arXiv subjects

Jean-Philip Piquemal

Publications and source records attributed to Jean-Philip Piquemal.

At least 19 recordsLinked to original sources

arXiv2026

Real-Space Chemistry on Quantum Computers: A Fault-Tolerant Algorithm with Adaptive Grids and Transcorrelated Extension

First-quantized, real-space formulations of quantum chemistry on quantum computers are appealing: qubit count scales logarithmically with spatial resolution, and Coulomb operators achieve quadratic instead of quartic computational scaling of two-electron interactions. However, existing schemes employ uniform discretizations, so the resolution required to capture electron-nuclear cusps in high-density regions oversamples low-density regions, wasting computational resources. We address this by deploying non-uniform, molecule-adaptive grids that concentrate points where electronic density is high. Using Voronoi partitions of these grids, the molecular Hamiltonian is expressed in a Hermitian form and in a transcorrelated, isospectral form that eliminates Coulomb singularities and yields cusp-free eigenfunctions. Both formulations slot naturally into quantum eigenvalue solvers: Hermitian Quantum Phase Estimation (QPE) and the recent generalised Quantum Eigenvalue Estimation (QEVE) protocol for its non-Hermitian, transcorrelated counterpart. Numerical validation on benchmark systems confirms that this non-heuristic ab initio framework offers a promising path for accurate ground-state chemistry on quantum hardware.

quant-ph↗

arXiv2026

Experimental Realization of the Markov Chain Monte Carlo Algorithm on a Quantum Computer

Quantum algorithms present a quadratically improved complexity over classical ones for certain sampling tasks. For instance, the Quantum Amplitude Estimation (QAE) algorithm promises to speed up the estimation of the mean of certain functions, given access to the quantum state corresponding to the probability distribution to be sampled from. Classically, samples are often obtained by simulating a Markov chain. In this work, we experimentally use encodings of Markov chains to prepare quantum states and run a quantum Markov Chain Monte Carlo (qMCMC) algorithm on Quantinuum System Model H2 and Quantinuum Helios quantum computers. We first demonstrate that it is possible to obtain accurate results by operating directly on the physical qubits. Crucially, to pave the way toward fault-tolerant execution, we also implement these algorithms using logical qubits protected by the Iceberg Quantum Error Detection (QED) code. By applying multiple rounds of mid-circuit QED during a random walk, we successfully catch and filter out hardware errors. These experiments demonstrate the feasibility of qMCMC on quantum hardware, bringing us closer to realizing quadratic quantum speedups with broad applications ranging from molecular modeling to machine learning and finance.

quant-ph↗

arXiv2026

An Optimized Construction of Lie Algebra Generator Pools for Variational Quantum Eigensolvers in Chemistry

Lie algebras are essential mathematical structures used in physics to describe sets of quantum operators. Identifying a minimal set of generators to construct these algebras is a central challenge. The traditional search for such generators relies on greedy construction steps applied to an exponentially growing number of candidate operators, making it computationally intractable. Here we show a general, polynomial-scaling strategy, based on fundamental Lie-algebraic properties, to overcome this bottleneck. We apply this framework to quantum chemistry, specifically to adaptive variational algorithms that simulate molecular ground states. By integrating our mathematically verified generator pools into a batched algorithmic framework, we reduce the required quantum resources and improve convergence for strongly correlated systems. Furthermore, this approach eliminates computational bottlenecks that previously restricted fixed-ansatz non-iterative coupled-cluster methods to small molecules, enabling simulations of complex systems well beyond previous limits. This foundational framework also presents broad applications across quantum computing, including quantum error correction, machine learning, and hardware control.

quant-ph↗

arXiv2026

Probing Extended Recognition Sites in Zn-Metalloproteins via Quantum Chemistry and Polarizable Molecular Dynamics

