DIFFMD: A Geometric Diffusion Model for Molecular Dynamics Simulations

Fang Wu, Stan Z. Li

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

1 Scopus citations

Abstract

Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on intermediate variables such as the potential energy or force fields to update atomic positions, which requires additional computations to perform back-propagation. To waive this requirement, we propose a novel model called DIFFMD by directly estimating the gradient of the log density of molecular conformations. DIFFMD relies on a score-based denoising diffusion generative model that perturbs the molecular structure with a conditional noise depending on atomic accelerations and treats conformations at previous timeframes as the prior distribution for sampling. Another challenge of modeling such a conformation generation process is that a molecule is kinetic instead of static, which no prior works have strictly studied. To solve this challenge, we propose an equivariant geometric Transformer as the score function in the diffusion process to calculate corresponding gradients. It incorporates the directions and velocities of atomic motions via 3D spherical Fourier-Bessel representations. With multiple architectural improvements, we outperform state-of-the-art baselines on MD17 and isomers of C7O2H10 datasets. This work contributes to accelerating material and drug discovery.

Original languageEnglish
Title of host publicationAAAI-23 Technical Tracks 4
EditorsBrian Williams, Yiling Chen, Jennifer Neville
PublisherAAAI press
Pages5321-5329
Number of pages9
ISBN (Electronic)9781577358800
StatePublished - 27 Jun 2023
Externally publishedYes
Event37th AAAI Conference on Artificial Intelligence, AAAI 2023 - Washington, United States
Duration: 7 Feb 202314 Feb 2023

Publication series

NameProceedings of the 37th AAAI Conference on Artificial Intelligence, AAAI 2023
Volume37

Conference

Conference37th AAAI Conference on Artificial Intelligence, AAAI 2023
Country/TerritoryUnited States
CityWashington
Period7/02/2314/02/23

ASJC Scopus subject areas

  • Artificial Intelligence

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