DenoiseVAE: Learning Molecule-Adaptive Noise Distributions for Denoising-based 3D Molecular Pre-training
Summary of Liu et al.'s ICLR 2025 paper introducing DenoiseVAE, a novel pre-training framework that learns …
Computational Chemistry Summaries
Location of Saddle Points and Minimum Energy Paths by a Constrained Simplex Optimization Procedure
Summary of Müller and Brown's 1979 paper introducing a novel gradient-free method based on constrained simplex …
The Dark Side of the Forces: Assessing Non-Conservative Force Models for Atomistic Machine Learning
Summary of Bigi et al.'s 2025 paper that critically evaluates the trend of using non-conservative force models in …
Efficient and Scalable Density Functional Theory Hamiltonian Prediction through Adaptive Sparsity
Summary of Luo et al.'s 2025 paper introducing SPHNet, an SE(3)-equivariant network that uses adaptive sparsity to …
Learning Smooth and Expressive Interatomic Potentials for Physical Property Prediction
Summary of Fu et al.'s 2025 paper that bridges the gap between test-set accuracy and downstream task performance for …
Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling
Summary of Lu et al.'s 2025 paper introducing SpaceFormer, a Transformer-based framework that models the entire 3D space …
Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals
Summary of Daw and Baskes's 1984 paper that introduces the Embedded-Atom Method (EAM), a semi-empirical, many-body …
Nonphysical Sampling Distributions in Monte Carlo Free-Energy Estimation: Umbrella Sampling
Summary of Torrie and Valleau's 1977 paper that introduces Umbrella Sampling, a powerful and general importance sampling …
Correlations in the Motion of Atoms in Liquid Argon
Summary of Aneesur Rahman's 1964 paper that effectively founded the field of molecular dynamics simulation by …
Processes of Adsorption and Diffusion on Solid Surfaces
Summary of Lennard-Jones's 1932 paper introducing a potential energy surface model to unify physical and chemical …
970 Million Druglike Small Molecules for Virtual Screening in the Chemical Universe Database GDB-13
A summary of the 2009 JACS paper by Blum and Reymond introducing the GDB-13 database, an enumeration of nearly one …