arXiv subjects

Rodolphe Vuilleumier

Publications and source records attributed to Rodolphe Vuilleumier.

At least 19 recordsLinked to original sources

arXiv2025

Liquid water under vibrational strong coupling: an extended cavity Born-Oppenheimer molecular dynamics study

A computational study of liquid water when the system is coupled with a (model) Fabry-Perot cavity is reported. At this end, the Cavity Born-Oppenheimer Molecular Dynamics approach proposed recently (Li et al., Proc. Nat. Acad. Sci. USA, 2020, 117, 18324-18331) is employed and different properties of water under vibrational strong coupling (VSC) are investigated. Different cavity frequencies are considered, corresponding to different modes in the IR spectrum of liquid water: high frequency (corresponding to O-H stretching modes), medium frequency (corresponding to water molecule bending) and low frequencies (corresponding to librational modes). Simulations were done both using classical and quantum nuclear dynamics, this last via Ring Polymer Molecular Dynamics. Similar effects of the cavity are obtained in both cases. Namely, whereas the infrared spectrum is observed to be split for all cavity frequencies, no effects on structural properties are detected. In addition, transport and dynamical properties, including the diffusion coefficient, molecular reorientation and hydrogen bond (HB) jump exchange times, show no effect due to cavity coupling when an extended statistical analysis is performed.

physics.chem-ph↗

arXiv2025

Anharmonic phonons via quantum thermal bath simulations

Lattice vibrations within crystalline solids, or phonons, provide information on a variety of important material characteristics, from thermal qualities to optical properties and phase transition behaviour. When the material contains light ions, or is subjected to sufficiently low temperatures and/or high pressures, anharmonic and nuclear quantum effects (NQEs) may significantly alter its phonon characteristics. Unfortunately, accurate inclusion of these two effects within numerical simulations typically incurs a substantial computational cost. In this work, we present a novel approach which promises to mitigate this problem. The scheme leverages the recently introduced quantum correlators approach for the extraction of anharmonic phonon frequencies from molecular dynamics data. To account for NQEs without excessive increase of the computational cost, we include nuclear quantum effects via the quantum thermal bath (QTB) method. This is the first full exploration of the use of QTB for the calculation of phonon dispersion relations. We demonstrate the noteworthy efficiency and accuracy of the scheme, and analyze its upsides and drawbacks by first considering 1-dimensional systems, and then the physically interesting case of solid neon.

physics.comp-ph↗

arXiv2025

Clustering data by reordering them

Grouping elements into families to analyse them separately is a standard analysis procedure in many areas of sciences. We propose herein a new algorithm based on the simple idea that members from a family look like each other, and don't resemble elements foreign to the family. After reordering the data according to the distance between elements, the analysis is automatically performed with easily-understandable parameters. Noise is explicitly taken into account to deal with the variety of problems of a data-driven world. We applied the algorithm to sort biomolecules conformations, gene sequences, cells, images, and experimental conditions.

cs.CV↗

arXiv2025

Constructing and explaining machine learning models for chemistry: example of the exploration and design of boron-based Lewis acids

The integration of machine learning (ML) into chemistry offers transformative potential in the design of molecules with targeted properties. However, the focus has often been on creating highly efficient predictive models, sometimes at the expense of interpretability. In this study, we leverage explainable AI techniques to explore the rational design of boron-based Lewis acids, which play a pivotal role in organic reactions due to their electron-ccepting properties. Using Fluoride Ion Affinity as a proxy for Lewis acidity, we developed interpretable ML models based on chemically meaningful descriptors, including ab initio computed features and substituent-based parameters derived from the Hammett linear free-energy relationship. By constraining the chemical space to well-defined molecular scaffolds, we achieved highly accurate predictions (mean absolute error < 6 kJ/mol), surpassing conventional black-box deep learning models in low-data regimes. Interpretability analyses of the models shed light on the origin of Lewis acidity in these compounds and identified actionable levers to modulate it through the nature and positioning of substituents on the molecular scaffold. This work bridges ML and chemist's way of thinking, demonstrating how explainable models can inspire molecular design and enhance scientific understanding of chemical reactivity.

