用扩散模型高效采样罕见构象,精准计算自由能。
Enhanced Diffusion Sampling: Efficient Rare Event Sampling and Free Energy Calculation with Diffusion Models
- 通过受控引导生成偏差样本,再精确重加权还原平衡态
- 三种算法在蛋白质折叠等系统中实现毫秒至小时级准确估算
- 适合需要快速高精度自由能计算的生物分子模拟研究者
稀有事件采样长期制约分子动力学模拟,尤其在生物分子体系中。尽管如BioEmu等扩散模型已能高效生成复杂分子分布的独立样本,消除了过渡态采样成本,但在计算依赖罕见平衡态的可观测量(如折叠自由能)时仍面临挑战。本文提出增强扩散采样框架,可在保持无偏热力学估计的前提下高效探索稀有事件区域。核心思路是设计定量精确的引导协议生成偏差系综,并通过精确重加权恢复平衡统计。我们实现了三种算法:UmbrellaDiff(基于扩散模型的伞形采样)、MetaDiff(元动力学的批处理类比)和ΔG-Diff(通过倾斜系综计算自由能差)。在模型系统、蛋白质折叠景观及折叠自由能计算中,方法实现快速、准确、可扩展的平衡性质估计,单系统耗时仅需GPU分钟至数小时,填补了扩散模型平衡采样后遗留的稀有事件采样空白。
原文摘要 · Abstract (English)
The rare-event sampling problem has long been the central limiting factor in molecular dynamics (MD), especially in biomolecular simulation. Recently, diffusion models such as BioEmu have emerged as powerful equilibrium samplers that generate independent samples from complex molecular distributions, eliminating the cost of sampling rare transition events. However, a sampling problem remains when computing observables that rely on states which are rare in equilibrium, for example folding free energies. Here, we introduce enhanced diffusion sampling, enabling efficient exploration of rare-event regions while preserving unbiased thermodynamic estimators. The key idea is to perform quantitatively accurate steering protocols to generate biased ensembles and subsequently recover equilibrium statistics via exact reweighting. We instantiate our framework in three algorithms: UmbrellaDiff (umbrella sampling with diffusion models), MetaDiff (a batchwise analogue for metadynamics), and $Δ$G-Diff (free-energy differences via tilted ensembles). Across toy systems, protein folding landscapes and folding free energies, our methods achieve fast, accurate, and scalable estimation of equilibrium properties within GPU-minutes to hours per system-closing the rare-event sampling gap that remained after the advent of diffusion-model equilibrium samplers.
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