Zn-metalloproteins play vital roles in numerous metabolic processes, making them high-value targets for structure-based drug design. To advance these efforts, it is useful to unravel the individual components of the intermolecular interaction energies (DE) that stabilize the Znbinding cavity, both in the absence and presence of bound protein ligands. Here, we utilize quantum chemistry (QC) to decompose DE into distinct physical contributions. The relative magnitudes of these components vary significantly depending on the coordination number (four to six) and the chemical nature ('hard' vs. 'soft') of the Zn-coordinating ligands. These high-level QC analyses serve to calibrate and validate polarizable molecular mechanics potentials, effectively extending the accurate description of electronic effects beyond the immediate Zn-binding cavity to enlarged recognition sites and, ultimately, entire protein systems over long molecular dynamics (MD) simulation timescales. Following a concise overview of our QC methodology, we present validation studies on complexes containing up to 300 atoms and discuss the prospects of applying this framework to large-scale simulations of Zn-metalloprotein-ligand complexes. Finally, the structural and energetic role of discrete, highly polarizable water molecules is highlighted.

physics.chem-ph↗

arXiv2026

Faster Molecular Dynamics with Neural Network Potentials via Distilled Multiple Time-Stepping and Non-Conservative Forces

Following our previous work (J. Phys. Chem. Lett., 2026, 17, 5, 1288-1295), we propose the DMTS-NC approach, a distilled multi-time-step (DMTS) strategy using non-conservative (NC) forces to further accelerate atomistic molecular dynamics simulations using foundation neural network models such as FeNNix-Bio1. There, a dual-level reversible reference system propagator algorithm (RESPA) formalism couples a target accurate conservative potential to a simplified distilled representation optimized for the production of non-conservative forces. Despite being non-conservative, the distilled architecture is designed to enforce key physical priors, such as equivariance under rotation and cancellation of atomic force components. These choices facilitate the distillation process and therefore improve drastically the robustness of simulation, significantly limiting abnormal discrepancies between the two models, thus achieving excellent agreement with the forces data. Overall, the DMTS-NC scheme is found to be more stable and efficient than its conservative counterpart with additional speedups reaching 15-30% over DMTS. Requiring no fine-tuning steps, it is easier to implement and can be pushed to the limit of the systems physical resonances to maintain accuracy while providing maximum efficiency. We obtain additional speedup by combining hydrogen mass repartitioning (HMR), High Hydrogen Friction (HHF) to further extended the largest timestep up to 10fs of our schemes while conserving stability and accuracy. As for DMTS, DMTS-NC is applicable to any neural network potential and can be applied to approaches that are computationally heavier than FeNNix-Bio1. We show a proof of principle applying the approach to the distillation of MACE-OFF23 with consequent speedups ranging from 3.66 to 5.64 compared to single timestep.

physics.chem-ph↗

arXiv2026

Quantum Circuits for the Metropolis-Hastings Algorithm

Szegedy's quantization of a reversible Markov chain provides a quantum walk whose spectral gap is quadratically larger than that of the classical walk. Quantum computers are therefore expected to provide a speedup of Metropolis-Hastings (MH) simulations. Existing generic methods to implement the quantum walk require coherently computing the transition probabilities of the underlying Markov kernel. However, reversible computing methods require a number of qubits that scales with the complexity of the computation. This overhead is undesirable in near-term fault-tolerant quantum computing, where few logical qubits are available. In this work, we present a Szegedy quantum walk construction which follows the classical proposal-acceptance logic, and does not require further reversible computing methods. We also compare this construction with an alternative to Szegedy's approach which also provides a quadratic gap amplification. Since each step of the quantum walks uses a constant number of proposal and acceptance steps, we expect the end-to-end quadratic speedup to hold for MH Markov Chain Monte-Carlo simulations.

quant-ph↗

arXiv2026

Dual-LAO for calculating fast and robust relative binding free energies of simple and complex transformations

