Computational Chemistry
Adaptive grid merging visualization for benzene molecule showing multi-resolution spatial discretization

Beyond Atoms: 3D Space Modeling for Molecular Pretraining

Lu et al. introduce SpaceFormer, a Transformer that models entire 3D molecular space (not just atoms) for superior …

Computational Chemistry
Atomic structure of a spherical fullerene

Dark Side of Forces: Non-Conservative ML Force Models

Bigi et al. critique non-conservative force models in ML potentials, showing their simulation failures and proposing …

Computational Chemistry
Spherical harmonics visualization

Efficient DFT Hamiltonian Prediction via Adaptive Sparsity

Luo et al. introduce SPHNet, using adaptive sparsity to dramatically improve SE(3)-equivariant Hamiltonian prediction …

Computational Chemistry
Atomic structure of a spherical fullerene

Learning Smooth Interatomic Potentials with eSEN

Fu et al. propose energy conservation as a key MLIP diagnostic and introduce eSEN, bridging test accuracy and real …

Computational Chemistry
Radial distribution function of liquid argon

Liquid Argon: LAMMPS Simulation

LAMMPS molecular dynamics simulation of liquid argon demonstrating fundamental liquid-state behavior and molecular …

Computational Chemistry
Embedding energy and effective charge functions for Ni and Pd from the original EAM paper

Embedded-Atom Method: Impurities and Defects in Metals

Daw and Baskes's foundational 1984 paper introducing the Embedded-Atom Method (EAM), a many-body potential for metal …

Computational Chemistry
Protein folding funnel diagram illustrating energy landscape

Umbrella Sampling: Monte Carlo Free-Energy Estimation

Torrie and Valleau's 1977 paper introducing Umbrella Sampling, an importance sampling technique for Monte Carlo …

Computational Chemistry
Schematic showing atom-surface interaction using the method of images

Adsorption and Diffusion on Surfaces

Lennard-Jones's 1932 foundational paper introducing potential energy surface models to unify physical and chemical …

Computational Chemistry
GDB-13 molecule structure showing CCCC(O)(CO)CC1CC1CN

GDB-13: Chemical Universe Database (970M Molecules)

A dataset card for the Generated Database 13 (GDB-13), a database of nearly 1 billion small organic molecules for …

Computational Chemistry
GDB-17 molecule structure showing complex polycyclic architecture

GDB-17: Chemical Universe Database (166B Molecules)

Dataset card for GDB-17, containing 166 billion small organic molecules representing the largest enumerated chemical …

Computational Chemistry
Comparison of 2D molecular graph versus 3D conformer ensemble showing latanoprost molecule in multiple conformations

GEOM Dataset: 3D Molecular Conformer Generation

Learn how GEOM transforms 2D molecular graphs into dynamic 3D conformer ensembles for molecular machine learning …

Computational Chemistry
SELFIES robustness demonstration

Invalid SMILES Benefit Chemical Language Models: A Study

Skinnider (2024) shows that generating invalid SMILES actually improves chemical language model performance through …