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

Fast Reactions01:27

Fast Reactions

Fast reactions occurring in times shorter than the time needed to mix reactants pose a unique challenge for investigation. In a liquid-phase continuous-flow system, reactants A and B are swiftly pushed into the mixing chamber, where mixing occurs within 1 ms. The reaction mixture then flows through an observation tube, and one measures light absorption to determine species concentrations at various points of the tube. This method is most appropriate when relatively large volumes of reactants...
Reaction Mechanisms: The Steady-State Approximation01:26

Reaction Mechanisms: The Steady-State Approximation

The steady-state approximation, also referred to as the quasi-steady-state approximation to differentiate it from a true steady state, is a widely used method for simplifying calculations in complex reaction mechanisms. This approach is particularly useful when dealing with multi-step reactions that involve reverse reactions or several steps, which can significantly increase mathematical complexity and make the reactions nearly unsolvable analytically.The steady-state approximation operates on...
Reaction Mechanisms: Rate-limiting Step Approximation01:29

Reaction Mechanisms: Rate-limiting Step Approximation

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...
Predicting Reaction Outcomes02:24

Predicting Reaction Outcomes

Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...
Reaction Mechanisms03:06

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:
Temperature Dependence on Reaction Rate02:55

Temperature Dependence on Reaction Rate

The Collision Theory
Atoms, molecules, or ions must collide before they can react with each other. Atoms must be close together to form chemical bonds. This premise is the basis for a theory that explains many observations regarding chemical kinetics, including factors affecting reaction rates.
The collision theory is based on the postulates that (i) the reaction rate is proportional to the rate of reactant collisions, (ii) the reacting species collide in an orientation allowing contact between...

You might also read

Related Articles

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

Sort by
Same author

DRIVE v3: Command Line Application for Identity-by-Descent Haplotype Clustering in Large Biobank Scale Data.

Genetic epidemiology·2026
Same author

Natural Language Processing for Substance Use Disorder Information Extraction: A Systematic Literature Review.

Current addiction reports·2026
Same author

Mitochondrial Haplogroups and Left Ventricular Diastolic Dysfunction in People Living With and Without HIV.

The Journal of infectious diseases·2026
Same author

Mitochondrial DNA Variation, Antiretroviral Therapy, and Incidence of Diabetes Among Men With and Without HIV.

Open forum infectious diseases·2026
Same author

The Centralized Pain Score: A Method to Identify Nociplastic Pain in Electronic Health Records.

Pain management nursing : official journal of the American Society of Pain Management Nurses·2026
Same author

Common variant approaches to study Mendelian disease gene function identify novel phenome and pathways associated with <i>PLOD3</i>.

medRxiv : the preprint server for health sciences·2025
Same journal

1,2-Aminothiol-specific conjugation for dual-color fluorescent labeling via ultrafast TAMM conjugates.

Methods in enzymology·2026
Same journal

Nitrone dipoles in bioorthogonal chemistry applications.

Methods in enzymology·2026
Same journal

Bioorthogonal labeling of sialic acid isomers for detection of glycoconjugates by mass spectrometry imaging and microscopy.

Methods in enzymology·2026
Same journal

Bioorthogonal photocatalytic proximity labeling for quantitative mapping of cell-cell interactions.

Methods in enzymology·2026
Same journal

inCu-click: Enabling copper-catalyzed click chemistry inside living cells.

Methods in enzymology·2026
Same journal

Site-specific antibody labeling via endo-S2 mediated Fc glycan remodeling.

Methods in enzymology·2026
See all related articles

Related Experiment Video

Updated: Jun 25, 2026

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

Discrete stochastic simulation methods for chemically reacting systems.

Yang Cao1, David C Samuels

  • 1Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA.

Methods in Enzymology
|February 17, 2009
PubMed
Summary
This summary is machine-generated.

Discrete stochastic chemical kinetics accounts for random, integer populations in chemical reactions, crucial for single-cell dynamics. This review covers simulation methods like Gillespie

More Related Videos

Precise Electrochemical Sizing of Individual Electro-Inactive Particles
05:03

Precise Electrochemical Sizing of Individual Electro-Inactive Particles

Published on: August 4, 2023

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
06:37

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

Related Experiment Videos

Last Updated: Jun 25, 2026

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

Precise Electrochemical Sizing of Individual Electro-Inactive Particles
05:03

Precise Electrochemical Sizing of Individual Electro-Inactive Particles

Published on: August 4, 2023

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
06:37

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

Area of Science:

  • Biochemistry
  • Chemical Kinetics
  • Computational Biology

Background:

  • Classical chemical kinetics uses deterministic differential equations, which may fail for systems with small molecular counts.
  • Cellular systems often exhibit low molecule numbers, necessitating stochastic approaches.
  • Discrete stochastic chemical kinetics models systems with integer populations and inherent randomness.

Purpose of the Study:

  • To review the fundamental theory of discrete stochastic chemical kinetics.
  • To discuss and compare major simulation methods for these systems.
  • To introduce and demonstrate an efficient hybrid simulation strategy.

Main Methods:

  • Review of Gillespie's stochastic simulation algorithm (SSA).
  • Discussion of the tau-leaping method for non-stiff biochemical systems.
  • Introduction of a hybrid SSA/tau-leaping method combining strengths of both.

Main Results:

  • The hybrid SSA/tau-leaping method offers a simple and efficient simulation strategy.
  • Implementation details and a software package for the hybrid method are provided.
  • The hybrid method is demonstrated on simple biochemical systems.

Conclusions:

  • Stochastic simulation methods are essential for accurately modeling biochemical dynamics in cellular systems.
  • The hybrid SSA/tau-leaping method provides an effective approach for simulating non-stiff biochemical systems.
  • This work facilitates the application of stochastic kinetics in computational biology.