Relative Binding Free Energy (RBFE) calculations are a cornerstone of rational hit-to-lead and lead optimization in modern drug discovery. However, the high computational cost and limited reliability in tackling large or complex molecular transformations often prevent their routine, high-throughput use. Here we introduce dual-LAO, a novel, highly efficient method for calculating RBFE. Building on the Lambda-ABF-OPES framework, this method combines a dual-topology setup and suitable restraints to dramatically accelerate free energy convergence. We demonstrate that dual-LAO, in combination with the AMOEBA polarizable force field, achieves an unprecedented acceleration factor of 15 to 30 times compared to current state-of-the-art methods on standard drug targets. Crucially, the approach maintains high accuracy and successfully tackles previously prohibitive molecular changes, including scaffold-hopping, buried water displacement, charge changes, ring-opening, and binding pose perturbations. This significant leap in efficiency allows for the widespread, routine integration of predictive molecular simulations into the rapid optimization cycles of drug discovery, enabling chemists to confidently model historically challenging systems in timescales compatible with real-world project deadlines.

physics.chem-ph↗

arXiv2026

The Convergence Frontier: Integrating Machine Learning and High Performance Quantum Computing for Next-Generation Drug Discovery

Integrating quantum mechanics into drug discovery marks a decisive shift from empirical trial-and-error toward quantitative precision. However, the prohibitive cost of ab initio molecular dynamics has historically forced a compromise between chemical accuracy and computational scalability. This paper identifies the convergence of High-Performance Computing (HPC), Machine Learning (ML), and Quantum Computing (QC) as the definitive solution to this bottleneck. While ML foundation models, such as FeNNix-Bio1, enable quantum-accurate simulations, they remain tethered to the inherent limits of classical data generation. We detail how High-Performance Quantum Computing (HPQC), utilizing hybrid QPU-GPU architectures, will serve as the ultimate accelerator for quantum chemistry data. By leveraging Hilbert space mapping, these systems can achieve true chemical accuracy while bypassing the heuristics of classical approximations. We show how this tripartite convergence optimizes the drug discovery pipeline, spanning from initial system preparation to ML-driven, high-fidelity simulations. Finally, we position quantum-enhanced sampling as the beyond GPU frontier for modeling reactive cellular systems and pioneering next-generation materials.

quant-ph↗

arXiv2026

High Performance Quantum Emulation for Chemistry Applications with Hyperion

The strategic demand for quantum hardware currently outpaces the availability of near-term devices, necessitating high-performance software emulators to validate novel protocols. We introduce Hyperion, a massively parallel, GPU-accelerated quantum emulator architected to bypass the classical memory walls inherent in strongly correlated quantum chemistry simulations. Hyperion leverages custom-optimized Sparse Matrix-Sparse Vector (SpMspV) kernels to natively accelerate exact matrix-vector multiplications, enabling strictly accurate State-Vector (SV) ADAPT-VQE simulations for up to 32 qubits on multi-node platforms. To scale beyond this hardware limit, we address the trade-off in pure Matrix Product State (MPS) emulators, where standard compression yields severe truncation errors and strict compression triggers intractable tensor rank explosions. We propose a novel partitioned emulation, namely the SV-MPS strategy: by routing non-interacting terms into an exact sparse SV core and delegating interacting terms to the MPS engine, this approach achieves emulation of 36 to 40 qubits with controlled approximations. This partitioning significantly reduces GPU resource requirements while maintaining robust accuracy across ADAPT-VQE iterations. Ultimately, Hyperion offers a high-fidelity platform dedicated to the development of new quantum algorithms for chemistry, enabling the modeling of realistic chemical systems at accuracies approaching the exact Full Configuration Interaction (FCI) / Complete Basis Set (CBS) limit.

quant-ph↗

arXiv2026

Logarithmic-depth quantum state preparation of polynomials

Quantum state preparation is a central primitive in many quantum algorithms, yet it is generally resource intensive, with efficient constructions known only for structured families of states. This work introduces a method for preparing quantum states whose amplitudes are given by a degree$-d$ polynomial, using circuits with logarithmic depth in the number $n$ of qubits and only $\mathcal O(n)$ ancilla qubits, improving previous approaches that required linear-depth circuits. The construction first relies on a block-encoding of an affine diagonal operator based on its Pauli-basis decomposition, which involves only $n$ terms. A modified linear-combination-of-unitaries (LCU) technique is introduced to implement this decomposition in logarithmic depth, together with a novel circuit for the EXACT-one oracle that flags basis states in which exactly one qubit is in the state $|1\rangle$. It then uses a generalized quantum eigenvalue transformation (GQET) to promote this affine operator to an arbitrary degree polynomial. Theoretical analysis and numerical simulations are reported along with a proof-of-principle implementation on a trapped-ion quantum processor using $14$ qubits and more than $500$ primitive quantum gates. Because polynomial approximations are ubiquitous in scientific computing, this construction provides a scalable and resource-efficient approach to quantum state preparation, further improving the potential of quantum algorithms in fields such as chemistry, physics, engineering, and finance.

