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

Block Diagram Reduction01:22

Block Diagram Reduction

183
The process of deriving the transfer function of a control system often involves reducing its block diagram to a single block. This simplification can be achieved through a series of strategic operations, including relocating branch points and comparators. These operations preserve the overall function of the system while allowing for easier manipulation and combination of blocks.
The first step in this process is the identification and relocation of a branch point. A branch point, where a...
183
Dynamic Equilibrium02:20

Dynamic Equilibrium

50.9K
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;...
50.9K
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

2.1K
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...
2.1K
Non-equilibrium in the Cell01:16

Non-equilibrium in the Cell

4.3K
An important concept in studying metabolism and energy is that of chemical equilibrium. Most chemical reactions are reversible. They can proceed in both directions, releasing energy into their environment in one direction, and absorbing it from the environment in the other direction. The same is true for the chemical reactions involved in cell metabolism, such as the breaking down and building up of proteins into and from individual amino acids, respectively. Reactants within a closed system...
4.3K
Redox Equilibria: Overview01:23

Redox Equilibria: Overview

544
A reduction-oxidation reaction is commonly called a redox reaction. In a redox reaction, electrons are transferred from one species to another rather than being shared between or among atoms. The reducing agent or reductant is the species that loses electrons and gets oxidized in the process. The species that gains electrons and gets reduced in the process is the oxidizing agent or oxidant. Redox reactions are represented as two separate equations called half-reactions, where one equation...
544
Fundamental Mathematical Principles in Pharmacokinetics: Calculus and Graphs01:21

Fundamental Mathematical Principles in Pharmacokinetics: Calculus and Graphs

1.2K
The fundamental mathematical principles, such as calculus and graphs, play crucial roles in analyzing drug movement and determining pharmacokinetic parameters. Differential calculus examines rates of change and helps to determine the dissolution rate of drugs in biofluids, as well as how drug concentrations change over time. For instance, it can help calculate the rate of elimination of a drug from the body based on its concentration-time profile.
On the other hand, integral calculus focuses on...
1.2K

You might also read

Related Articles

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

Sort by
Same author

Parametric Sensitivity Analysis of Oscillatory Delay Systems with an Application to Gene Regulation.

Bulletin of mathematical biology·2017
Same journal

Phenotypic plasticity trade-offs in an age-structured model of bacterial growth under stress.

Journal of mathematical biology·2026
Same journal

Intraspecific interactions facilitate mutualism across multilayer networks under weak selection.

Journal of mathematical biology·2026
Same journal

A two-species competition model on a compact metric graph for the invasion and competition of Aedes Aegypti and Aedes Albopictus mosquitoes in Florida.

Journal of mathematical biology·2026
Same journal

Superinfection and the hypnozoite reservoir for Plasmodium vivax: a multitype branching process approximation.

Journal of mathematical biology·2026
Same journal

Correction to: Superinfection and the hypnozoite reservoir for Plasmodium vivax: a general framework.

Journal of mathematical biology·2026
Same journal

Stoichiometric balance and sustained rhythms.

Journal of mathematical biology·2026
See all related articles

Related Experiment Video

Updated: Jun 13, 2025

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

2.1K

Graph-based, dynamics-preserving reduction of (bio)chemical systems.

Marc R Roussel1, Talmon Soares2

  • 1Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada. roussel@uleth.ca.

Journal of Mathematical Biology
|September 13, 2024
PubMed
Summary
This summary is machine-generated.

This study introduces a parameter-independent method to simplify complex biochemical models by identifying essential reaction subnetworks, called critical fragments, that preserve key system dynamics like oscillations and bistability.

Keywords:
Chemical reaction networksControl of gene expressionGraph-theoretical methodsMass-action modelingModel reductionNitric oxide metabolism

More Related Videos

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

17.6K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.1K

Related Experiment Videos

Last Updated: Jun 13, 2025

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

2.1K
A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

17.6K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.1K

Area of Science:

  • Biochemistry
  • Systems Biology
  • Chemical Engineering

Background:

  • Complex biochemical models often contain numerous parameters, making analysis challenging.
  • Identifying essential components for specific dynamics (e.g., oscillations, bistability) is crucial for understanding biological systems.
  • Model reduction techniques are needed to manage complexity and parameter uncertainty in (bio)chemical systems.

Purpose of the Study:

  • To develop a dynamics-preserving model reduction scheme for mass-action biochemical systems.
  • To identify and preserve critical fragments (instability-generating subnetworks) within larger models.
  • To apply these reduction methods to a specific biological case study.

Main Methods:

  • Model reduction based on critical fragments, focusing on structural conditions for instability.
  • Parameter-independent analysis to ensure robustness.
  • Application to a model of nitric oxide detoxification enzyme (Hmp) synthesis in Escherichia coli.

Main Results:

  • A method for reducing mass-action biochemical models while preserving essential dynamics.
  • Identification of critical fragments that govern system behavior, independent of specific parameter values.
  • Successful application to an E. coli model exhibiting bistability.

Conclusions:

  • Parameter-independent model reduction using critical fragments is an effective strategy for simplifying complex biochemical systems.
  • This approach facilitates the analysis of specific dynamical behaviors like bistability.
  • The method offers a valuable tool for studying large-scale (bio)chemical models with parametric uncertainties.