arXiv subjects

Francois Gygi

Publications and source records attributed to Francois Gygi.

16 recordsLinked to original sources

arXiv2026

Large-scale first-principle simulations of amorphous indium oxide

Amorphous indium oxide (a-In$_2$O$_3$) is a high-electron-mobility semiconductor of central importance in thin-film transistors and a promising photoanode for solar-driven water oxidation. Despite sustained experimental and computational investigations, the structural motifs underlying its unusual transport properties and the existence of O-O peroxide-like bonds within its network have remained unresolved. Here we develop a MACE-based machine-learned interatomic potential trained on first-principles molecular dynamics trajectories and use it to generate and analyze amorphous structures containing up to 5120 atoms, two orders of magnitude larger than those adopted in typical ab initio studies. We find X-ray structure factors in excellent quantitative agreement with experiment and we confirm that In$_2$O$_3$ is a poor glass former, with the likely presence of quasi-crystalline regions in amorphous samples. Our large-scale structural analysis reveals extended chains of edge-sharing InO$_k$ polyhedra providing a concrete structural basis for the high electron mobility of a-In$_2$O$_3$. Our results strongly support the formation of O-O peroxide-like bonds in the amorphous network, with a mean length of 1.5 \AA{}. We show that these bonds introduce localized in-gap states near the conduction band minimum, acting as a source of intrinsic n-type self-doping and enhancing sub-gap optical absorption. These effects are detectable via a distinct Raman feature near 850 cm$^{-1}$ that is absent in the IR spectrum. Overall, our results establish a comprehensive structure-property picture of a-In$_2$O$_3$, provide directly testable experimental predictions, and suggest that controlled amorphization is a viable strategy for improving the photoelectrochemical activity of a-In$_2$O$_3$.

cond-mat.mtrl-sci↗

arXiv2025

Characterizing Defect Dynamics in Silicon Carbide Using Symmetry-Adapted Collective Variables and Machine Learning Interatomic Potentials

Silicon carbide (SiC) divacancies are attractive candidates for spin defect qubits possessing long coherence times and optical addressability. The high activation barriers associated with SiC defect formation and motion pose challenges for their study by first-principles molecular dynamics. In this work, we develop and deploy machine learning interatomic potentials (MLIPs) to accelerate defect dynamics simulations while retaining ab initio accuracy. We employ an active learning strategy comprising symmetry-adapted collective variable discovery and enhanced sampling to compile configurationally diverse training data, calculation of energies and forces using density functional theory (DFT), and training of an E(3)-equivariant MLIP based on the Allegro model. The trained MLIP reproduces DFT-level accuracy in defect transition activation free energy barriers, enables the efficient and stable simulation of multi-defect 216-atom supercells, and permits an analysis of the temperature dependence of defect thermodynamic stability and formation/annihilation kinetics to propose an optimal annealing temperature to maximally stabilize VV divacancies.

cond-mat.mtrl-sci↗

arXiv2025

Computational study of indium oxide photoelectrodes

Using a combination of first principles molecular dynamics simulations (FPMD) and electronic structure calculations, we characterize the atomistic structure and vibrational properties of a photocatalytic surface of In$_2$O$_3$, a promising photoelectrode for the production of hydrogen peroxide. We then investigate the surface in contact with water and show that the electronic states of In$_2$O$_3$ are appropriately positioned in energy to facilitate the two-electron water oxidation reaction (WOR) over the competing four-electron oxygen evolution reaction. We further propose that the use of strained thin films interfaced with water is beneficial in decreasing the optical gap of In$_2$O$_3$ and thus utilizing a wider portion of the solar spectrum for the WOR.

cond-mat.mtrl-sci↗

arXiv2024

Towards Verifying Exact Conditions for Implementations of Density Functional Approximations

Density Functional Theory (DFT) is used extensively in the computation of electronic properties of matter, with various applications. Approximating the exchange-correlation (XC) functional is the key to the Kohn-Sham DFT approach, the basis of most DFT calculations. The choice of this density functional approximation (DFA) depends crucially on the particular system under study, which has resulted in the development of hundreds of DFAs. Though the exact density functional is not known, researchers have discovered analytical properties of this exact functional. Furthermore, these exact conditions are used when designing DFAs. We present XCVerifier, the first approach for verifying whether a DFA implementation satisfies the DFT exact conditions. XCVerifier was evaluated on five DFAs from the popular Libxc library and seven exact conditions from recent work. XCVerifier was able to verify or find violations for a majority of the DFA/condition pairs, demonstrating the feasibility of using formal methods to verify DFA implementations.

