arXiv subjects

Kenneth M. Merz Jr

Publications and source records attributed to Kenneth M. Merz Jr.

14 recordsLinked to original sources

arXiv2026

Quantum Computing Enabled ab initio Molecular Dynamics Simulations

We demonstrate a quantum-classical workflow for ab initio molecular dynamics (AIMD) in which quantum measurements from a chemistry-inspired LUCJ ansatz are post-processed using Sample-based Quantum Diagonalization (SQD) to recover determinant subspaces and deliver energies and analytical nuclear gradients for dynamics. As an exact benchmark, we use full configuration interaction (FCI) in the STO-3G basis, enabling a direct assessment of the accuracy of SQD. In gas-phase benchmarks, SQD reproduces FCI energies and gradients to within 1 kcal mol$^{-1}$ of the FCI reference and yields stable AIMD trajectories. In explicit-solvent QM/MM simulations, SQD retains this agreement, matching FCI energy fluctuations and RMS gradient profiles and reproducing solute-solvent structure as quantified by radial distribution functions. Overall, these benchmarks establish LUCJ+SQD as a practical route for integrating current quantum hardware into QM/MM molecular dynamics and provide an early demonstration of condensed-phase QM/MM dynamics driven by a quantum electronic-structure engine.

physics.chem-ph↗

arXiv2026

Quantum-Centric Geometry Optimization with Wave-Function-Based Embedding

The EWF-(FCI,SQD) method, a wave-function-based embedding approach combining full configuration interaction (FCI) and sample-based quantum diagonalization (SQD), is a promising new tool for the simulation of molecular systems. However, applications of EWF-(FCI,SQD) have so far been limited to single-point calculations, whereas the study of complex chemical processes requires the ability to explore potential energy surfaces. In this work, we demonstrate geometry optimization with EWF-(FCI,SQD), scaling our simulations to molecules as large as menthone and benzidine within the STO-3G basis set. Without fragmentation, these systems comprise 73 and 82 molecular orbitals respectively, presenting an intractable Hilbert space for conventional exact or high-level subspace solvers and establishing a clear necessity for fragmentation-based methodologies. The underlying fragment SQD simulations in the EWF-(FCI,SQD) geometry optimizations use up to 70 qubits. The resulting geometries show exceptional accuracy relative to the classical reference, with deviations below 4 picometers.

quant-ph↗

arXiv2026

A Quantum Multi-Programming Framework to Maximize Quantum Resources for the LUCJ Ansatz

In the context of quantum computing, efficient resource management is crucial for optimizing throughput on cloud-based platforms and maximizing hardware utilization. In the present work, we propose an approach to tackle quantum chemistry problems via quantum multi-programming of the Local Unitary Cluster Jastrow (LUCJ) ans\"atze. The ground-state energy of the molecular system is obtained via Sample-based quantum diagonalization (SQD), further refined by its extended version (ext-SQD). Building upon the Qiskit Experiments package, which already supports parallel execution functionality for general tasks, we developed a novel parallel experiment class tailored for quantum chemistry problems. Cross-talk is a known issue in the multi-programming frameworks and can corrupt the ground-energy estimation of the simulated systems. To assess its impact within our approach, we simulated two conformations of the ethanol molecule: one at the equilibrium state (EtOH$_{Eq}$), and one with the O-H bond stretched to 1.2 ${{\AA}}$ (EtOH$_{1.2}$). We defined three different layouts that we executed in a randomized fashion, alternating serial and parallel execution within 10 independent replicates. The single modality of each circuit was kept as a baseline to evaluate the effect of cross-talk induced by quantum multi-programming. The energies obtained at the first-, last- and ext-SQD iteration were compared to the classical Heat-bath Configuration Interaction (HCI) reference. Our findings highlight the viability of a quantum multi-programming workflow for quantum chemistry as the robust post-processing protocol effectively mitigates possible cross-talk induced noise. At the final step of the configuration recovery process, the energy difference relative to the HCI reference is negligible, within 0.001 kcal/mol.

quant-ph↗

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.

quant-ph↗

arXiv2025

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.

quant-ph↗

arXiv2025

Quantum Algorithm for Protein Structure Prediction Using the Face-Centered Cubic Lattice

In this work, we present the first implementation of the face-centered cubic (FCC) lattice model for protein structure prediction with a quantum algorithm. Our motivation to encode the FCC lattice stems from our observation that the FCC lattice is more capable in terms of modeling realistic secondary structures in proteins compared to other lattices, as demonstrated using root mean square deviation (RMSD). We utilize two quantum methods to solve this problem: a polynomial fitting approach (PolyFit) and the Variational Quantum Eigensolver with constraints (VQEC) based on the Lagrangian duality principle. Both methods are successfully deployed on Eagle R3 (ibm_cleveland) and Heron R2 (ibm_kingston) quantum computers, where we are able to recover ground state configurations for the 6-amino acid sequence KLVFFA under noise. A comparative analysis of the outcomes generated by the two QPUs reveals a significant enhancement (reaching nearly a two-fold improvement for PolyFit and a three-fold improvement for VQEC) in the prediction and sampling of the optimal solution (ground state conformations) on the newer Heron R2 architecture, highlighting the impact of quantum hardware advancements for this application.