quant-ph↗

arXiv2026

Accelerating Molecular Dynamics Simulations with Foundation Neural Network Models using Multiple Time-Step and Distillation

We present a distilled multi-time-step (DMTS) strategy to accelerate molecular dynamics simulations using foundation neural network models. DMTS uses a dual-level neural network where the target accurate potential is coupled to a simpler but faster model obtained via a distillation process. The 3.5 Å-cutoff distilled model is sufficient to capture the fast-varying forces, i.e., mainly bonded interactions, from the accurate potential allowing its use in a reversible reference system propagator algorithms (RESPA)-like formalism. The approach conserves accuracy, preserving both static and dynamical properties, while enabling to evaluate the costly model only every 3 to 6 fs depending on the system. Consequently, large simulation speedups over standard 1 fs integration are observed: nearly 4-fold in homogeneous systems and 3-fold in large solvated proteins through leveraging active learning for enhanced stability. Such a strategy is applicable to any neural network potential and reduces their performance gap with classical force fields.

physics.chem-ph↗

arXiv2025

Practical protein-pocket hydration-site prediction for drug discovery on a quantum computer

Demonstrating the practical utility of Noisy Intermediate-Scale Quantum (NISQ) hardware for recurrent tasks in Computer-Aided Drug Discovery is of paramount importance. We tackle this challenge by performing three-dimensional protein pockets hydration-site prediction on a quantum computer. Formulating the water placement problem as a Quadratic Unconstrained Binary Optimization (QUBO), we use a hybrid approach coupling a classical three-dimensional reference-interaction site model (3D-RISM) to an efficient quantum optimization solver, to run various hardware experiments up to 123 qubits. Matching the precision of classical approaches, our results reproduced experimental predictions on real-life protein-ligand complexes. Furthermore, through a detailed resource estimation analysis, we show that accuracy can be systematically improved with increasing number of qubits, indicating that full quantum utility is in reach. Finally, we provide evidence that advantageous situations could be found for systems where classical optimization struggles to provide optimal solutions. The method has potential for assisting simulations of protein-ligand complexes for drug lead optimization and setup of docking calculations.

quant-ph↗

arXiv2025

Quantum Speedup for Nonreversible Markov Chains

Quantum algorithms can potentially solve a handful of problems more efficiently than their classical counterparts. In that context, it has been discussed that Markov chains problems could be solved significantly faster using quantum computing. Indeed, previous work suggests that quantum computers could accelerate sampling from the stationary distribution of reversible Markov chains. However, in practice, certain physical processes of interest are nonreversible in the probabilistic sense and reversible Markov chains can sometimes be replaced by more efficient nonreversible chains targeting the same stationary distribution. This study constructs Markov chain reversibilizations and develops quantum algorithmic techniques to accelerate nonreversible processes. Such an up-to-exponential quantum speedup goes beyond the predicted quadratic quantum acceleration for reversible chains and is likely to have a decisive impact on many applications ranging from statistics and machine learning to computational modeling in physics, chemistry, biology and finance.

quant-ph↗

arXiv2025

VTX: Real-time high-performance molecular structure and dynamics visualization software