cond-mat.mtrl-sci↗

arXiv2023

Engineering the formation of spin-defects from first principles

The full realization of spin qubits for quantum technologies relies on the ability to control and design the formation processes of spin defects in semiconductors and insulators. We present a computational protocol to investigate the synthesis of point-defects at the atomistic level, and we apply it to the study of a promising spin-qubit in silicon carbide, the divacancy (VV). Our strategy combines electronic structure calculations based on density functional theory and enhanced sampling techniques coupled with first principles molecular dynamics. We predict the optimal annealing temperatures for the formation of VVs at high temperature and show how to engineer the Fermi level of the material to optimize the defect's yield for several polytypes of silicon carbide. Our results are in excellent agreement with available experimental data and provide novel atomistic insights into point defect formation and annihilation processes as a function of temperature.

cond-mat.mtrl-sci↗

arXiv2021

Quantum vibronic effects on the electronic properties of solid and molecular carbon

We study the effect of quantum vibronic coupling on the electronic properties of carbon allotropes, including molecules and solids, by combining path integral first principles molecular dynamics (FPMD) with a colored noise thermostat. In addition to avoiding several approximations commonly adopted in calculations of electron-phonon coupling, our approach only adds a moderate computational cost to FPMD simulations and hence it is applicable to large supercells, such as those required to describe amorphous solids. We predict the effect of electron-phonon coupling on the fundamental gap of amorphous carbon, and we show that in diamond the zero-phonon renormalization of the band gap is larger than previously reported.

cond-mat.mtrl-sci↗

arXiv2019

Dimensionality and heat transport in Si-Ge superlattices

We investigated how dimensionality affects heat transport in Si-Ge superlattices by computing the thermal conductivity of planar superlattices and arrays of Ge nanowires and nanodots embedded in Si. We studied superlattices with $\sim$10 nm periods using a fully atomistic Monte Carlo solution of the Boltzmann transport equation in the relaxation time approximation. We found that for periods larger than 4 nm, the room temperature cross-plane conductivity of planar superlattices with equally thick Si and Ge layers is larger than that of their nanowire and dot counterparts of similar sizes (up to 100\%), while the trend is reversed below 4 nm.

cond-mat.mes-hall↗

arXiv2019

A finite field approach to solving the Bethe Salpeter equation

We present a method to compute optical spectra and exciton binding energies of molecules and solids based on the solution of the Bethe-Salpeter equation (BSE) and the calculation of the screened Coulomb interaction in finite field. The method does not require the explicit evaluation of dielectric matrices nor of virtual electronic states, and can be easily applied without resorting to the random phase approximation. In addition it utilizes localized orbitals obtained from Bloch states using bisection techniques, thus greatly reducing the complexity of the calculation and enabling the efficient use of hybrid functionals to obtain single particle wavefunctions. We report exciton binding energies of several molecules and absorption spectra of condensed systems of unprecedented size, including water and ice samples with hundreds of atoms.

cond-mat.mtrl-sci↗

arXiv2018

A Finite-field Approach for $GW$ Calculations Beyond the Random Phase Approximation

We describe a finite-field approach to compute density response functions, which allows for efficient $G_0W_0$ and $G_0W_0\Gamma_0$ calculations beyond the random phase approximation. The method is easily applicable to density functional calculations performed with hybrid functionals. We present results for the electronic properties of molecules and solids and we discuss a general scheme to overcome slow convergence of quasiparticle energies obtained from $G_0W_0\Gamma_0$ calculations, as a function of the basis set used to represent the dielectric matrix.