quant-ph↗

arXiv2025

Improving GANs by leveraging the quantum noise from real hardware

We propose a novel approach to generative adversarial networks (GANs) in which the standard i.i.d. Gaussian latent prior is replaced or hybridized with a quantum-correlated prior derived from measurements of a 16-qubit entangling circuit. Each latent sample is generated by grouping repeated shots per qubit into a binary fraction, applying the inverse Gaussian CDF to obtain a 16-dimensional Gaussian vector whose joint copula reflects genuine quantum entanglement, and then projecting into the high-dimensional space via a fixed random matrix. By pre-sampling tens of millions of bitstrings, either from a noiseless simulator or from IBM hardware, we build large pools of independent but internally quantum-correlated latents. We integrate this prior into three representative architectures (WGAN, SNGAN, BigGAN) on CIFAR-10, making no changes to the neural network structure or training hyperparameters. The hybrid latent representations incorporating hardware-derived noise consistently lower the FID relative to both the classical baseline and the simulator variant, especially when the quantum component constitutes a substantial fraction of the prior. In addition, we execute on the QPU in parallel to not only save computing time but also further decrease the FID up to 17% in BigGAN. These results indicate that intrinsic quantum randomness and device-specific imperfections can provide a structured inductive bias that enhances GAN performance. Our work demonstrates a practical pipeline for leveraging noisy quantum hardware to enrich deep-generative modeling, opening a new interface between quantum information and machine learning. All code and data are available at https://github.com/Neon8988/GAN_QN.git.

quant-ph↗

arXiv2025

Quantum-Centric Alchemical Free Energy Calculations

In the present work, we present a hybrid quantum-classical workflow aimed at improving the accuracy of alchemical free energy (AFE) predictions by incorporating configuration interaction (CI) simulations using the book-ending correction method. This approach applies the Multistate Bennett Acceptance Ratio (MBAR) over a coupling parameter {\lambda} to smoothly transition the system from molecular mechanics (MM) ({\lambda} = 0) to a quantum mechanics (QM) ({\lambda} = 1) description. The resulting correction is then applied to the classically (MM) computed AFE to account for the more accurate QM treatment. The standard book-ending procedure uses AMBER to simulate the MM region, and QUICK, AMBER's default QM engine, to handle the QM region with either the Hartree-Fock (HF) method or density functional theory (DFT). In this work, we introduce a novel interface to QUICK, via sander, that enables CI simulations, and can operate in two ways: A) via PySCF backend to perform full configuration interaction (FCI) using conventional computing resources, B) quantum-centric sample-based quantum diagonalization (SQD) workflow via Qiskit which leverages both quantum hardware and post-processing on conventional computing resources for CI simulations. In this workflow QUICK performs most steps of the calculations, but at user-defined intervals, it redirects the computation to either FCI or SQD backend to get the CI result. We computed the book-end corrections for the hydration free energy (HFE) of three small organic molecules (ammonia, methane, and water) to benchmark the proposed approach and demonstrate how quantum-computers can be used in AFE calculations. We believe that this approach can be scaled to more complex systems like drug-receptor interactions in future studies.

physics.chem-ph↗

arXiv2025

QFGN: A Quantum Approach to High-Fidelity Implicit Neural Representations

Implicit neural representations have shown potential in various applications. However, accurately reconstructing the image or providing clear details via image super-resolution remains challenging. This paper introduces Quantum Fourier Gaussian Network (QFGN), a quantum-based machine learning model for better signal representations. The frequency spectrum is well balanced by penalizing the low-frequency components, leading to the improved expressivity of quantum circuits. The results demonstrate that with minimal parameters, QFGN outperforms the current state-of-the-art (SOTA) models. Despite noise on hardware, the model achieves accuracy comparable to that of SIREN, highlighting the potential applications of quantum machine learning in this field.

quant-ph↗

arXiv2025

Benchmarking MedMNIST dataset on real quantum hardware

Quantum machine learning (QML) has emerged as a promising domain to leverage the computational capabilities of quantum systems to solve complex classification tasks. In this work, we present the first comprehensive QML study by benchmarking the MedMNIST-a diverse collection of medical imaging datasets on a 127-qubit real IBM quantum hardware, to evaluate the feasibility and performance of quantum models (without any classical neural networks) in practical applications. This study explores recent advancements in quantum computing such as device-aware quantum circuits, error suppression, and mitigation for medical image classification. Our methodology is comprised of three stages: preprocessing, generation of noise-resilient and hardware-efficient quantum circuits, optimizing/training of quantum circuits on classical hardware, and inference on real IBM quantum hardware. Firstly, we process all input images in the preprocessing stage to reduce the spatial dimension due to quantum hardware limitations. We generate hardware-efficient quantum circuits using backend properties expressible to learn complex patterns for medical image classification. After classical optimization of QML models, we perform inference on real quantum hardware. We also incorporate advanced error suppression and mitigation techniques in our QML workflow, including dynamical decoupling (DD), gate twirling, and matrix-free measurement mitigation (M3) to mitigate the effects of noise and improve classification performance. The experimental results showcase the potential of quantum computing for medical imaging and establish a benchmark for future advancements in QML applied to healthcare.