physics.chem-ph↗

arXiv2023

Rényi entropy of quantum anharmonic chain at non-zero temperature

The interplay of quantum and classical fluctuations in the vicinity of a quantum critical point (QCP) gives rise to various regimes or phases with distinct quantum character. In this work, we show that the Rényi entropy is a precious tool to characterize the phase diagram of critical systems not only around the QCP but also away from it, thanks to its capability to detect the emergence of local order at finite temperature. For an efficient evaluation of the Rényi entropy, we introduce a new algorithm based on a path integral Langevin dynamics combined with a previously proposed thermodynamic integration method built on regularized paths. We apply this framework to study the critical behavior of a linear chain of anharmonic oscillators, a particular realization of the $ϕ^4$ model. We fully resolved its phase diagram, as a function of both temperature and interaction strength. At finite temperature, we find a sequence of three regimes - para, disordered and quasi long-range ordered -, met as the interaction is increased. The Rényi entropy divergence coincides with the crossover between the para and disordered regime, which shows no temperature dependence. The occurrence of quasi long-range order, on the other hand, is temperature dependent. The two crossover lines merge in proximity of the QCP, at zero temperature, where the Rényi entropy is sharply peaked. Via its subsystem-size scaling, we confirm that the transition belongs to the two-dimensional Ising universality class. This phenomenology is expected to happen in all $ϕ^4$-like systems, as well as in the elusive water ice transition across phases VII, VIII and X.

cond-mat.stat-mech↗

arXiv2023

Predicting the Charge Density Response in Metal Electrodes

The computational study of energy storage and conversion processes calls for simulation techniques that can reproduce the electronic response of metal electrodes under electric fields. Despite recent advancements in machine-learning methods applied to electronic-structure properties, predicting the non-local behavior of the charge density in electronic conductors remains a major open challenge. We combine long-range and equivariant kernel methods to predict the Kohn-Sham electron density of metal electrodes in response to various kinds of electric field perturbations. By taking slabs of gold as an example, we first show how the non-local electronic polarization generated by the interaction with an ionic species can be accurately reproduced in electrodes of arbitrary thickness. A finite-field extension of the method is then introduced, which allows us to predict the charge transfer and the electrostatic potential drop induced by the application of a homogeneous and constant electric field. Finally, we demonstrate the capability of the method to reproduce the charge-density response in a gold/electrolyte capacitor under an applied voltage, predicting the system polarization with a greater accuracy than state-of-the-art classical atomic-charge models.

cond-mat.mtrl-sci↗

arXiv2023

Quasi-classical simulations of resonance Raman spectra based on path integral linearization

Based on a linearization approximation coupled with path integral formalism, we propose a method derived from the propagation of quasi-classical trajectories to simulate resonance Raman spectra. This method is based on a ground state sampling followed by an ensemble of trajectories on the mean surface between the ground and excited states. The method was tested on three models and compared to quantum mechanics solution based on a sum-over-states approach: harmonic and anharmonic oscillators and the HOCl molecule (hypochlorous acid). The method proposed is able to correctly characterize resonance Raman scattering and enhancement, including the description of overtones and combination bands. The absorption spectrum is obtained at the same time and the vibrational fine structure can be reproduced for long excited state relaxation times. The method can be applied also to dissociating excited states (as is the case for HOCl).

physics.chem-ph↗

arXiv2023

Thermal dependence of the hydrated proton and optimal proton transfer

Water is a key ingredient for life and plays a central role as solvent in many biochemical reactions. However, the intrinsically quantum nature of the hydrogen nucleus, revealing itself in a large variety of physical manifestations, including proton transfer, gives rise to unexpected phenomena whose description is still elusive. Here we study, by an unprecedented combination of state-of-the-art quantum Monte Carlo methods and path-integral molecular dynamics, the structure and hydrogen-bond dynamics of the protonated water hexamer, the fundamental unit for the hydrated proton. We report a remarkably low thermal expansion of the hydrogen bond from zero temperature up to 300 K, owing to the presence of short-Zundel configurations, characterised by proton delocalisation and favoured by the synergy of nuclear quantum effects and thermal activation. The hydrogen bond strength progressively weakens above 300 K, when localised Eigen-like configurations become relevant. Our analysis, supported by the instanton statistics of shuttling protons, reveals that the near-room-temperature range from 250 K to 300 K is a ``sweet spot'' for proton transfer, and thus for many phenomena depending on it, including life.

