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

Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

4.7K
Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
4.7K
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

1.9K
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...
1.9K

You might also read

Related Articles

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

Sort by
Same author

HCR-Proxy resolves site-specific proximal RNA microenvironments at subcompartmental resolution.

Nucleic acids research·2026
Same author

A nonavalent BODIPY with a multivalent arrangement of α-mannosides enables lectins recognition in fluorescence-based assays.

RSC chemical biology·2026
Same author

Integrative profiling of condensation-prone RNAs during early development.

Cell genomics·2025
Same author

Synthesis of a Water-Soluble BODIPY for Targeting and Assessing the Function of Endoplasmic Reticulum.

ACS bio & med chem Au·2025
Same author

A deep dive into spin-labeled polysorbate's interaction with therapeutic antibody using 2D NMR, EPR and MD simulations.

European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V·2025
Same author

Synthesis and evaluation of lipophilic fluorescent probes for the labelling of Listeria and their impact on biofilm formation.

Journal of microbiological methods·2025

Related Experiment Video

Updated: May 2, 2026

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA
12:05

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

Published on: October 1, 2017

11.0K

Recovering position-dependent diffusion from biased molecular dynamics simulations.

Ajasja Ljubetič1, Iztok Urbančič1, Janez Štrancar1

  • 1Laboratory of Biophysics, Condensed Matter Physics Department, "Jožef Stefan" Institute, 1000 Ljubljana, Slovenia.

The Journal of Chemical Physics
|March 5, 2014
PubMed
Summary

This study introduces a method to calculate diffusion coefficients from molecular dynamics (MD) trajectories. This allows extending short MD simulations to longer timescales for biophysical system analysis.

More Related Videos

Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules
10:20

Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules

Published on: September 5, 2019

7.9K
Mapping Molecular Diffusion in the Plasma Membrane by Multiple-Target Tracing MTT
12:19

Mapping Molecular Diffusion in the Plasma Membrane by Multiple-Target Tracing MTT

Published on: May 27, 2012

16.1K

Related Experiment Videos

Last Updated: May 2, 2026

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA
12:05

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

Published on: October 1, 2017

11.0K
Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules
10:20

Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules

Published on: September 5, 2019

7.9K
Mapping Molecular Diffusion in the Plasma Membrane by Multiple-Target Tracing MTT
12:19

Mapping Molecular Diffusion in the Plasma Membrane by Multiple-Target Tracing MTT

Published on: May 27, 2012

16.1K

Area of Science:

  • Biophysics
  • Computational Chemistry
  • Statistical Mechanics

Background:

  • All-atom molecular dynamics (MD) simulations offer insights into biophysical systems but are computationally expensive, limiting simulation length.
  • Simulating long-term diffusive dynamics (Langevin dynamics or Brownian motion) of user-defined collective variables (colvars) can reduce computational cost.
  • Existing MD trajectories can be used to extend simulations to millisecond timescales in the colvars subspace with minimal computational overhead.

Purpose of the Study:

  • To develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) from existing MD trajectories.
  • To analyze changes in collective variables (colvars) to extract diffusion information.
  • To provide an open-source tool for calculating and visualizing diffusion coefficients.

Main Methods:

  • Analysis of collective variable (colvar) changes within an existing molecular dynamics (MD) trajectory.
  • Development of a method to determine multidimensional anisotropic diffusion coefficients (D).
  • Application of the method to dihedral angles of alanine dipeptide as a test case.

Main Results:

  • A method was developed to calculate multidimensional anisotropic diffusion coefficients (D) from MD data.
  • Diffusion coefficients (D) were successfully obtained for the dihedral angles of alanine dipeptide.
  • An open-source Mathematica package was created for determining and visualizing diffusion coefficients in one or two dimensions.

Conclusions:

  • The developed method enables efficient calculation of diffusion coefficients from MD trajectories.
  • The open-source package facilitates the analysis and extension of biophysical simulations.
  • The package can generate diffusive trajectories when free energy and diffusion coefficients are known.