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

Tight Junctions

Tight Junctions

Tight junctions are molecular seals between cells that prevent the leaking of fluids, ions, and other small solutes across cavities and compartments in multicellular organisms. They are mainly composed of claudin and occludin transmembrane proteins, and other proteins such as tricellulin and JAM (junctional adhesion molecule). All these proteins are 4-pass transmembrane proteins, except JAM, which is a single-pass transmembrane protein belonging to the immunoglobulin superfamily. The...

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.

Linear Circuits

Linear Circuits

A linear circuit is characterized by its output having a direct proportionality to its input, adhering to the linearity property, which encompasses the principles of homogeneity (scaling) and additivity. Homogeneity dictates that when the input, also referred to as the excitation, is multiplied by a constant factor, the output, known as the response, is correspondingly scaled by the same constant factor. For instance, if the current is multiplied by a constant 'k,' the voltage likewise...

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

Cooperative Binding of Transcription Regulators

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...

Trial and Error and Algorithm

Trial and Error and Algorithm

A problem-solving strategy is a plan of action used to find a solution. Different strategies have distinct action plans. Trial and error involves trying different solutions until one works. For instance, to fix a broken printer, you might check ink levels, ensure the paper tray isn't jammed, and verify the printer's connection to your laptop. This method can be time-consuming but is commonly used. Thomas Edison, for example, used trial and error to find a suitable filament for the light...

You might also read

Related Articles

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

Sort by

Same author

[Trends and projections of global and Chinese disease burden of lower respiratory tract infections, 1990-2021: a multi-model analysis based on Global Burden of Disease Study data].

Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi·2025

Same author

Synovial chondromatosis in a patient with atypical rheumatoid arthritis confirmed by clinical, radiographic, and pathological evidence: a case report.

Scandinavian journal of rheumatology·2025

Same author

Antiprotons and Elementary Particles over a Solar Cycle: Results from the Alpha Magnetic Spectrometer.

Physical review letters·2025

Same author

Solar Modulation of Cosmic Nuclei over a Solar Cycle: Results from the Alpha Magnetic Spectrometer.

Physical review letters·2025

Same author

[Challenges and coping strategies of cancer screening research and practice in China: Taking esophageal cancer as an example].

Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi·2024

Same author

Zhou et al. Reply.

Physical review letters·2024

Same journal

Quantum simulation of alignment dependent differential cross sections in co-propagating molecular beams at cold collision energies.

The Journal of chemical physics·2026

Same journal

Non-additive ion effects on the coil-globule equilibrium of a generic polymer in aqueous salt solutions.

The Journal of chemical physics·2026

Same journal

Insights into the unexpected small reduction of the temperature of maximum density of water by lithium chloride addition.

The Journal of chemical physics·2026

Same journal

Optical frequency comb double-resonance spectroscopy of the 9030-9175 cm-1 states of ethylene.

The Journal of chemical physics·2026

Same journal

Time reversal breaking of colloidal particles in cells.

The Journal of chemical physics·2026

Same journal

Photodynamics of amino acids under UV excitation: Extraterrestrial amino acids.

The Journal of chemical physics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 27, 2026

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

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

Published on: May 20, 2020

Linear scaling algorithm for tight-binding molecular dynamics simulations.

Z H He¹, X B Ye², B C Pan¹

¹Key Laboratory of Strongly-Coupled Quantum Matter Physics, Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.

The Journal of Chemical Physics

|March 24, 2019

Summary

This summary is machine-generated.

A new linear scaling algorithm for large-scale tight-binding molecular dynamics simulations was developed. This divide-and-conquer method accurately calculates physical properties of large systems, offering efficiency and reduced memory usage.

More Related Videos

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

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

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

Related Experiment Videos

Last Updated: Jan 27, 2026

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

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

Published on: May 20, 2020

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

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

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

Area of Science:

Computational physics
Materials science
Quantum chemistry

Background:

Linear scaling (O(N)) methods enable theoretical treatment of large atomic systems.
Efficient algorithms are crucial for large-scale molecular dynamics simulations.

Purpose of the Study:

To develop a novel linear scaling algorithm for tight-binding molecular dynamics.
To enable accurate simulation of large systems without full matrix diagonalization.

Main Methods:

A divide-and-conquer approach was implemented, dividing the system into subsystems.
The method avoids constructing the density matrix or electronic density.
Physical properties are accessed through subsystem calculations.

Main Results:

The algorithm was applied to a tungsten metallic system.
Results for atomic structures, melting point, defect formation energy, and electronic properties matched exact diagonalization.
The method demonstrated linear scaling complexity and high parallel efficiency.

Conclusions:

The proposed method is effective for large-scale tight-binding molecular dynamics simulations.
It offers advantages in linear scaling, memory consumption, and parallel efficiency.
This approach facilitates the study of complex, large material systems.