Can You Hear the Shape of a Molecule? (Part Three)
Supervised learning reveals hidden eigenvalue patterns that clustering missed, testing k-NN and logistic regression on …
Computational Chemistry
Can You Hear the Shape of a Molecule? (Part Two)
Clustering analysis reveals why Coulomb matrix eigenvalues struggle with larger alkanes, using Dunn Index and silhouette …
Can You Hear the Shape of a Molecule?
Explore molecular shape recognition using Coulomb matrix eigenvalues. Analysis of alkane isomers from data generation to …
Understanding Coulomb Matrices for Molecular Machine Learning
Learn how Coulomb matrices encode 3D molecular structure for machine learning—from basic theory to Python implementation …
Copper Adatom Diffusion on Cu(100): LAMMPS Simulation
LAMMPS molecular dynamics simulation of copper adatom diffusion on a Cu(100) surface, showing atomic mobility …
LAMMPS Tutorial: Copper Adatom Diffusion
LAMMPS tutorial for copper surface diffusion simulation and ML training data generation. Includes setup, analysis, and …
Platinum Adatom Diffusion on Pt(100) Surface
LAMMPS tutorial for platinum adatom diffusion simulation and ML training data. Learn how heavier atoms behave …
Platinum Adatom Diffusion on Pt(100): LAMMPS Simulation
LAMMPS molecular dynamics simulation of platinum adatom diffusion on a Pt(100) surface, showing atomic mobility …
Generating Mini-Protein Trajectories with GROMACS
Systematic GROMACS workflows for simulating mini-proteins across multiple amino acids to generate diverse MD …
Mini-Protein Trajectory Generation
GROMACS workflows for amino acid dipeptide trajectories across nine residue types, creating diverse MD datasets for ML …
SELFIES and the Future of Molecular String Representations
A comprehensive perspective on molecular string representations, focusing on SELFIES as a 100% robust alternative to …...
IMG2SMI: Translating Molecular Structure Images to SMILES
Campos & Ji's method for converting 2D molecular images to SMILES strings using Transformers and SELFIES representation....