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

Physiological Pharmacokinetic Models: Blood Flow-Limited Versus Diffusion-Limited Models00:57

Physiological Pharmacokinetic Models: Blood Flow-Limited Versus Diffusion-Limited Models

436
Physiological pharmacokinetic models, often called flow-limited or perfusion models, typically assume a swift drug distribution between tissue and venous blood, creating a rapid drug equilibrium. This premise is based on the idea that drug diffusion is extremely fast, and the cell membrane presents no barrier to drug permeation. In this scenario, where no drug binding occurs, the drug concentration in the tissue equals that of the venous blood leaving the tissue. This greatly simplifies the...
436
Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

6.2K
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...
6.2K
Turbulent Flow: Problem Solving01:09

Turbulent Flow: Problem Solving

545
Carbonation is a process used to dissolve carbon dioxide gas in a liquid, commonly used in the production of carbonated beverages. Achieving efficient carbonation requires careful control of temperature, pressure, and flow conditions. By adjusting these parameters, carbonation efficiency can be maximized, producing a higher concentration of CO2 in the liquid.
Temperature is a key factor in CO2 solubility. In this case, the CO2 gas and the liquid are cooled to 20°C. Lower temperatures enhance...
545
Three-Dimensional Force System:Problem Solving01:30

Three-Dimensional Force System:Problem Solving

1.5K
A three-dimensional force system refers to a scenario in which three forces act simultaneously in three different directions. This type of problem is commonly encountered in physics and engineering, where it is necessary to calculate the resultant force on the system, which can then be used to predict or analyze the behavior of the object or structure under consideration.
To solve a three-dimensional force system, first resolve each force into its respective scalar components. Do this using...
1.5K
Distribution of Molecular Speeds01:27

Distribution of Molecular Speeds

6.0K
The motion of molecules in a gas is random in magnitude and direction for individual molecules, but a gas of many molecules has a predictable distribution of molecular speeds. This predictable distribution of molecular speeds is known as the Maxwell-Boltzmann distribution. The distribution of molecular speeds in liquids is comparable to that of gases but not identical and can help to understand the phenomenon of the boiling and vapor pressure of a liquid. Consider that a molecule requires a...
6.0K
Navier–Stokes Equations01:28

Navier–Stokes Equations

2.7K
For incompressible Newtonian fluids, where density remains constant, stresses show a linear relationship with the deformation rate, defined by normal and shear stresses. Normal stresses depend on the pressure exerted on the fluid and the rate of deformation in specific directions, which determines how fluid flows under varying pressures. Shear stresses, on the other hand, act tangentially across fluid layers. They explain how adjacent fluid layers slide relative to one another, connecting...
2.7K

You might also read

Related Articles

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

Sort by
Same author

Tumor-immune trajectory context connects static tissue architecture to clinical outcomes.

bioRxiv : the preprint server for biology·2026
Same author

A Novel Computational Pipeline for Acquiring Pressure-Volume Hemodynamics of the Right Ventricle in Pulmonary Hypertension.

JACC. Heart failure·2025
Same author

BIWT: a bioinformatics walkthrough for embedding spatial multiomics in agent-based models for virtual cells.

Bioinformatics (Oxford, England)·2025
Same author

Total solar eclipse triggers dawn behavior in birds: Insights from acoustic recordings and community science.

Science (New York, N.Y.)·2025
Same author

Drug-loaded nanoparticles for cancer therapy: A high-throughput multicellular agent-based modeling study.

Journal of theoretical biology·2025
Same author

Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories.

Cell·2025
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
Same journal

KASSPer: Kinase Active Site Structure Prediction using Protein and Ligand Language Models and Its Application to Virtual Screening.

Bioinformatics (Oxford, England)·2026
Same journal

IDR searcher: a search engine solution for public image resources.

Bioinformatics (Oxford, England)·2026
Same journal

KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles.

Bioinformatics (Oxford, England)·2026
Same journal

Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.

Bioinformatics (Oxford, England)·2026
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Mar 28, 2026

A Method for Determination and Simulation of Permeability and Diffusion in a 3D Tissue Model in a Membrane Insert System for Multi-well Plates
10:33

A Method for Determination and Simulation of Permeability and Diffusion in a 3D Tissue Model in a Membrane Insert System for Multi-well Plates

Published on: February 23, 2018

26.3K

BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations.

Ahmadreza Ghaffarizadeh1, Samuel H Friedman1, Paul Macklin1

  • 1Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA 90033, USA.

Bioinformatics (Oxford, England)
|December 15, 2015
PubMed
Summary
This summary is machine-generated.

BioFVM is a new C++ computational tool that efficiently simulates the diffusion of multiple substances in 3D multicellular systems. This solver is stable, scalable, and suitable for complex biological modeling.

More Related Videos

Spot Variation Fluorescence Correlation Spectroscopy for Analysis of Molecular Diffusion at the Plasma Membrane of Living Cells
05:56

Spot Variation Fluorescence Correlation Spectroscopy for Analysis of Molecular Diffusion at the Plasma Membrane of Living Cells

Published on: November 12, 2020

3.4K
Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

2.1K

Related Experiment Videos

Last Updated: Mar 28, 2026

A Method for Determination and Simulation of Permeability and Diffusion in a 3D Tissue Model in a Membrane Insert System for Multi-well Plates
10:33

A Method for Determination and Simulation of Permeability and Diffusion in a 3D Tissue Model in a Membrane Insert System for Multi-well Plates

Published on: February 23, 2018

26.3K
Spot Variation Fluorescence Correlation Spectroscopy for Analysis of Molecular Diffusion at the Plasma Membrane of Living Cells
05:56

Spot Variation Fluorescence Correlation Spectroscopy for Analysis of Molecular Diffusion at the Plasma Membrane of Living Cells

Published on: November 12, 2020

3.4K
Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

2.1K

Area of Science:

  • Computational biology
  • Mathematical modeling
  • Biophysics

Background:

  • Multicellular computational models necessitate solving complex partial differential equations (PDEs) for substrate dynamics.
  • Simulating the release, uptake, decay, and diffusion of multiple substrates in 3D is computationally intensive.
  • Incorporating drug effects, growth factors, and signaling pathways adds further complexity to these models.

Purpose of the Study:

  • Introduce BioFVM, a novel diffusive transport solver specifically designed for biological applications.
  • Enable efficient and accurate simulation of substrate transport in large 3D multicellular systems.
  • Provide a stable and scalable computational tool for systems biology research.

Main Methods:

  • Developed BioFVM in C++ utilizing OpenMP for parallelization.
  • Implemented algorithms for simulating release, uptake, diffusion, and decay of multiple substrates.
  • Ensured stability for large time steps and achieved linear computational cost scaling.
  • Validated solutions for first-order temporal and second-order spatial accuracy.

Main Results:

  • BioFVM efficiently simulates the release, uptake, diffusion, and decay of numerous substrates in 3D.
  • The solver demonstrates stability with large time steps and linear computational cost scaling.
  • Parallelization with OpenMP allows for efficient execution on standard computing resources.
  • Solutions exhibit first-order accuracy in time and second-order accuracy in space.

Conclusions:

  • BioFVM provides a robust and efficient solution for simulating diffusive transport in multicellular systems.
  • The tool is suitable for integration into larger simulation frameworks or standalone use.
  • BioFVM facilitates advanced computational modeling in systems biology and related fields.
  • The open-source availability promotes wider adoption and development in the scientific community.