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Scientific-Computing

Scientific Computing
Grid of complex molecular structures rendered from SELFIES and SMILES strings

Molecular String Renderer: Robust Visualization Infrastructure

A robust, type-safe Python library for converting chemical string representations (SMILES, SELFIES, InChI) into …...

Computational Chemistry
The transformation from a 2D chemical structure image to a SMILES representation

What is Optical Chemical Structure Recognition (OCSR)?

A micro-review of Optical Chemical Structure Recognition (OCSR), tracing its evolution from rule-based systems to …

Computational Chemistry
Aspirin molecular structure generated from SMILES string

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.

Computational Chemistry
Müller-Brown Potential Energy Surface showing the three minima and two saddle points

Müller-Brown Potential

The Müller-Brown potential: a classic two-dimensional analytical benchmark for testing optimization algorithms, reaction …...

Scientific Computing
Comparison of exponential sampling methods showing histograms from both inverse transform and von Neumann methods overlaid with the theoretical exponential distribution

Exponential Random Number Generation: Two Classic Algorithms Compared

Compare inverse transform sampling and von Neumann's rejection method for exponential random numbers with Python …

Computational Chemistry
Müller-Brown Potential Energy Surface showing the three minima and two saddle points

High-Performance Müller-Brown Potential: A PyTorch Testbed for Machine Learning and Molecular Dynamics

High-performance, GPU-accelerated PyTorch framework for the Müller-Brown potential, featuring JIT compilation, …...

Computational Chemistry
Müller-Brown Potential Energy Surface showing the three minima and two saddle points

Implementing the Müller-Brown Potential in PyTorch

Guide to implementing the Müller-Brown potential in PyTorch, comparing analytical vs automatic differentiation with …

Computational Chemistry

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 …...

Computational Chemistry

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 …...

Computational Chemistry
Coulomb matrix heatmap visualization showing molecular structure encoding on logarithmic scale

Understanding Coulomb Matrices for Molecular Machine Learning

Learn how Coulomb matrices encode 3D molecular structure for machine learning from basic theory to Python implementation …

Computational Social Science
Top features for Economics and Public Finance policy classification across Congresses

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, …

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 …