arXiv subjects

Thaddeus Pellegrini

Publications and source records attributed to Thaddeus Pellegrini.

6 recordsLinked to original sources

arXiv2026

Crossing the 12,000-atom barrier with heterogeneous quantum-classical supercomputing: quantum chemistry of protein-ligand complexes

We develop a workflow decomposing a molecule into fragments via quantum embedding and simulating them with a heterogeneous quantum-classical (HQC) method. We sample fragment electronic configurations on two 156-qubit quantum processors (ibm$\_$cleveland, ibm$\_$kobe), using up to 94 qubits, running 21,006 circuits for over 239 hours, collecting $3.0 \cdot 10^9$ measurement outcomes -- the most resource-intensive HQC computation for quantum chemistry to date. We compute fragment wavefunctions via optimized subspace diagonalization on supercomputers Fugaku, Miyabi-G, and ROQUO, achieving 72.5$\%$ parallel efficiency with scalable distributed linear algebra kernels. We simulate two protein-ligand complexes spanning dispersion- and electrostatics-dominated regimes (11,608, 12,635 atoms), demonstrate $>40\times$ increase in system size and up to $210\times$ improvement in accuracy over previous state-of-the-art, with HQC matching coupled-cluster (CCSD) accuracy in fragment energies. We present the first HQC protein-ligand binding prediction using a mixed-basis set and an automated end-to-end workflow enabling practical HQC calculations of large protein systems.

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arXiv2026

Quantum Computations on Fusion Blanket Molten Salts

Molten salts such as FLiBe (2LiF--BeF$_2$) are leading blanket materials for breeding and recovering tritium in fusion reactors. Predicting tritium speciation requires accurate electronic ground-state energies for representative molten-salt clusters, a demanding task for correlated electronic-structure methods. Here we report the first application of heterogeneous quantum--classical computing to tritium binding in FLiBe. Clusters drawn from ab initio molecular dynamics are partitioned by an embedded-wavefunction (EWF) method into atom-centered fragments, and the largest fragments are solved on IBM quantum hardware using extended sample-based quantum diagonalization (ext-SQD). Across nine clusters, the heterogeneous quantum--classical workflow reproduces fragment ground-state energies with agreement to full configuration interaction within 0.7~kcal/mol and a mean absolute deviation of 0.3~kcal/mol. In contrast, fragmented and unfragmented conformational energy differences and tritium binding energies differ by 12~kcal/mol and 110~kcal/mol on average, respectively, identifying fragment construction rather than fragment solution as the dominant source of algorithmic bias. To the best of our knowledge, this is the first such demonstration for a charged ionic system and in particular an inorganic molten salt, where electrostatic and polarization effects make the accurate treatment of electronic correlation particularly challenging. These results also identify areas of future research towards an accurate and scalable quantum--classical workflow to compute free-energy estimates of tritium speciation in fusion blankets.

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arXiv2026

Protein-Ligand Free Energy Perturbation on Quantum Hardware

The use of free energy perturbation (FEP) methods to study protein-ligand complexes is one of the most important tools in structure-based drug design. Because FEP methods typically rely on force fields, they may suffer from force field parameter-related issues. Herein, we present a quantum mechanics/molecular mechanics (QM/MM) hybrid method to overcome deficiencies in force-field models by using QM bookending approaches on both classical and quantum hardware. In the MM part of this QM/MM FEP method, AMBER is used to simulate the protein receptor and the unperturbed moiety of the ligand, with the ff19SB and GAFF2 force fields. In the QM part, QUICK was used to conduct Hartree-Fock (HF) calculations, followed by heat-bath configuration interaction (HCI) as a benchmark on classical devices. To enable the HCI function in QUICK, we developed a Python-based interface to execute HCI from IBM's qiskit-addon-dice-solver. Moreover, the same interface also enabled this work to execute QM/MM FEP calculations on quantum hardware using the Local Unitary Cluster Jastrow (LUCJ) ansatz, followed by sample-based diagonalization (SQD) and extended-SQD (extSQD) post-processing. Using a series of thermolysis inhibitors as an example, we find reasonable agreement with experiment between the classical HCI method and the LUCJ-SQD/extSQD method, with the latter yielding a result closer to the experimental value. The execution time between the HCI-based FEP method and the LUCJ-SQD/extSQD-based FEP method is also comparable, indicating a high potential for utility in the noisy intermediate-scale quantum (NISQ) era.

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arXiv2026

Molecular Quantum Computations on a Protein

This work presents the implementation of a fragment-based, quantum-centric supercomputing workflow for computing molecular electronic structure using quantum hardware. The workflow is applied to predict the relative energies of two conformers of the 300-atom Trp-cage miniprotein. The methodology employs wave function-based embedding (EWF) as the underlying fragmentation framework, in which all atoms in the system are explicitly included in the CI treatment. CI calculations for individual fragments are performed using either sample-based quantum diagonalization (SQD) for challenging fragments or full configuration interaction (FCI) for trivial fragments. To assess the accuracy of SQD for fragment CI calculations, EWF-(FCI,SQD) results are compared against EWF-MP2 and EWF-CCSD benchmarks. Overall, the results demonstrate that large-scale electronic configuration interaction (CI) simulations of protein systems containing hundreds or even thousands of atoms can be realized through the combined use of quantum and classical computing resources.

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arXiv2025

Domain-Aware Quantum Circuit for QML

Designing parameterized quantum circuits (PQCs) that are expressive, trainable, and robust to hardware noise is a central challenge for quantum machine learning (QML) on noisy intermediate-scale quantum (NISQ) devices. We present a Domain-Aware Quantum Circuit (DAQC) that leverages image priors to guide locality-preserving encoding and entanglement via non-overlapping DCT-style zigzag windows. The design employs interleaved encode-entangle-train cycles, where entanglement is applied among qubits hosting neighboring pixels, aligned to device connectivity. This staged, locality-preserving information flow expands the effective receptive field without deep global mixing, enabling efficient use of limited depth and qubits. The design concentrates representational capacity on short-range correlations, reduces long-range two-qubit operations, and encourages stable optimization, thereby mitigating depth-induced and globally entangled barren-plateau effects. We evaluate DAQC on MNIST, FashionMNIST, and PneumoniaMNIST datasets. On quantum hardware, DAQC achieves performance competitive with strong classical baselines (e.g., ResNet-18/50, DenseNet-121, EfficientNet-B0) and substantially outperforming Quantum Circuit Search (QCS) baselines. To the best of our knowledge, DAQC, which uses a quantum feature extractor with only a linear classical readout (no deep classical backbone), currently achieves the best reported performance on real quantum hardware for QML-based image classification tasks. Code and pretrained models are available at: https://github.com/gurinder-hub/DAQC.

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arXiv2024

Simulation of a Diels-Alder Reaction on a Quantum Computer

The simulation of chemical reactions is an anticipated application of quantum computers. Using a Diels-Alder reaction as a test case, in this study we explore the potential applications of quantum algorithms and hardware in investigating chemical reactions. Our specific goal is to calculate the activation barrier of a reaction between ethylene and cyclopentadiene forming a transition state. To achieve this goal, we use quantum algorithms for near-term quantum hardware (entanglement forging and quantum subspace expansion) and classical post-processing (many-body perturbation theory) in concert. We conduct simulations on IBM quantum hardware using up to 8 qubits, and compute accurate activation barriers in the reaction between cyclopentadiene and ethylene by accounting for both static and dynamic electronic correlation. This work illustrates a hybrid quantum-classical computational workflow to study chemical reactions on near-term quantum devices, showcasing the potential of quantum algorithms and hardware in accurately calculating activation barriers.

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