README.md

Introduction to kinetic Monte Carlo (kMC) Simulations with Examples in Jupyter Notebooks

The notebooks contain the basic concepts of kinetic Monte Carlo simluations and its applications in both well-mixed and lattice systems taken from the literature.

For lattice kMC, the software named zacros is used. Its Python Wrapper can be downloaded or cloned from Zacros-Wrapper GitHub repository.

Developers

• Yifan Wang ([email protected])
• Jake Kalscheur ([email protected])

Chapters

Well-mixed kMC:

1. Intro to kMC with a Michaelis-Menten Example

2. Samlping and Computing Average with a Gene Expression Mechanism

3. Modeling Oscilliations with an Auto Catalysis Mechanism

Lattice kMC:

4. CO Oxidation Example on Pd(111) by Zacros and Zacros Wrapper

Click to play with the interactive notebooks on your browser