Computational Biology
Four types of protein folding energy landscapes from left to right - smooth funnel

Funnels, Pathways, and Energy Landscapes

Foundational paper establishing the energy landscape theory, folding funnels, and the principle of minimal frustration.

Computational Chemistry
Graph Perception for Chemical Structure OCR

Graph Perception for Chemical Structure OCR

A 1990 methodological paper presenting an early OCR system for digitizing chemical structure images into connectivity …

Machine Learning Fundamentals
Visualization of inverse problem showing one input mapping to multiple valid outputs

Mixture Density Networks

Seminal 1994 paper introducing MDNs to model arbitrary conditional probability distributions using neural networks.

Computational Chemistry
Early optical recognition system converts scanned chemical diagrams to connection tables

Optical Recognition of Chemical Graphics

A 1993 prototype system for converting scanned chemical diagrams into connection tables using vectorization and …

Computational Chemistry
Five-stage pipeline for reconstructing chemical molecules from raster images

Reconstruction of Chemical Molecules from Images

A 5-module system converting raster images of chemical structures into machine-readable SDF files with custom …

Scientific Computing
Three-dimensional Brownian motion trajectory showing random walk behavior

Second-Order Langevin Equation for Field Simulations

Hyperbolic Algorithm adds second-order derivatives to Langevin dynamics, reducing systematic errors to O(ε²) for lattice …

Computational Social Science
Hierarchical Ideal Point Topic Model visualization showing political polarization

Tea Party in the House

A hierarchical probabilistic model combining roll call votes, bill text, and legislative speeches to analyze political …

Computational Chemistry
Optical chemical structure recognition example

MolRec: Rule-Based OCSR System

Rule-based system for optical chemical structure recognition using vectorization and geometric analysis, achieving 95% …

Computational Chemistry
ChemInfty: Chemical Structure Recognition in Patent Images

ChemInfty: Chemical Structure Recognition in Patent Images

Fujiyoshi et al.'s segment-based approach for recognizing chemical structures in challenging Japanese patent images with …

Computational Biology
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 constitutional alkane isomers.

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 Numbers: Two Classic Algorithms

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