arXiv subjects

Victor Onofre

Publications and source records attributed to Victor Onofre.

5 recordsLinked to original sources

arXiv2025

A Scalable Heuristic for Molecular Docking on Neutral-Atom Quantum Processors

Molecular docking is a critical computational method in drug discovery used to predict the binding conformation and orientation of a ligand within a protein's binding site. Mapping this challenge onto a graph-based problem, specifically the Maximum Weighted Independent Set (MWIS) problem, allows it to be addressed by specialized hardware such as neutral-atom quantum processors. However, a significant bottleneck has been the size mismatch between biologically relevant molecular systems and the limited capacity of near-term quantum devices. In this work, we overcome this scaling limitation by the use of a divide-and-conquer heuristic introduced in Cazals 2025. This algorithm decomposes a single, intractable graph instance into smaller sub-problems that can be solved sequentially on a neutral-atom quantum emulator, incurring only a linear computational overhead. We benchmark this approach on 10 real-world protein-ligand complexes, including 9 from the Astex Diverse Set, with graphs ranging from 225 to 585 vertices. The quantum heuristic consistently outperforms a greedy baseline and achieves the provably optimal solution on a 540-node instance (TACE-AS). We further assess the biological relevance of the reconstructed poses via the fraction of native contacts, and benchmark the full workflow on a standard dataset of diverse protein-ligand complexes. Our work establishes a scalable blueprint for applying quantum optimization to molecular docking, while identifying concrete directions for improving both the algorithmic strategy and the underlying graph model.

quant-ph↗

arXiv2025

Quantum Optimization on Rydberg Atom Arrays with Arbitrary Connectivity: Gadgets Limitations and a Heuristic Approach

Programmable quantum systems based on Rydberg atom arrays have recently emerged as a promising testbed for combinatorial optimization. Indeed, the Maximum Weighted Independent Set problem on unit-disk graphs can be efficiently mapped to such systems due to their geometric constraints. However, extending this capability to arbitrary graph instances typically necessitates the use of reduction gadgets, which introduce additional experimental overhead and complexity. Here, we analyze the complexity-theoretic limits of polynomial reductions from arbitrary graphs to unit-disk instances. We prove any such reduction incurs a quadratic blow-up in vertex count and degrades solution approximation guarantees. As a practical alternative, we propose a divide-and-conquer heuristic with only linear overhead which leverages precalibrated atomic layouts. We benchmark it on Erd\"os-R\'enyi graphs, and demonstrate feasibility on the Orion Alpha processor.

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arXiv2024

Towards molecular docking with neutral atoms

New computational strategies, such as molecular docking, are emerging to speed up the drug discovery process. This method predicts the activity of molecules at the binding site of proteins, helping to select the ones that exhibit desirable behavior and rejecting the rest. However, for large chemical libraries, it is essential to search and score configurations using fewer computational resources while maintaining high precision. In this work, we map the molecular docking problem to a graph problem, a maximum-weight independent set problem on a unit-disk graph in a physical neutral atom quantum processor. Here, each vertex represents an atom trapped by optical tweezers. The Variational Quantum Adiabatic Algorithm (VQAA) approach is used to solve the generic graph problem with two optimization methods, Scipy and Hyperopt. Additionally, a machine learning method is explored using the adiabatic algorithm. Results for multiple graphs are presented, and a small instance of the molecular docking problem is solved, demonstrating the potential for near-term quantum applications.

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arXiv2024

Simulating open quantum systems using noise models and NISQ devices with error mitigation

In this work, we present simulations of two Open Quantum System models, Collisional and Markovian Reservoir, with noise simulations, the IBM devices ($\textit{ibm_kyoto}$, $\textit{ibm_osaka}$) and the OQC device Lucy. Extending the results of García-Pérez, et al. [npj Quantum Information 6.1 (2020): 1]. Using the Mitiq toolkit, we apply Zero-Noise extrapolation (ZNE), an error mitigation technique, and analyze their deviation from the theoretical results for the models under study. For both models, by applying ZNE, we were able to reduce the error and overlap it with the theoretical results. All our simulations and experiments were done in the qBraid environment.

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arXiv2024

Quantum artificial vision for defect detection in manufacturing

In this paper we consider several algorithms for quantum computer vision using Noisy Intermediate-Scale Quantum (NISQ) devices, and benchmark them for a real problem against their classical counterparts. Specifically, we consider two approaches: a quantum Support Vector Machine (QSVM) on a universal gate-based quantum computer, and QBoost on a quantum annealer. The quantum vision systems are benchmarked for an unbalanced dataset of images where the aim is to detect defects in manufactured car pieces. We see that the quantum algorithms outperform their classical counterparts in several ways, with QBoost allowing for larger problems to be analyzed with present-day quantum annealers. Data preprocessing, including dimensionality reduction and contrast enhancement, is also discussed, as well as hyperparameter tuning in QBoost. To the best of our knowledge, this is the first implementation of quantum computer vision systems for a problem of industrial relevance in a manufacturing production line.

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