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

Reaction Mechanisms03:06

Reaction Mechanisms

33.5K
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.
For instance, the decomposition of ozone appears to follow a mechanism with two steps:
33.5K
Catalysis02:50

Catalysis

32.6K
The presence of a catalyst affects the rate of a chemical reaction. A catalyst is a substance that can increase the reaction rate without being consumed during the process. A basic comprehension of a catalysts’ role during chemical reactions can be understood from the concept of reaction mechanisms and energy diagrams.
32.6K
Reaction Mechanisms: Rate-limiting Step Approximation01:29

Reaction Mechanisms: Rate-limiting Step Approximation

81
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...
81
Predicting Reaction Outcomes02:24

Predicting Reaction Outcomes

11.6K
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,...
11.6K
Heterogeneous Catalysis01:22

Heterogeneous Catalysis

129
Heterogeneous catalysis involves a catalyst in a different phase from the reactants. It is a process where the catalyst and the reactants are in distinct phases, typically solid and gas or liquid.Most heterogeneous catalysts are metals, metal oxides, or acids. The list includes transition metals like iron (Fe), cobalt (Co), nickel (Ni), palladium (Pd), platinum (Pt), chromium (Cr), manganese (Mn), tungsten (W), silver (Ag), and copper (Cu). These metals possess partially vacant d orbitals that...
129
Measuring Reaction Rates03:09

Measuring Reaction Rates

34.0K
Polarimetry finds application in chemical kinetics to measure the concentration and reaction kinetics of optically active substances during a chemical reaction. Optically active substances have the capability of rotating the plane of polarization of linearly polarized light passing through them—a feature called optical rotation. Optical activity is attributed to the molecular structure of substances. Normal monochromatic light is unpolarized and possesses oscillations of the electrical...
34.0K

You might also read

Related Articles

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

Sort by
Same author

Scalable Boltzmann generators for equilibrium sampling of large-scale materials.

Nature communications·2026
Same author

Assessing generative modeling approaches for free energy estimates in condensed matter.

The Journal of chemical physics·2026
Same author

MXtalTools: A Toolkit for Machine Learning on Molecular Crystals.

Journal of chemical information and modeling·2026
Same author

Size-Consistent Adiabatic Connection Functionals via Orbital-Based Matrix Interpolation.

Journal of chemical theory and computation·2026
Same author

Automated Machine Learning Pipeline: Large Language Models-Assisted Automated Data set Generation for Training Machine-Learned Interatomic Potentials.

Journal of chemical theory and computation·2025
Same author

An Exact Multiple-Time-Step Variational Formulation for the Committor and the Transition Rate.

The journal of physical chemistry. B·2025
Same journal

Analytic Nuclear Gradients Including Oriented External Electric Fields in a Molecule-Fixed Frame.

Journal of chemical theory and computation·2026
Same journal

Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.

Journal of chemical theory and computation·2026
Same journal

Generalizable Protein Folding Pathway Exploration with DA2-GRASP: Extending Beyond Miniproteins.

Journal of chemical theory and computation·2026
Same journal

Improving PCM in Protic Media: Markov State Models for TD-DFT Calculations.

Journal of chemical theory and computation·2026
Same journal

Efficient Coupled-Cluster Python Frameworks for Next-Generation GPUs: A Comparative Study of CuPy and PyTorch on the Hopper and Grace Hopper Architecture.

Journal of chemical theory and computation·2026
Same journal

Extending the MARTINI 3 Coarse-Grained Force Field to Polypeptoids.

Journal of chemical theory and computation·2026
See all related articles

Related Experiment Video

Updated: Apr 18, 2026

Preparation and 3D Tracking of Catalytic Swimming Devices
06:50

Preparation and 3D Tracking of Catalytic Swimming Devices

Published on: July 1, 2016

8.0K

Markov State Models for Tracking Reaction Dynamics on Catalytic Nanoparticles.

Caitlin A McCandler1, Chatipat Lorpaiboon1, Timothy C Berkelbach1,2

  • 1Initiative for Computational Catalysis, Flatiron Institute, New York, New York 10010, United States.

Journal of Chemical Theory and Computation
|April 16, 2026
PubMed
Summary
This summary is machine-generated.

Markov state models (MSMs) analyze complex catalytic dynamics. For rhodium catalysts, MSMs reveal nanoparticle effects on hydrogen interactions, improving upon standard transition state theory (TST).

More Related Videos

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

13.5K
Ligand-Mediated Nucleation and Growth of Palladium Metal Nanoparticles
11:54

Ligand-Mediated Nucleation and Growth of Palladium Metal Nanoparticles

Published on: June 25, 2018

10.9K

Related Experiment Videos

Last Updated: Apr 18, 2026

Preparation and 3D Tracking of Catalytic Swimming Devices
06:50

Preparation and 3D Tracking of Catalytic Swimming Devices

Published on: July 1, 2016

8.0K
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

13.5K
Ligand-Mediated Nucleation and Growth of Palladium Metal Nanoparticles
11:54

Ligand-Mediated Nucleation and Growth of Palladium Metal Nanoparticles

Published on: June 25, 2018

10.9K

Area of Science:

  • Physical Chemistry
  • Surface Science
  • Computational Chemistry

Background:

  • Markov state models (MSMs) are essential for analyzing complex dynamical data in heterogeneous catalysis.
  • Standard transition state theory (TST) is insufficient for complex catalytic systems with fluctuating surfaces and multiple reactants.
  • Machine-learned interatomic potentials enable feasible molecular dynamics (MD) simulations of intricate catalytic processes.

Purpose of the Study:

  • To extend Markov state models (MSMs) for dynamic coarse-graining of molecular dynamics (MD) simulation data.
  • To analyze hydrogen dynamics on rhodium catalysts with varying geometries (slab and nanoparticle) and surface concentrations.
  • To investigate the influence of nanoparticle features and hydrogen-hydrogen interactions on catalytic rates.

Main Methods:

  • Utilizing machine-learned interatomic potentials for molecular dynamics (MD) simulations.
  • Applying Markov state models (MSMs) to coarse-grain MD data and extract kinetic information.
  • Analyzing hydrogen dynamics on rhodium surfaces, comparing slab and nanoparticle geometries.

Main Results:

  • Nanoparticle features (corners, edges) significantly slow hydrogen association/dissociation rates.
  • Hydrogen-hydrogen interactions exhibit cooperative behavior, leading to nonmonotonic rate dependencies on concentration.
  • Results highlight limitations of standard transition state theory (TST) for these complex systems.

Conclusions:

  • Markov state models (MSMs) effectively capture complex dynamics in heterogeneous catalysis.
  • Nanoparticle geometry and hydrogen interactions critically influence reaction kinetics.
  • This approach provides physical insight beyond traditional methods for complex catalytic systems.