cond-mat.mtrl-sci↗

arXiv2022

Mass-Zero constrained dynamics for simulations based on orbital-free density functional theory

A new algorithm for efficient and fully time-reversible integration of first-principles molecular dynamics based on orbital-free density functional theory (OFDFT) is presented. The algorithm adapts to this nontrivial case the recently introduced Mass-Zero (MaZe) constrained dynamics. The formalism ensures that full adiabatic separation is enforced between nuclear and electronic degrees of freedom and, consequently, that the exact Born-Oppenheimer probability for the nuclei is sampled. Numerical integration of the MaZe dynamics combines standard molecular dynamics algorithms, e.g. Verlet or velocity Verlet, with the SHAKE method to impose the minimum conditions on the electronic degrees of freedom as a set of constraints. The developments presented in this work, that include a bespoke adaptation of the standard SHAKE algorithm, ensure that the quasilinear scaling of OFDFT is preserved by the new method for a broad range of kinetic and exchange-correlation functionals, including nonlocal ones. The efficiency and accuracy of the approach is demonstrated via calculations of static and dynamic properties of liquid sodium in the constant energy and constant temperature ensembles.

cond-mat.stat-mech↗

arXiv2022

Quantum Rényi entropy by optimal thermodynamic integration paths

Despite being a well-established operational approach to quantify entanglement, Rényi entropy calculations have been plagued by their computational complexity. We introduce here a theoretical framework based on an optimal thermodynamic integration scheme, where the Rényi entropy can be efficiently evaluated using regularizing paths. This approach avoids slowly convergent fluctuating contributions and leads to low-variance estimates. In this way, large system sizes and high levels of entanglement in model or first-principles Hamiltonians are within our reach. We demonstrate it in the one-dimensional quantum Ising model and perform the evaluation of entanglement entropy in the formic acid dimer, by discovering that its two shared protons are entangled even above room temperature.

cond-mat.stat-mech↗

arXiv2022

Hydrogen phase-IV characterization by full account of quantum anharmonicity

We devise a framework to compute accurate phonons in molecular crystals even in case of strong quantum anharmonicity. Our approach is based on the calculation of the static limit of the phononic Matsubara Green's function from path integral molecular dynamics simulations. Our method enjoys a remarkably low variance, which allows one to compute accurate phonon frequencies after a few picoseconds of nuclear dynamics, and it is further stabilized by the use of appropriate constrained displacement operators. We applied it to solid hydrogen at high pressure. For phase III, our predicted infrared (IR) and Raman active vibrons agree very well with experiments. We then characterize the crystalline symmetry of phase IV by direct comparison with vibrational data and we determine the character of its Raman and IR vibron peaks.

cond-mat.mtrl-sci↗

arXiv2021

Probing anharmonic phonons by quantum correlators: A path integral approach

We devise an efficient scheme to determine vibrational properties from Path Integral Molecular Dynamics (PIMD) simulations. The method is based on zero-time Kubo-transformed correlation functions and captures the anharmonicity of the potential due to both temperature and quantum effects. Using analytical derivations and numerical calculations on toy-model potentials, we show that two different estimators built upon PIMD correlation functions fully characterize the phonon spectra and the anharmonicity strength. The first estimator is associated with force-force quantum correlators and gives access to the fundamental frequencies and thermodynamic properties of the quantum system. The second one is instead connected to displacement-displacement correlators and probes the lowest-energy phonon excitations with high accuracy. We also prove that the use of generalized eigenvalue equations, in place of the standard normal mode equations, leads to a significant speed-up in the PIMD phonon calculations, both in terms of faster convergence rate and smaller time-step bias. Within this framework, using ab initio PIMD simulations, we compute phonon dispersions of diamond and of the high-pressure I41/amd phase of atomic hydrogen. We find that, in the latter case, the anharmonicity is stronger than previously estimated and yields a sizeable red-shift in the vibrational spectrum of atomic hydrogen.

