Computational Chemistry

SELFIES: The Original Paper (Krenn et al. 2020)

A summary of the foundational 2020 paper that introduced SELFIES - the 100% robust molecular string representation …

Computational Chemistry

SMILES: The Original Paper (Weininger 1988)

A summary of David Weininger's foundational 1988 paper that introduced SMILES notation - the string-based molecular …

Machine Learning Fundamentals
Sphere packing illustration showing Shannon's geometric interpretation of channel capacity

Communication in the Presence of Noise

Shannon's 1949 foundational paper establishing information theory, channel capacity, and the sampling theorem for …...

Computational Chemistry
Protein folding energy landscape funnel showing high-energy unfolded states converging to the native state

How to Fold Graciously: The Levinthal Paradox

A perspective paper defining the Grand Challenge of protein folding: distinguishing kinetic pathways from thermodynamic …...

Computational Chemistry
Log-scale plot showing exponential growth of alkane isomer counts from C1 to C40

The Number of Isomeric Hydrocarbons of the Methane Series

Henze and Blair's 1931 JACS paper deriving exact recursive formulas for counting alkane isomers and establishing the …

Scientific Computing
Venus as seen by Mariner 10, showing swirling cloud patterns in the dense atmosphere

The Surface of Venus

A review of Basilevsky and Head's synthesis of Venus's geology and surface features, emphasizing radar imaging and …...

Scientific Computing
Velocity Autocorrelation Function showing the signature negative region characteristic of liquid dynamics

Digital Restoration: Modernizing Rahman's 1964 Argon Simulation

How I used modern software engineering (caching, vectorization, and dependency locking) to reproduce a 60-year-old …...

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

Digital Restoration: Modernizing Rahman's 1964 Argon Simulation

A high-fidelity replication of foundational molecular dynamics using modern software engineering practices: caching, …...