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arXiv 提交日期: 2026-02-02
📄 Abstract - Scalable Spatio-Temporal SE(3) Diffusion for Long-Horizon Protein Dynamics

Molecular dynamics (MD) simulations remain the gold standard for studying protein dynamics, but their computational cost limits access to biologically relevant timescales. Recent generative models have shown promise in accelerating simulations, yet they struggle with long-horizon generation due to architectural constraints, error accumulation, and inadequate modeling of spatio-temporal dynamics. We present STAR-MD (Spatio-Temporal Autoregressive Rollout for Molecular Dynamics), a scalable SE(3)-equivariant diffusion model that generates physically plausible protein trajectories over microsecond timescales. Our key innovation is a causal diffusion transformer with joint spatio-temporal attention that efficiently captures complex space-time dependencies while avoiding the memory bottlenecks of existing methods. On the standard ATLAS benchmark, STAR-MD achieves state-of-the-art performance across all metrics--substantially improving conformational coverage, structural validity, and dynamic fidelity compared to previous methods. STAR-MD successfully extrapolates to generate stable microsecond-scale trajectories where baseline methods fail catastrophically, maintaining high structural quality throughout the extended rollout. Our comprehensive evaluation reveals severe limitations in current models for long-horizon generation, while demonstrating that STAR-MD's joint spatio-temporal modeling enables robust dynamics simulation at biologically relevant timescales, paving the way for accelerated exploration of protein function.

顶级标签: biology model training machine learning
详细标签: protein dynamics diffusion models se(3) equivariance molecular simulation generative modeling 或 搜索:

面向长时程蛋白质动力学的可扩展时空SE(3)扩散模型 / Scalable Spatio-Temporal SE(3) Diffusion for Long-Horizon Protein Dynamics


1️⃣ 一句话总结

这篇论文提出了一种名为STAR-MD的新型人工智能模型,它能够像‘快进’一样,高效且准确地模拟蛋白质在微秒级时间尺度上的动态变化,解决了传统模拟方法速度慢、现有生成模型难以预测长时间行为的难题。

源自 arXiv: 2602.02128