Torrie and Valleau’s 1977 paper introducing importance sampling with non-physical distributions to overcome the sampling gap problem in Monte Carlo free-energy calculations, particularly for phase transitions.
Learn to align molecular structures and point clouds using the Kabsch algorithm, with differentiable implementations for modern ML frameworks.
Watch copper atoms move across a crystal surface in this molecular dynamics simulation. This video demonstrates surface diffusion mechanisms important for understanding catalysis and crystal growth processes.
Step-by-step LAMMPS tutorial for simulating copper and platinum adatom diffusion. Learn surface dynamics simulation, trajectory analysis, and how atomic mass affects diffusion for machine learning datasets.
Visualize platinum atom diffusion on crystal surfaces in this LAMMPS molecular dynamics simulation. Understand surface mobility mechanisms crucial for catalysis and materials design.
A complete input-to-analysis workflow for simulating adatom diffusion on FCC metal surfaces using LAMMPS and EAM potentials, providing comparative datasets for copper and platinum that demonstrate how atomic mass and bonding strength affect surface dynamics, with automated Python analysis generating publication-ready visualizations.
A practical guide to simulating mini-proteins using GROMACS; from alanine dipeptide to tryptophan systems for ML training data generation.
An automated GROMACS pipeline for generating high-fidelity molecular dynamics datasets suitable for machine learning, simulating capped dipeptides across nine residue types with 0.1 ps resolution and atomic force extraction optimized for training Neural Network Potentials.