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Reaction Mechanisms

Reaction Mechanisms

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:

Basic Postulates of Kinetic Molecular Theory: Particle Size, Energy, and Collision

Basic Postulates of Kinetic Molecular Theory: Particle Size, Energy, and Collision

The ideal-gas equation, which is empirical, describes the behavior of gases by establishing relationships between their macroscopic properties. For example, Charles’ law states that volume and temperature are directly related. Gases, therefore, expand when heated at constant pressure. Although gas laws explain how the macroscopic properties change relative to one another, it does not explain the rationale behind it.

Equilibrium Conditions for a Particle

Equilibrium Conditions for a Particle

When an object is in equilibrium, it is either at rest or moving with a constant velocity. There are two types of equilibrium: static and dynamic. Static equilibrium occurs when an object is at rest, while dynamic equilibrium occurs when an object is moving with a constant velocity. In both cases, there must be a balance of forces acting on the object.
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Multi-Step Reactions

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Rate-Determining Steps

Rate-Determining Steps

Relating Reaction Mechanisms
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The concept of rate-determining step can be understood from the analogy of a 4-lane freeway with a short-stretch of traffic-bottleneck caused due to...

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

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

Published on: August 9, 2024

Particle-based simulation of non-elementary bimolecular kinetics.

Taylor Kearney¹, Mark B Flegg¹

¹Monash University, Victoria, Australia.

Mathematical Biosciences

|November 26, 2025

Summary

Particle-based simulations now directly handle complex biochemical reactions. This novel framework efficiently simulates non-elementary kinetics, reducing computational cost for systems biology research.

Keywords:

Circadian oscillations Michaelis-Menten kinetics Non-elementary bimolecular kinetics Particle-based simulation Proximity-based reaction conditions Quasi-steadystate approximation

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Area of Science:

Biochemistry
Computational Biology
Chemical Kinetics

Background:

Particle-based simulations are crucial for biochemical systems, bridging scales between molecular dynamics and reaction-diffusion models.
Current methods are limited to elementary (mass-action) kinetics, restricting the simulation of complex biological processes.

Purpose of the Study:

To develop a novel framework for directly simulating non-elementary bimolecular kinetics in particle-based simulations.
To adapt non-elementary reaction conditions, typically for trimolecular interactions, to biomolecular reactions.

Main Methods:

Implemented a novel approach using a third implicit reactant to mimic non-elementary kinetics.
Utilized an event-driven simulation framework.
Validated the method by reproducing Michaelis-Menten kinetics and simulating the Goldbeter circadian rhythm model.

Main Results:

Successfully simulated non-elementary bimolecular kinetics without explicitly modeling underlying fast elementary reactions.
Accurately reproduced Michaelis-Menten kinetics and the Goldbeter model dynamics.
Significantly reduced computational cost compared to simulating all elementary steps.

Conclusions:

The developed framework expands the scope of reaction networks accessible to particle-based simulations.
Offers a practical and computationally efficient alternative for simulating systems with non-elementary kinetics where quasi-steady-state approximations apply.