Jove
Visualize
Contact Us

Related Concept Videos

Cellular Membranes and Drug Transport01:24

Cellular Membranes and Drug Transport

1.7K
Drugs must traverse multiple biological barriers, such as multi-layered skin, single-layered intestinal epithelium, and the plasma membrane, to reach their target sites within the body. The plasma membrane, a highly structured composite of phospholipids, carbohydrates, and proteins, is the cell's protective boundary, facilitating selective substance exchange.
Phospholipids arrange themselves into a bilayer, with hydrophilic heads oriented outward and hydrophobic tails facing inward.
1.7K
Subatomic Particles03:37

Subatomic Particles

114.2K
Dalton was only partially correct about the particles that make up matter. All matter is composed of atoms, and atoms are composed of three smaller subatomic particles: protons, neutrons, and electrons. These three particles account for the mass and the charge of an atom.
114.2K
The Nucleosome Core Particle02:10

The Nucleosome Core Particle

14.6K
Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
14.6K
The Nucleosome Core Particle01:12

The Nucleosome Core Particle

2.5K
Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their primary aim is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. On the other hand, they must allow polymerase enzymes to access histone-bound DNA during...
2.5K
Dynamic Equilibrium02:20

Dynamic Equilibrium

63.5K
A reversible chemical reaction represents a chemical process that proceeds in both forward (left to right) and reverse (right to left) directions. When the rates of the forward and reverse reactions are equal, the concentrations of the reactant and product species remain constant over time and the system is at equilibrium. A special double arrow is used to emphasize the reversible nature of the reaction. The relative concentrations of reactants and products in equilibrium systems vary greatly;...
63.5K
Basic Postulates of Kinetic Molecular Theory: Particle Size, Energy, and Collision02:43

Basic Postulates of Kinetic Molecular Theory: Particle Size, Energy, and Collision

38.0K
The ideal-gas equation, which is empirical, describes the behavior of gases by establishing relationships between their macroscopic properties. For example, Charles’ law states that volume and temperature are directly related. Gases, therefore, expand when heated at constant pressure. Although gas laws explain how the macroscopic properties change relative to one another, it does not explain the rationale behind it.
38.0K

You might also read

Related Articles

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

Sort by
Same author

Progress in deep Markov state modeling: Coarse graining and experimental data restraints.

The Journal of chemical physics·2021
Same author

Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics.

The Journal of chemical physics·2021
Same author

Hydrodynamic coupling for particle-based solvent-free membrane models.

The Journal of chemical physics·2021
Same author

Machine learning implicit solvation for molecular dynamics.

The Journal of chemical physics·2021
Same author

Multi-body effects in a coarse-grained protein force field.

The Journal of chemical physics·2021
Same author

Convergence to the fixed-node limit in deep variational Monte Carlo.

The Journal of chemical physics·2021
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 Experiment Video

Updated: Feb 15, 2026

Mass-Sensitive Particle Tracking to Characterize Membrane-Associated Macromolecule Dynamics
13:30

Mass-Sensitive Particle Tracking to Characterize Membrane-Associated Macromolecule Dynamics

Published on: February 18, 2022

5.0K

Particle-based membrane model for mesoscopic simulation of cellular dynamics.

Mohsen Sadeghi1, Thomas R Weikl2, Frank Noé1

  • 1Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany.

The Journal of Chemical Physics
|February 3, 2018
PubMed
Summary

We developed a computationally efficient, coarse-grained model for lipid bilayer membranes, suitable for reaction-diffusion simulations. This particle-based model accurately captures membrane mechanics and fluidity, enabling studies of cellular processes.

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

3.2K
A Model Membrane Platform for Reconstituting Mitochondrial Membrane Dynamics
10:31

A Model Membrane Platform for Reconstituting Mitochondrial Membrane Dynamics

Published on: September 2, 2020

8.1K

Related Experiment Videos

Last Updated: Feb 15, 2026

Mass-Sensitive Particle Tracking to Characterize Membrane-Associated Macromolecule Dynamics
13:30

Mass-Sensitive Particle Tracking to Characterize Membrane-Associated Macromolecule Dynamics

Published on: February 18, 2022

5.0K
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

3.2K
A Model Membrane Platform for Reconstituting Mitochondrial Membrane Dynamics
10:31

A Model Membrane Platform for Reconstituting Mitochondrial Membrane Dynamics

Published on: September 2, 2020

8.1K

Area of Science:

  • Computational Biophysics
  • Materials Science
  • Biomembranes

Background:

  • Simulating lipid bilayer membranes is crucial for understanding cellular processes.
  • Existing models often lack computational efficiency or solvent-free capabilities.
  • Bridging coarse-grained and reaction-diffusion simulations requires specialized membrane models.

Purpose of the Study:

  • To present a simple, computationally efficient, coarse-grained, and solvent-free model for lipid bilayer membranes.
  • To parameterize the model for accurate reproduction of local membrane mechanics and in-plane fluidity.
  • To validate the model's physical accuracy through multiple quantitative tests and comparisons with continuum models.

Main Methods:

  • Developed a particle-based model where particles represent coarse patches of lipid monolayers.
  • Incorporated nearest-neighbor bond-stretching and angle-bending interactions, parameterized using Helfrich energy density.
  • Implemented in-plane fluidity via Monte Carlo bond-flipping moves.
  • Validated the model using power spectrum analysis of undulations, bending stiffness recovery, area compressibility modulus, shear flow viscosity, and nanoparticle interaction simulations.

Main Results:

  • The model accurately reproduces equilibrium thermal undulations and recovers input bending stiffness.
  • Isothermal area compressibility modulus is tunable and independent of bending rigidity.
  • Effective in-plane viscosity is measurable and can be specified.
  • Simulations of membrane deformation and budding, including interaction with nanoparticles, align with continuum model predictions.
  • The model successfully mimics expected budding behavior.

Conclusions:

  • The developed coarse-grained, solvent-free model offers a computationally efficient and physically accurate representation of lipid bilayer membranes.
  • It effectively captures essential membrane properties like mechanics, fluidity, and large-scale deformations.
  • The model is highly practical for integration with particle-based reaction-diffusion and ultra coarse-grained molecular dynamics simulations of biological systems.