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Scientific-Computing

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.

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

Implementing the Müller-Brown Potential in PyTorch

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

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

Müller-Brown Potential in PyTorch

PyTorch implementation of the Müller-Brown potential with performance optimizations, MD simulations, and analytical vs …...

Scientific Computing
Velocity Autocorrelation Function showing the signature negative region characteristic of liquid dynamics and the cage effect discovered by Rahman

Rahman's 1964 Liquid Argon Simulation Replication

Replication of Rahman's 1964 molecular dynamics simulation using modern LAMMPS and Python, achieving quantitative …...

Scientific Computing
Velocity Autocorrelation Function showing the signature negative region characteristic of liquid dynamics and the cage effect discovered by Rahman

Replicating Rahman's 1964 Liquid Argon Simulation

Recreating the foundational 1964 molecular dynamics simulation with modern Python and LAMMPS, testing whether Rahman's …...

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 …...

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 …

Computational Chemistry
Ball model representation of a crystal surface with steps, kinks, adatoms, and vacancies showing various surface features

LAMMPS Tutorial: Copper Adatom Diffusion

LAMMPS tutorial for copper surface diffusion simulation and ML training data generation. Includes setup, analysis, and …

Computational Chemistry
Ball model representation of a crystal surface with steps, kinks, adatoms, and vacancies showing various surface features

Platinum Adatom Diffusion on Pt(100) Surface

LAMMPS tutorial for platinum adatom diffusion simulation and ML training data. Learn how heavier atoms behave …

Computational Chemistry

Generating Mini-Protein Trajectories with GROMACS

Systematic GROMACS workflows for simulating mini-proteins across multiple amino acids to generate diverse MD …