UniSim: A Unified Simulator for Time-Coarsened Dynamics of Biomolecules

• URL: http://arxiv.org/abs/2506.03157v2
• Date: Thu, 05 Jun 2025 07:10:52 GMT
• Title: UniSim: A Unified Simulator for Time-Coarsened Dynamics of Biomolecules
• Authors: Ziyang Yu, Wenbing Huang, Yang Liu,
• Abstract summary: We propose textbfUnified bfSimulator (UniSim), which leverages cross-domain knowledge to enhance the understanding of atomic interactions.<n>UniSim achieves highly competitive performance across small molecules, peptides, and proteins.
• Score: 17.559471937824767
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off between accuracy and efficiency, while recent deep learning-based improvements have mostly focused on single-domain molecules, lacking transferability to unfamiliar molecular systems. Therefore, we propose \textbf{Uni}fied \textbf{Sim}ulator (UniSim), which leverages cross-domain knowledge to enhance the understanding of atomic interactions. First, we employ a multi-head pretraining approach to learn a unified atomic representation model from a large and diverse set of molecular data. Then, based on the stochastic interpolant framework, we learn the state transition patterns over long timesteps from MD trajectories, and introduce a force guidance module for rapidly adapting to different chemical environments. Our experiments demonstrate that UniSim achieves highly competitive performance across small molecules, peptides, and proteins.

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