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arXiv · 2501.17319

MDDM: A Molecular Dynamics Diffusion Model to Predict Particle Self-Assembly

Kevin Ferguson·Yu-hsuan Chen·Levent Burak Kara
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Abstract

The discovery and study of new material systems rely on molecular simulations that often come with significant computational expense. We propose MDDM, a Molecular Dynamics Diffusion Model, which is capable of predicting a valid output conformation for a given input pair potential function. After training MDDM on a large dataset of molecular dynamics self-assembly results, the proposed model can convert uniform noise into a meaningful output particle structure corresponding to an arbitrary input potential. The model's architecture has domain-specific properties built-in, such as satisfying periodic boundaries and being invariant to translation. The model significantly outperforms the baseline point-cloud diffusion model for both unconditional and conditional generation tasks.

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Kevin Ferguson, Yu-hsuan Chen, Levent Burak Kara. 2025-01-28. MDDM: A Molecular Dynamics Diffusion Model to Predict Particle Self-Assembly. https://arxiv.org/abs/2501.17319

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