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

Multi-Step Reactions02:31

Multi-Step Reactions

8.5K
Chemical reactions often occur in a stepwise fashion involving two or more distinct reactions taking place in a sequence. A balanced equation indicates the reacting species and the product species, but it reveals no details about how the reaction occurs at the molecular level. The reaction mechanism (or reaction path) provides details regarding the precise, step-by-step process by which a reaction occurs. Each of the steps in a reaction mechanism is called an elementary reaction. These...
8.5K
Coupled Reactions01:17

Coupled Reactions

10.5K
Cellular processes such as building and breaking down complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Cells often couple the energy-releasing reaction with the energy-requiring one to carry out important cell functions. 
Energy in adenosine triphosphate or ATP molecules is easily accessible to do work. ATP powers the majority of energy-requiring cellular reactions....
10.5K
Synthesis and Decomposition Reactions02:17

Synthesis and Decomposition Reactions

37.8K
Synthesis and decomposition are two types of redox reactions. Synthesis means to make something, whereas decomposition means to break something. The reactions are accompanied by chemical and energy changes. 
37.8K
Phase I Reactions: Reductive Reactions01:27

Phase I Reactions: Reductive Reactions

482
Phase I biotransformation reductive reactions are chemical processes that modify drugs by introducing or revealing polar functional groups via reduction. Enzymes called reductases catalyze these reactions, playing a pivotal role in drug metabolism by transforming lipophilic drugs into more polar, water-soluble metabolites for easy excretion. An essential type of reductive reaction is the carbonyl group reduction, where aldehydes and ketones are reduced to alcohols. An example is the...
482
Ladder Diagrams: Complexation Equilibria01:07

Ladder Diagrams: Complexation Equilibria

559
Ladder diagrams are useful for evaluating equilibria involving metal-ligand complexes. The vertical scale of the ladder diagram represents the concentration of unreacted or free ligand, pL. The horizontal lines on the scale depict the log of stepwise formation constants for metal-ligand complexes and indicate the dominant species in all the regions.
The formation constant, K1, for the formation of Cd(NH3)2+ complex from cadmium and ammonia is 3.55 × 102. Log K1 (i.e. pNH3) is 2.55, and...
559
Ladder Diagrams: Redox Equilibria01:30

Ladder Diagrams: Redox Equilibria

702
Ladder diagrams are useful tools for understanding redox equilibrium reactions, especially the effects of concentration changes on the electrochemical potential of the reaction. The vertical axis in the redox ladder diagrams represents the electrochemical potential, E. The area of predominance is demarcated using the Nernst equation.
Consider the Fe3+/Fe2+ half-reaction, which has a standard-state potential of +0.771 V. At potentials more positive than +0.771 V, Fe3+ predominates, whereas Fe2+...
702

You might also read

Related Articles

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

Sort by
Same author

An agent-based learning model integrating sex differences in renal cell carcinoma.

Frontiers in immunology·2026
Same author

A systematic literature review of spatio-temporal graph neural network models for time series forecasting and classification.

Neural networks : the official journal of the International Neural Network Society·2025
Same author

Secure and Decentralized Hybrid Multi-Face Recognition for IoT Applications.

Sensors (Basel, Switzerland)·2025
Same author

Lightweight Vision Transformer for Frame-Level Ergonomic Posture Classification in Industrial Workflows.

Sensors (Basel, Switzerland)·2025
Same author

Automatic generation of pseudoknotted RNAs taxonomy.

BMC bioinformatics·2023
Same author

RNA secondary structure factorization in prime tangles.

BMC bioinformatics·2022
Same journal

Efficacy of Tinospora cordifolia bioactives as agonists of Smoothened (Smo) receptor to promote oligodendroglial lineage induction for remyelination-based therapy.

Journal of molecular graphics & modelling·2026
Same journal

Dynamic remodeling of USP28 by the selective inhibitor CAS-010: Insights from DFT and molecular dynamics simulations.

Journal of molecular graphics & modelling·2026
Same journal

Beyond the catalytic site: Voxilaprevir and Pasireotide as repurposed therapeutics for conformational inhibition of ADAR1.

Journal of molecular graphics & modelling·2026
Same journal

A mechanism-guided framework for prioritizing membrane-interaction anti-Vibrio peptides from peptidomics data.

Journal of molecular graphics & modelling·2026
Same journal

A multi-Level Study of 20S proteasome inhibitors: an integrated approach combining chemistry and Modelling.

Journal of molecular graphics & modelling·2026
Same journal

In silico identification of DNMT1 inhibitors from the PlantCyc database through computational approach to assess the anti-cancer potential of nutraceutical compounds in breast cancer.

Journal of molecular graphics & modelling·2026
See all related articles

Related Experiment Video

Updated: Dec 26, 2025

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

18.4K

Visualising 2-simplex formation in metabolic reactions.

Marco Piangerelli1, Stefano Maestri2, Emanuela Merelli1

  • 1Computer Science, School of Science and Technologies, University of Camerino, Via Madonna delle Carceri 7, Camerino, 62032, Italy.

Journal of Molecular Graphics & Modelling
|March 18, 2020
PubMed
Summary
This summary is machine-generated.

This study uses a multiagent system to visualize metabolic reactions like glycolysis. Topological data analysis reveals emerging patterns, offering a qualitative view of complex system behavior.

Keywords:
Interactive computationMetabolic reactionsMultiagent modelling and simulationSpatial simulatorTopological data analysis

More Related Videos

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

11.1K
Metabolic Pathway Confirmation and Discovery Through 13C-labeling of Proteinogenic Amino Acids
07:26

Metabolic Pathway Confirmation and Discovery Through 13C-labeling of Proteinogenic Amino Acids

Published on: January 26, 2012

24.9K

Related Experiment Videos

Last Updated: Dec 26, 2025

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

18.4K
Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

11.1K
Metabolic Pathway Confirmation and Discovery Through 13C-labeling of Proteinogenic Amino Acids
07:26

Metabolic Pathway Confirmation and Discovery Through 13C-labeling of Proteinogenic Amino Acids

Published on: January 26, 2012

24.9K

Area of Science:

  • Systems Biology
  • Computational Biology
  • Biophysics

Background:

  • * Current tools for visualizing molecular interactions in silico primarily focus on quantitative aspects.
  • * Visualizing the emergent behavior of complex biological systems, such as metabolic pathways, remains a challenge.
  • * A topological interpretation of interaction-as-perception in multiagent systems offers a novel approach.

Purpose of the Study:

  • * To investigate the potential of a topological approach for visualizing complex system behavior.
  • * To model and simulate the glycolysis process using a multiagent system.
  • * To apply topological data analysis to understand emergent patterns in metabolic reactions.

Main Methods:

  • * Modeling and simulation of glycolysis as a multiagent system.
  • * Performing topological data analysis on molecular perception graphs during enzymatic complex formation.
  • * Identifying simplicial structures within the graphs to represent emergent patterns.

Main Results:

  • * Visualization of emergent patterns in glycolysis simulation using topological data analysis.
  • * Characterization of metabolic reactions from a qualitative perspective through identified patterns.
  • * Correlation of topological patterns with simulation reactivity trends.

Conclusions:

  • * Topological interpretation of interaction-as-perception provides a qualitative framework for understanding complex metabolic systems.
  • * This approach can reveal emergent patterns and simulation reactivity trends in biological processes like glycolysis.
  • * The study highlights the utility of multiagent systems and topological data analysis in systems biology.