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Related Concept Videos

Reaction Mechanisms03:06

Reaction Mechanisms

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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.
For instance, the decomposition of ozone appears to follow a mechanism with two steps:
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Multi-Step Reactions02:31

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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...
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Introduction to Chemical Reactions01:23

Introduction to Chemical Reactions

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All chemical reactions begin with a reactant, the general term for one or more substances entering the reaction. Sodium and chloride ions, for example, are the reactants in the production of table salt. One or more substances produced by a chemical reaction are called the product. Chemical reactions follow the law of conservation of mass, which means that matter cannot be created nor destroyed in a chemical reaction. The components of the reactants—the number of atoms and the...
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Ribozymes02:47

Ribozymes

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The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can...
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Reaction Mechanisms: Rate-limiting Step Approximation01:29

Reaction Mechanisms: Rate-limiting Step Approximation

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The rate-determining step, or RDS, in a chemical reaction is the slowest step that determines the overall reaction rate. It is identified by using the observed rate law and typically involves approximation methods like the RDS approximation or the steady-state approximation.In the RDS approximation, also known as the rate-limiting-step or equilibrium approximation, the reaction mechanism consists of one or more reversible reactions near equilibrium, followed by a slower RDS, and then one or...
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Chemical Reactions02:26

Chemical Reactions

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A balanced chemical equation provides the information of chemical formulas of the reactants and products involved in the chemical change. A reaction’s stoichiometry helps predict how much of the reactant is needed to produce the desired amount of product, or in some cases, how much product will be formed from a specific amount of the reactant.
The relative amounts of reactants and products represented in a balanced chemical equation are often referred to as stoichiometric amounts.
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Updated: Apr 16, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
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KIMMDY: a biomolecular reaction emulator.

Eric Hartmann1,2, Jannik Buhr1,2, Kai Riedmiller1,2

  • 1Heidelberg Institute for Theoretical Studies, Am Schloss-Wolfsbrunnenweg 35, Heidelberg, Germany.

Nature Communications
|April 14, 2026
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Summary

We developed KIMMDY, a biomolecular reaction emulator using kinetic Monte Carlo and graph neural networks. This tool models complex biochemical reactions in large systems, improving our understanding of biological processes.

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Area of Science:

  • Computational Biology
  • Biochemistry
  • Molecular Dynamics

Background:

  • Molecular simulations are crucial in biology but struggle with modeling biochemical reactions.
  • Directly simulating biochemical reactions in large, dynamic systems is computationally intensive.

Purpose of the Study:

  • To present KIMMDY, a novel biomolecular reaction emulator.
  • To enable accurate modeling of biochemical reactions across conformational ensembles.

Main Methods:

  • Utilizing kinetic Monte Carlo simulations.
  • Employing graph neural networks for reaction rate prediction.
  • Integrating physics-based or heuristic models.

Main Results:

  • KIMMDY successfully models dynamic, large-scale systems with competing reactions.
  • Validated against experimental data for radical reactions, nucleophilic substitutions, and photodimerization.
  • Demonstrated versatility across protein and DNA systems.

Conclusions:

  • KIMMDY enhances understanding of biochemical reaction cascades.
  • Provides a tool for re-interpreting experimental data.
  • Inspires future experimental investigations in molecular biology.