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Related Concept Videos

Facilitated Diffusion01:16

Facilitated Diffusion

The plasma membrane, a critical structure in cellular biology, houses an array of transporters, or carrier proteins, interspersed within its lipid bilayer. These proteins play a crucial role in solute transport through facilitated diffusion, a form of passive diffusion that uses transporters to move the molecules across the membrane.
In this process, substrates such as organic compounds and ions interact with a transporter on one side, triggering conformational changes in proteins that enable...
Facilitated Transport01:19

Facilitated Transport

The chemical and physical properties of plasma membranes cause them to be selectively permeable. Since plasma membranes have both hydrophobic and hydrophilic regions, substances need to be able to transverse both regions. The hydrophobic area of membranes repels substances such as charged ions. Therefore, such substances need special membrane proteins to cross a membrane successfully. In  facilitated transport, also known as facilitated diffusion, molecules and ions travel across a membrane via...
Facilitated Transport01:19

Facilitated Transport

The chemical and physical properties of plasma membranes cause them to be selectively permeable. Since plasma membranes have both hydrophobic and hydrophilic regions, substances need to be able to transverse both regions. The hydrophobic area of membranes repels substances such as charged ions. Therefore, such substances need special membrane proteins to cross a membrane successfully. In  facilitated transport, also known as facilitated diffusion, molecules and ions travel across a membrane via...
Physiological Pharmacokinetic Models: Blood Flow-Limited Versus Diffusion-Limited Models00:57

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

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...
The Significance of Membrane Transport01:44

The Significance of Membrane Transport

The transport of solutes across the cell membrane is essential for metabolic processes, like maintaining cell size and volume, generating the action potential, exchanging nutrients and gases, etc. Membrane transport can be either passive or active. It can be simple diffusion, facilitated, or mediated transport aided by transport proteins such as transporters and channels.
Transporters facilitate either an active or passive movement of solutes. They can allow a single-molecule transport down its...
Model Approaches for Pharmacokinetic Data: Distributed Parameter Models01:06

Model Approaches for Pharmacokinetic Data: Distributed Parameter Models

Pharmacokinetic models are mathematical constructs that represent and predict the time course of drug concentrations in the body, providing meaningful pharmacokinetic parameters. These models are categorized into compartment, physiological, and distributed parameter models.
The distributed parameter models are specifically designed to account for variations and differences in some drug classes. This model is particularly useful for assessing regional concentrations of anticancer or...

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Related Experiment Video

Updated: May 19, 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

Computational models for large-scale simulations of facilitated diffusion.

Nicolae Radu Zabet1, Boris Adryan

  • 1Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1QR, UK. n.r.zabet@gen.cam.ac.uk

Molecular Biosystems
|August 16, 2012
PubMed
Summary
This summary is machine-generated.

Transcription factors find target DNA sites using facilitated diffusion, a mix of 3D movement and 1D DNA walks. Stochastic simulations can help answer remaining questions about this gene regulation search mechanism.

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Related Experiment Videos

Last Updated: May 19, 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

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies
07:31

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Published on: September 1, 2023

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

Area of Science:

  • Molecular Biology
  • Biophysics
  • Computational Biology

Background:

  • Gene regulation relies on transcription factors binding specific genomic sites.
  • Transcription factors are low-abundance proteins searching a vast genome.
  • The search process is rapid, suggesting an efficient mechanism.

Purpose of the Study:

  • To review the current understanding of the facilitated diffusion mechanism for transcription factor binding.
  • To identify knowledge gaps and unanswered questions regarding facilitated diffusion.
  • To advocate for the use of stochastic simulations in addressing these questions.

Main Methods:

  • Review of existing literature on transcription factor binding and facilitated diffusion.
  • Discussion of the principles of three-dimensional diffusion and one-dimensional random walks on DNA.
  • Exploration of the utility of stochastic simulations for modeling these processes.

Main Results:

  • Facilitated diffusion combines 3D diffusion and 1D DNA translocation for efficient target searching.
  • Several key questions regarding the dynamics and regulation of this search remain unanswered.
  • Stochastic simulations offer a powerful computational approach to investigate these complex mechanisms.

Conclusions:

  • Facilitated diffusion is a crucial mechanism for rapid and specific transcription factor binding.
  • Further research using computational modeling, particularly stochastic simulations, is needed to fully elucidate the process.
  • Defining necessary biological parameters for accurate computational models is essential for advancing our understanding.