What is Optical Chemical Structure Recognition (OCSR)?
A micro-review of Optical Chemical Structure Recognition (OCSR), tracing its evolution from rule-based systems to …
Scientific-Computing
Converting SMILES Strings to 2D Molecular Images
Learn how to create 2D molecular images from SMILES strings using RDKit and PIL, with proper formatting and legends.
Müller-Brown Potential
The Müller-Brown potential: a classic two-dimensional analytical benchmark for testing optimization algorithms, reaction …...
Exponential Random Number Generation: Two Classic Algorithms Compared
Compare inverse transform sampling and von Neumann's rejection method for exponential random numbers with Python …
Implementing the Müller-Brown Potential in PyTorch
Guide to implementing the Müller-Brown potential in PyTorch, comparing analytical vs automatic differentiation with …
Müller-Brown Potential in PyTorch
PyTorch implementation of the Müller-Brown potential with performance optimizations, MD simulations, and analytical vs …...
Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals
Daw and Baskes's foundational 1984 paper introducing the Embedded-Atom Method (EAM), a many-body potential for metal …...
Nonphysical Sampling Distributions in Monte Carlo Free-Energy Estimation: Umbrella Sampling
Torrie and Valleau's 1977 paper introducing Umbrella Sampling, an importance sampling technique for Monte Carlo …...
Understanding Coulomb Matrices for Molecular Machine Learning
Learn how Coulomb matrices encode 3D molecular structure for machine learning—from basic theory to Python implementation …
How Does Congress Actually Work? Data from 15K Bills
What happens to bills in Congress? Analyzing 15K+ bills from the 117th Congress to understand legislative patterns, …
Kabsch Algorithm: NumPy, PyTorch, TensorFlow, and JAX
Learn about the Kabsch algorithm for optimal point alignment with implementations in NumPy, PyTorch, TensorFlow, and JAX …
Generating Mini-Protein Trajectories with GROMACS
Systematic GROMACS workflows for simulating mini-proteins across multiple amino acids to generate diverse MD …