Pranav Chandarana

We report the largest trapped-ion hardware demonstration of lattice protein-folding optimization to date, using bias-field digitized counterdiabatic quantum optimization (BF-DCQO) on a fully connected 64-qubit Barium development system similar to the forthcoming IonQ Tempo line. Six peptide sequences with 14-16 amino-acid residues are encoded using a coarse-grained tetrahedral lattice model, yielding higher-order spin-glass Hamiltonians with long-range interactions involving up to five-body terms and mapped to 46-61 qubits. The resulting instances are demanding for near-term quantum hardware because low-energy configurations must satisfy backbone-geometry constraints while optimizing dense residue-contact interactions. BF-DCQO uses a non-variational bias-feedback mechanism, where low-energy samples from each round define longitudinal fields that guide subsequent quantum evolutions. Across the studied instances, BF-DCQO shifts raw sampled energy distributions toward lower energies than uniform random sampling, with the strongest improvements appearing in residue-contact variables. To preserve this signal, we introduce a consensus-based post-processing pipeline that combines quantum-learned contact information with feasible backbone geometries. The resulting hybrid workflow reaches the classical reference energy in multiple instances and improves over the corresponding random-seeded pipeline. These results show that BF-DCQO can generate structured samples for dense protein-folding Hamiltonians at previously unexplored trapped-ion scales.

Hardware-tested workflow for portfolio optimization on trapped-ion processors using decomposition, BF-DCQO, recombination, and post-processing.

We propose a hybrid classical-quantum digitized-counterdiabatic algorithm to tackle the protein folding problem on a tetrahedral lattice. Digitized-counterdiabatic quantum computing is a paradigm developed to compress quantum algorithms via the digitization of the counterdiabatic acceleration of a given adiabatic quantum computation. Finding the lowest energy configuration of the amino acid sequence is an NP-hard optimization problem that plays a prominent role in chemistry, biology, and drug design. We outperform state-of-the-art quantum algorithms using problem-inspired and hardware-efficient variational quantum circuits. We apply our method to proteins with up to 9 amino acids, using up to 17 qubits on quantum hardware. Specifically, we benchmark our quantum algorithm with Quantinuum's trapped ions, Google's and IBM's superconducting circuits, obtaining high success probabilities with low-depth circuits as required in the NISQ era.