Summary: VTX is a molecular visualization software capable to handle most molecular structures and dynamics trajectories file formats. It features a real-time high-performance molecular graphics engine, based on modern OpenGL, optimized for the visualization of massive molecular systems and molecular dynamics trajectories. VTX includes multiple interactive camera and user interaction features, notably free-fly navigation and a fully modular graphical user interface designed for increased usability. It allows the production of high-resolution images for presentations and posters with custom background. VTX design is focused on performance and usability for research, teaching and educative purposes. Availability and implementation: VTX is open source and free for non commercial use. Builds for Windows and Ubuntu Linux are available at http://vtx.drugdesign.fr. The source code is available at https://github.com/VTX-Molecular-Visualization . Supplementary Information: A video displaying free-fly navigation in a whole-cell model is available

cs.GR↗

arXiv2025

The Q-AMOEBA (CF) Polarizable Potential

We present Q-AMOEBA (CF), an enhanced version of the Q-AMOEBA polarizable model that integrates a geometry-dependent charge flux (CF) term while designed for an explicit treatment of nuclear quantum effects (NQE). The inclusion of CF effects allows matching experimental data for the molecular structure of water in both gas and liquid phases, addressing limitations faced by most force fields. We show that Q-AMOEBA (CF) provides highly accurate results for a wide range of thermodynamical properties of liquid water. Using the computational efficiency of the adaptive Quantum Thermal Bath method, which accounts for NQE at a cost comparable to classical molecular dynamics, we evaluate the robustness and transferability of Q-AMOEBA (CF) by calculating hydration free energies of various ions and organic molecules. Finally, we apply this methodology to the alanine dipeptide and compute the corresponding dihedral angle potential of mean force and hydration free energy. Unexpectedly, the latter quantity displays significant NQE. These results pave the way to a finer understanding of their role in biochemical systems.

physics.chem-ph↗

arXiv2025

Lambda-ABF-OPES: Faster Convergence with High Accuracy in Alchemical Free Energy Calculations

Predicting the binding affinity between small molecules and target macromolecules while combining both speed and accuracy, is a cornerstone of modern computational drug discovery which is critical for accelerating therapeutic development. Despite recent progresses in molecular dynamics (MD) simulations, such as advanced polarizable force fields and enhanced-sampling techniques, estimating absolute binding free energies (ABFE) remains computationally challenging. To overcome these difficulties, we introduce a highly efficient, hybrid methodology that couples the Lambda-Adaptive Biasing Force (Lambda-ABF) scheme with On-the-fly Probability Enhanced Sampling (OPES). This approach achieves up to a nine-fold improvement in sampling efficiency and computational speed compared to the original Lambda-ABF when used in conjunction with the AMOEBA polarizable force field, yielding converged results at a fraction of the cost of standard techniques.

physics.chem-ph↗

arXiv2025

Pushing the Accuracy Limit of Foundation Neural Network Models with Quantum Monte Carlo Forces and Path Integrals

We propose an end-to-end integrated strategy to produce highly accurate quantum chemistry (QC) synthetic datasets (energies and forces) aimed at deriving Foundation Machine Learning models for molecular simulation. Starting from Density Functional Theory (DFT), a "Jacob's Ladder" approach leverages computationally-optimized layers of massively GPU-accelerated software with increasing accuracy. Thanks to Exascale, this is the first time that the computationally intensive calculation of Quantum Monte Carlo forces (QMC), and the combination of multi-determinant QMC energies and forces with selected-Configuration Interaction wavefunctions, are computed at such scale at the complete basis-set limit. To bridge the gap between accurate QC and condensed-phase Molecular Dynamics, we leverage transfer learning to improve the DFT-based FeNNix-Bio1 foundation model. The resulting approach is coupled to path integrals adaptive sampling quantum dynamics to perform nanosecond reactive simulations at unprecedented accuracy. These results demonstrate the promise of Exascale to deepen our understanding of the inner machinery of complex biosystems.

physics.chem-ph↗

arXiv2025

The need to implement FAIR principles in biomolecular simulations

This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necessity of a collaborative effort to create, establish, and sustain a database that allows findability, accessibility, interoperability, and reusability of molecular dynamics simulation data. Such a development would democratize the field and significantly improve the impact of MD simulations on life science research. This will transform our working paradigm, pushing the field to a new frontier. We invite you to support our initiative at the MDDB community (https://mddbr.eu/community/) Now published as: Amaro, R.E., et al. The need to implement FAIR principles in biomolecular simulations. Nat Methods (2025) https://doi.org/10.1038/s41592-025-02635-0

q-bio.BM↗