quant-ph↗

arXiv2025

Implicit solvent sample-based quantum diagonalization

The sample-based quantum diagonalization (SQD) method shows great promise in quantum-centric simulations of ground state energies in molecular systems. Inclusion of solute-solvent interactions in simulations of electronic structure is critical for biochemical and medical applications. However, all of the previous applications of the SQD method were shown for gas-phase simulations of the electronic structure. The present work aims to bridge this gap by introducing the integral equation formalism polarizable continuum model (IEF-PCM) of solvent into the SQD calculations. We perform SQD/cc-pVDZ IEF-PCM simulations of methanol, methylamine, ethanol, and water in aqueous solution using quantum hardware and compare our results to CASCI/cc-pVDZ IEF-PCM simulations. Our simulations on ibm_cleveland, ibm_kyiv, and ibm_marrakesh quantum devices are performed with 27, 30, 41, and 52 qubits demonstrating the scalability of SQD IEF-PCM simulations.

quant-ph↗

arXiv2024

Integrating Machine Learning and Quantum Circuits for Proton Affinity Predictions

A key step in interpreting gas-phase ion mobility coupled with mass spectrometry (IM-MS) data for unknown structure prediction involves identifying the most favorable protonated structure. In the gas phase, the site of protonation is determined using proton affinity (PA) measurements. Currently, mass spectrometry and ab initio computation methods are widely used to evaluate PA; however, both methods are resource-intensive and time-consuming. Therefore, there is a critical need for efficient methods to estimate PA, enabling the rapid identification of the most favorable protonation site in complex organic molecules with multiple proton binding sites. In this work, we developed a fast and accurate method for PA prediction by using multiple descriptors in combination with machine learning (ML) models. Using a comprehensive set of 186 descriptors, our model demonstrated strong predictive performance, with an R2 of 0.96 and a MAE of 2.47kcal/mol, comparable to experimental uncertainty. Furthermore, we designed quantum circuits as feature encoders for a classical neural network. To evaluate the effectiveness of this hybrid quantum-classical model, we compared its performance with traditional ML models using a reduced feature set derived from the full set. The result showed that this hybrid model achieved consistent performance comparable to traditional ML models with the same reduced feature set on both a noiseless simulator and real quantum hardware, highlighting the potential of quantum machine learning for accurate and efficient PA predictions.

cs.LG↗

arXiv2024

Towards quantum-centric simulations of extended molecules: sample-based quantum diagonalization enhanced with density matrix embedding theory

Computing ground-state properties of molecules is a promising application for quantum computers operating in concert with classical high-performance computing resources. Quantum embedding methods are a family of algorithms particularly suited to these computational platforms: they combine high-level calculations on active regions of a molecule with low-level calculations on the surrounding environment, thereby avoiding expensive high-level full-molecule calculations and allowing to distribute computational cost across multiple and heterogeneous computing units. Here, we present the first density matrix embedding theory (DMET) simulations performed in combination with the sample-based quantum diagonalization (SQD) method. We employ the DMET-SQD formalism to compute the ground-state energy of a ring of 18 hydrogen atoms, and the relative energies of the chair, half-chair, twist-boat, and boat conformers of cyclohexane. The full-molecule 41- and 89-qubit simulations are decomposed into 27- and 32-qubit active-region simulations, that we carry out on the ibm_cleveland device, obtaining results in agreement with reference classical methods. Our DMET-SQD calculations mark a tangible progress in the size of active regions that can be accurately tackled by near-term quantum computers, and are an early demonstration of the potential for quantum-centric simulations to accurately treat the electronic structure of large molecules, with the ultimate goal of tackling systems such as peptides and proteins.

quant-ph↗

arXiv2024

Accurate quantum-centric simulations of supramolecular interactions

We present the first quantum-centric simulations of noncovalent interactions using a supramolecular approach. We simulate the potential energy surfaces (PES) of the water and methane dimers, featuring hydrophilic and hydrophobic interactions, respectively, with a sample-based quantum diagonalization (SQD) approach. Our simulations on quantum processors, using 27- and 36-qubit circuits, are in remarkable agreement with classical methods, deviating from complete active space configuration interaction (CASCI) and coupled-cluster singles, doubles, and perturbative triples (CCSD(T)) within 1 kcal/mol in the equilibrium regions of the PES. Finally, we test the capacity limits of the quantum methods for capturing hydrophobic interactions with an experiment on 54 qubits. These results mark significant progress in the application of quantum computing to chemical problems, paving the way for more accurate modeling of noncovalent interactions in complex systems critical to the biological, chemical and pharmaceutical sciences.

quant-ph↗