Identifying the entanglement structure of a many-body quantum state, namely how its constituents partition into unentangled blocks, is a central task in quantum information science, yet conventional tomography scales exponentially with system size. Here we introduce a scalable framework that recognizes large-scale entanglement structures directly from local correlation fingerprints. By choosing a representative local Pauli basis that satisfies a boundary-matching condition p_1 = p_R, the entire chain is read out in a single measurement configuration, keeping the measurement effort independent of system size. In noisy simulations, this single-basis protocol classifies GHZ-, W-, and cluster-type structures among 30 candidate partitions with a mean accuracy exceeding 95% for systems of up to 100 qubits. We further validate the protocol on a superconducting quantum processor, where it reliably classifies block structures for systems of up to 13 qubits before noise- and depth-induced degradation sets in at larger sizes. By mapping these failure modes explicitly, our results delineate the boundary of hardware-level scalability and point to a concrete strategy for characterizing entanglement structure on near-term quantum devices.
Protein structure predictors achieve high single-state accuracy, but it remains unclear whether they can recover functionally relevant conformational ensembles or account for the presence of ligands and/or binding partners. Here, we benchmark AlphaFold3, Boltz-2, Chai-1, and BioEmu on four canonical multi-state proteins (Pf-MATE, LAO, SecA, and β2AR), quantifying state bias and sampling breadth against experimental reference structures. Models frequently default to a dominant state represented in the PDB; small-molecule ligands have weak or inconsistent effects, while large protein partners drive clear conformational switching between states. Multiple sequence alignment (MSA)-based approaches (AF-Cluster and random subsampling) recapitulate similar biases, indicating that this behavior is not unique to newer architectures. These results underscore current limitations for multi-state protein structure prediction and structure-guided ligand discovery. TOC Graphic
Muhui Ye, Yu-Hong Wang, M. Brogi et al.· bioRxiv· 0 citations