cond-mat.mtrl-sci↗

arXiv2020

Mass-zero constrained molecular dynamics for electrode charges in simulations of electrochemical systems

Classical molecular dynamics simulations have recently become a standard tool for the study of electrochemical systems. State-of-the-art approaches represent the electrodes as perfect conductors, modelling their responses to the charge distribution of electrolytes via the so-called fluctuating charge model. These fluctuating charges are additional degrees of freedom that, in a Born-Oppenheimer spirit, adapt instantaneously to changes in the environment to keep each electrode at a constant potential. Here we show that this model can be treated in the framework of constrained molecular dynamics, leading to a symplectic and time-reversible algorithm for the evolution of all the degrees of freedom of the system. The computational cost and the accuracy of the new method are similar to current alternative implementations of the model. The advantage lies in the accuracy and long term stability guaranteed by the formal properties of the algorithm and in the possibility to systematically introduce additional kinematic conditions of arbitrary number and form. We illustrate the performance of the constrained dynamics approach by enforcing the electroneutrality of the electrodes in a simple capacitor consisting of two graphite electrodes separated by a slab of liquid water.

cond-mat.stat-mech↗

arXiv2020

Adiabatic motion and statistical mechanics via mass zero constrained dynamics

In recent work [Coretti et al., The Journal of Chemical Physics, 2018, 149, 191102], a new algorithm to solve numerically the dynamics of the shell model for polarization was presented. The approach, broadly applicable to systems involving adiabatically separated dynamical variables, employs constrained molecular dynamics to strictly enforce the condition that the force on the fast degrees of freedom, modeled as having zero mass, is null at each time step. The algorithm is symplectic and fully time reversible, and results in stable and efficient propagation. In this paper we complete the discussion of the mechanics of mass zero constrained dynamics by showing how to adapt it to problems where the fast degrees of freedom must satisfy additional conditions. This extension includes, in particular, the important case of first principles molecular dynamics. We then consider the statistical mechanics of the mass zero constrained dynamical system demonstrating that the marginal probability sampled by the dynamics in the physical phase space recovers the form of the Born-Oppenheimer probability density.

cond-mat.stat-mech↗

arXiv2019

Direct observation of water mediated single proton transport between hBN surface defects

Aqueous proton transport at interfaces is ubiquitous and crucial for a number of fields, ranging from cellular transport and signaling, to catalysis and membrane science. However, due to their light mass, small size and high chemical reactivity, uncovering single proton surface transport at room temperature and in aqueous environment has so far remained out-of-reach of conventional atomic-scale surface science techniques, such as STM. Here, we use single-molecule localization microscopy techniques to resolve optically the transport of individual excess protons at the interface of hexagonal boron nitride crystals and aqueous solutions at room temperature. Our label-free approach relies on the successive protonation and activation of optically active defects at the surface of the crystal allowing us to resolve interfacial proton transport at the single molecule scale with nanometric resolution and over micrometer range. Proton trajectories are revealed as a succession of jumps between proton-binding defects, mediated by interfacial water. We demonstrate unexpected interfacial proton mobility under illumination, limited by proton desorption from individual defects. The proposed mechanism is supported by ab initio molecular dynamics simulations of defected and pristine hBN/water interface. Our observations provide direct experimental evidence at the single molecule scale that interfacial water provides a preferential pathway for lateral proton transport. Our findings have fundamental and general implications for water-mediated molecular charge transport at interfaces.

cond-mat.mes-hall↗

arXiv2019

Computing three-dimensional densities from force densities improves statistical efficiency

