arXiv subjects

Shijia Sun

Publications and source records attributed to Shijia Sun.

3 recordsLinked to original sources

arXiv2026

Qutrit entanglement and joint multi-parameter estimation in an optical clock platform

Quantum metrology harnesses entanglement to improve measurement precision beyond classical limits. While standard protocols rely on two-level qubits to estimate a single parameter, extending them to entangled multi-level qudits enables the optimal simultaneous estimation of multiple parameters within a single probe. However, generating such multi-level entanglement and harnessing it for joint multi-parameter estimation in atomic clocks has remained an outstanding challenge. Here, we experimentally demonstrate genuine qutrit entanglement and joint multi-parameter estimation in an optical clock platform. Leveraging control over the ground state and two fine-structure clock states of $^{88}\text{Sr}$ atoms trapped in triple-magic optical tweezers, we generate a maximally entangled two-qutrit state with a loss-postselected fidelity of F = 0.85(1), certifying genuine multi-level entanglement. Taking advantage of this high-dimensional entanglement, we theoretically construct and experimentally realize an optimal two-qutrit metrological probe state and noise-robust readout circuit to simultaneously estimate injected phases on two optical clock transitions. We observe a joint estimation variance below the ideal individual two-level sensing threshold, and show theoretically that this advantage persists at state-of-the-art atom numbers under circuit-level noise. These results demonstrate the key building blocks towards quantum information science with high-dimensional states encoded in the internal energy levels of neutral atoms.

quant-ph↗

arXiv2026

Velocity-Enabled Quantum Computing with Neutral Atoms

Realizing error-corrected logical qubits is a central goal for the current development of digital quantum computers. Neutral atoms offer the opportunity to coherently shuttle atoms for realizing efficient quantum error correction based on long-range connectivity and parallel atom transport. Nevertheless, time overheads in shuttling atoms and complex control hardware pose challenges to scaling current architectures. Here, we introduce atom velocity as a new degree of freedom in neutral-atom architectures tailored to quantum error correction. Through controlled Doppler shifts, we demonstrate velocity-selective mid-circuit state preparation and measurement on moving atoms, leaving spectator atoms unaffected. Furthermore, we achieve on-the-fly local single-qubit rotations by mapping micron-scale atom displacements to the spatial phase of global control beams. Complementing these techniques with CZ entangling gates with a fidelity of 99.86(4)%, we experimentally implement key primitives for quantum error correction and measurement-based quantum computing. We generate an eight-qubit entangled cluster state with an average stabilizer value of 0.830(4), realize an [[4,2,2]] error-detection code with 99.0(3) % logical Bell-state fidelity, and perform stabilizer measurements using a flying ancilla. By enabling selective operations on continuously moving atoms using only global beams, this velocity-enabled architecture reduces hardware overhead while minimizing shuttling and transfer delays, opening a new pathway for fast, large-scale atom-based quantum computation.

quant-ph↗

arXiv2025

CONFIDE: Hallucination Assessment for Reliable Biomolecular Structure Prediction and Design

Reliable evaluation of protein structure predictions remains challenging, as metrics like pLDDT capture energetic stability but often miss subtle errors such as atomic clashes or conformational traps reflecting topological frustration within the protein folding energy landscape. We present CODE (Chain of Diffusion Embeddings), a self evaluating metric empirically found to quantify topological frustration directly from the latent diffusion embeddings of the AlphaFold3 series of structure predictors in a fully unsupervised manner. Integrating this with pLDDT, we propose CONFIDE, a unified evaluation framework that combines energetic and topological perspectives to improve the reliability of AlphaFold3 and related models. CODE strongly correlates with protein folding rates driven by topological frustration, achieving a correlation of 0.82 compared to pLDDT's 0.33 (a relative improvement of 148\%). CONFIDE significantly enhances the reliability of quality evaluation in molecular glue structure prediction benchmarks, achieving a Spearman correlation of 0.73 with RMSD, compared to pLDDT's correlation of 0.42, a relative improvement of 73.8\%. Beyond quality assessment, our approach applies to diverse drug design tasks, including all-atom binder design, enzymatic active site mapping, mutation induced binding affinity prediction, nucleic acid aptamer screening, and flexible protein modeling. By combining data driven embeddings with theoretical insight, CODE and CONFIDE outperform existing metrics across a wide range of biomolecular systems, offering robust and versatile tools to refine structure predictions, advance structural biology, and accelerate drug discovery.

q-bio.BM↗