physics.chem-ph↗

arXiv2015

Optimization Algorithm for the Generation of ONCV Pseudopotentials

We present an optimization algorithm to construct pseudopotentials and use it to generate a set of Optimized Norm-Conserving Vanderbilt (ONCV) pseudopotentials for elements up to Z=83 (Bi) (excluding Lanthanides). We introduce a quality function that assesses the agreement of a pseudopotential calculation with all-electron FLAPW results, and the necessary plane-wave energy cutoff. This quality function allows us to use a Nelder-Mead optimization algorithm on a training set of materials to optimize the input parameters of the pseudopotential construction for most of the periodic table. We control the accuracy of the resulting pseudopotentials on a test set of materials independent of the training set. We find that the automatically constructed pseudopotentials provide a good agreement with the all-electron results obtained using the FLEUR code with a plane-wave energy cutoff of approximately 60 Ry.

cond-mat.mtrl-sci↗

arXiv2010

Ab initio investigation of the melting line of nitrogen at high pressure

Understanding the behavior of molecular systems under pressure is a fundamental problem in condensed matter physics. In the case of nitrogen, the determination of the phase diagram and in particular of the melting line, are largely open problems. Two independent experiments have reported the presence of a maximum in the nitrogen melting curve, below 90 GPa, however the position and the interpretation of the origin of such maximum differ. By means of ab initio molecular dynamics simulations based on density functional theory and thermodynamic integration techniques, we have determined the phase diagram of nitrogen in the range between 20 and 100 GPa. We find a maximum in the melting line, related to a transformation in the liquid, from molecular N_2 to polymeric nitrogen accompanied by an insulator-to-metal transition.

cond-mat.mtrl-sci↗

arXiv2005

A unified electrostatic and cavitation model for first-principles molecular dynamics in solution

The electrostatic continuum solvent model developed by Fattebert and Gygi is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. Our model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution, and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. We apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon.

cond-mat.mtrl-sci↗

arXiv2003

Structure and bonding of dense liquid oxygen from first principles simulations

Using first principles simulations we have investigated the structural and bonding properties of dense fluid oxygen up to 180 GPa. We have found that band gap closure occurs in the molecular liquid, with a "slow" transition from a semi-conducting to a poor metallic state occurring over a wide pressure range. At approximately 80 GPa, molecular dissociation is observed in the metallic fluid. Spin fluctuations play a key role in determining the electronic structure of the low pressure fluid, while they are suppressed at high pressure.

cond-mat.mtrl-sci↗

arXiv2000

On the structure and stability of germanium nanoparticles

In order to control and tailor the properties of nanodots, it is essential to separate the effects of quantum confinement from those due to the surface, and to gain insight into the influence of preparation conditions on the dot physical properties. We address these issues for the case of small Ge clusters (1-3 nm), using a combination of empirical and first-principles molecular dynamics techniques. Our results show that over a wide temperature range the diamond structure is more stable than tetragonal, ST12-like structures for clusters containing more than 50 atoms; however, the magnitude of the energy difference between the two geometries is strongly dependent on the surface properties. Based on our structural data, we propose a mechanism which may be responsible for the formation of metastable ST12 clusters in vapor deposition experiments, by cold quenching of amorphous nanoparticles with unsaturated, reconstructed surfaces.

cond-mat.mtrl-sci↗

arXiv1995

Real-Space Adaptive-Coordinate Electronic Structure Calculations

We present a real-space adaptive-coordinate method, which combines the advantages of the finite-difference approach with the accuracy and flexibility of the adaptive coordinate method. The discretized Kohn-Sham equations are written in generalized curvilinear coordinates and solved self-consistently by means of an iterative approach. The Poisson equation is solved in real space using the Multigrid algorithm. We implemented the method on a massively parallel computer, and applied it to the calculation of the equilibrium geometry and harmonic vibrational frequencies of the CO_2, CO, N_2 and F_2 molecules, yielding excellent agreement with the results of accurate quantum chemistry and Local Density Functional calculations.

mtrl-th↗

arXiv1995

Ab initio Molecular Dynamics in Adaptive Coordinates

We present a new formulation of ab initio molecular dynamics which exploits the efficiency of plane waves in adaptive curvilinear coordinates, and thus provides an accurate treatment of first-row elements. The method is used to perform a molecular dynamics simulation of the CO_2 molecule, and allows to reproduce detailed features of its vibrational spectrum such as the splitting of the Raman sigma+_g mode caused by Fermi resonance. This new approach opens the way to highly accurate ab initio simulations of organic compounds.

mtrl-th↗