The extraction of inhomogeneous 3-dimensional densities around tagged solutes from molecular simulations is known to have a very high computational cost because this is traditionally performed by collecting histograms, with each discrete voxel in three-dimensional space needing to be visited significantly. This paper presents an extension of a previous methodology for the extraction of 3D solvent number densities with a reduced variance principle [Borgis et al., Mol. Phys. 111, 3486-3492 (2013)] to other 3D densities such as charge and polarization densities. The approach is also generalized to cover molecular solvents with structures described using rigid geometrical constraints, which include in particular popular water models such as SPC/E and TIPnP class of models. The noise reduction is illustrated for the microscopic hydration structure of a small molecule, in various simulation conditions, and for a protein. The method has large applicability to simulations of solvation in many fields, for example around biomolecules, nanoparticles, or within porous materials.

physics.chem-ph↗

arXiv2019

The MgCO$_3$-CaCO$_3$-Li$_2$CO$_3$-Na$_2$CO$_3$-K$_2$CO$_3$ Carbonate Melts: Thermodynamics and Transport Properties by Atomistic Simulations

Atomistic simulations provide a meaningful way to determine the physico-chemical properties of liquids in a consistent theoretical framework. This approach takes on particular usefulness for the study of molten carbonates, in a context where thermodynamic and transport data are crucially needed over a large domain of temperatures and pressures (to ascertain the role of these melts in geochemical processes) but are very scarce in the literature, especially for the calco-magnesian compositions prevailing in the Earth's mantle. Following our work on Li2CO3-Na2CO3-K2CO3 melts, we extend our force field to incorporate Ca and Mg components. The empirical interaction potentials are benchmarked on the density data available in the experimental literature (for the crystals and the K2Ca(CO3)2 melt) and on the liquid structure issued from ab initio molecular dynamics simulations. Molecular dynamics simulations are then performed to study the thermodynamics, the microscopic structure, the diffusion coefficients, the electrical conductivity and the viscosity of molten Ca, Mg-bearing carbonates up to 2073 K and 15 GPa. Additionally, the equation of state of a Na-Ca-K mixture representative of the lavas emitted at Ol Doinyo Lengai (Tanzania) is evaluated. The overall agreement between the MD results and the existing experimental data is very satisfying and provides evidence for the ability of the force field to accurately model any MgCO3-CaCO3-Li2CO3-Na2CO3-K2CO3 melt over a large T - P range. Moreover it is the first report of a force field allowing to study the transport properties of molten magnesite (MgCO3) and molten dolomite (CaMg(CO3)2).

physics.chem-ph↗

arXiv2019

Atomistic simulations of molten carbonates: thermodynamic and transport properties of the Li2CO3-Na2CO3-K2CO3 system

Although molten carbonates only represent, at most, a very minor phase in the Earth's mantle, they are thought to be implied in anomalous high-conductivity zones in its upper part (70-350 km). Besides the high electrical conductivity of these molten salts is also exploitable in fuel cells. Here we report quantitative calculations of their properties, over a large range of thermodynamic conditions and chemical compositions, that are a requisite to develop technological devices and to provide a better understanding of a number of geochemical processes. To model molten carbonates by atomistic simulations, we have developed an optimized classical force field based on experimental data of the literature and on the liquid structure issued from ab initio molecular dynamics simulations performed by ourselves. In implementing this force field into a molecular dynamics simulation code, we have evaluated the thermodynamics (equation of state and surface tension), the microscopic liquid structure and the transport properties (diffusion coefficients, electrical conductivity and viscosity) of molten alkali carbonates (Li2CO3, Na2CO3, K2CO3 and some of their binary and ternary mixtures) from the melting point up to the thermodynamic conditions prevailing in the Earth's upper mantle (~ 1100-2100 K, 0-15 GPa). Our results are in very good agreement with the data available in the literature. To our knowledge a reliable molecular model for molten alkali carbonates covering such a large domain of thermodynamic conditions, chemical compositions and physicochemical properties has never been published yet.

physics.chem-ph↗