Molecular Dynamics

This section covers classical molecular dynamics literature from the 1980s and 1990s. Notes concentrate on foundational interatomic potential models, surface diffusion phenomena on metal surfaces (particularly platinum), and oscillatory catalytic reactions on platinum.

Computational Chemistry

Embedding energy and effective charge functions for Ni and Pd from the original EAM paper

Embedded-Atom Method: Impurities and Defects in Metals

The foundational 1984 paper introducing EAM, a semi-empirical many-body interatomic potential that incorporates density functional theory concepts to accurately simulate metallic systems while maintaining computational efficiency comparable to pair potentials.

Computational Chemistry

Protein folding funnel diagram illustrating energy landscape

Umbrella Sampling: Monte Carlo Free-Energy Estimation

Torrie and Valleau’s 1977 methodological breakthrough introducing importance sampling with non-physical distributions to overcome the sampling gap problem in Monte Carlo free-energy calculations, particularly for rare events and phase transitions.