Breathing Life into a Classic: A Modern Replication of Rahman's 1964 Liquid Argon Simulation
A deep dive into a Python-based replication of Aneesur Rahman's seminal 1964 paper, exploring the foundations of molecular dynamics with modern tools …
Scientific-Computing
10 posts tagged with scientific-computing.
Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals
Summary of Daw and Baskes's 1984 paper that introduces the Embedded-Atom Method (EAM), a semi-empirical, many-body potential that became a cornerstone …
Nonphysical Sampling Distributions in Monte Carlo Free-Energy Estimation: Umbrella Sampling
Summary of Torrie and Valleau's 1977 paper that introduces Umbrella Sampling, a powerful and general importance sampling technique for overcoming the …
Various Techniques Used in Connection With Random Digits
Summary of John von Neumann's 1951 paper (transcribed by G. E. Forsythe) that lays the conceptual groundwork for modern pseudo-random number …
Correlations in the Motion of Atoms in Liquid Argon
Summary of Aneesur Rahman's 1964 paper that effectively founded the field of molecular dynamics simulation by demonstrating its power to reveal the …
Von Neumann's Trick: Generating Randomness Without a Logarithm
A Python tutorial replicating John von Neumann's clever comparison-based algorithm for exponential sampling and comparing its performance to the …
Kabsch Algorithm: NumPy, PyTorch, TensorFlow, and JAX
Learn about the Kabsch algorithm for optimal point alignment with implementations in NumPy, PyTorch, TensorFlow, and JAX for ML applications.
LAMMPS Simulation: Pt Adatom Diffusion on Pt(100) Surface
Build LAMMPS molecular dynamics simulations of platinum surface diffusion. Setup and analysis tutorial for generating trajectory data.
Generating Mini-Protein Trajectories with GROMACS
Build GROMACS workflows for simulating mini-proteins across multiple amino acids. Generate diverse MD trajectories for machine learning.
LAMMPS Adatom Diffusion Series
Molecular dynamics simulations studying atomic diffusion on metal surfaces, designed to generate high-quality trajectory data for machine learning …