Computational Chemistry
Schematic showing atom-surface interaction using the method of images

Adsorption and Diffusion on Surfaces

Lennard-Jones's 1932 foundational paper introducing potential energy surface models to unify physical and chemical …

Scientific Computing
Molecular structure alignment showing protein conformations and RMSD calculation

Kabsch Algorithm: NumPy, PyTorch, TensorFlow, and JAX

Learn about the Kabsch algorithm for optimal point alignment with implementations in NumPy, PyTorch, TensorFlow, and JAX …

Computational Chemistry
Copper adatom trajectory on Cu(100) surface

Copper Adatom Diffusion on Cu(100): LAMMPS Simulation

LAMMPS molecular dynamics simulation of copper adatom diffusion on a Cu(100) surface, showing atomic mobility …

Computational Chemistry
Ball model representation of a crystal surface with steps, kinks, adatoms, and vacancies showing various surface features

Platinum Adatom Diffusion on Pt(100) Surface

LAMMPS tutorial for platinum adatom diffusion simulation and ML training data. Learn how heavier atoms behave …

Computational Chemistry
Schematic showing atom-surface interaction

Platinum Adatom Diffusion on Pt(100): LAMMPS Simulation

LAMMPS molecular dynamics simulation of platinum adatom diffusion on a Pt(100) surface, showing atomic mobility …

Scientific Computing
Energy conservation plot showing kinetic, potential, and total energy oscillations for a copper adatom diffusion simulation

Automated Adatom Diffusion Workflow

Python-wrapped reference implementation for surface diffusion simulations using LAMMPS and EAM potentials, with …