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arXiv · 2506.07866

Protein folding with an all-to-all trapped-ion quantum computer

Sebastián V. Romero·Alejandro Gomez Cadavid·Pavle Nikačević·Enrique Solano·Narendra N. Hegade·Miguel Angel Lopez-Ruiz·Claudio Girotto·Masako Yamada·Panagiotis Kl. Barkoutsos·Ananth Kaushik·Martin Roetteler
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Abstract

We experimentally demonstrate that the bias-field digitized counterdiabatic quantum optimization (BF-DCQO) algorithm, implemented on IonQ's fully connected trapped-ion quantum processors, offers an efficient approach to solving dense higher-order unconstrained binary optimization (HUBO) problems. Specifically, we tackle protein folding on a tetrahedral lattice for up to 12 amino acids, representing the largest quantum hardware implementations of protein folding problems reported to date. Additionally, we address MAX 4-SAT instances at the computational phase transition and fully connected spin-glass problems using all 36 available qubits. Across all considered cases, our method consistently achieves optimal solutions, highlighting the powerful synergy between non-variational quantum optimization approaches and the intrinsic all-to-all connectivity of trapped-ion architectures. Given the expected scalability of trapped-ion quantum systems, BF-DCQO represents a promising pathway toward practical quantum advantage for dense HUBO problems with significant industrial and scientific relevance.

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Sebastián V. Romero, Alejandro Gomez Cadavid, Pavle Nikačević, Enrique Solano, Narendra N. Hegade, Miguel Angel Lopez-Ruiz, Claudio Girotto, Masako Yamada, Panagiotis Kl. Barkoutsos, Ananth Kaushik, Martin Roetteler. 2025-06-09. Protein folding with an all-to-all trapped-ion quantum computer. https://arxiv.org/abs/2506.07866

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