Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling
Lu et al. introduce SpaceFormer, a Transformer that models entire 3D molecular space—not just atoms—for superior …...
Computational Chemistry
Efficient and Scalable Density Functional Theory Hamiltonian Prediction through Adaptive Sparsity
Luo et al. introduce SPHNet, using adaptive sparsity to dramatically improve SE(3)-equivariant Hamiltonian prediction …...
Learning Smooth and Expressive Interatomic Potentials for Physical Property Prediction
Fu et al. propose energy conservation as a key MLIP diagnostic and introduce eSEN, bridging test accuracy and real …...
Liquid Argon: LAMMPS Simulation
LAMMPS molecular dynamics simulation of liquid argon demonstrating fundamental liquid-state behavior and molecular …
The Dark Side of the Forces: Assessing Non-Conservative Force Models for Atomistic Machine Learning
Bigi et al. critique non-conservative force models in ML potentials, showing their simulation failures and proposing …...
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 …...
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 …...
Processes of Adsorption and Diffusion on Solid Surfaces
Lennard-Jones's 1932 foundational paper introducing potential energy surface models to unify physical and chemical …...
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 …
GDB-17: Chemical Universe Database (166B Molecules)
Dataset card for GDB-17, containing 166 billion small organic molecules representing the largest enumerated chemical …
GEOM Dataset: 3D Molecular Conformer Generation
Learn how GEOM transforms 2D molecular graphs into dynamic 3D conformer ensembles for molecular machine learning …
Invalid SMILES are Beneficial Rather than Detrimental to Chemical Language Models
Skinnider's 2024 Nature Machine Intelligence paper demonstrates that the ability to generate invalid SMILES is actually …...