolecular forces enhances the model's predictive power.
This approach holds significant potential for advancing large-scale polypeptide and protein simulations.